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Sample records for ancestry highly correlated

  1. A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations.

    Science.gov (United States)

    Gompert, Zachariah

    2016-01-01

    Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20) SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure), particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur) and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among chromosomes in the Uyghur

  2. A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations.

    Directory of Open Access Journals (Sweden)

    Zachariah Gompert

    Full Text Available Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20 SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure, particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among

  3. Unexpected inverse correlation between Native American ancestry and Asian American variants of HPV16 in admixed Colombian cervical cancer cases.

    Science.gov (United States)

    Lopera, Esteban A; Baena, Armando; Florez, Victor; Montiel, Jehidys; Duque, Constanza; Ramirez, Tatiana; Borrero, Mauricio; Cordoba, Carlos M; Rojas, Fredy; Pareja, Rene; Bedoya, Astrid M; Bedoya, Gabriel; Sanchez, Gloria I

    2014-12-01

    European (E) variants of HPV 16 are evenly distributed among world regions, meanwhile Non-European variants such as European-Asian (EAs), Asian American (AA) and African (Af) are mostly confined to Eastern Asia, The Americas and African regions respectively. Several studies have shown that genetic variation of HPV 16 is associated with the risk of cervical cancer, which also seems to be dependent on the population. This relationship between ethnicity and variants have led to the suggestion that there is co-evolution of variants with humankind. Our aim was to evaluate the relationship between the individual ancestry proportion and infection with HPV 16 variants in cervical cancer. We examined the association between ancestry and HPV 16 variants in samples of 82 cervical cancer cases from different regions of Colombia. Individual ancestry proportions (European, African and Native American) were estimated by genotyping 106 ancestry informative markers. Variants were identified by PCR amplification of the E6 gene, followed by reverse line blot hybridization (RLB) with variants specific probes. Overall European (E) and Asian American (AA) variants frequency was 66.5% and 33.5% respectively. Similar distribution was observed in cases with higher proportions of European or African ancestry. A higher Native American ancestry was significantly associated with higher frequency of E variants (median ancestry>23.6%, Age and place of birth adjusted OR: 3.55, 95% CI: 1.26-10.03, p=0.01). Even further, an inverse geographic correlation between Native American ancestry and frequency of infections with AA variants was observed (ρ=-0.825, p=0.008). Regions with higher proportion of Native American ancestry had a lower frequency of AA variants of HPV 16. This study suggests replacement of AA variants by E variants of human papillomavirus 16 in cervical cancer cases with high Native American ancestry. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Education of Non-European Ancestry Immigrant Students in Suburban High Schools

    Science.gov (United States)

    Shodavaram, Mary P.; Jones, Lisa A.; Weaver, Laurie R.; Marquez, Judith A.; Ensle, Anne L.

    2009-01-01

    The purpose of this study was to examine suburban high school teachers' beliefs about non-European ancestry immigrant students; more specifically, suburban teachers' beliefs regarding the impact of students' cultural backgrounds on academic performance were examined. Non-European ancestry immigrant students are those students whose ancestral…

  5. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

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    Ng, Maggie C Y; Graff, Mariaelisa; Lu, Yingchang; Justice, Anne E; Mudgal, Poorva; Liu, Ching-Ti; Young, Kristin; Yanek, Lisa R; Feitosa, Mary F; Wojczynski, Mary K; Rand, Kristin; Brody, Jennifer A; Cade, Brian E; Dimitrov, Latchezar; Duan, Qing; Guo, Xiuqing; Lange, Leslie A; Nalls, Michael A; Okut, Hayrettin; Tajuddin, Salman M; Tayo, Bamidele O; Vedantam, Sailaja; Bradfield, Jonathan P; Chen, Guanjie; Chen, Wei-Min; Chesi, Alessandra; Irvin, Marguerite R; Padhukasahasram, Badri; Smith, Jennifer A; Zheng, Wei; Allison, Matthew A; Ambrosone, Christine B; Bandera, Elisa V; Bartz, Traci M; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bottinger, Erwin P; Carpten, John; Chanock, Stephen J; Chen, Yii-Der Ida; Conti, David V; Cooper, Richard S; Fornage, Myriam; Freedman, Barry I; Garcia, Melissa; Goodman, Phyllis J; Hsu, Yu-Han H; Hu, Jennifer; Huff, Chad D; Ingles, Sue A; John, Esther M; Kittles, Rick; Klein, Eric; Li, Jin; McKnight, Barbara; Nayak, Uma; Nemesure, Barbara; Ogunniyi, Adesola; Olshan, Andrew; Press, Michael F; Rohde, Rebecca; Rybicki, Benjamin A; Salako, Babatunde; Sanderson, Maureen; Shao, Yaming; Siscovick, David S; Stanford, Janet L; Stevens, Victoria L; Stram, Alex; Strom, Sara S; Vaidya, Dhananjay; Witte, John S; Yao, Jie; Zhu, Xiaofeng; Ziegler, Regina G; Zonderman, Alan B; Adeyemo, Adebowale; Ambs, Stefan; Cushman, Mary; Faul, Jessica D; Hakonarson, Hakon; Levin, Albert M; Nathanson, Katherine L; Ware, Erin B; Weir, David R; Zhao, Wei; Zhi, Degui; Arnett, Donna K; Grant, Struan F A; Kardia, Sharon L R; Oloapde, Olufunmilayo I; Rao, D C; Rotimi, Charles N; Sale, Michele M; Williams, L Keoki; Zemel, Babette S; Becker, Diane M; Borecki, Ingrid B; Evans, Michele K; Harris, Tamara B; Hirschhorn, Joel N; Li, Yun; Patel, Sanjay R; Psaty, Bruce M; Rotter, Jerome I; Wilson, James G; Bowden, Donald W; Cupples, L Adrienne; Haiman, Christopher A; Loos, Ruth J F; North, Kari E

    2017-04-01

    Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

  6. High Molecular Weight Adiponectin Levels are Neither Influenced by Adiponectin Polymorphisms Nor Associated with Insulin Resistance in Mixed-Ancestry Hyperglycemic Subjects from South Africa

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    Zemlin Annalise E

    2016-10-01

    Full Text Available Background: High molecular weight (HMW adiponectin has antiatherogenic, antiinflammatory and antidiabetic properties and these effects have been linked to its effect on high density lipoprotein cholesterol (HDL-c. Single nucleotide polymorphisms (SNPs in the adiponectin gene influence adiponectin levels. We examined the relationship between HMW-adiponectin levels and cardiometabolic traits in normo- and hyperglycemic mixed ancestry South Africans and correlated these levels to two common polymorphisms.

  7. African Ancestry Influences CCR5 –2459G>A Genotype-Associated Virologic Success of Highly Active Antiretroviral Therapy

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    Cheruvu, Vinay K.; Igo, Robert P.; Jurevic, Richard J.; Serre, David; Zimmerman, Peter A.; Rodriguez, Benigno; Mehlotra, Rajeev K.

    2014-01-01

    Introduction In a North American, HIV-positive, highly active antiretroviral therapy (HAART)-treated, adherent cohort of self-identified white and black patients, we previously observed that chemokine (C-C motif) receptor 5 (CCR5) –2459G>A genotype had a strong association with time to achieve virologic success (TVLS) in black but not in white patients. Methods Using 128 genome-wide ancestry informative markers, we performed a quantitative assessment of ancestry in these patients (n = 310) to determine (1) whether CCR5 –2459G>A genotype is still associated with TVLS of HAART when ancestry, not self-identified race, is considered and (2) whether this association is influenced by varying African ancestry. Results We found that the interaction between CCR5 –2459G>A genotype and African ancestry (≤0.125 vs. ≥0.425 and A genotype and TVLS was stronger in patients with African ancestry ≥0.71 than in patients with African ancestry ≥0.452, in both Kaplan-Meier (log-rank P = 0.039 and 0.057, respectively, for AA, GA, and GG) and Cox proportional hazards regression (relative hazard for GG compared with AA 2.59 [95% CI, 1.27–5.22; P = 0.01] and 2.26 [95% CI, 1.18–4.32; P = 0.01], respectively) analyses. Conclusions We observed that the association between CCR5 –2459G>A genotype and TVLS of HAART increased with stronger African ancestry. Understanding the genomic mechanisms by which African ancestry influences this association is critical, and requires further studies. PMID:24714069

  8. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry.

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    do Rego Borges, Andrea; Sá, Jamile; Hoshi, Ryuichi; Viena, Camila Sane; Mariano, Lorena C; de Castro Veiga, Patricia; Medrado, Alena Peixoto; Machado, Renato Assis; de Aquino, Sibele Nascimento; Messetti, Ana Camila; Spritz, Richard A; Coletta, Ricardo D; Reis, Silvia R A

    2015-10-01

    Nonsyndromic cleft lip with or without cleft palate (NSCL ± P) is the most common orofacial birth defect, exhibiting variable prevalence around the world, often attributed to ethnic and environmental differences. Linkage analyses and genome-wide association studies have identified several genomic susceptibility regions for NSCL ± P, mostly in European-derived or Asian populations. Genetic predisposition to NSCL ± P is ethnicity-dependent, and the genetic basis of susceptibility to NSCL ± P likely varies among populations. The population of Brazil is highly admixed, with highly variable ancestry; thus, the genetic determinants of NSCL ± P susceptibility may be quite different. This study tested association of 8 single-nucleotide polymorphisms (SNPs), previously identified by genome-wide studies in other populations, with NSCL ± P in a Brazilian population with high African ancestry. SNPs rs560426, rs642961, rs1530300, rs987525, rs3758249, rs7078160, rs17085106, and rs13041247 were genotyped in 293 Brazilian patients with NSCL ± P and 352 unaffected Brazilian controls. Each sample was also genotyped for 40 biallelic short insertion/deletion polymorphic markers to characterize genetic ancestry. The average African ancestry background was 31.1% for the NSCL ± P group and 36.7% for the control group. After adjustment for ancestry and multiple testing, the minor alleles of rs3758249 (OR: 1.58, 95% CI: 1.25-2.01, P = 0.0001) and rs7078160 (OR: 1.59, 95% CI: 1.21-2.07, P = 0.0002) were significantly associated with risk of NSCL ± P. Polymorphisms located in IRF6 (rs642961) and 8q24 (rs1530300 and rs987525) showed marginal associations in this Brazilian population with high African ancestry. These results indicate that rs3758249 at 9q22 and rs7078160 at 10q25.3 represent risk loci for NSCL ± P in the Brazilian population with high African ancestry. © 2015 Wiley Periodicals, Inc.

  9. African ancestry protects against Alzheimer's disease-related neuropathology.

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    Schlesinger, D; Grinberg, L T; Alba, J G; Naslavsky, M S; Licinio, L; Farfel, J M; Suemoto, C K; de Lucena Ferretti, R E; Leite, R E P; de Andrade, M P; dos Santos, A C F; Brentani, H; Pasqualucci, C A; Nitrini, R; Jacob-Filho, W; Zatz, M

    2013-01-01

    Previous studies in dementia epidemiology have reported higher Alzheimer's disease rates in African-Americans when compared with White Americans. To determine whether genetically determined African ancestry is associated with neuropathological changes commonly associated with dementia, we analyzed a population-based brain bank in the highly admixed city of São Paulo, Brazil. African ancestry was estimated through the use of previously described ancestry-informative markers. Risk of presence of neuritic plaques, neurofibrillary tangles, small vessel disease, brain infarcts and Lewy bodies in subjects with significant African ancestry versus those without was determined. Results were adjusted for multiple environmental risk factors, demographic variables and apolipoprotein E genotype. African ancestry was inversely correlated with neuritic plaques (P=0.03). Subjects with significant African ancestry (n=112, 55.4%) showed lower prevalence of neuritic plaques in the univariate analysis (odds ratio (OR) 0.72, 95% confidence interval (CI) 0.55-0.95, P=0.01) and when adjusted for age, sex, APOE genotype and environmental risk factors (OR 0.43, 95% CI 0.21-0.89, P=0.02). There were no significant differences for the presence of other neuropathological alterations. We show for the first time, using genetically determined ancestry, that African ancestry may be highly protective of Alzheimer's disease neuropathology, functioning through either genetic variants or unknown environmental factors. Epidemiological studies correlating African-American race/ethnicity with increased Alzheimer's disease rates should not be interpreted as surrogates of genetic ancestry or considered to represent African-derived populations from the developing nations such as Brazil.

  10. The Relationship between Native American Ancestry, Body Mass Index and Diabetes Risk among Mexican-Americans.

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    Hu, Hao; Huff, Chad D; Yamamura, Yuko; Wu, Xifeng; Strom, Sara S

    2015-01-01

    Higher body mass index (BMI) is a well-established risk factor for type 2 diabetes, and rates of obesity and type 2 diabetes are substantially higher among Mexican-Americans relative to non-Hispanic European Americans. Mexican-Americans are genetically diverse, with a highly variable distribution of Native American, European, and African ancestries. Here, we evaluate the role of Native American ancestry on BMI and diabetes risk in a well-defined Mexican-American population. Participants were randomly selected among individuals residing in the Houston area who are enrolled in the Mexican-American Cohort study. Using a custom Illumina GoldenGate Panel, we genotyped DNA from 4,662 cohort participants for 87 Ancestry-Informative Markers. On average, the participants were of 50.2% Native American ancestry, 42.7% European ancestry and 7.1% African ancestry. Using multivariate linear regression, we found BMI and Native American ancestry were inversely correlated; individuals with ancestry were 2.5 times more likely to be severely obese compared to those with >80% Native American ancestry. Furthermore, we demonstrated an interaction between BMI and Native American ancestry in diabetes risk among women; Native American ancestry was a strong risk factor for diabetes only among overweight and obese women (OR = 1.190 for each 10% increase in Native American ancestry). This study offers new insight into the complex relationship between obesity, genetic ancestry, and their respective effects on diabetes risk. Findings from this study may improve the diabetes risk prediction among Mexican-American individuals thereby facilitating targeted prevention strategies.

  11. Surname-inferred Andean ancestry is associated with child stature and limb lengths at high altitude in Peru, but not at sea level.

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    Pomeroy, Emma; Wells, Jonathan C K; Stanojevic, Sanja; Miranda, J Jaime; Moore, Lorna G; Cole, Tim J; Stock, Jay T

    2015-01-01

    Native Andean ancestry gives partial protection from reduced birthweight at high altitude in the Andes compared with European ancestry. Whether Andean ancestry is also associated with body proportions and greater postnatal body size at altitude is unknown. Therefore, we tested whether a greater proportion of Andean ancestry is associated with stature and body proportions among Peruvian children at high and low altitude. Height, head circumference, head-trunk height, upper and lower limb lengths, and tibia, ulna, hand and foot lengths, were measured in 133 highland and 169 lowland children aged 6 months to 8.5 years. For highland and lowland groups separately, age-sex-adjusted anthropometry z scores were regressed on the number of indigenous parental surnames as a proxy for Andean ancestry, adjusting for potential confounders (maternal age and education, parity, altitude [highlands only]). Among highland children, greater Andean ancestry was negatively associated with stature and tibia, ulna, and lower limb lengths, independent of negative associations with greater altitude for these measurements. Relationships were strongest for tibia length: each additional Andean surname or 1,000 m increase at altitude among highland children was associated with 0.18 and 0.65 z score decreases in tibia length, respectively. Anthropometry was not significantly associated with ancestry among lowland children. Greater Andean ancestry is associated with shorter stature and limb measurements at high but not low altitude. Gene-environment interactions between high altitude and Andean ancestry may exacerbate the trade-off between chest dimensions and stature that was proposed previously, though we could not test this directly. © 2015 Wiley Periodicals, Inc.

  12. What Is Genetic Ancestry Testing?

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    ... What is genetic ancestry testing? What is genetic ancestry testing? Genetic ancestry testing, or genetic genealogy, is ... with other groups. For more information about genetic ancestry testing: The University of Utah provides video tutorials ...

  13. Highly discrepant proportions of female and male Scandinavian and British Isles ancestry within the isolated population of the Faroe Islands

    DEFF Research Database (Denmark)

    Als, Thomas D; Jorgensen, Tove H; Børglum, Anders D

    2006-01-01

    Isles ancestry. In the present study we used 122 new and 19 previously published hypervariable region I sequences of the mitochondrial control region to analyse the genetic diversity of the Faroese population and compare it with other populations in the North Atlantic region. The analyses suggested...... that the Faroese mtDNA pool has been affected by genetic drift, and is among the most homogenous and isolated in the North Atlantic region. This will have implications for attempts to locate genes for complex disorders. To obtain estimates of Scandinavian vs British Isles ancestry proportions, we applied...... a frequency-based admixture approach taking private haplotypes into account by the use of phylogenetic information. While previous studies have suggested an excess of Scandinavian ancestry among the male settlers of the Faroe Islands, the current study indicates an excess of British Isles ancestry among...

  14. Denisovan Ancestry in East Eurasian and Native American Populations.

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    Qin, Pengfei; Stoneking, Mark

    2015-10-01

    Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide single nucleotide polymorphism data from 2,493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Highly discrepant proportions of female and male Scandinavian and British Isles ancestry within the isolated population of the Faroe Islands

    DEFF Research Database (Denmark)

    Als, Thomas Damm; TH, Jørgensen; Børglum, Anders

    2006-01-01

    The Faroe Islands in the North Atlantic Ocean are inhabited by a small population, whose origin is thought to date back to the Viking Age. Historical, archaeological and linguistic evidence indicates that the present population of the Faroe Islands may have a mixture of Scandinavian and British...... a frequency-based admixture approach taking private haplotypes into account by the use of phylogenetic information. While previous studies have suggested an excess of Scandinavian ancestry among the male settlers of the Faroe Islands, the current study indicates an excess of British Isles ancestry among...

  16. Amerind ancestry, socioeconomic status and the genetics of type 2 diabetes in a Colombian population.

    Directory of Open Access Journals (Sweden)

    Desmond D Campbell

    Full Text Available The "thrifty genotype" hypothesis proposes that the high prevalence of type 2 diabetes (T2D in Native Americans and admixed Latin Americans has a genetic basis and reflects an evolutionary adaptation to a past low calorie/high exercise lifestyle. However, identification of the gene variants underpinning this hypothesis remains elusive. Here we assessed the role of Native American ancestry, socioeconomic status (SES and 21 candidate gene loci in susceptibility to T2D in a sample of 876 T2D cases and 399 controls from Antioquia (Colombia. Although mean Native American ancestry is significantly higher in T2D cases than in controls (32% v 29%, this difference is confounded by the correlation of ancestry with SES, which is a stronger predictor of disease status. Nominally significant association (P1 was observed for markers selected from previous T2D genome-wide association studies, consistent with a role for Old World variants in susceptibility to T2D in Latin Americans. No association was found to the only known Native American-specific gene variant previously associated with T2D in a Mexican sample (rs9282541 in ABCA1. An admixture mapping scan with 1,536 ancestry informative markers (AIMs did not identify genome regions with significant deviation of ancestry in Antioquia. Exclusion analysis indicates that this scan rules out ~95% of the genome as harboring loci with ancestry risk ratios >1.22 (at P < 0.05.

  17. Effects of Amerindian Genetic Ancestry on Clinical Variables and Therapy in Patients with Rheumatoid Arthritis.

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    Sánchez, Elena; García de la Torre, Ignacio; Sacnún, Mónica; Goñi, Mario; Berbotto, Guillermo; Paira, Sergio; Musuruana, Jorge Luis; Graf, César; Alvarellos, Alejandro; Messina, Osvaldo D; Babini, Alejandra; Strusberg, Ingrid; Marcos, Juan Carlos; Scherbarth, Hugo; Spindler, Alberto; Quinteros, Ana; Toloza, Sergio; Moreno, José Luis C; Catoggio, Luis J; Tate, Guillermo; Eimon, Alicia; Citera, Gustavo; Pellet, Antonio Catalán; Nasswetter, Gustavo; Cardiel, Mario H; Miranda, Pedro; Ballesteros, Francisco; Esquivel-Valerio, Jorge A; Maradiaga-Ceceña, Marco A; Acevedo-Vásquez, Eduardo M; García, Conrado García; Tusié-Luna, Teresa; Pons-Estel, Bernardo A; Alarcón-Riquelme, Marta E

    2017-12-01

    To define whether Amerindian genetic ancestry correlates with clinical and therapeutic variables in admixed individuals with rheumatoid arthritis (RA) from Latin America. Patients with RA (n = 1347) and healthy controls (n = 1012) from Argentina, Mexico, Chile, and Peru were included. Samples were genotyped for the Immunochip v1 using the Illumina platform. Clinical data were obtained through interviews or the clinical history. Percentage of Amerindian ancestry was comparable between cases and controls. Morning stiffness (p ancestry after Bonferroni correction. Higher Amerindian ancestry correlated only with weight loss (p Bonferroni ancestry correlated with higher doses of azathioprine (p ancestry protects against most major clinical criteria of RA, but regarding the association of RF with increased European ancestry, age, sex, and smoking are modifiers. Ancestry also correlates with the therapeutic profiles.

  18. A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy.

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    Corbett-Detig, Russell; Nielsen, Rasmus

    2017-01-01

    Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry

  19. A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set.

    Science.gov (United States)

    Santos, Hadassa C; Horimoto, Andréa V R; Tarazona-Santos, Eduardo; Rodrigues-Soares, Fernanda; Barreto, Mauricio L; Horta, Bernardo L; Lima-Costa, Maria F; Gouveia, Mateus H; Machado, Moara; Silva, Thiago M; Sanches, José M; Esteban, Nubia; Magalhaes, Wagner C S; Rodrigues, Maíra R; Kehdy, Fernanda S G; Pereira, Alexandre C

    2016-05-01

    The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.

  20. African ancestry and its correlation to type 2 diabetes in African Americans: a genetic admixture analysis in three U.S. population cohorts.

    Directory of Open Access Journals (Sweden)

    Ching-Yu Cheng

    Full Text Available The risk of type 2 diabetes is approximately 2-fold higher in African Americans than in European Americans even after adjusting for known environmental risk factors, including socioeconomic status (SES, suggesting that genetic factors may explain some of this population difference in disease risk. However, relatively few genetic studies have examined this hypothesis in a large sample of African Americans with and without diabetes. Therefore, we performed an admixture analysis using 2,189 ancestry-informative markers in 7,021 African Americans (2,373 with type 2 diabetes and 4,648 without from the Atherosclerosis Risk in Communities Study, the Jackson Heart Study, and the Multiethnic Cohort to 1 determine the association of type 2 diabetes and its related quantitative traits with African ancestry controlling for measures of SES and 2 identify genetic loci for type 2 diabetes through a genome-wide admixture mapping scan. The median percentage of African ancestry of diabetic participants was slightly greater than that of non-diabetic participants (study-adjusted difference = 1.6%, P<0.001. The odds ratio for diabetes comparing participants in the highest vs. lowest tertile of African ancestry was 1.33 (95% confidence interval 1.13-1.55, after adjustment for age, sex, study, body mass index (BMI, and SES. Admixture scans identified two potential loci for diabetes at 12p13.31 (LOD = 4.0 and 13q14.3 (Z score = 4.5, P = 6.6 × 10(-6. In conclusion, genetic ancestry has a significant association with type 2 diabetes above and beyond its association with non-genetic risk factors for type 2 diabetes in African Americans, but no single gene with a major effect is sufficient to explain a large portion of the observed population difference in risk of diabetes. There undoubtedly is a complex interplay among specific genetic loci and non-genetic factors, which may both be associated with overall admixture, leading to the observed ethnic differences in diabetes

  1. Genomics assisted ancestry deconvolution in grape.

    Directory of Open Access Journals (Sweden)

    Jason Sawler

    Full Text Available The genus Vitis (the grapevine is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world's most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a principal components analysis (PCA based ancestry estimation method to calculate admixture proportions of hybrid grapes in the United States Department of Agriculture grape germplasm collection using genome-wide polymorphism data. We find that grape breeders have backcrossed to both the domesticated V. vinifera and wild Vitis species and that reasonably accurate genome-wide ancestry estimation can be performed on interspecific Vitis hybrids using a panel of fewer than 50 ancestry informative markers (AIMs. We compare measures of ancestry informativeness used in selecting SNP panels for two-way admixture estimation, and verify the accuracy of our method on simulated populations of admixed offspring. Our method of ancestry deconvolution provides a first step towards selection at the seed or seedling stage for desirable admixture profiles, which will facilitate marker-assisted breeding that aims to introgress traits from wild Vitis species while retaining the desirable characteristics of elite V. vinifera cultivars.

  2. Genomics Assisted Ancestry Deconvolution in Grape

    Science.gov (United States)

    Sawler, Jason; Reisch, Bruce; Aradhya, Mallikarjuna K.; Prins, Bernard; Zhong, Gan-Yuan; Schwaninger, Heidi; Simon, Charles; Buckler, Edward; Myles, Sean

    2013-01-01

    The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a principal components analysis (PCA) based ancestry estimation method to calculate admixture proportions of hybrid grapes in the United States Department of Agriculture grape germplasm collection using genome-wide polymorphism data. We find that grape breeders have backcrossed to both the domesticated V. vinifera and wild Vitis species and that reasonably accurate genome-wide ancestry estimation can be performed on interspecific Vitis hybrids using a panel of fewer than 50 ancestry informative markers (AIMs). We compare measures of ancestry informativeness used in selecting SNP panels for two-way admixture estimation, and verify the accuracy of our method on simulated populations of admixed offspring. Our method of ancestry deconvolution provides a first step towards selection at the seed or seedling stage for desirable admixture profiles, which will facilitate marker-assisted breeding that aims to introgress traits from wild Vitis species while retaining the desirable characteristics of elite V. vinifera cultivars. PMID:24244717

  3. Genetic and environmental risk factors for rheumatoid arthritis in a UK African ancestry population: the GENRA case-control study.

    Science.gov (United States)

    Traylor, Matthew; Curtis, Charles; Patel, Hamel; Breen, Gerome; Hyuck Lee, Sang; Xu, Xiaohui; Newhouse, Stephen; Dobson, Richard; Steer, Sophia; Cope, Andrew P; Markus, Hugh S; Lewis, Cathryn M; Scott, Ian C

    2017-08-01

    To evaluate whether genetic and environmental factors associated with RA in European and Asian ancestry populations are also associated with RA in African ancestry individuals. A case-control study was undertaken in 197 RA cases and 868 controls of African ancestry (Black African, Black Caribbean or Black British ethnicity) from South London. Smoking and alcohol consumption data at RA diagnosis was captured. Genotyping was undertaken (Multi-Ethnic Genotyping Array) and human leukocyte antigen (HLA) alleles imputed. The following European/Asian RA susceptibility factors were tested: 99 genome-wide loci combined into a genetic risk score; HLA region [20 haplotypes; shared epitope (SE)]; smoking; and alcohol consumption. The SE was tested for its association with radiological erosions. Logistic regression models were used, including ancestry-informative principal components, to control for admixture. European/Asian susceptibility loci were associated with RA in African ancestry individuals. The genetic risk score provided an odds ratio (OR) for RA of 1.53 (95% CI: 1.31, 1.79; P = 1.3 × 10 - 7 ). HLA haplotype ORs in European and African ancestry individuals were highly correlated ( r = 0.83, 95% CI: 0.56, 0.94; P = 1.1 × 10 - 4 ). Ever-smoking increased (OR = 2.36, 95% CI: 1.46, 3.82; P = 4.6 × 10 - 4 ) and drinking alcohol reduced (OR = 0.34, 95% CI: 0.20, 0.56; P = 2.7 × 10 - 5 ) RA risk in African ancestry individuals. The SE was associated with erosions (OR = 2.61, 95% CI: 1.36, 5.01; P = 3.9 × 10 - 3 ). Gene-environment RA risk factors identified in European/Asian ancestry populations are relevant in African ancestry individuals. As modern statistical methods facilitate analysing ancestrally diverse populations, future genetic studies should incorporate African ancestry individuals to ensure their implications for precision medicine are universally applicable. © The Author 2017. Published by Oxford University Press on behalf of the British Society for

  4. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels

    DEFF Research Database (Denmark)

    Santos, C; Fondevila, M; Ballard, D

    2015-01-01

    that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory...... relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using...... the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95...

  5. Crinoid ancestry without blastozoans

    Directory of Open Access Journals (Sweden)

    Thomas E. Guensburg

    2016-06-01

    Full Text Available At present, a debate in the paleontologic literature focuses on whether or not the immediate ancestry of the Crinoidea lies in an unidentified member of the Blastozoa, which includes eocrinoids and an assemblage known variously as the “cystoids”. Those proposing to derive crinoids from within the blastozoans have recently argued for homologies in the construction of the oral region of certain derived taxa from both groups. An opposing viewpoint, outlined here, finds evidence that aside from plesiomorphies, proposed similarities are superficial and homoplastic. We suggest these superficialities represent convergent adaptive strategies. Earliest crinoids express ambulacral traits unlike any blastozoan but that are expressed in the only other pentaradial echinoderms with a known record early enough to be considered in the context of crinoid origins, edrioasteroids and edrioasteroid-like stem echinoderms.

  6. Inferring Genetic Ancestry: Opportunities, Challenges, and Implications

    OpenAIRE

    Royal, Charmaine D.; Novembre, John; Fullerton, Stephanie M.; Goldstein, David B.; Long, Jeffrey C.; Bamshad, Michael J.; Clark, Andrew G.

    2010-01-01

    Increasing public interest in direct-to-consumer (DTC) genetic ancestry testing has been accompanied by growing concern about issues ranging from the personal and societal implications of the testing to the scientific validity of ancestry inference. The very concept of “ancestry” is subject to misunderstanding in both the general and scientific communities. What do we mean by ancestry? How exactly is ancestry measured? How far back can such ancestry be defined and by which genetic tools? How ...

  7. What Is Genetic Ancestry Testing?

    Science.gov (United States)

    ... consumer genetic testing? What kinds of direct-to-consumer genetic tests are available? What is genetic ancestry testing? What are the benefits and risks of direct-to-consumer genetic testing? ...

  8. What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression.

    Science.gov (United States)

    Hernandez-Pacheco, Natalia; Flores, Carlos; Oh, Sam S; Burchard, Esteban G; Pino-Yanes, Maria

    2016-07-01

    Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.

  9. The common ancestry of life

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2010-11-01

    Full Text Available Abstract Background It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a common-ancestry model and a multiple-ancestry model to predict sequences of universally conserved proteins. Results We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis. Conclusion A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming. Reviewers this article was reviewed by William Martin, Ivan Iossifov (nominated by Andrey Rzhetsky and Arcady Mushegian. For the complete reviews, see the Reviewers' Report section.

  10. High accurate volume holographic correlator with 4000 parallel correlation channels

    Science.gov (United States)

    Ni, Kai; Qu, Zongyao; Cao, Liangcai; Su, Ping; He, Qingsheng; Jin, Guofan

    2008-03-01

    Volume holographic correlator allows simultaneously calculate the two-dimensional inner product between the input image and each stored image. We have recently experimentally implemented in VHC 4000 parallel correlation channels with better than 98% output accuracy in a single location in a crystal. The speckle modulation is used to suppress the sidelobes of the correlation patterns, allowing more correlation spots to be contained in the output plane. A modified exposure schedule is designed to ensure the hologram in each channel with unity diffraction efficiency. In this schedule, a restricted coefficient was introduced into the original exposure schedule to solve the problem that the sensitivity and time constant of the crystal will change as a time function when in high-capacity storage. An interleaving method is proposed to improve the output accuracy. By unifying the distribution of the input and stored image patterns without changing the inner products between them, this method could eliminate the impact of correlation pattern variety on calculated inner product values. Moreover, by using this method, the maximum correlation spot size is reduced, which decreases the required minimum safe clearance between neighboring spots in the output plane, allowing more spots to be parallely detected without crosstalk. The experimental results are given and analyzed.

  11. Explicit Modeling of Ancestry Improves Polygenic Risk Scores and BLUP Prediction.

    Science.gov (United States)

    Chen, Chia-Yen; Han, Jiali; Hunter, David J; Kraft, Peter; Price, Alkes L

    2015-09-01

    Polygenic prediction using genome-wide SNPs can provide high prediction accuracy for complex traits. Here, we investigate the question of how to account for genetic ancestry when conducting polygenic prediction. We show that the accuracy of polygenic prediction in structured populations may be partly due to genetic ancestry. However, we hypothesized that explicitly modeling ancestry could improve polygenic prediction accuracy. We analyzed three GWAS of hair color (HC), tanning ability (TA), and basal cell carcinoma (BCC) in European Americans (sample size from 7,440 to 9,822) and considered two widely used polygenic prediction approaches: polygenic risk scores (PRSs) and best linear unbiased prediction (BLUP). We compared polygenic prediction without correction for ancestry to polygenic prediction with ancestry as a separate component in the model. In 10-fold cross-validation using the PRS approach, the R(2) for HC increased by 66% (0.0456-0.0755; P ancestry, which prevents ancestry effects from entering into each SNP effect and being overweighted. Surprisingly, explicitly modeling ancestry produces a similar improvement when using the BLUP approach, which fits all SNPs simultaneously in a single variance component and causes ancestry to be underweighted. We validate our findings via simulations, which show that the differences in prediction accuracy will increase in magnitude as sample sizes increase. In summary, our results show that explicitly modeling ancestry can be important in both PRS and BLUP prediction. © 2015 WILEY PERIODICALS, INC.

  12. AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

    Science.gov (United States)

    Schaefer, Nathan K; Shapiro, Beth; Green, Richard E

    2017-04-04

    Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.

  13. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.

    Science.gov (United States)

    Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

    2014-09-01

    The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

  14. Particle correlations in high-multiplicity reactions

    International Nuclear Information System (INIS)

    Hayot, Fernand.

    1976-01-01

    A comprehensive review of the results obtained in the study of short range correlations in high-multiplicity events is presented: introduction of the fundamental short-range order hypothesis, introduction of clusters in nondiffractive events (only the production of identical, independent, and neutral clusters was considered); search for short range dynamical effects between particles coming from the decay of a same cluster by studying two-particle rapidity correlations in inclusive and semi-inclusive experiments; study of transverse momentum correlations [fr

  15. Angular correlations and high energy evolution

    International Nuclear Information System (INIS)

    Kovner, Alex; Lublinsky, Michael

    2011-01-01

    We address the question of to what extent JIMWLK evolution is capable of taking into account angular correlations in a high energy hadronic wave function. Our conclusion is that angular (and indeed other) correlations in the wave function cannot be reliably calculated without taking into account Pomeron loops in the evolution. As an example we study numerically the energy evolution of angular correlations between dipole scattering amplitudes in the framework of the large N c approximation to JIMWLK evolution (the 'projectile dipole model'). Target correlations are introduced via averaging over an (isotropic) ensemble of anisotropic initial conditions. We find that correlations disappear very quickly with rapidity even inside the saturation radius. This is in accordance with our physical picture of JIMWLK evolution. The actual correlations inside the saturation radius in the target QCD wave function, on the other hand, should remain sizable at any rapidity.

  16. Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses

    Science.gov (United States)

    Ramey, Andy M.; Reeves, Andrew; Teslaa, Joshua L.; Nashold, Sean W.; Donnelly, Tyrone F.; Bahl, Justin; Hall, Jeffrey S.

    2016-01-01

    Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November–December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses. Results of phylogenetic analyses and estimates for times of most recent common ancestry support migratory birds sampled in Beringia as maintaining viral diversity closely related to novel highly pathogenic influenza A virus genotypes detected in North America. Although our results do not elucidate the route by which highly pathogenic influenza A viruses were introduced into North America, genetic evidence is consistent with the hypothesized trans-Beringian route of introduction via migratory birds.

  17. Dihadron correlations at high pT

    International Nuclear Information System (INIS)

    Filimonov, Kirill

    2004-01-01

    Jet quenching in the matter created in high energy nucleus/nucleus collisions provides a tomographic tool to probe the medium properties. Recent experimental results from the Relativistic Heavy-Ion Collider (RHIC) on characterization of jet production via dihadron correlations at high transverse momentum are reviewed. Expectations from the dihadron measurements for the lower energy √s NN = 62.4 GeV RHIC run are discussed

  18. Uniparental ancestry markers in Chilean populations

    Directory of Open Access Journals (Sweden)

    Camilla Dutra Vieira-Machado

    Full Text Available Abstract The presence of Native Americans, Europeans, and Africans has led to the development of a multi-ethnic, admixed population in Chile. This study aimed to contribute to the characterization of the uniparental genetic structure of three Chilean regions. Newborns from seven hospitals in Independencia, Providencia, Santiago, Curicó, Cauquenes, Valdívia, and Puerto Montt communes, belonging to the Chilean regions of Santiago, Maule, and Los Lagos, were studied. The presence of Native American mitochondrial DNA (mtDNA haplogroups and two markers present in the non-recombinant region of the Y chromosome, DYS199 and DYS287, indicative of Native American and African ancestry, respectively, was determined. A high Native American matrilineal contribution and a low Native American and African patrilineal contributions were found in all three studied regions. As previously found in Chilean admixed populations, the Native American matrilineal contribution was lower in Santiago than in the other studied regions. However, there was an unexpectedly higher contribution of Native American ancestry in one of the studied communes in Santiago, probably due to the high rate of immigration from other regions of the country. The population genetic sub-structure we detected in Santiago using few uniparental markers requires further confirmation, owing to possible stratification for autosomal and X-chromosome markers.

  19. Genomic ancestry as a predictor of haemodynamic profile in heart failure.

    Science.gov (United States)

    Bernardez-Pereira, Sabrina; Gioli-Pereira, Luciana; Marcondes-Braga, Fabiana G; Santos, Paulo Caleb Junior Lima; Spina, Joceli Mabel Rocha; Horimoto, Andréa Roseli Vançan Russo; Santos, Hadassa Campos; Bacal, Fernando; Fernandes, Fábio; Mansur, Alfredo Jose; Pietrobon, Ricardo; Krieger, José Eduardo; Mesquita, Evandro Tinoco; Pereira, Alexandre Costa

    2016-01-01

    The aim of this study is to assess the association between genetic ancestry, self-declared race and haemodynamic parameters in patients with chronic heart failure (HF). Observational, cross-sectional study. Eligible participants were aged between 18 and 80 years; ejection fraction was ≤50%. Patients underwent genetic analysis of ancestry informative markers, echocardiography and impedance cardiography (ICG). Race was determined by self-classification into two groups: white and non-white. Genomic ancestry was estimated using a panel of 101 348 polymorphic markers and three continental reference populations (European, African and Native American). Our study included 362 patients with HF between August 2012 and August 2014. 123 patients with HF declared themselves as white and 234 patients declared themselves as non-white. No statistically significant differences were found regarding the ICG parameters according to self-declared race. The Amerindian ancestry was positively correlated with systolic time ratio (r=0.109, pancestry. In multiple linear regression, African ancestry remained associated with the E/e' ratio, even after adjustment to risk factors. The African genetic ancestry was associated with worse parameters of diastolic function; the Amerindian ancestry correlated with a worse pattern of ventricular contractility, while self-declared colour was not helpful to infer haemodynamic profiles in HF. NTC02043431.

  20. Ancestry as a potential modifier of gene expression in breast tumors from Colombian women.

    Science.gov (United States)

    Serrano-Gómez, Silvia J; Sanabria-Salas, María Carolina; Garay, Jone; Baddoo, Melody C; Hernández-Suarez, Gustavo; Mejía, Juan Carlos; García, Oscar; Miele, Lucio; Fejerman, Laura; Zabaleta, Jovanny

    2017-01-01

    Hispanic/Latino populations are a genetically admixed and heterogeneous group, with variable fractions of European, Indigenous American and African ancestries. The molecular profile of breast cancer has been widely described in non-Hispanic Whites but equivalent knowledge is lacking in Hispanic/Latinas. We have previously reported that the most prevalent breast cancer intrinsic subtype in Colombian women was Luminal B as defined by St. Gallen 2013 criteria. In this study we explored ancestry-associated differences in molecular profiles of Luminal B tumors among these highly admixed women. We performed whole-transcriptome RNA-seq analysis in 42 Luminal tumors (21 Luminal A and 21 Luminal B) from Colombian women. Genetic ancestry was estimated from a panel of 80 ancestry-informative markers (AIM). We categorized patients according to Luminal subtype and to the proportion of European and Indigenous American ancestry and performed differential expression analysis comparing Luminal B against Luminal A tumors according to the assigned ancestry groups. We found 5 genes potentially modulated by genetic ancestry: ERBB2 (log2FC = 2.367, padjancestry (p = 0.02, B = 3.11). This association was not biased by the distribution of HER2+ tumors among the groups analyzed. Our results suggest that genetic ancestry in Hispanic/Latina women might modify ERBB2 gene expression in Luminal tumors. Further analyses are needed to confirm these findings and explore their prognostic value.

  1. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise.

    Science.gov (United States)

    Santos, C; Fondevila, M; Ballard, D; Banemann, R; Bento, A M; Børsting, C; Branicki, W; Brisighelli, F; Burrington, M; Capal, T; Chaitanya, L; Daniel, R; Decroyer, V; England, R; Gettings, K B; Gross, T E; Haas, C; Harteveld, J; Hoff-Olsen, P; Hoffmann, A; Kayser, M; Kohler, P; Linacre, A; Mayr-Eduardoff, M; McGovern, C; Morling, N; O'Donnell, G; Parson, W; Pascali, V L; Porto, M J; Roseth, A; Schneider, P M; Sijen, T; Stenzl, V; Court, D Syndercombe; Templeton, J E; Turanska, M; Vallone, P M; Oorschot, R A H van; Zatkalikova, L; Carracedo, Á; Phillips, C

    2015-11-01

    There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain

  2. Higher percent body fat in young women with lower physical activity level and greater proportion Pacific Islander ancestry.

    Science.gov (United States)

    Black, Nate; Nabokov, Vanessa; Vijayadeva, Vinutha; Novotny, Rachel

    2011-11-01

    Samoan women exhibit high rates of obesity, which can possibly be attenuated through diet and physical activity. Obesity, and body fatness in particular, is associated with increased risk for chronic diseases. Ancestry, physical activity, and dietary patterns have been associated with body composition. Using a cross-sectional design, the relative importance of proportion of Pacific Islander (PI) ancestry, level of physical activity, and macronutrients among healthy women in Honolulu, Hawai'i, ages 18 to 28 years was examined. All data were collected between January 2003 and December 2004. Percent body fat (%BF) was determined by whole body dual energy x-ray absorptiometry (DXA). Nutrient data were derived from a three-day food record. Means and standard deviations were computed for all variables of interest. Bivariate correlation analysis was used to determine correlates of %BF. Multiple regression analysis was used to determine relative contribution of variables significantly associated with %BF. Proportion of PI ancestry was significantly positively associated with %BF (P=0.0001). Physical activity level was significantly negatively associated with %BF (P=0.0006). Intervention to increase physical activity level of young Samoan women may be effective to decrease body fat and improve health. CRC-NIH grant: 0216.

  3. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  4. Mitochondrial and genomic ancestry are associated with etiology of heart failure in Brazilian patients.

    Science.gov (United States)

    Cardena, M M S G; Ribeiro-Dos-Santos, A K; Santos, S E B; Mansur, A J; Bernardez-Pereira, S; Santos, P C J L; Pereira, A C; Fridman, C

    2016-02-01

    There is a high prevalence of heart failure (HF) in the general population, but it is more common in black people. We evaluated the association between genomic ancestry and mitochondrial haplogroups (mt-haplogroups) with HF etiology in 503 Brazilian patients. We elicited Mt-haplogroups by analyzing the control region of mitochondrial DNA, and genomic ancestry, by using 48 autosomal insertion-deletion ancestry informative markers. Hypertensive (28.6%, n=144) and ischemic (28.4%, n=143) etiologies of HF were the most prevalent herein. Our results showed that 233 individuals (46.3%) presented African mitochondrial (mt)-haplogroups, and the major contribution in the genomic ancestry analysis was the European ancestry (57.5% (±22.1%)). African mt-haplogroups were positively associated with a diagnosis of hypertensive cardiomyopathy (odds ratio, OR 1.55, confidence interval, CI 95% 1.04-2.44, P=0.04) when compared with European mt-haplogroups. Regarding the genomic ancestry, the African ancestry variant had higher risks (OR 7.84, 95% CI 2.81-21.91, Pancestry variant had lower risks (OR 0.14, 95% CI 0.04-5.00, Pancestry showed an OR of 4.05 (CI 95% 1.53-10.74, P=0.005), whereas African ancestry showed an OR of 0.17 (CI 95% 0.06-0.48, P=0.001) for developing ischemic etiology. In conclusion, this study supports the importance of using ancestry informative markers and mitochondrial DNA to study the genetics of complex diseases in admixed populations to improve the management, treatment and prevention of these illnesses. Therefore, the ancestry informative markers and mt-haplogroups could provide new biomarkers to be associated with HF etiologies and be used as a premise for more specific management.

  5. High-order nonuniformly correlated beams

    Science.gov (United States)

    Wu, Dan; Wang, Fei; Cai, Yangjian

    2018-02-01

    We have introduced a class of partially coherent beams with spatially varying correlations named high-order nonuniformly correlated (HNUC) beams, as an extension of conventional nonuniformly correlated (NUC) beams. Such beams bring a new parameter (mode order) which is used to tailor the spatial coherence properties. The behavior of the spectral density of the HNUC beams on propagation has been investigated through numerical examples with the help of discrete model decomposition and fast Fourier transform (FFT) algorithm. Our results reveal that by selecting the mode order appropriately, the more sharpened intensity maxima can be achieved at a certain propagation distance compared to that of the NUC beams, and the lateral shift of the intensity maxima on propagation is closed related to the mode order. Furthermore, analytical expressions for the r.m.s width and the propagation factor of the HNUC beams on free-space propagation are derived by means of Wigner distribution function. The influence of initial beam parameters on the evolution of the r.m.s width and the propagation factor, and the relation between the r.m.s width and the occurring of the sharpened intensity maxima on propagation have been studied and discussed in detail.

  6. LAIT: a local ancestry inference toolkit.

    Science.gov (United States)

    Hui, Daniel; Fang, Zhou; Lin, Jerome; Duan, Qing; Li, Yun; Hu, Ming; Chen, Wei

    2017-09-06

    Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. We developed a tool set, Local Ancestry Inference Toolkit (LAIT), which can convert standardized files into software-specific input file formats as well as standardize and summarize inference results for four popular local ancestry inference software: HAPMIX, LAMP, LAMP-LD, and ELAI. We tested LAIT using both simulated and real data sets and demonstrated that LAIT provides convenience to run multiple local ancestry inference software. In addition, we evaluated the performance of local ancestry software among different supported software packages, mainly focusing on inference accuracy and computational resources used. We provided a toolkit to facilitate the use of local ancestry inference software, especially for users with limited bioinformatics background.

  7. The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected.

    Directory of Open Access Journals (Sweden)

    Sérgio D J Pena

    2011-02-01

    Full Text Available Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a "total ancestry" estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries--a phenomenon described and intended as the "whitening of Brazil"--is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil

  8. Population genetics models of local ancestry.

    Science.gov (United States)

    Gravel, Simon

    2012-06-01

    Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

  9. Highly-correlated charges in polyelectrolyte gels

    Science.gov (United States)

    Sing, Charles; Zwanikken, Johannes; Olvera de La Cruz, Monica

    2013-03-01

    Polyelectrolyte gels are ubiquitous in polymer physics due to their attractive combination of structural and chemical features that permit the realization of ``environmentally responsive'' systems. The conventional conceptual picture of the volume response of these systems is based on a competition between osmotic and elastic effects. We elaborate on this fundamental understanding by including ion correlations through the use of liquid-state integral equation theory. This allows for a statistical mechanical representation of the state of the system that not only surpasses traditional Poisson-Boltzmann theories but also renders structural features in a highly accurate fashion. In particular, the local ion structure is elucidated, allowing for detailed articulation of charge inversion and condensation effects in the context of gel swelling. The inclusion of correlations has a number of ramifications that become apparent, with enhanced gel collapse and excluded volume competitions that give rise to novel and ion-dependent reentrant swelling effects. We expect this rigorous theory to prove instructive in understanding any number of gelated structures, such as chromosomes or designed synthetic materials for drug delivery.

  10. Dissecting the within-Africa ancestry of populations of African descent in the Americas.

    Science.gov (United States)

    Stefflova, Klara; Dulik, Matthew C; Barnholtz-Sloan, Jill S; Pai, Athma A; Walker, Amy H; Rebbeck, Timothy R

    2011-01-06

    The ancestry of African-descended Americans is known to be drawn from three distinct populations: African, European, and Native American. While many studies consider this continental admixture, few account for the genetically distinct sources of ancestry within Africa--the continent with the highest genetic variation. Here, we dissect the within-Africa genetic ancestry of various populations of the Americas self-identified as having primarily African ancestry using uniparentally inherited mitochondrial DNA. We first confirmed that our results obtained using uniparentally-derived group admixture estimates are correlated with the average autosomal-derived individual admixture estimates (hence are relevant to genomic ancestry) by assessing continental admixture using both types of markers (mtDNA and Y-chromosome vs. ancestry informative markers). We then focused on the within-Africa maternal ancestry, mining our comprehensive database of published mtDNA variation (∼5800 individuals from 143 African populations) that helped us thoroughly dissect the African mtDNA pool. Using this well-defined African mtDNA variation, we quantified the relative contributions of maternal genetic ancestry from multiple W/WC/SW/SE (West to South East) African populations to the different pools of today's African-descended Americans of North and South America and the Caribbean. Our analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled

  11. Lumbee Native American ancestry and the incidence of aggressive histologic subtypes of endometrial cancer

    Directory of Open Access Journals (Sweden)

    Chelsea Zhang

    2015-08-01

    Conclusion: In this retrospective cohort analysis, Lumbee Native American ancestry was not a significant independent predictor of rates of high-risk histological subtypes of endometrial cancer or poor survival outcomes.

  12. Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study.

    Directory of Open Access Journals (Sweden)

    Melinda C Aldrich

    Full Text Available BACKGROUND: Smoking tobacco reduces lung function. African Americans have both lower lung function and decreased metabolism of tobacco smoke compared to European Americans. African ancestry is also associated with lower pulmonary function in African Americans. We aimed to determine whether African ancestry modifies the association between smoking and lung function and its rate of decline in African Americans. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated a prospective ongoing cohort of 1,281 African Americans participating in the Health, Aging, and Body Composition (Health ABC Study initiated in 1997. We also examined an ongoing prospective cohort initiated in 1985 of 1,223 African Americans in the Coronary Artery Disease in Young Adults (CARDIA Study. Pulmonary function and tobacco smoking exposure were measured at baseline and repeatedly over the follow-up period. Individual genetic ancestry proportions were estimated using ancestry informative markers selected to distinguish European and West African ancestry. African Americans with a high proportion of African ancestry had lower baseline forced expiratory volume in one second (FEV₁ per pack-year of smoking (-5.7 ml FEV₁/ smoking pack-year compared with smokers with lower African ancestry (-4.6 ml in FEV₁/ smoking pack-year (interaction P value  = 0.17. Longitudinal analyses revealed a suggestive interaction between smoking, and African ancestry on the rate of FEV(1 decline in Health ABC and independently replicated in CARDIA. CONCLUSIONS/SIGNIFICANCE: African American individuals with a high proportion of African ancestry are at greater risk for losing lung function while smoking.

  13. Inference of biogeographical ancestry across central regions of Eurasia.

    Science.gov (United States)

    Bulbul, O; Filoglu, G; Zorlu, T; Altuncul, H; Freire-Aradas, A; Söchtig, J; Ruiz, Y; Klintschar, M; Triki-Fendri, S; Rebai, A; Phillips, C; Lareu, M V; Carracedo, Á; Schneider, P M

    2016-01-01

    The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

  14. A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín.

    Science.gov (United States)

    Conley, Andrew B; Rishishwar, Lavanya; Norris, Emily T; Valderrama-Aguirre, Augusto; Mariño-Ramírez, Leonardo; Medina-Rivas, Miguel A; Jordan, I King

    2017-10-05

    At least 20% of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia's Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared with 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to overestimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population, and Medellín having relatively more shared ancestry with West African populations in Sierra

  15. Electronic behavior of highly correlated metals

    International Nuclear Information System (INIS)

    Reich, A.

    1988-10-01

    This thesis addresses the question of the strongly interacting many-body problem: that is, systems where the interparticle correlations are so strong as to defy perturbative approaches. These subtle correlations occur in narrow band materials, such as the lanthanides and actinides, wherein the f-electrons are so localized that a variety of new phenomena, including intermediate-valence and heavy-fermionic behavior, may occur. As well, one has the alloying problem, where local interactions are paramount in determining the overall behavior. The technique employed in dealing with these systems is the Small Cluster method, wherein the full many-body Hamiltonian for a small grouping of atoms, coupled with periodic boundary conditions, is solved exactly. This is tantamount to solving a bulk crystal at the high points of symmetry in the Brillouin Zone. The mathematical overhead is further reduced by employing the full space group and spin symmetries. By its very nature, the Small Cluster method is well able to handle short-range interactions, as well as the combinatorial complexity of the many-body problem, on an equal footing. The nature of long-range order and phase transition behavior cannot be incorporated, but sometimes clues as to their origin can be discerned. The calculations presented include: a two-band Anderson model for an intermediate-valence system, wherein photoemission and fluctuation behavior is examined; a single-band Hubbard model for a ternary alloy system, such as copper-silver-gold; and a Hubbard model for a heavy- fermion system, wherein Fermi surface, transport, magnetic and superconducting properties are discussed. 148 refs., 31 figs., 24 tabs

  16. Self-declared ethnicity and genomic ancestry in prostate cancer patients from Brazil.

    Science.gov (United States)

    Oliveira, J S; Ferreira, R S; Santos, L M; Marin, L J; Corrêa, R X; Luizon, M R; Simões, A L; Gadelha, S R; Sousa, S M B

    2016-10-17

    Some studies of polymorphisms in prostate cancer (PCa) analyze individuals in a uniform manner, regardless of genetic ancestry. However, PCa aggressiveness differs between subjects of African descent and those of European extraction. Thus, genetic ancestry analysis may be used to detect population stratification in case-control association studies. We genotyped 11 ancestry informative markers to estimate the contributions of African, European, and Amerindian ancestries in a case-control sample of 213 individuals from Bahia State, Northeast Brazil, including 104 PCa patients. We compared this data with self-reported ancestry and the stratification of cases by PCa aggressiveness according to Gleason score. A larger African genetic contribution (44%) was detected among cases, and a greater European contribution (61%) among controls. Self-declaration data revealed that 74% of PCa patients considered themselves non-white (black and brown), and 41.3% of controls viewed themselves as white. Our data showed a higher degree of European ancestry among fast-growing cancer cases than those of intermediate and slow development. This differs from many previous studies, in which the prevalence of African ancestry has been reported for all grades. Differences were observed between degrees of PCa aggressiveness in terms of genetic ancestry. In particular, the greater European contribution among patients with high-grade PCa indicates that a population's genetic structure can influence case-control studies. This investigation contributes to our understanding of the genetic basis of tumor aggressiveness among groups of different genetic ancestries, especially admixed populations, and has significant implications for the assessment of inter-population heterogeneity in drug treatment effects.

  17. High precision studies of directional correlations

    International Nuclear Information System (INIS)

    El-khosht, M.

    1980-01-01

    Two applications of the method of directional correlations are described. The first part deals with gamma-gamma directional correlations measurements. A total of 27 cascades have been studied in 97 Tc, 206 Pb and 206 Bi. Information is obtained on the angular momenta of levels, multipolarities of electromagnetic transitions and further, reduced transition probabilities. The later part of this thesis describes a determination of anisotropic directional correlation between gamma-rays and LX-rays in 160 Dy. To the authors' knowledge this is the first observation of an anisotropic correlation between gamma rays and X-rays following internal conversion. (Auth.)

  18. Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit.

    Science.gov (United States)

    Ramani, Anantharaman; Wong, Yongxun; Tan, Si Zhen; Shue, Bing Hong; Syn, Christopher

    2017-11-01

    ) was generally high in the absence of admixture. Misclassification occurred in admixed individuals, who were likely offspring of inter-ethnic marriages, and hence whose self-reported bio-geographic ancestries were dependent on that of their fathers, and in individuals of minority sub-populations with inter-ethnic beliefs. The ancestry prediction capabilities of the 59 SNPs on the ForenSeq kit were reasonably effective in differentiating the Singapore Chinese, Malay and Indian sub-populations, and will be of use for investigative purposes. However, there is potential for more accurate prediction through the evaluation of other AIM sets. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Genomic ancestry and education level independently influence abdominal fat distributions in a Brazilian admixed population.

    Science.gov (United States)

    França, Giovanny Vinícius Araújo de; De Lucia Rolfe, Emanuella; Horta, Bernardo Lessa; Gigante, Denise Petrucci; Yudkin, John S; Ong, Ken K; Victora, Cesar Gomes

    2017-01-01

    We aimed to identify the independent associations of genomic ancestry and education level with abdominal fat distributions in the 1982 Pelotas birth cohort study, Brazil. In 2,890 participants (1,409 men and 1,481 women), genomic ancestry was assessed using genotype data on 370,539 genome-wide variants to quantify ancestral proportions in each individual. Years of completed education was used to indicate socio-economic position. Visceral fat depth and subcutaneous abdominal fat thickness were measured by ultrasound at age 29-31y; these measures were adjusted for BMI to indicate abdominal fat distributions. Linear regression models were performed, separately by sex. Admixture was observed between European (median proportion 85.3), African (6.6), and Native American (6.3) ancestries, with a strong inverse correlation between the African and European ancestry scores (ρ = -0.93; pabdominal fat distributions in men (both P = 0.001), and inversely associated with subcutaneous abdominal fat distribution in women (p = 0.009). Independent of genomic ancestry, higher education level was associated with lower visceral fat, but higher subcutaneous fat, in both men and women (all pabdominal fat distribution in adults. African ancestry appeared to lower abdominal fat distributions, particularly in men.

  20. Interaction between common breast cancer susceptibility variants, genetic ancestry, and nongenetic risk factors in Hispanic women.

    Science.gov (United States)

    Fejerman, Laura; Stern, Mariana C; John, Esther M; Torres-Mejía, Gabriela; Hines, Lisa M; Wolff, Roger K; Baumgartner, Kathy B; Giuliano, Anna R; Ziv, Elad; Pérez-Stable, Eliseo J; Slattery, Martha L

    2015-11-01

    Most genetic variants associated with breast cancer risk have been discovered in women of European ancestry, and only a few genome-wide association studies (GWAS) have been conducted in minority groups. This research disparity persists in post-GWAS gene-environment interaction analyses. We tested the interaction between hormonal and lifestyle risk factors for breast cancer, and ten GWAS-identified SNPs among 2,107 Hispanic women with breast cancer and 2,587 unaffected controls, to gain insight into a previously reported gene by ancestry interaction in this population. We estimated genetic ancestry with a set of 104 ancestry-informative markers selected to discriminate between Indigenous American and European ancestry. We used logistic regression models to evaluate main effects and interactions. We found that the rs13387042-2q35(G/A) SNP was associated with breast cancer risk only among postmenopausal women who never used hormone therapy [per A allele OR: 0.94 (95% confidence intervals, 0.74-1.20), 1.20 (0.94-1.53), and 1.49 (1.28-1.75) for current, former, and never hormone therapy users, respectively, Pinteraction 0.002] and premenopausal women who breastfed >12 months [OR: 1.01 (0.72-1.42), 1.19 (0.98-1.45), and 1.69 (1.26-2.26) for never, 12 months breastfeeding, respectively, Pinteraction 0.014]. The correlation between genetic ancestry, hormone replacement therapy use, and breastfeeding behavior partially explained a previously reported interaction between a breast cancer risk variant and genetic ancestry in Hispanic women. These results highlight the importance of understanding the interplay between genetic ancestry, genetics, and nongenetic risk factors and their contribution to breast cancer risk. ©2015 American Association for Cancer Research.

  1. Ancestry dependent DNA methylation and influence of maternal nutrition.

    Directory of Open Access Journals (Sweden)

    Khyobeni Mozhui

    Full Text Available There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112 and European American (EA; N = 91 participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood. Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition--specifically, plasma levels of vitamin D and folate during pregnancy--on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC. Overall, there is lower global methylation in African ancestral groups. Plasma levels of 25-hydroxy vitamin D are also considerably lower among AA mothers and about 60% of AA and 40% of EA mothers have concentrations below 20 ng/ml. Using a weighted correlation analysis, we define a network of CpG sites that is jointly modulated by ancestry and maternal vitamin D. Our results show that differences in DNA methylation patterns are remarkably stable and maternal micronutrients can exert an influence on the child epigenome.

  2. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

    Directory of Open Access Journals (Sweden)

    Theobald Douglas L

    2011-11-01

    Full Text Available Abstract Background The universal common ancestry (UCA of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the status and nature of UCA has been questioned. In earlier work I presented a formal, quantitative test of UCA in which model selection criteria overwhelmingly choose common ancestry over independent ancestry, based on a dataset of universally conserved proteins. These model-based tests are founded in likelihoodist and Bayesian probability theory, in opposition to classical frequentist null hypothesis tests such as Karlin-Altschul E-values for sequence similarity. In a recent comment, Koonin and Wolf (K&W claim that the model preference for UCA is "a trivial consequence of significant sequence similarity". They support this claim with a computational simulation, derived from universally conserved proteins, which produces similar sequences lacking phylogenetic structure. The model selection tests prefer common ancestry for this artificial data set. Results For the real universal protein sequences, hierarchical phylogenetic structure (induced by genealogical history is the overriding reason for why the tests choose UCA; sequence similarity is a relatively minor factor. First, for cases of conflicting phylogenetic structure, the tests choose independent ancestry even with highly similar sequences. Second, certain models, like star trees and K&W's profile model (corresponding to their simulation, readily explain sequence similarity yet lack phylogenetic structure. However, these are extremely poor models for the real proteins, even worse than independent ancestry models, though they explain K&W's artificial data well. Finally, K&W's simulation is an implementation of a well-known phylogenetic model, and it produces sequences that mimic homologous proteins. Therefore the model selection tests work appropriately with the artificial

  3. High-Fidelity Coding with Correlated Neurons

    Science.gov (United States)

    da Silveira, Rava Azeredo; Berry, Michael J.

    2014-01-01

    Positive correlations in the activity of neurons are widely observed in the brain. Previous studies have shown these correlations to be detrimental to the fidelity of population codes, or at best marginally favorable compared to independent codes. Here, we show that positive correlations can enhance coding performance by astronomical factors. Specifically, the probability of discrimination error can be suppressed by many orders of magnitude. Likewise, the number of stimuli encoded—the capacity—can be enhanced more than tenfold. These effects do not necessitate unrealistic correlation values, and can occur for populations with a few tens of neurons. We further show that both effects benefit from heterogeneity commonly seen in population activity. Error suppression and capacity enhancement rest upon a pattern of correlation. Tuning of one or several effective parameters can yield a limit of perfect coding: the corresponding pattern of positive correlation leads to a ‘lock-in’ of response probabilities that eliminates variability in the subspace relevant for stimulus discrimination. We discuss the nature of this pattern and we suggest experimental tests to identify it. PMID:25412463

  4. Analysis of ancestry informative markers in three main ethnic groups from Ecuador supports a trihybrid origin of Ecuadorians.

    Science.gov (United States)

    Santangelo, Roberta; González-Andrade, Fabricio; Børsting, Claus; Torroni, Antonio; Pereira, Vania; Morling, Niels

    2017-11-01

    Ancestry inference is traditionally done using autosomal SNPs that present great allele frequency differences among populations from different geographic regions. These ancestry informative markers (AIMs) are useful for determining the most likely biogeographic ancestry or population of origin of an individual. Due to the growing interest in AIMs and their applicability in different fields, commercial companies have started to develop AIM multiplexes targeted for Massive Parallel Sequencing platforms. This project focused on the study of three main ethnic groups from Ecuador (Kichwa, Mestizo, and Afro-Ecuadorian) using the Precision ID Ancestry panel (Thermo Fisher Scientific). In total, 162 Ecuadorian individuals were investigated. The Afro-Ecuadorian and Mestizo showed higher average genetic diversities compared to the Kichwa. These results are consistent with the highly admixed nature of the first two groups. The Kichwa showed the highest proportion of Native Amerindian (NAM) ancestry relative to the other two groups. The Mestizo had an admixed ancestry of NAM and European with a larger European component, whereas the Afro-Ecuadorian were highly admixed presenting proportions of African, Native Amerindian, and European ancestries. The comparison of our results with previous studies based on uniparental markers (i.e. Y chromosome and mtDNA) highlighted the sex-biased admixture process in the Ecuadorian Mestizo. Overall, the data generated in this work represent one important step to assess the application of ancestry inference in admixed populations in a forensic context. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    Full Text Available Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. We applied this approach to a complex, uniquely admixed South African population. Using genome-wide SNP data from over 764 individuals, we accurately estimate the genetic contributions from the best ancestral populations: isiXhosa [Formula: see text], ‡Khomani SAN [Formula: see text], European [Formula: see text], Indian [Formula: see text], and Chinese [Formula: see text]. We also demonstrate that the ancestral allele frequency differences correlate with increased linkage disequilibrium in the South African population, which originates from admixture events rather than population bottlenecks.The collective term for people of mixed ancestry in southern Africa is "Coloured," and this is officially recognized in South

  6. Neither self-reported ethnicity nor declared family origin are reliable indicators of genomic ancestry.

    Science.gov (United States)

    Ramos, Bruna Ribeiro de Andrade; D'Elia, Maria Paula Barbieri; Amador, Marcos Antônio Trindade; Santos, Ney Pereira Carneiro; Santos, Sidney Emanuel Batista; da Cruz Castelli, Erick; Witkin, Steven S; Miot, Hélio Amante; Miot, Luciane Donida Bartoli; da Silva, Márcia Guimarães

    2016-06-01

    Ancestry information can be useful in investigations of diseases with a genetic or infectious background. As the Brazilian population is highly admixed physical traits tend to be poor indicators of ancestry. The assessment of ancestry by ancestry informative markers (AIMs) can exclude the subjectivity of self-declared ethnicity and reported family origin. We aimed to evaluate the reliability of self-reported ethnicity or reported family origin as indicators of genomic ancestry in a female population from the Southeast of Brazil. Two cohorts were included: 404 women asked to self-report their ethnicity (Pop1) and 234 women asked to report their family's origin (Pop2). Identification of AIMs was performed using a panel of 61 markers and results were plotted against parental populations-Amerindian, Western European and Sub-Saharan African-using Structure v2.3.4. In Pop1 57.4 % of women self-reported as white, 34.6 % as brown and 8.0 % as black. Median global European, Amerindian and African contributions were 66.8, 12.6 and 16.6 %. In Pop2, 66.4 % of women declared European origin, 23.9 % African origin and 26.9 % Amerindian. Median global European, Amerindian and African contributions were 80.8, 7.3 and 7.6 %, respectively. Only 31.0 and 21.0 % of the global variation in African and European contributions, respectively, could be explained by self-reported ethnicity and reported family origin only accounted for 20.0 and 5.0 % of the variations observed in African and European ancestries, respectively. Amerindian ancestry did not influence self-reported ethnicity or declared family origin. Neither self-reported ethnicity nor declared family origin are reliable indicators of genomic ancestry in these Brazilian populations.

  7. Analysis of the genetic ancestry of patients with oral clefts from South American admixed populations.

    Science.gov (United States)

    Vieira-Machado, Camilla D; de Carvalho, Flavia M; Santana da Silva, Luiz C; Dos Santos, Sidney E; Martins, Claudia; Poletta, Fernando A; Mereb, Juan C; Vieira, Alexandre R; Castilla, Eduardo E; Orioli, Iêda M

    2016-08-01

    Increased susceptibility to cleft lip, with or without cleft palate (CL±P) has been observed in South America, as related to Amerindian ancestry, using epidemiological data, uniparental markers, and blood groups. In this study, it was evaluated whether this increased risk remains when Amerindian ancestry is estimated using autosomal markers and considered in the predictive model. Ancestry was estimated through genotyping 62 insertion and deletion (INDEL) markers in sample sets of patients with CL±P, patients with cleft palate (CP), and controls, from Patagonia in southern Argentina and Belém in northern Brazil. The Amerindian ancestry in patients from Patagonia with CL±P was greater than in controls although it did not reach statistical significance. The European ancestry in patients with CL±P from Belém and in patients with CP from Belém and Patagonia was higher than in controls and statistically significant for patients with CP who were from Belém. This high contribution of European genetic ancestry among patients with CP who were from Belém has not been previously observed in American populations. Our results do not corroborate the currently accepted risks for CL±P and CP estimated by epidemiological studies in the North American populations and probably reflect the higher admixture found in South American ethnic groups when compared with the same ethnic groups from the North American populations. © 2016 Eur J Oral Sci.

  8. Maximum-likelihood estimation of recent shared ancestry (ERSA).

    Science.gov (United States)

    Huff, Chad D; Witherspoon, David J; Simonson, Tatum S; Xing, Jinchuan; Watkins, W Scott; Zhang, Yuhua; Tuohy, Therese M; Neklason, Deborah W; Burt, Randall W; Guthery, Stephen L; Woodward, Scott R; Jorde, Lynn B

    2011-05-01

    Accurate estimation of recent shared ancestry is important for genetics, evolution, medicine, conservation biology, and forensics. Established methods estimate kinship accurately for first-degree through third-degree relatives. We demonstrate that chromosomal segments shared by two individuals due to identity by descent (IBD) provide much additional information about shared ancestry. We developed a maximum-likelihood method for the estimation of recent shared ancestry (ERSA) from the number and lengths of IBD segments derived from high-density SNP or whole-genome sequence data. We used ERSA to estimate relationships from SNP genotypes in 169 individuals from three large, well-defined human pedigrees. ERSA is accurate to within one degree of relationship for 97% of first-degree through fifth-degree relatives and 80% of sixth-degree and seventh-degree relatives. We demonstrate that ERSA's statistical power approaches the maximum theoretical limit imposed by the fact that distant relatives frequently share no DNA through a common ancestor. ERSA greatly expands the range of relationships that can be estimated from genetic data and is implemented in a freely available software package.

  9. Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

    Science.gov (United States)

    Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

    2014-01-01

    The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry. PMID:25254375

  10. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  11. Ancestry, admixture and fitness in Colombian genomes

    Science.gov (United States)

    Rishishwar, Lavanya; Conley, Andrew B.; Wigington, Charles H.; Wang, Lu; Valderrama-Aguirre, Augusto; King Jordan, I.

    2015-01-01

    The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment. PMID:26197429

  12. Highly noise resistant multiqubit quantum correlations

    Science.gov (United States)

    Laskowski, Wiesław; Vértesi, Tamás; Wieśniak, Marcin

    2015-11-01

    We analyze robustness of correlations of the N-qubit GHZ and Dicke states against white noise admixture. For sufficiently large N, the Dicke states (for any number of excitations) lead to more robust violation of local realism than the GHZ states (e.g. for N > 8 for the W state). We also identify states that are the most resistant to white noise. Surprisingly, it turns out that these states are the GHZ states augmented with fully product states. Based on our numerical analysis conducted up to N = 8, and an analytical formula derived for any N parties, we conjecture that the three-qubit GHZ state augmented with a product of (N - 3) pure qubits is the most robust against white noise admixture among any N-qubit state. As a by-product, we derive a single Bell inequality and show that it is violated by all pure entangled states of a given number of parties. This gives an alternative proof of Gisin’s theorem.

  13. Highly noise resistant multiqubit quantum correlations

    International Nuclear Information System (INIS)

    Laskowski, Wiesław; Wieśniak, Marcin; Vértesi, Tamás

    2015-01-01

    We analyze robustness of correlations of the N-qubit GHZ and Dicke states against white noise admixture. For sufficiently large N, the Dicke states (for any number of excitations) lead to more robust violation of local realism than the GHZ states (e.g. for N > 8 for the W state). We also identify states that are the most resistant to white noise. Surprisingly, it turns out that these states are the GHZ states augmented with fully product states. Based on our numerical analysis conducted up to N = 8, and an analytical formula derived for any N parties, we conjecture that the three-qubit GHZ state augmented with a product of (N − 3) pure qubits is the most robust against white noise admixture among any N-qubit state. As a by-product, we derive a single Bell inequality and show that it is violated by all pure entangled states of a given number of parties. This gives an alternative proof of Gisin’s theorem. (paper)

  14. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    Science.gov (United States)

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-05

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  15. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.

    Science.gov (United States)

    Crawford, Nicholas; Prendergast, D'Arcy; Oehlert, John W; Shaw, Gary M; Stevenson, David K; Rappaport, Nadav; Sirota, Marina; Tishkoff, Sarah A; Sondheimer, Neal

    2018-03-01

    To examine linkages between mitochondrial genetics and preterm birth by assessing the risk for preterm birth associated with the inheritance of nuclear haplotypes that are ancestrally distinct from mitochondrial haplogroup. Genome-wide genotyping studies of cohorts of preterm and term individuals were evaluated. We determined the mitochondrial haplogroup and nuclear ancestry for individuals and developed a scoring for the degree to which mitochondrial ancestry is divergent from nuclear ancestry. Infants with higher degrees of divergent mitochondrial ancestry were at increased risk for preterm birth (0.124 for preterm vs 0.105 for term infants; Pancestry correlated with earlier delivery within the primary study population, but this finding was not replicated in secondary cohorts born preterm. Individuals with divergent patterns of mitochondrial and nuclear ancestry are at increased risk for preterm birth. These findings may in part explain the higher rates of preterm birth in African Americans and in individuals with a matrilineal family history of preterm birth. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation

    Science.gov (United States)

    Phillips, Christopher; Prieto, Lourdes; Fondevila, Manuel; Salas, Antonio; Gómez-Tato, Antonio; Álvarez-Dios, José; Alonso, Antonio; Blanco-Verea, Alejandro; Brión, María; Montesino, Marta; Carracedo, Ángel; Lareu, María Victoria

    2009-01-01

    The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results

  17. Denisovan Ancestry in East Eurasian and Native American Populations.

    OpenAIRE

    Stoneking, Mark; Qin, Pengfei

    2015-01-01

    Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide pop...

  18. Ancestry and dental development: A geographic and genetic perspective

    NARCIS (Netherlands)

    B. Dhamo (Brunilda); L. Kragt (Lea); Grgic, O. (Olja); S. Vucic (Strahinja); M.C. Medina-Gomez (Carolina); Rivadeneira, F. (Fernando); V.W.V. Jaddoe (Vincent); E.B. Wolvius (Eppo); E.M. Ongkosuwito (Edwin)

    2017-01-01

    textabstractObjective: In this study, we investigated the influence of ancestry on dental development in the Generation R Study. Methods: Information on geographic ancestry was available in 3,600 children (1,810 boys and 1,790 girls, mean age 9.81±0.35 years) and information about genetic ancestry

  19. Analysis of iris surface features in populations of diverse ancestry

    Science.gov (United States)

    Edwards, Melissa; Cha, David; Krithika, S.; Johnson, Monique; Parra, Esteban J.

    2016-01-01

    There are many textural elements that can be found in the human eye, including Fuchs’ crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs’ crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs’ crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest. PMID:26909168

  20. Chromosome Connections: Compelling Clues to Common Ancestry

    Science.gov (United States)

    Flammer, Larry

    2013-01-01

    Students compare banding patterns on hominid chromosomes and see striking evidence of their common ancestry. To test this, human chromosome no. 2 is matched with two shorter chimpanzee chromosomes, leading to the hypothesis that human chromosome 2 resulted from the fusion of the two shorter chromosomes. Students test that hypothesis by looking for…

  1. Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile.

    Directory of Open Access Journals (Sweden)

    Justo Lorenzo Bermejo

    2017-05-01

    Full Text Available Latin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention. Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26. By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1-4.3%, P = 6×10-27. Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data.

  2. Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile.

    Science.gov (United States)

    Lorenzo Bermejo, Justo; Boekstegers, Felix; González Silos, Rosa; Marcelain, Katherine; Baez Benavides, Pablo; Barahona Ponce, Carol; Müller, Bettina; Ferreccio, Catterina; Koshiol, Jill; Fischer, Christine; Peil, Barbara; Sinsheimer, Janet; Fuentes Guajardo, Macarena; Barajas, Olga; Gonzalez-Jose, Rolando; Bedoya, Gabriel; Cátira Bortolini, Maria; Canizales-Quinteros, Samuel; Gallo, Carla; Ruiz Linares, Andres; Rothhammer, Francisco

    2017-05-01

    Latin Americans are highly heterogeneous regarding the type of Native American ancestry. Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention. Here we investigate possible associations between the type of Native American ancestry and leading causes of death. After an aggregate-data study based on genome-wide genotype data from 1805 admixed Chileans and 639,789 deaths, we validate an identified association with gallbladder cancer relying on individual data from 64 gallbladder cancer patients, with and without a family history, and 170 healthy controls. Native American proportions were markedly underestimated when the two main types of Native American ancestry in Chile, originated from the Mapuche and Aymara indigenous peoples, were combined together. Consideration of the type of Native American ancestry was crucial to identify disease associations. Native American ancestry showed no association with gallbladder cancer mortality (P = 0.26). By contrast, each 1% increase in the Mapuche proportion represented a 3.7% increased mortality risk by gallbladder cancer (95%CI 3.1-4.3%, P = 6×10-27). Individual-data results and extensive sensitivity analyses confirmed the association between Mapuche ancestry and gallbladder cancer. Increasing Mapuche proportions were also associated with an increased mortality due to asthma and, interestingly, with a decreased mortality by diabetes. The mortality due to skin, bladder, larynx, bronchus and lung cancers increased with increasing Aymara proportions. Described methods should be considered in future studies on human population genetics and human health. Complementary individual-based studies are needed to apportion the genetic and non-genetic components of associations identified relying on aggregate-data.

  3. Phenotypic variance explained by local ancestry in admixed African Americans.

    Science.gov (United States)

    Shriner, Daniel; Bentley, Amy R; Doumatey, Ayo P; Chen, Guanjie; Zhou, Jie; Adeyemo, Adebowale; Rotimi, Charles N

    2015-01-01

    We surveyed 26 quantitative traits and disease outcomes to understand the proportion of phenotypic variance explained by local ancestry in admixed African Americans. After inferring local ancestry as the number of African-ancestry chromosomes at hundreds of thousands of genotyped loci across all autosomes, we used a linear mixed effects model to estimate the variance explained by local ancestry in two large independent samples of unrelated African Americans. We found that local ancestry at major and polygenic effect genes can explain up to 20 and 8% of phenotypic variance, respectively. These findings provide evidence that most but not all additive genetic variance is explained by genetic markers undifferentiated by ancestry. These results also inform the proportion of health disparities due to genetic risk factors and the magnitude of error in association studies not controlling for local ancestry.

  4. Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures

    Science.gov (United States)

    Galanter, Joshua M; Gignoux, Christopher R; Oh, Sam S; Torgerson, Dara; Pino-Yanes, Maria; Thakur, Neeta; Eng, Celeste; Hu, Donglei; Huntsman, Scott; Farber, Harold J; Avila, Pedro C; Brigino-Buenaventura, Emerita; LeNoir, Michael A; Meade, Kelly; Serebrisky, Denise; Rodríguez-Cintrón, William; Kumar, Rajesh; Rodríguez-Santana, Jose R; Seibold, Max A; Borrell, Luisa N; Burchard, Esteban G; Zaitlen, Noah

    2017-01-01

    Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a significant enrichment (p=4.2×10-64) of ethnicity-associated sites amongst loci previously associated environmental exposures, particularly maternal smoking during pregnancy. We conclude that differential methylation between ethnic groups is partially explained by the shared genetic ancestry but that environmental factors not captured by ancestry significantly contribute to variation in methylation. DOI: http://dx.doi.org/10.7554/eLife.20532.001 PMID:28044981

  5. Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening.

    Science.gov (United States)

    Shraga, Roman; Yarnall, Sarah; Elango, Sonya; Manoharan, Arun; Rodriguez, Sally Ann; Bristow, Sara L; Kumar, Neha; Niknazar, Mohammad; Hoffman, David; Ghadir, Shahin; Vassena, Rita; Chen, Serena H; Hershlag, Avner; Grifo, Jamie; Puig, Oscar

    2017-11-28

    Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks.

  6. Entropy measure of credit risk in highly correlated markets

    Science.gov (United States)

    Gottschalk, Sylvia

    2017-07-01

    We compare the single and multi-factor structural models of corporate default by calculating the Jeffreys-Kullback-Leibler divergence between their predicted default probabilities when asset correlations are either high or low. Single-factor structural models assume that the stochastic process driving the value of a firm is independent of that of other companies. A multi-factor structural model, on the contrary, is built on the assumption that a single firm's value follows a stochastic process correlated with that of other companies. Our main results show that the divergence between the two models increases in highly correlated, volatile, and large markets, but that it is closer to zero in small markets, when asset correlations are low and firms are highly leveraged. These findings suggest that during periods of financial instability, when asset volatility and correlations increase, one of the models misreports actual default risk.

  7. Differentiation of African components of ancestry to stratify groups in a case-control study of a Brazilian urban population.

    Science.gov (United States)

    Silbiger, Vivian N; Hirata, Mario H; Luchessi, Andre D; Genvigir, Fabiana D V; Cerda, Alvaro; Rodrigues, Alice C; Willrich, Maria A V; Arazi, Simone S; Dorea, Egidio L; Bernik, Marcia M S; Faludi, Andre A; Bertolami, Marcelo C; Santos, Carla; Carracedo, Angel; Salas, Antonio; Freire, Ana; Lareu, Maria Victoria; Phillips, Christopher; Porras-Hurtado, Liliana; Fondevila, Manuel; Hirata, Rosario D C

    2012-06-01

    Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies. We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case-control association study of a Brazilian urban sample. One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA 0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers.

  8. Rapidity and multiplicity correlations in high energy hadronic collisions

    International Nuclear Information System (INIS)

    Heiselberg, H.

    1993-01-01

    Rapidity and multiplicity correlations of particle production in high energy hadronic collisions are studied. A simple model including short range correlations in rapidity due to clustering and long range correlations due to energy conservation is able to describe the two-body correlation functions well hadron-nucleon collisions around lab energies of 250 GeV. In this model fractional moments are calculated and compared to data. The strong rise of the factorial moments in rapidity intervals by size δy∝1 can be explained by long and short range correlation alone whereas the factorial moments approach a constant value at very small δy due to lack of correlations also in agreement with experiment. There is therefore no need for introducing intermittency in the particle production in hadronic collisions at these energies. (orig.)

  9. RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

    Science.gov (United States)

    Maples, Brian K.; Gravel, Simon; Kenny, Eimear E.; Bustamante, Carlos D.

    2013-01-01

    Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (∼30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American ancestry (∼0.4%). PMID:23910464

  10. Impact of ancestry categorisations on residential segregation measures using Swedish register data.

    Science.gov (United States)

    Jarvis, Benjamin; Kawalerowicz, Juta; Valdez, Sarah

    2017-07-01

    Country-of-birth data contained in registers are often aggregated to create broad ancestry group categories. We examine how measures of residential segregation vary according to levels of aggregation. We use Swedish register data to calculate pairwise dissimilarity indices from 1990 to 2012 for ancestry groups defined at four nested levels of aggregation: (1) micro-groups containing 50 categories, (2) meso-groups containing 16 categories, (3) macro-groups containing six categories and (4) a broad Western/non-Western binary. We find variation in segregation levels between ancestry groups that is obscured by data aggregation. This study demonstrates that the practice of aggregating country-of-birth statistics in register data can hinder the ability to identify highly segregated groups and therefore design effective policy to remedy both intergroup and intergenerational inequalities.

  11. Local ancestry transitions modify snp-trait associations.

    Science.gov (United States)

    Fish, Alexandra E; Crawford, Dana C; Capra, John A; Bush, William S

    2018-01-01

    Genomic maps of local ancestry identify ancestry transitions - points on a chromosome where recent recombination events in admixed individuals have joined two different ancestral haplotypes. These events bring together alleles that evolved within separate continential populations, providing a unique opportunity to evaluate the joint effect of these alleles on health outcomes. In this work, we evaluate the impact of genetic variants in the context of nearby local ancestry transitions within a sample of nearly 10,000 adults of African ancestry with traits derived from electronic health records. Genetic data was located using the Metabochip, and used to derive local ancestry. We develop a model that captures the effect of both single variants and local ancestry, and use it to identify examples where local ancestry transitions significantly interact with nearby variants to influence metabolic traits. In our most compelling example, we find that the minor allele of rs16890640 occuring on a European background with a downstream local ancestry transition to African ancestry results in significantly lower mean corpuscular hemoglobin and volume. This finding represents a new way of discovering genetic interactions, and is supported by molecular data that suggest changes to local ancestry may impact local chromatin looping.

  12. Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates.

    Science.gov (United States)

    Jia, Jing; Wei, Yi-Liang; Qin, Cui-Jiao; Hu, Lan; Wan, Li-Hua; Li, Cai-Xia

    2014-01-01

    Inferring the ancestral origin of DNA samples can be helpful in correcting population stratification in disease association studies or guiding crime investigations. Populations throughout the world vary in appearance features and biological characteristics. Based on this idea, we performed a genome-wide scan for SNPs within genes that are related to physical and biological traits. Using the HapMap database, we screened 52 genes and their flanking regions. Thirty-five SNPs that displayed highly contrasting allele frequencies (F(st)>0.3, linkage disequilibrium r(2)0.001) among Africans, Europeans, and East Asians were selected and validated. A multiplexed assay was developed to genotype these 35 SNPs in 357 individuals from 10 populations worldwide. This panel provided accurate estimates of individual ancestry proportions with balanced discriminatory power among the three continental ancestries: Africans, Europeans, and East Asians. It also proved very effective in evaluating admixed populations living in joint regions of continents (e.g., Uyghurs and Indians) and discriminating some subpopulations within each of the three continents. Structure analysis was performed to establish and evaluate the panel of ancestry-informative markers, and the components of each population were also described to indicate the structural composition. The 21 population structures in our study are consistent with geographic patterns, and individuals were properly assigned to their original ancestral populations with proportion analyses and random match probability calculations. Thus, the panel and its population information will be useful resources to minimize the effects of population stratification in association analyses and to assign the most likely origin of an unknown DNA contributor in forensic investigations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  13. Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND).

    Science.gov (United States)

    Williams, Robert C; Elston, Robert C; Kumar, Pankaj; Knowler, William C; Abboud, Hanna E; Adler, Sharon; Bowden, Donald W; Divers, Jasmin; Freedman, Barry I; Igo, Robert P; Ipp, Eli; Iyengar, Sudha K; Kimmel, Paul L; Klag, Michael J; Kohn, Orly; Langefeld, Carl D; Leehey, David J; Nelson, Robert G; Nicholas, Susanne B; Pahl, Madeleine V; Parekh, Rulan S; Rotter, Jerome I; Schelling, Jeffrey R; Sedor, John R; Shah, Vallabh O; Smith, Michael W; Taylor, Kent D; Thameem, Farook; Thornley-Brown, Denyse; Winkler, Cheryl A; Guo, Xiuqing; Zager, Phillip; Hanson, Robert L

    2016-05-04

    The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample. A fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy. The identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased

  14. Quantum correlation of high dimensional system in a dephasing environment

    Science.gov (United States)

    Ji, Yinghua; Ke, Qiang; Hu, Juju

    2018-05-01

    For a high dimensional spin-S system embedded in a dephasing environment, we theoretically analyze the time evolutions of quantum correlation and entanglement via Frobenius norm and negativity. The quantum correlation dynamics can be considered as a function of the decoherence parameters, including the ratio between the system oscillator frequency ω0 and the reservoir cutoff frequency ωc , and the different environment temperature. It is shown that the quantum correlation can not only measure nonclassical correlation of the considered system, but also perform a better robustness against the dissipation. In addition, the decoherence presents the non-Markovian features and the quantum correlation freeze phenomenon. The former is much weaker than that in the sub-Ohmic or Ohmic thermal reservoir environment.

  15. Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations.

    Science.gov (United States)

    Yoneyama, S; Yao, J; Guo, X; Fernandez-Rhodes, L; Lim, U; Boston, J; Buzková, P; Carlson, C S; Cheng, I; Cochran, B; Cooper, R; Ehret, G; Fornage, M; Gong, J; Gross, M; Gu, C C; Haessler, J; Haiman, C A; Henderson, B; Hindorff, L A; Houston, D; Irvin, M R; Jackson, R; Kuller, L; Leppert, M; Lewis, C E; Li, R; Le Marchand, L; Matise, T C; Nguyen, K-Dh; Chakravarti, A; Pankow, J S; Pankratz, N; Pooler, L; Ritchie, M D; Bien, S A; Wassel, C L; Chen, Y-D I; Taylor, K D; Allison, M; Rotter, J I; Schreiner, P J; Schumacher, F; Wilkens, L; Boerwinkle, E; Kooperberg, C; Peters, U; Buyske, S; Graff, M; North, K E

    2017-02-01

    Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of body mass index (BMI) and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine-mapping cardiovascular-associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Of the 17 WHR loci, eight single-nucleotide polymorphisms (SNPs) located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine-mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female-stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Of 17 previously identified loci, four loci replicated in the African ancestry populations of this

  16. Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations

    Science.gov (United States)

    Yoneyama, Sachiko; Yao, Jie; Guo, Xiuqing; Fernandez-Rhodes, Lindsay; Lim, Unhee; Boston, Jonathan; Buzková, Petra; Carlson, Christopher S.; Cheng, Iona; Cochran, Barbara; Cooper, Richard; Ehret, Georg; Fornage, Myriam; Gong, Jian; Gross, Myron; Gu, C. Charles; Haessler, Jeff; Haiman, Christopher A.; Henderson, Brian; Hindorff, Lucia A.; Houston, Denise; Irvin, Marguerite R.; Jackson, Rebecca; Kuller, Lew; Leppert, Mark; Lewis, Cora E.; Li, Rongling; Le Marchand, Loic; Matise, Tara C.; Nguyen, Khanh-Dung H.; Chakravarti, Aravinda; Pankow, James S.; Pankratz, Nathan; Pooler, Loreall; Ritchie, Marylyn D.; Bien, Stephanie A.; Wassel, Christina L.; Chen, Yii-Der I.; Taylor, Kent D.; Allison, Matthew; Rotter, Jerome I.; Schreiner, Pamela J.; Schumacher, Fredrick; Wilkens, Lynne; Boerwinkle, Eric; Kooperberg, Charles; Peters, Ulrike; Buyske, Steven; Graff, Mariaelisa; North, Kari E.

    2016-01-01

    Background/Objectives Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of BMI and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. Subjects/Methods To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine mapping cardiovascular associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Results Of the 17 WHR loci, eight SNPs located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Conclusions Of 17 previously identified loci, four loci replicated in the African ancestry populations of

  17. African ancestry is associated with facial melasma in women: a cross-sectional study.

    Science.gov (United States)

    D'Elia, Maria Paula Barbieri; Brandão, Marcela Calixto; de Andrade Ramos, Bruna Ribeiro; da Silva, Márcia Guimarães; Miot, Luciane Donida Bartoli; Dos Santos, Sidney Emanuel Batista; Miot, Hélio Amante

    2017-02-17

    Melasma is a chronic acquired focal hypermelanosis affecting photoexposed areas, especially for women during fertile age. Several factors contribute to its development: sun exposure, sex steroids, medicines, and family history. Melanic pigmentation pathway discloses several SNPs in different populations. Here, we evaluated the association between genetic ancestry and facial melasma. A cross-sectional study involving women with melasma and an age-matched control group from outpatients at FMB-Unesp, Botucatu-SP, Brazil was performed. DNA was extracted from oral mucosa swabs and ancestry determined by studying 61 INDELs. The genetic ancestry components were adjusted by other known risk factors by multiple logistic regression. We evaluated 119 women with facial melasma and 119 controls. Mean age was 39 ± 9 years. Mean age at beginning of disease was 27 ± 8 years. Pregnancy (40%), sun exposure (37%), and hormonal oral contraception (22%) were the most frequently reported melasma triggers. All subjects presented admixed ancestry, African and European genetic contributions were significantly different between cases and controls (respectively 10% vs 6%; 77% vs 82%; p ancestry (OR = 1.04; 95% CI 1.01 to 1.07), first generation family history (OR = 3.04; 95% CI 1.56 to 5.94), low education level (OR = 4.04; 95% CI 1.56 to 5.94), and use of antidepressants by individuals with affected family members (OR = 6.15; 95% CI 1.13 to 33.37) were associated with melasma, independently of other known risk factors. Facial melasma was independently associated with African ancestry in a highly admixed population.

  18. Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

    Science.gov (United States)

    Santos, Carla; Phillips, Christopher; Fondevila, Manuel; Daniel, Runa; van Oorschot, Roland A H; Burchard, Esteban G; Schanfield, Moses S; Souto, Luis; Uacyisrael, Jolame; Via, Marc; Carracedo, Ángel; Lareu, Maria V

    2016-01-01

    The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry

  19. Correlation between high-risk pregnancy and developmental delay ...

    African Journals Online (AJOL)

    Background: The future development of children is considered more than ever now due to the advances in medical knowledge and thus the increase in survival rates of high-risk infants. This study investigated the correlation between high-risk pregnancy and developmental delay in children aged 4- 60 months. Methods: ...

  20. Fanconi Anaemia in South African Patients with Afrikaner Ancestry

    Directory of Open Access Journals (Sweden)

    C Feben

    2017-10-01

    Full Text Available Background. Fanconi anaemia (FA is a rare genetic disorder of impaired DNA repair that results in physical and haematological consequences in affected individuals. In South Africa (SA, individuals with Afrikaner ancestry are at an increased risk of inheriting disease-causing FA mutations, owing to the three common FANCA (FA, complementation group A founder mutations present in this population subgroup. Objectives. To describe the physical phenotype of SA patients with FANCA mutations for the purpose of recommending appropriate care for affected individuals. Methods. A structured clinical examination and file-based review were used to evaluate the physical phenotype of 7 patients with compound heterozygous and homozygous FANCA founder mutations, and 1 patient with confirmed FANCA complementation analysis. Descriptive statistical analysis was used to determine the frequency of physical anomalies in Afrikaner patients and to compare the described phenotype to other FA cohorts, including a previously clinically characterised black SA FA cohort. Results. An earlier age of diagnosis of FA in Afrikaner patients, a high frequency of somatic anomalies and a higher-than-expected incidence of the VACTERL/H phenotype were noted. Conclusions. Based on our findings, recommendations for the care of FA patients with Afrikaner ancestry are made, including renal ultrasound evaluation at diagnosis and hearing screening

  1. Ultraconserved words point to deep language ancestry across Eurasia.

    Science.gov (United States)

    Pagel, Mark; Atkinson, Quentin D; S Calude, Andreea; Meade, Andrew

    2013-05-21

    The search for ever deeper relationships among the World's languages is bedeviled by the fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 to 9,000 y. On the other hand, quantitative modeling indicates that some "ultraconserved" words exist that might be used to find evidence for deep linguistic relationships beyond that time barrier. Here we use a statistical model, which takes into account the frequency with which words are used in common everyday speech, to predict the existence of a set of such highly conserved words among seven language families of Eurasia postulated to form a linguistic superfamily that evolved from a common ancestor around 15,000 y ago. We derive a dated phylogenetic tree of this proposed superfamily with a time-depth of ~14,450 y, implying that some frequently used words have been retained in related forms since the end of the last ice age. Words used more than once per 1,000 in everyday speech were 7- to 10-times more likely to show deep ancestry on this tree. Our results suggest a remarkable fidelity in the transmission of some words and give theoretical justification to the search for features of language that might be preserved across wide spans of time and geography.

  2. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.

    Science.gov (United States)

    Wei, Yi-Liang; Wei, Li; Zhao, Lei; Sun, Qi-Fan; Jiang, Li; Zhang, Tao; Liu, Hai-Bo; Chen, Jian-Gang; Ye, Jian; Hu, Lan; Li, Cai-Xia

    2016-01-01

    A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r (2) ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

  3. Health and genetic ancestry testing: time to bridge the gap.

    Science.gov (United States)

    Smart, Andrew; Bolnick, Deborah A; Tutton, Richard

    2017-01-09

    It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health risks associated with particular ancestral lineages. Because some of the proposed associations have received little attention from oversight agencies and professional genetic associations, scientific developments are currently outpacing governance regimes for consumer genetic testing. We highlight the recent and unremarked upon emergence of biomedical studies linking markers of genetic ancestry to disease risks, and show that this body of scientific research is becoming part of public discourse connecting ancestry and health. For instance, data on genome-wide ancestry informative markers are being used to assess health risks, and we document over 100 biomedical research articles that propose associations between mitochondrial DNA and Y chromosome markers of genetic ancestry and a wide variety of disease risks. Taking as an example an association between coronary heart disease and British men belonging to Y chromosome haplogroup I, we show how this science was translated into mainstream and online media, and how it circulates among consumers of genetic tests for ancestry. We find wide variations in how the science is interpreted, which suggests the potential for confusion or misunderstanding. We recommend that stakeholders involved in creating and using estimates of genetic ancestry reconsider their policies for communicating with each other and with the public about the health implications of ancestry information.

  4. Ancestry, Plasmodium cynomolgi prevalence and rhesus macaque admixture in cynomolgus macaques (Macaca fascicularis) bred for export in Chinese breeding farms.

    Science.gov (United States)

    Zhang, Xinjun; Meng, Yuhuan; Houghton, Paul; Liu, Mingyu; Kanthaswamy, Sreetharan; Oldt, Robert; Ng, Jillian; Trask, Jessica Satkoski; Huang, Ren; Singh, Balbir; Du, Hongli; Smith, David Glenn

    2017-04-01

    Most cynomolgus macaques (Macaca fascicularis) used in the United States as animal models are imported from Chinese breeding farms without documented ancestry. Cynomolgus macaques with varying rhesus macaque ancestry proportions may exhibit differences, such as susceptibility to malaria, that affect their suitability as a research model. DNA of 400 cynomolgus macaques from 10 Chinese breeding farms was genotyped to characterize their regional origin and rhesus ancestry proportion. A nested PCR assay was used to detect Plasmodium cynomolgi infection in sampled individuals. All populations exhibited high levels of genetic heterogeneity and low levels of inbreeding and genetic subdivision. Almost all individuals exhibited an Indochinese origin and a rhesus ancestry proportion of 5%-48%. The incidence of P. cynomolgi infection in cynomolgus macaques is strongly associated with proportion of rhesus ancestry. The varying amount of rhesus ancestry in cynomolgus macaques underscores the importance of monitoring their genetic similarity in malaria research. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Correlations in hadron-hadron interactions at high energy

    International Nuclear Information System (INIS)

    Nguyen Huu Khanh

    1978-01-01

    Some main features of the experimental results on the correlations in hadron-hadron interactions at high energy are considered. Particular attention is paid to the long-range correlation, short-range correlation and Bose-Einstein effect. Long-range correlations are confirmed by the variation of the number of charged particles produced in the final state depending on energy, violation of Koba-Nielsen- Olesen scaling and the analysis of correlation betWeen the numbers of charged particles emitted in the forward and backward hemispheres. Short-range correlations are discussed from the point of view of ISR pp, 195 GeV/c pN and 32 GeV/c k + p experiments. Bose-Einstein effects are studied up to now only between pions. Pions are not produced directly but from the decay of heavier objects. Some experimental results seem to support the evidence for dynamical long-range correlations. Most of the data are compatible with the independent cluster model

  6. High Temperature, high pressure equation of state density correlations and viscosity correlations

    Energy Technology Data Exchange (ETDEWEB)

    Tapriyal, D.; Enick, R.; McHugh, M.; Gamwo, I.; Morreale, B.

    2012-07-31

    Global increase in oil demand and depleting reserves has derived a need to find new oil resources. To find these untapped reservoirs, oil companies are exploring various remote and harsh locations such as deep waters in Gulf of Mexico, remote arctic regions, unexplored deep deserts, etc. Further, the depth of new oil/gas wells being drilled has increased considerably to tap these new resources. With the increase in the well depth, the bottomhole temperature and pressure are also increasing to extreme values (i.e. up to 500 F and 35,000 psi). The density and viscosity of natural gas and crude oil at reservoir conditions are critical fundamental properties required for accurate assessment of the amount of recoverable petroleum within a reservoir and the modeling of the flow of these fluids within the porous media. These properties are also used to design appropriate drilling and production equipment such as blow out preventers, risers, etc. With the present state of art, there is no accurate database for these fluid properties at extreme conditions. As we have begun to expand this experimental database it has become apparent that there are neither equations of state for density or transport models for viscosity that can be used to predict these fundamental properties of multi-component hydrocarbon mixtures over a wide range of temperature and pressure. Presently, oil companies are using correlations based on lower temperature and pressure databases that exhibit an unsatisfactory predictive capability at extreme conditions (e.g. as great as {+-} 50%). From the perspective of these oil companies that are committed to safely producing these resources, accurately predicting flow rates, and assuring the integrity of the flow, the absence of an extensive experimental database at extreme conditions and models capable of predicting these properties over an extremely wide range of temperature and pressure (including extreme conditions) makes their task even more daunting.

  7. Genomic African and Native American Ancestry and Chagas Disease: The Bambui (Brazil) Epigen Cohort Study of Aging.

    Science.gov (United States)

    Lima-Costa, M Fernanda; Macinko, James; Mambrini, Juliana Vaz de Mello; Peixoto, Sérgio Viana; Pereira, Alexandre Costa; Tarazona-Santos, Eduardo; Ribeiro, Antonio Luiz Pinho

    2016-05-01

    The influence of genetic ancestry on Trypanosoma cruzi infection and Chagas disease outcomes is unknown. We used 370,539 Single Nucleotide Polymorphisms (SNPs) to examine the association between individual proportions of African, European and Native American genomic ancestry with T. cruzi infection and related outcomes in 1,341 participants (aged ≥ 60 years) of the Bambui (Brazil) population-based cohort study of aging. Potential confounding variables included sociodemographic characteristics and an array of health measures. The prevalence of T. cruzi infection was 37.5% and 56.3% of those infected had a major ECG abnormality. Baseline T. cruzi infection was correlated with higher levels of African and Native American ancestry, which in turn were strongly associated with poor socioeconomic circumstances. Cardiomyopathy in infected persons was not significantly associated with African or Native American ancestry levels. Infected persons with a major ECG abnormality were at increased risk of 15-year mortality relative to their counterparts with no such abnormalities (adjusted hazard ratio = 1.80; 95% 1.41, 2.32). African and Native American ancestry levels had no significant effect modifying this association. Our findings indicate that African and Native American ancestry have no influence on the presence of major ECG abnormalities and had no influence on the ability of an ECG abnormality to predict mortality in older people infected with T. cruzi. In contrast, our results revealed a strong and independent association between prevalent T. cruzi infection and higher levels of African and Native American ancestry. Whether this association is a consequence of genetic background or differential exposure to infection remains to be determined.

  8. Read-only high accuracy volume holographic optical correlator

    Science.gov (United States)

    Zhao, Tian; Li, Jingming; Cao, Liangcai; He, Qingsheng; Jin, Guofan

    2011-10-01

    A read-only volume holographic correlator (VHC) is proposed. After the recording of all of the correlation database pages by angular multiplexing, a stand-alone read-only high accuracy VHC will be separated from the VHC recording facilities which include the high-power laser and the angular multiplexing system. The stand-alone VHC has its own low power readout laser and very compact and simple structure. Since there are two lasers that are employed for recording and readout, respectively, the optical alignment tolerance of the laser illumination on the SLM is very sensitive. The twodimensional angular tolerance is analyzed based on the theoretical model of the volume holographic correlator. The experimental demonstration of the proposed read-only VHC is introduced and discussed.

  9. Socioeconomic and nutritional factors account for the association of gastric cancer with Amerindian ancestry in a Latin American admixed population.

    Directory of Open Access Journals (Sweden)

    Latife Pereira

    Full Text Available Gastric cancer is one of the most lethal types of cancer and its incidence varies worldwide, with the Andean region of South America showing high incidence rates. We evaluated the genetic structure of the population from Lima (Peru and performed a case-control genetic association study to test the contribution of African, European, or Native American ancestry to risk for gastric cancer, controlling for the effect of non-genetic factors. A wide set of socioeconomic, dietary, and clinic information was collected for each participant in the study and ancestry was estimated based on 103 ancestry informative markers. Although the urban population from Lima is usually considered as mestizo (i.e., admixed from Africans, Europeans, and Native Americans, we observed a high fraction of Native American ancestry (78.4% for the cases and 74.6% for the controls and a very low African ancestry (<5%. We determined that higher Native American individual ancestry is associated with gastric cancer, but socioeconomic factors associated both with gastric cancer and Native American ethnicity account for this association. Therefore, the high incidence of gastric cancer in Peru does not seem to be related to susceptibility alleles common in this population. Instead, our result suggests a predominant role for ethnic-associated socioeconomic factors and disparities in access to health services. Since Native Americans are a neglected group in genomic studies, we suggest that the population from Lima and other large cities from Western South America with high Native American ancestry background may be convenient targets for epidemiological studies focused on this ethnic group.

  10. Alternative High School Students: Prevalence and Correlates of Overweight

    Science.gov (United States)

    Kubik, Martha Y.; Davey, Cynthia; Fulkerson, Jayne A.; Sirard, John; Story, Mary; Arcan, Chrisa

    2009-01-01

    Objective: To determine prevalence and correlates of overweight among adolescents attending alternative high schools (AHS). Methods: AHS students (n=145) from 6 schools completed surveys and anthropometric measures. Cross-sectional associations were assessed using mixed model multivariate logistic regression. Results: Among students, 42% were…

  11. Correlates of highly active antiretroviral therapy adherence among ...

    African Journals Online (AJOL)

    Correlates of highly active antiretroviral therapy adherence among urban Ethiopian clients. ... clients' self-reported adherence to HAART medication, a descriptive, comparative cross-sectional study was carried out among adults receiving HAART medication at the Zewditu Memorial Hospital ART clinic in Addis Ababa.

  12. Inference for High-dimensional Differential Correlation Matrices.

    Science.gov (United States)

    Cai, T Tony; Zhang, Anru

    2016-01-01

    Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical guarantees are given. Minimax rate of convergence is established and the proposed estimator is shown to be adaptively rate-optimal over collections of paired correlation matrices with approximately sparse differences. Simulation results show that the procedure significantly outperforms two other natural methods that are based on separate estimation of the individual correlation matrices. The procedure is also illustrated through an analysis of a breast cancer dataset, which provides evidence at the gene co-expression level that several genes, of which a subset has been previously verified, are associated with the breast cancer. Hypothesis testing on the differential correlation matrices is also considered. A test, which is particularly well suited for testing against sparse alternatives, is introduced. In addition, other related problems, including estimation of a single sparse correlation matrix, estimation of the differential covariance matrices, and estimation of the differential cross-correlation matrices, are also discussed.

  13. High-speed technique based on a parallel projection correlation procedure for digital image correlation

    Science.gov (United States)

    Zaripov, D. I.; Renfu, Li

    2018-05-01

    The implementation of high-efficiency digital image correlation methods based on a zero-normalized cross-correlation (ZNCC) procedure for high-speed, time-resolved measurements using a high-resolution digital camera is associated with big data processing and is often time consuming. In order to speed-up ZNCC computation, a high-speed technique based on a parallel projection correlation procedure is proposed. The proposed technique involves the use of interrogation window projections instead of its two-dimensional field of luminous intensity. This simplification allows acceleration of ZNCC computation up to 28.8 times compared to ZNCC calculated directly, depending on the size of interrogation window and region of interest. The results of three synthetic test cases, such as a one-dimensional uniform flow, a linear shear flow and a turbulent boundary-layer flow, are discussed in terms of accuracy. In the latter case, the proposed technique is implemented together with an iterative window-deformation technique. On the basis of the results of the present work, the proposed technique is recommended to be used for initial velocity field calculation, with further correction using more accurate techniques.

  14. Association of breast cancer risk and the mTOR pathway in women of African ancestry in 'The Root' Consortium.

    Science.gov (United States)

    Wang, Shengfeng; Huo, Dezheng; Ogundiran, Temidayo O; Ojengbede, Oladosu; Zheng, Wei; Nathanson, Katherine L; Nemesure, Barbara; Ambs, Stefan; Olopade, Olufunmilayo I; Zheng, Yonglan

    2017-08-01

    Functional studies have elucidated the role of the mammalian target of rapamycin (mTOR) pathway in breast carcinogenesis, but to date, there is a paucity of data on its contribution to breast cancer risk in women of African ancestry. We examined 47628 SNPs in 61 mTOR pathway genes in the genome wide association study of breast cancer in the African Diaspora study (The Root consortium), which included 3686 participants (1657 cases). Pathway- and gene-level analyses were conducted using the adaptive rank truncated product (ARTP) test for 10994 SNPs that were not highly correlated (r2 studies of breast cancer in the African Diaspora. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. African Ancestry Is Associated with Higher Intraocular Pressure in Latinos.

    Science.gov (United States)

    Nannini, Drew; Torres, Mina; Chen, Yii-Der I; Taylor, Kent D; Rotter, Jerome I; Varma, Rohit; Gao, Xiaoyi

    2016-01-01

    Intraocular pressure (IOP) is a major risk factor, as well as the only modifiable risk factor, for glaucoma. Racial differences have been observed in IOP measurements with individuals of African descent experiencing the highest IOP when compared with other ethnic groups. The purpose of this study was to examine the relationship between genetic ancestry and IOP in Latinos. Population-based genetic association study. A total of 3541 participants recruited from the Los Angeles Latino Eye Study. Study participants were genotyped using the Illumina OmniExpress BeadChip (∼730K markers). We used STRUCTURE to estimate individual genetic ancestry. Simple and multiple linear regression, as well as quantile regression, analyses were performed to investigate the relationship between genetic ancestry and IOP. The relationship between genetic ancestry and IOP in Latinos. African ancestry was significantly associated with higher IOP in Latinos in our simple linear regression analysis (P = 0.002). After adjusting for age, gender, body mass index, systolic blood pressure, central corneal thickness, and type 2 diabetes, this association remained significant (P = 0.0005). The main association was modified by a significant interaction between African ancestry and hypertension (P = 0.037), with hypertensive individuals experiencing a greater increase in IOP with increasing African ancestry. To our knowledge, we demonstrate for the first time that African ancestry and its interaction with hypertension are associated with higher IOP in Latinos. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  16. Ancestry and Severity of Disability: A National Study.

    Science.gov (United States)

    Wheaton, Joe E.; Hertzfeld, Jennifer

    2002-01-01

    Examines effects of ancestry and severity of disability of vocational rehabilitation consumers. European Americans, individuals with higher costs, and persons who received assistive technology were more likely to be closed rehabilitated. Individuals from other ancestry groups, who were coded severely disabled, or who had been in the system for…

  17. European ancestry predominates in neuromyelitis optica and multiple sclerosis patients from Brazil.

    Directory of Open Access Journals (Sweden)

    Doralina Guimarães Brum

    Full Text Available BACKGROUND: Neuromyelitis optica (NMO is considered relatively more common in non-Whites, whereas multiple sclerosis (MS presents a high prevalence rate, particularly in Whites from Western countries populations. However, no study has used ancestry informative markers (AIMs to estimate the genetic ancestry contribution to NMO patients. METHODS: Twelve AIMs were selected based on the large allele frequency differences among European, African, and Amerindian populations, in order to investigate the genetic contribution of each ancestral group in 236 patients with MS and NMO, diagnosed using the McDonald and Wingerchuck criteria, respectively. All 128 MS patients were recruited at the Faculty of Medicine of Ribeirão Preto (MS-RP, Southeastern Brazil, as well as 108 healthy bone marrow donors considered as healthy controls. A total of 108 NMO patients were recruited from five Neurology centers from different Brazilian regions, including Ribeirão Preto (NMO-RP. PRINCIPAL FINDINGS: European ancestry contribution was higher in MS-RP than in NMO-RP (78.5% vs. 68.7% patients. In contrast, African ancestry estimates were higher in NMO-RP than in MS-RP (20.5% vs. 12.5% patients. Moreover, principal component analyses showed that groups of NMO patients from different Brazilian regions were clustered close to the European ancestral population. CONCLUSIONS: Our findings demonstrate that European genetic contribution predominates in NMO and MS patients from Brazil.

  18. Paracoccidioidomycosis: High-resolution computed tomography-pathologic correlation

    International Nuclear Information System (INIS)

    Marchiori, Edson; Valiante, Paulo Marcos; Mano, Claudia Mauro; Zanetti, Glaucia; Escuissato, Dante L.; Souza, Arthur Soares; Capone, Domenico

    2011-01-01

    Objective: The purpose of this study was to describe the high-resolution computed tomography (HRCT) features of pulmonary paracoccidioidomycosis and to correlate them with pathologic findings. Methods: The study included 23 adult patients with pulmonary paracoccidioidomycosis. All patients had undergone HRCT, and the images were retrospectively analyzed by two chest radiologists, who reached decisions by consensus. An experienced lung pathologist reviewed all pathological specimens. The HRCT findings were correlated with histopathologic data. Results: The predominant HRCT findings included areas of ground-glass opacities, nodules, interlobular septal thickening, airspace consolidation, cavitation, and fibrosis. The main pathological features consisted of alveolar and interlobular septal inflammatory infiltration, granulomas, alveolar exudate, cavitation secondary to necrosis, and fibrosis. Conclusion: Paracoccidioidomycosis can present different tomography patterns, which can involve both the interstitium and the airspace. These abnormalities can be pathologically correlated with inflammatory infiltration, granulomatous reaction, and fibrosis.

  19. A study of highly correlated classical and quantum fluids

    International Nuclear Information System (INIS)

    Clements, B.E.

    1988-01-01

    We have determined, by molecular dynamics simulation, the l = 0, 2, 4, and 6 Legendre coefficients of the static pair-pair correlation function Q(r,r'), the dynamic pair-pair correlation function Q(r,r';t) and the dynamic four point correlation function S 4 (k, -k,q, -q;t). The interaction potential was taken to be Lennard-Jones. The simulation was carried out at two different values of density and temperature; one coinciding with that of liquid argon near its triple point and the other coinciding with high density argon at room temperature. We argue that an important contribution to the pair-pair correlation function comes from the thee-body correlations. We find that the Legendre coefficients of Q(r,r') provide strong evidence that, upon freezing, the resulting crystalline structure will be a close-packed structure. A study of dynamical fluctuations characterized by Legendre coefficients of the dynamic pair-pair correlation function support this assertion. Finally, we provide a discussion on a decoupling scheme, used in the literature, to approximate the static and dynamic four point correlation function. A variational calculation with the Penrose-Reatto-Chester-Jastrow density matrix is used to study the finite temperature properties of Bose quantum fluids. This analysis provides a systematic method for adding correction terms to the density matrix approach of Campbell, Ristig, Kurten and Senger. We find that the excitation spectrum for the elementary excitations has the proper temperature dependence in contrast to earlier calculations

  20. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

    DEFF Research Database (Denmark)

    Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.

    2014-01-01

    ,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic......The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24...... that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans....

  1. A comparison of high-frequency cross-correlation measures

    Science.gov (United States)

    Precup, Ovidiu V.; Iori, Giulia

    2004-12-01

    On a high-frequency scale the time series are not homogeneous, therefore standard correlation measures cannot be directly applied to the raw data. There are two ways to deal with this problem. The time series can be homogenised through an interpolation method (An Introduction to High-Frequency Finance, Academic Press, NY, 2001) (linear or previous tick) and then the Pearson correlation statistic computed. Recently, methods that can handle raw non-synchronous time series have been developed (Int. J. Theor. Appl. Finance 6(1) (2003) 87; J. Empirical Finance 4 (1997) 259). This paper compares two traditional methods that use interpolation with an alternative method applied directly to the actual time series.

  2. Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

    Science.gov (United States)

    Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

    2017-03-15

    Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved

  3. pp spin correlations at high p/sub T/

    International Nuclear Information System (INIS)

    Auer, I.P.; Colton, E.; Ditzler, W.R.

    1980-01-01

    New data are presented for measurements of the spin correlation in pp reactions with longitudinally polarized beam and target. Data were obtained at 11.75 GeV/c for both elastic scattering and for π + - and π - -production at high p/sub T/ in pp reactions at 11.75 GeV/c. A comparison is made with recent predictions of quark-parton models

  4. WDR1 and CLNK gene polymorphisms correlate with serum glucose and high-density lipoprotein levels in Tibetan gout patients.

    Science.gov (United States)

    Lan, Bing; Chen, Peng; Jiri, Mutu; He, Na; Feng, Tian; Liu, Kai; Jin, Tianbo; Kang, Longli

    2016-03-01

    Current evidence suggests heredity and metabolic syndrome contributes to gout progression. Specifically, the WDR1 and CLNK genes may play a role in gout progression in European ancestry populations. However, no studies have focused on Chinese populations, especially Tibetan individuals. This study aims to determine whether variations in these two genes correlate with gout-related indices in Chinese-Tibetan gout patients. Eleven single-nucleotide polymorphisms in the WDR1 and CLNK genes were detected in 319 Chinese-Tibetan gout patients and 318 controls. We used one-way analysis of variance to evaluate the polymorphisms' effects on gout based on mean serum levels of metabolism indicators, such as albumin, glucose (GLU), triglycerides, cholesterol, high-density lipoproteins (HDL-C), creatinine, and uric acid, from fasting venous blood samples. All p values were Bonferroni corrected. Polymorphisms of the WDR1 and CLNK genes affected multiple risk factors for gout development. Significant differences in serum GLU levels were detected between different genotypic groups with WDRI polymorphisms rs4604059 (p = 0.005) and rs12498927 (p = 0.005). In addition, significant differences in serum HDL-C levels were detected between different genotypic groups with the CLNK polymorphism rs2041215 (p = 0.001). Polymorphisms of CLNK also affected levels of albumin, triglycerides, and creatinine. This study is the first to investigate and identify positive correlations between WDR1 and CLNK gene polymorphisms in Chinese-Tibetan populations. Our findings provide significant evidence for the effect of genetic polymorphisms on gout-related factors in Chinese-Tibetan populations.

  5. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations.

    Science.gov (United States)

    Duan, Qing; Xu, Zheng; Raffield, Laura M; Chang, Suhua; Wu, Di; Lange, Ethan M; Reiner, Alex P; Li, Yun

    2018-04-01

    Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA. © 2017 WILEY PERIODICALS, INC.

  6. Energy homeostasis genes and breast cancer risk: The influence of ancestry, body size, and menopausal status, the breast cancer health disparities study.

    Science.gov (United States)

    Slattery, Martha L; Lundgreen, Abbie; Hines, Lisa; Wolff, Roger K; Torres-Mejia, Gabriella; Baumgartner, Kathy N; John, Esther M

    2015-12-01

    Obesity and breast cancer risk is multifaceted and genes associated with energy homeostasis may modify this relationship. We evaluated 10 genes that have been associated with obesity and energy homeostasis to determine their association with breast cancer risk in Hispanic/Native American (2111 cases, 2597 controls) and non-Hispanic white (1481 cases, 1585 controls) women. Cholecystokinin (CCK) rs747455 and proopiomelanocortin (POMC) rs6713532 and rs7565877 (for low Indigenous American (IA) ancestry); CCK rs8192472 and neuropeptide Y (NYP) rs16141 and rs14129 (intermediate IA ancestry); and leptin receptor (LEPR) rs11585329 (high IA ancestry) were strongly associated with multiple indicators of body size. There were no significant associations with breast cancer risk between genes and SNPs overall. However, LEPR was significantly associated with breast cancer risk among women with low IA ancestry (PARTP=0.024); POMC was significantly associated with breast cancer risk among women with intermediate (PARTP=0.015) and high (PARTP=0.012) IA ancestry. The overall pathway was statistically significant for pre-menopausal women with low IA ancestry (PARTP=0.05), as was cocaine and amphetamine regulated transcript protein (CARTPT) (PARTP=0.014) and ghrelin (GHRL) (PARTP=0.007). POMC was significantly associated with breast cancer risk among post-menopausal women with higher IA ancestry (PARTP=0.005). Three SNPs in LEPR (rs6704167, rs17412175, and rs7626141), and adiponectin (ADIPOQ); rs822391) showed significant 4-way interactions (GxExMenopausexAncestry) for multiple indicators of body size among pre-menopausal women. Energy homeostasis genes were associated with breast cancer risk; menopausal status, body size, and genetic ancestry influenced this relationship. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Genetic ancestry in relation to the metabolic response to a US versus traditional Mexican diet: a randomized crossover feeding trial among women of Mexican descent.

    Science.gov (United States)

    Santiago-Torres, M; De Dieu Tapsoba, J; Kratz, M; Lampe, J W; Breymeyer, K L; Levy, L; Song, X; Villaseñor, A; Wang, C-Y; Fejerman, L; Neuhouser, M L; Carlson, C S

    2017-03-01

    Certain populations with a large proportion of indigenous American (IA) genetic ancestry may be evolutionarily adapted to traditional diets high in legumes and complex carbohydrates, and may have a detrimental metabolic response to US diets high in refined carbohydrates and added sugars. We tested whether IA ancestry modified the metabolic response to a US versus traditional Mexican diet in a controlled dietary intervention. First and second generation Mexican immigrant women (n=53) completed a randomized crossover feeding trial testing the effects of a US versus traditional Mexican diet. The metabolic response to the diets was measured by fasting serum concentrations of glucose, insulin, insulin-like growth factor-1 (IGF-1), IGF-binding protein-3 (IGFBP-3), adiponectin, C-reactive protein, interleukin-6 and computed homeostasis model assessment for insulin resistance (HOMA IR ). Blood collected at baseline was used for genotyping, and estimation of African, European and IA ancestries with the use of 214 ancestry informative markers. The genetic ancestral background was 56% IA, 38% European and 6% African. Women in the highest IA ancestry tertile (>62%) were shorter in height, less educated and less acculturated to the US lifestyle, and tended to have higher waist-to-hip ratio compared with women in the middle and lowest IA ancestry tertiles, respectively. Compared with the US diet, the traditional Mexican diet tended to reduce glucose, insulin, IGF-1, IGFBP-3 and HOMA IR among women in the middle IA ancestry group (IA ancestry ⩽45-62%), whereas having no effect on biomarkers related to inflammation. We observed modest interactions between IA ancestry and the metabolic response to a US versus traditional Mexican diet among Mexican immigrant women.

  8. Variation in APOL1 Contributes to Ancestry-Level Differences in HDLc-Kidney Function Association

    Directory of Open Access Journals (Sweden)

    Amy Rebecca Bentley

    2012-01-01

    Full Text Available Low levels of high-density cholesterol (HDLc accompany chronic kidney disease, but the association between HDLc and the estimated glomerular filtration rate (eGFR in the general population is unclear. We investigated the HDLc-eGFR association in nondiabetic Han Chinese (HC, n=1100, West Africans (WA, n=1497, and African Americans (AA, n=1539. There were significant differences by ancestry: HDLc was positively associated with eGFR in HC (β=0.13, P<0.0001, but negatively associated among African ancestry populations (WA: −0.19, P<0.0001; AA: −0.09, P=0.02. These differences were also seen in nationally-representative NHANES data (among European Americans: 0.09, P=0.005; among African Americans −0.14, P=0.03. To further explore the findings in African ancestry populations, we investigated the role of an African ancestry-specific nephropathy risk variant, rs73885319, in the gene encoding HDL-associated APOL1. Among AA, an inverse HDLc-eGFR association was observed only with the risk genotype (−0.38 versus 0.001; P=0.03. This interaction was not seen in WA. In summary, counter to expectation, an inverse HDLc-eGFR association was observed among those of African ancestry. Given the APOL1 × HDLc interaction among AA, genetic factors may contribute to this paradoxical association. Notably, these findings suggest that the unexplained mechanism by which APOL1 affects kidney-disease risk may involve HDLc.

  9. Simultaneous correlative scanning electron and high-NA fluorescence microscopy.

    Directory of Open Access Journals (Sweden)

    Nalan Liv

    Full Text Available Correlative light and electron microscopy (CLEM is a unique method for investigating biological structure-function relations. With CLEM protein distributions visualized in fluorescence can be mapped onto the cellular ultrastructure measured with electron microscopy. Widespread application of correlative microscopy is hampered by elaborate experimental procedures related foremost to retrieving regions of interest in both modalities and/or compromises in integrated approaches. We present a novel approach to correlative microscopy, in which a high numerical aperture epi-fluorescence microscope and a scanning electron microscope illuminate the same area of a sample at the same time. This removes the need for retrieval of regions of interest leading to a drastic reduction of inspection times and the possibility for quantitative investigations of large areas and datasets with correlative microscopy. We demonstrate Simultaneous CLEM (SCLEM analyzing cell-cell connections and membrane protrusions in whole uncoated colon adenocarcinoma cell line cells stained for actin and cortactin with AlexaFluor488. SCLEM imaging of coverglass-mounted tissue sections with both electron-dense and fluorescence staining is also shown.

  10. Dynamics of Coulomb correlations in semiconductors in high magnetic fields

    International Nuclear Information System (INIS)

    Fromer, Neil Alan

    2002-01-01

    Current theories have been successful in explaining many nonlinear optical experiments in undoped semiconductors. However, these theories require a ground state which is assumed to be uncorrelated. Strongly correlated systems of current interest, such as a two dimensional electron gas in a high magnetic field, cannot be explained in this manner because the correlations in the ground state and the low energy collective excitations cause a breakdown of the conventional techniques. We perform ultrafast time-resolved four-wave mixing on $n$-modulation doped quantum wells, which contain a quasi-two dimensional electron gas, in a large magnetic field, when only a single Landau level is excited and also when two levels are excited together. We find evidence for memory effects and as strong coupling between the Landau levels induced by the electron gas. We compare our results with simulations based on a new microscopic approach capable of treating the collective effects and correlations of the doped electrons, and find a good qualitative agreement. By looking at the individual contributions to the model, we determine that the unusual correlation effects seen in the experiments are caused by the scattering of photo-excited electron-hole pairs with the electron gas, leading to new excited states which are not present in undoped semiconductors, and also by exciton-exciton interactions mediated by the long-lived collective excitations of the electron gas, inter-Landau level magnetoplasmons

  11. The Astrobiological Case for Our Cosmic Ancestry

    Science.gov (United States)

    Wickramasinghe, Chandra

    With steadily mounting evidence that points to a cosmic origin of terrestrial life, a cultural barrier prevails against admitting that such a connection exists. Astronomy continues to reveal the presence of organic molecules and organic dust on a huge cosmic scale, amounting to a third of interstellar carbon tied up in this form. Just as the overwhelming bulk of organics on Earth stored over geological timescales are derived from the degradation of living cells, so it seems most likely that interstellar organics in large measure also derive from biology. As we enter a new decade -- the year 2010 -- a clear pronouncement of our likely alien ancestry and of the existence of extraterrestrial life on a cosmic scale would seem to be overdue.

  12. Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

    Science.gov (United States)

    Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

    2013-01-01

    Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

  13. Genetic ancestry in relation to the metabolic response to a U.S. versus traditional Mexican diet: a randomized crossover feeding trial among women of Mexican descent

    OpenAIRE

    Santiago-Torres, Margarita; De Dieu Tapsoba, Jean; Kratz, Mario; Lampe, Johanna W.; Breymeyer, Kara L.; Levy, Lisa; Song, Xiaoling; Villase?or, Adriana; Wang, Ching-Yun; Fejerman, Laura; Neuhouser, Marian L.; Carlson, Christopher S.

    2016-01-01

    Background Certain populations with a large proportion of Indigenous American (IA) genetic ancestry may be evolutionarily adapted to traditional diets high in legumes and complex carbohydrates, and may have a detrimental metabolic response to U.S. diets high in refined carbohydrates and added sugars. We tested whether IA ancestry modified the metabolic response to a U.S. versus traditional Mexican diet in a controlled dietary intervention. Methods First and second generation Mexican immigrant...

  14. Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

    Science.gov (United States)

    Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

    2013-01-01

    Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

  15. Complex correlation approach for high frequency financial data

    Science.gov (United States)

    Wilinski, Mateusz; Ikeda, Yuichi; Aoyama, Hideaki

    2018-02-01

    We propose a novel approach that allows the calculation of a Hilbert transform based complex correlation for unevenly spaced data. This method is especially suitable for high frequency trading data, which are of a particular interest in finance. Its most important feature is the ability to take into account lead-lag relations on different scales, without knowing them in advance. We also present results obtained with this approach while working on Tokyo Stock Exchange intraday quotations. We show that individual sectors and subsectors tend to form important market components which may follow each other with small but significant delays. These components may be recognized by analysing eigenvectors of complex correlation matrix for Nikkei 225 stocks. Interestingly, sectorial components are also found in eigenvectors corresponding to the bulk eigenvalues, traditionally treated as noise.

  16. On discriminant analysis techniques and correlation structures in high dimensions

    DEFF Research Database (Denmark)

    Clemmensen, Line Katrine Harder

    This paper compares several recently proposed techniques for performing discriminant analysis in high dimensions, and illustrates that the various sparse methods dier in prediction abilities depending on their underlying assumptions about the correlation structures in the data. The techniques...... the methods in two: Those who assume independence between the variables and thus use a diagonal estimate of the within-class covariance matrix, and those who assume dependence between the variables and thus use an estimate of the within-class covariance matrix, which also estimates the correlations between...... variables. The two groups of methods are compared and the pros and cons are exemplied using dierent cases of simulated data. The results illustrate that the estimate of the covariance matrix is an important factor with respect to choice of method, and the choice of method should thus be driven by the nature...

  17. Orbitals, correlation, valencies in high-Tc superconductors

    International Nuclear Information System (INIS)

    Khomskii, D.I.

    1990-09-01

    The survey is given of certain properties of high-Tc superconductors connected with the details of their electronic structure such as the kind of orbitals involved and the degree of correlation. Special attention is paid to the properties of cuprates at high doping level. The problem whether there exists a ''Mott transition'' at high electron or a hole concentration is discussed. We also discuss physical factors (d-p Coulomb interaction, orbital mixing) leading to the partial occupation of copper d x 2 -orbital. In particular we show that in localized picture (x 2 -y 2 ) and z 2 -levels in La 2-x Sr x CuO 4 may cross at x approx. 0.4 which may be responsible for a marked change of many properties at this doping. The possible role of x 2 -electrons in pairing is discussed in connection with some recent experiments. (author). 28 refs, 6 figs, 1 tab

  18. Amerindian (but not African or European) ancestry is significantly associated with diurnal preference within an admixed Brazilian population.

    Science.gov (United States)

    Egan, Kieren J; Campos Santos, Hadassa; Beijamini, Felipe; Duarte, Núbia E; Horimoto, Andréa R V R; Taporoski, Tâmara P; Vallada, Homero; Negrão, André B; Krieger, José E; Pedrazzoli, Mário; Knutson, Kristen L; Pereira, Alexandre C; von Schantz, Malcolm

    2017-01-01

    Significant questions remain unanswered regarding the genetic versus environmental contributions to racial/ethnic differences in sleep and circadian rhythms. We addressed this question by investigating the association between diurnal preference, using the morningness-eveningness questionnaire (MEQ), and genetic ancestry within the Baependi Heart Study cohort, a highly admixed Brazilian population based in a rural town. Analysis was performed using measures of ancestry, using the Admixture program, and MEQ from 1,453 individuals. We found an association between the degree of Amerindian (but not European of African) ancestry and morningness, equating to 0.16 units for each additional percent of Amerindian ancestry, after adjustment for age, sex, education, and residential zone. To our knowledge, this is the first published report identifying an association between genetic ancestry and MEQ, and above all, the first one based on ancestral contributions within individuals living in the same community. This previously unknown ancestral dimension of diurnal preference suggests a stratification between racial/ethnic groups in an as yet unknown number of genetic polymorphisms.

  19. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.

    Directory of Open Access Journals (Sweden)

    Amidou N'Diaye

    2011-10-01

    Full Text Available Adult height is a classic polygenic trait of high heritability (h(2 approximately 0.8. More than 180 single nucleotide polymorphisms (SNPs, identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain approximately10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P = 3.4×10(-12 and 2p14-rs4315565, P = 1.2×10(-8. As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P = 1.7×10(-4 for overall replication. Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01. Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits.

  20. The Hmong Diaspora: preserved South-East Asian genetic ancestry in French Guianese Asians.

    Science.gov (United States)

    Brucato, Nicolas; Mazières, Stéphane; Guitard, Evelyne; Giscard, Pierre-Henri; Bois, Etienne; Larrouy, Georges; Dugoujon, Jean-Michel

    2012-01-01

    The Hmong Diaspora is one of the widest modern human migrations. Mainly localised in South-East Asia, the United States of America, and metropolitan France, a small community has also settled the Amazonian forest of French Guiana. We have biologically analysed 62 individuals of this unique Guianese population through three complementary genetic markers: mitochondrial DNA (HVS-I/II and coding region SNPs), Y-chromosome (SNPs and STRs), and the Gm allotypic system. All genetic systems showed a high conservation of the Asian gene pool (Asian ancestry: mtDNA=100.0%; NRY=99.1%; Gm=96.6%), without a trace of founder effect. When compared across various Asian populations, the highest correlations were observed with Hmong-Mien groups still living in South-East Asia (Fst<0.05; P-value<0.05). Despite a long history punctuated by exodus, the French Guianese Hmong have maintained their original genetic diversity. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  1. On temporal correlations in high-resolution frequency counting

    OpenAIRE

    Dunker, Tim; Hauglin, Harald; Rønningen, Ole Petter

    2016-01-01

    We analyze noise properties of time series of frequency data from different counting modes of a Keysight 53230A frequency counter. We use a 10 MHz reference signal from a passive hydrogen maser connected via phase-stable Huber+Suhner Sucoflex 104 cables to the reference and input connectors of the counter. We find that the high resolution gap-free (CONT) frequency counting process imposes long-term correlations in the output data, resulting in a modified Allan deviation that is characteristic...

  2. Near-side high-p (T) correlations: the ridge

    Czech Academy of Sciences Publication Activity Database

    Bielčíková, Jana

    2009-01-01

    Roč. 61, č. 4 (2009), s. 589-595 ISSN 1434-6044. [3rd International Conference on Hard and Electromagnetic Probes of High-Energy Nuclear Collisions. Illa da Toxa, 08.06.2008-14.06.2008] R&D Projects: GA ČR GA202/07/0079; GA MŠk LC07048 Institutional research plan: CEZ:AV0Z10480505 Keywords : QUARK-GLUON PLASMA * HEAVY ION COLLISION * particle correlations Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 2.746, year: 2009

  3. Analysis method of high-order collective-flow correlations based on the concept of correlative degree

    International Nuclear Information System (INIS)

    Zhang Weigang

    2000-01-01

    Based on the concept of correlative degree, a new method of high-order collective-flow measurement is constructed, with which azimuthal correlations, correlations of final state transverse momentum magnitude and transverse correlations can be inspected respectively. Using the new method the contributions of the azimuthal correlations of particles distribution and the correlations of transverse momentum magnitude of final state particles to high-order collective-flow correlations are analyzed respectively with 4π experimental events for 1.2 A GeV Ar + BaI 2 collisions at the Bevalac stream chamber. Comparing with the correlations of transverse momentum magnitude, the azimuthal correlations of final state particles distribution dominate high-order collective-flow correlations in experimental samples. The contributions of correlations of transverse momentum magnitude of final state particles not only enhance the strength of the high-order correlations of particle group, but also provide important information for the measurement of the collectivity of collective flow within the more constraint district

  4. Multiparticle correlations and intermittency in high energy collisions

    International Nuclear Information System (INIS)

    Bozek, P.

    1992-01-01

    The analysis of the intermittency signal observed in high energy experiments is presented using multiparticle distributions and correlation functions. The effect of the dimensional projection of the multiparticle distributions on one or two-dimensional subspace is discussed. The structure of the multiparticle cumulants is analyzed for the DELPHI e + e - annihilation data. The model of spatiotemporal intermittency is discussed in details and is shown to reproduce qualitatively the dependence of the intermittency strength on the target and projectile nuclei. A 1-dimensional (1D) cellular-automaton and a 1D forest-fire model is studied. On the example of the noncritical 1D Ising model the difficulties of the scaled factorial moment (SFM) method in extracting genuine scaling behaviour is illustrated. All these studies could serve as tools to test the sensibility of the SFM method as used in the analysis of the high energy production. (K.A.) 122 refs.; 38 figs.; 3 tabs

  5. Search for correlated high energy cosmic ray events with CHICOS

    International Nuclear Information System (INIS)

    Carlson, B E; Brobeck, E; Jillings, C J; Larson, M B; Lynn, T W; McKeown, R D; Hill, James E; Falkowski, B J; Seki, R; Sepikas, J; Yodh, G B

    2005-01-01

    We present the results of a search for time correlations in high energy cosmic ray data (primary E > 10 14 eV) collected by the California HIgh school Cosmic ray ObServatory (CHICOS) array. Data from 60 detector sites spread over an area of 400 km 2 were studied for evidence of isolated events separated by more than 1 km with coincidence times ranging from 1 μs up to 1 s. The results are consistent with the absence of excess coincidences except for a 2.9σ excess observed for coincidence times less than 10 μs. We report upper limits for the coincidence probability as a function of coincidence time

  6. Ancestry and dental development: A geographic and genetic perspective.

    Science.gov (United States)

    Dhamo, Brunilda; Kragt, Lea; Grgic, Olja; Vucic, Strahinja; Medina-Gomez, Carolina; Rivadeneira, Fernando; Jaddoe, Vincent W V; Wolvius, Eppo B; Ongkosuwito, Edwin M

    2018-02-01

    In this study, we investigated the influence of ancestry on dental development in the Generation R Study. Information on geographic ancestry was available in 3,600 children (1,810 boys and 1,790 girls, mean age 9.81 ± 0.35 years) and information about genetic ancestry was available in 2,786 children (1,387 boys and 1,399 girls, mean age 9.82 ± 0.34 years). Dental development was assessed in all children using the Demirjian method. The associations of geographic ancestry (Cape Verdean, Moroccan, Turkish, Dutch Antillean, Surinamese Creole and Surinamese Hindustani vs Dutch as the reference group) and genetic content of ancestry (European, African or Asian) with dental development was analyzed using linear regression models. In a geographic perspective of ancestry, Moroccan (β = 0.18; 95% CI: 0.07, 0.28), Turkish (β = 0.22; 95% CI: 0.12, 0.32), Dutch Antillean (β = 0.27; 95% CI: 0.12, 0.41), and Surinamese Creole (β = 0.16; 95% CI: 0.03, 0.30) preceded Dutch children in dental development. Moreover, in a genetic perspective of ancestry, a higher proportion of European ancestry was associated with decelerated dental development (β = -0.32; 95% CI: -.44, -.20). In contrast, a higher proportion of African ancestry (β = 0.29; 95% CI: 0.16, 0.43) and a higher proportion of Asian ancestry (β = 0.28; 95% CI: 0.09, 0.48) were associated with accelerated dental development. When investigating only European children, these effect estimates increased to twice as large in absolute value. Based on a geographic and genetic perspective, differences in dental development exist in a population of heterogeneous ancestry and should be considered when describing the physiological growth in children. © 2017 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.

  7. Human leukocyte antigen class I (A, B and C) allele and haplotype variation in a South African Mixed ancestry population.

    Science.gov (United States)

    Loubser, Shayne; Paximadis, Maria; Tiemessen, Caroline T

    South Africa has a large (∼53million), ethnically diverse population (black African, Caucasian, Indian/Asian and Mixed ancestry) and a high disease burden (particularly HIV-1 and Mycobacterium tuberculosis). The Mixed ancestry population constitutes ∼9% of the total population and was established ∼365years ago in the Western Cape region through interracial mixing of black Africans, Europeans and Asians. Admixed populations present unique opportunities to identify genetic factors involved in disease susceptibility. Since HLA genes are important mediators of host immunity, we investigated HLA-A, -B and -C allele and haplotype diversity in 50 healthy, unrelated individuals recruited from the Mixed ancestry population. Copyright © 2017. Published by Elsevier Inc.

  8. Ancestry Testing and the Practice of Genetic Counseling.

    Science.gov (United States)

    Kirkpatrick, Brianne E; Rashkin, Misha D

    2017-02-01

    Ancestry testing is a home DNA test with many dimensions; in some cases, the implications and outcomes of testing cross over into the health sphere. Common reasons for seeking ancestry testing include determining an estimate of customer's ethnic background, identifying genetic relatives, and securing a raw DNA data file that can be used for other purposes. As the ancestry test marketplace continues to grow, and third-party vendors empower the general public to analyze their own genetic material, the role of the genetic counselor is likely to evolve dramatically. Roles of the genetic counselor may include assisting clients with the interpretation of and adaptation to these results, as well as advising the companies involved in this sector on the ethical, legal, and social issues associated with testing. This paper reviews the history, fundamentals, intended uses, and unintended consequences of ancestry genetic testing. It also discusses the types of information in an ancestry testing result, situations that might involve a clinical genetic counselor, and the benefits, limitations, and functions that ancestry genetic testing can play in a clinical genetics setting.

  9. A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci.

    Science.gov (United States)

    Rand, Kristin A; Song, Chi; Dean, Eric; Serie, Daniel J; Curtin, Karen; Sheng, Xin; Hu, Donglei; Huff, Carol Ann; Bernal-Mizrachi, Leon; Tomasson, Michael H; Ailawadhi, Sikander; Singhal, Seema; Pawlish, Karen; Peters, Edward S; Bock, Cathryn H; Stram, Alex; Van Den Berg, David J; Edlund, Christopher K; Conti, David V; Zimmerman, Todd; Hwang, Amie E; Huntsman, Scott; Graff, John; Nooka, Ajay; Kong, Yinfei; Pregja, Silvana L; Berndt, Sonja I; Blot, William J; Carpten, John; Casey, Graham; Chu, Lisa; Diver, W Ryan; Stevens, Victoria L; Lieber, Michael R; Goodman, Phyllis J; Hennis, Anselm J M; Hsing, Ann W; Mehta, Jayesh; Kittles, Rick A; Kolb, Suzanne; Klein, Eric A; Leske, Cristina; Murphy, Adam B; Nemesure, Barbara; Neslund-Dudas, Christine; Strom, Sara S; Vij, Ravi; Rybicki, Benjamin A; Stanford, Janet L; Signorello, Lisa B; Witte, John S; Ambrosone, Christine B; Bhatti, Parveen; John, Esther M; Bernstein, Leslie; Zheng, Wei; Olshan, Andrew F; Hu, Jennifer J; Ziegler, Regina G; Nyante, Sarah J; Bandera, Elisa V; Birmann, Brenda M; Ingles, Sue A; Press, Michael F; Atanackovic, Djordje; Glenn, Martha J; Cannon-Albright, Lisa A; Jones, Brandt; Tricot, Guido; Martin, Thomas G; Kumar, Shaji K; Wolf, Jeffrey L; Deming Halverson, Sandra L; Rothman, Nathaniel; Brooks-Wilson, Angela R; Rajkumar, S Vincent; Kolonel, Laurence N; Chanock, Stephen J; Slager, Susan L; Severson, Richard K; Janakiraman, Nalini; Terebelo, Howard R; Brown, Elizabeth E; De Roos, Anneclaire J; Mohrbacher, Ann F; Colditz, Graham A; Giles, Graham G; Spinelli, John J; Chiu, Brian C; Munshi, Nikhil C; Anderson, Kenneth C; Levy, Joan; Zonder, Jeffrey A; Orlowski, Robert Z; Lonial, Sagar; Camp, Nicola J; Vachon, Celine M; Ziv, Elad; Stram, Daniel O; Hazelett, Dennis J; Haiman, Christopher A; Cozen, Wendy

    2016-12-01

    Genome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma. We performed association testing of common variation in eight regions in 1,318 patients with multiple myeloma and 1,480 controls of European ancestry and 1,305 patients with multiple myeloma and 7,078 controls of African ancestry and conducted a meta-analysis to localize the signals, with epigenetic annotation used to predict functionality. We found that variants in 7p15.3, 17p11.2, 22q13.1 were statistically significantly (P ancestry and persons of European ancestry, and the variant in 3p22.1 was associated in European ancestry only. In a combined African ancestry-European ancestry meta-analysis, variation in five regions (2p23.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) was statistically significantly associated with multiple myeloma risk. In 3p22.1, the correlated variants clustered within the gene body of ULK4 Correlated variants in 7p15.3 clustered around an enhancer at the 3' end of the CDCA7L transcription termination site. A missense variant at 17p11.2 (rs34562254, Pro251Leu, OR, 1.32; P = 2.93 × 10 -7 ) in TNFRSF13B encodes a lymphocyte-specific protein in the TNF receptor family that interacts with the NF-κB pathway. SNPs correlated with the index signal in 22q13.1 cluster around the promoter and enhancer regions of CBX7 CONCLUSIONS: We found that reported multiple myeloma susceptibility regions contain risk variants important across populations, supporting the use of multiple racial/ethnic groups with different underlying genetic architecture to enhance the localization and identification of putatively functional alleles. A subset of reported risk loci for multiple myeloma has consistent effects across populations and is likely to be functional. Cancer Epidemiol Biomarkers Prev; 25(12); 1609-18. ©2016 AACR. ©2016 American Association for Cancer Research.

  10. Correlation mediated superconductivity in a 'High-Tsub(c)' model

    International Nuclear Information System (INIS)

    Long, M.W.

    1987-08-01

    A simple model is presented to account for the High-Tsub(c) perovskite superconductors. The superconducting mechanism is purely electronic and comes from local Hubbard correlations. The model comprises a Hubbard model for the copper sites with a single particle oxygen band between the two copper Hubbard bands. The electrons move only between nearest neighbour atoms which are of different types. Using two very different approximation schemes, one related to 'Slave-Boson' mean field theory and the other based on an exact local Fermion transformation, the possibility of copper-oxygen or a mixture of copper-oxygen and oxygen-oxygen pairing is shown. The author believes that the most promising situation for superconductivity is with the Oxygen band over half-filled and closer in energy to the lower Hubbard band. (author)

  11. Multiparticle correlations and intermittency in high energy collisions

    CERN Document Server

    Bozek, P

    1992-01-01

    In this work the analysis of the intermittency signal observed in high energy experi- ments is done using multiparticle distributions and correlation functions. The effect of the dimensional projection of the multiparticle distributions on one or two-dimensional subspace is discussed. The structure of the multiparticle cumulants is analyzed for the DELPHI e + e~ annihilation data. The language of the self-similar distribution func- tions, which is used in this work, is shown to be largely equivalent to the well known a-model. In the case of the ultrarelativistic nuclear collisions, where the Monte-Carlo simulations fail to reproduce the data, we argue that the observed intermittency pattern is a signal of some nonlinear effect beyond the simple superposition of nucleon-nucleon collisions. The model of spatiotemporal intermittency is discussed in details and is shown to reproduce qualitatively the dependence of t...

  12. Oxidative stress at high altitude: genotype–phenotype correlations

    Directory of Open Access Journals (Sweden)

    Pandey P

    2014-05-01

    Full Text Available Priyanka Pandey,1,2 MA Qadar Pasha1,2 1CSIR-Institute of Genomics and Integrative Biology, Delhi, India; 2Department of Biotechnology, University of Pune, Ganeshkhind, Pune, India Abstract: It has been well-documented that the hypobaric hypoxic environment at high altitude (HA causes stress to both the permanent residents of HA and the sojourners. This oxidative stress primarily disturbs the oxygen-sensing and vascular homeostasis pathways, thereby upsetting normal human physiology, especially in sojourners. These environmental challenges have caused dynamic evolutionary changes within natives of HA, allowing them to develop adaptive plasticity. This review focuses on the genomic and biochemical features of the molecules involved in the oxygen-sensing and vascular homeostasis pathways with respect to HA pulmonary edema (HAPE and adaptation. We review the role of genetic markers such as HIF-prolyl hydroxylase 2, endothelial PAS domain-containing protein 1, endothelial nitric oxide synthase, endothelin 1, cytochrome b-245 alpha polypeptide, and glutathione S-transferase pi 1, as well as three circulatory biomarkers (nitric oxide, endothelin 1, and 8-iso-prostaglandin F2α, by highlighting approaches such as candidate gene and genome-wide, adopted in deciphering the pathways. A disagreement between the two approaches has also been highlighted. In addition, we discuss that an overrepresentation of wild-type alleles in HA natives and mutant alleles of same polymorphisms in HAPE patients implies that the allelic variants at the same locus are involved in adaptation and HAPE, respectively. Moreover, healthy sojourners present a number of genomic features similar to HA natives, further strengthening the concept of genetic predisposition. A trend in correlation between protective and risk alleles and altered levels of circulatory markers clearly documents the phenomenon of genotype–phenotype correlations. We conclude that the genetic and biochemical

  13. Ancestry informative markers: inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex.

    Science.gov (United States)

    Romanini, Carola; Romero, Magdalena; Salado Puerto, Mercedes; Catelli, Laura; Phillips, Christopher; Pereira, Rui; Gusmão, Leonor; Vullo, Carlos

    2015-05-01

    Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  14. An evaluation of non-metric cranial traits used to estimate ancestry in a South African sample.

    Science.gov (United States)

    L'Abbé, E N; Van Rooyen, C; Nawrocki, S P; Becker, P J

    2011-06-15

    Establishing ancestry from a skeleton for forensic purposes has been shown to be difficult. The purpose of this paper is to address the application of thirteen non-metric traits to estimate ancestry in three South African groups, namely White, Black and "Coloured". In doing so, the frequency distribution of thirteen non-metric traits among South Africans are presented; the relationship of these non-metric traits with ancestry, sex, age at death are evaluated; and Kappa statistics are utilized to assess the inter and intra-rater reliability. Crania of 520 known individuals were obtained from four skeletal samples in South Africa: the Pretoria Bone Collection, the Raymond A. Dart Collection, the Kirsten Collection and the Student Bone Collection from the University of the Free State. Average age at death was 51, with an age range between 18 and 90. Thirteen commonly used non-metric traits from the face and jaw were scored; definition and illustrations were taken from Hefner, Bass and Hauser and De Stephano. Frequency distributions, ordinal regression and Cohen's Kappa statistics were performed as a means to assess population variation and repeatability. Frequency distributions were highly variable among South Africans. Twelve of the 13 variables had a statistically significant relationship with ancestry. Sex significantly affected only one variable, inter-orbital breadth, and age at death affected two (anterior nasal spine and alveolar prognathism). The interaction of ancestry and sex independently affected three variables (nasal bone contour, nasal breadth, and interorbital breadth). Seven traits had moderate to excellent repeatability, while poor scoring consistency was noted for six variables. Difficulties in repeating several of the trait scores may require either a need for refinement of the definitions, or these character states may not adequately describe the observable morphology in the population. The application of the traditional experience-based approach

  15. A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population

    Science.gov (United States)

    Daya, Michelle; van der Merwe, Lize; Galal, Ushma; Möller, Marlo; Salie, Muneeb; Chimusa, Emile R.; Galanter, Joshua M.; van Helden, Paul D.; Henn, Brenna M.; Gignoux, Chris R.; Hoal, Eileen

    2013-01-01

    Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's -statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population. PMID:24376522

  16. Short range correlations in high energy heavy ion collisions

    International Nuclear Information System (INIS)

    Franco, V.; Nutt, W.T.

    1978-01-01

    We present a technique for including the effects of nucleon-nucleon correlations in the optical phase shift (chi) expansion of the nucleus-nucleus scattering amplitude and present the results for chi to second order. The total and inelastic cross sections are consistently higher than those obtained ignoring correlations, and are in better agreement with the data. Furthermore, the inclusion of correlations leads to second order phase shift functions which do not violate unitarity, in constrast to the case when correlations are ignored in very heavy nuclei (A 1 , A 2 > or approx. = 200). In elastic scattering differential cross sections, the effects of correlations can be quite large

  17. Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

    Science.gov (United States)

    Brown, Robert; Pasaniuc, Bogdan

    2014-01-01

    Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk loci, to inferring recombination rates, to mapping missing contigs in the human genome. Although many methods for local ancestry inference have been proposed, most are designed for use with genotyping arrays and fail to make use of the full spectrum of data available from sequencing. In addition, current haplotype-based approaches are very computationally demanding, requiring large computational time for moderately large sample sizes. Here we present new methods for local ancestry inference that leverage continent-specific variants (CSVs) to attain increased performance over existing approaches in sequenced admixed genomes. A key feature of our approach is that it incorporates the admixed genomes themselves jointly with public datasets, such as 1000 Genomes, to improve the accuracy of CSV calling. We use simulations to show that our approach attains accuracy similar to widely used computationally intensive haplotype-based approaches with large decreases in runtime. Most importantly, we show that our method recovers comparable local ancestries, as the 1000 Genomes consensus local ancestry calls in the real admixed individuals from the 1000 Genomes Project. We extend our approach to account for low-coverage sequencing and show that accurate local ancestry inference can be attained at low sequencing coverage. Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on the basis of sCSVs. PMID:24743331

  18. Genetic ancestry effects on the distribution of toll-like receptors (TLRs) gene polymorphisms in a population of the Atlantic Forest, São Paulo, Brazil.

    Science.gov (United States)

    Guimarães, Lilian O; Bajay, Miklos Maximiliano; Monteiro, Eliana F; Wunderlich, Gerhard; Santos, Sidney E; Kirchgatter, Karin

    2018-02-01

    The innate immune system governed by toll-like receptors (TLRs) provides the first line of defense against pathogens. Surface-localized TLR1 and TLR6 are known to detect parasite components. TLR encoding genes were shown to display signatures of recent positive selection in Europeans and might be involved in local adaptation at immune-related genes. To verify the influence of Brazilian population admixture on the distribution of polymorphisms in TLRs, we analyzed the genotype frequencies of 24 polymorphisms distributed across five TLR genes in a Southeastern Brazilian population where autochthonous cases of malaria occur in small foci of transmission. The estimation of ancestry showed mainly European ancestry (63%) followed by African ancestry (22%). Mean proportions of European ancestry differed significantly between the genotypes of the TLR1 (I602S) gene and in the TLR6 (P249S) gene. The chance of having the G allele in TLR1 gene increases as European ancestry increases as well as the chance of having the T allele in the TLR6 gene. The 602S allele is related to a ''hypo-responsiveness'' possibly explaining the high prevalence of asymptomatic malaria cases in areas of Southeastern Brazil. Our results underline the necessity to include informative ancestry markers in genetic association studies in order to avoid biased results. Copyright © 2017 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  19. Biogeographical ancestry is associated with socioenvironmental conditions and infections in a Latin American urban population

    Directory of Open Access Journals (Sweden)

    Thiago Magalhães da Silva

    2018-04-01

    Full Text Available Racial inequalities are observed for different diseases and are mainly caused by differences in socioeconomic status between ethnoracial groups. Genetic factors have also been implicated, and recently, several studies have investigated the association between biogeographical ancestry (BGA and complex diseases. However, the role of BGA as a proxy for non-genetic health determinants has been little investigated. Similarly, studies comparing the association of BGA and self-reported skin colour with these determinants are scarce. Here, we report the association of BGA and self-reported skin colour with socioenvironmental conditions and infections. We studied 1246 children living in a Brazilian urban poor area. The BGA was estimated using 370,539 genome-wide autosomal markers. Standardised questionnaires were administered to the children’s guardians to evaluate socioenvironmental conditions. Infection (or pathogen exposure was defined by the presence of positive serologic test results for IgG to seven pathogens (Toxocara spp, Toxoplasma gondii, Helicobacter pylori, and hepatitis A, herpes simplex, herpes zoster and Epstein-Barr viruses and the presence of intestinal helminth eggs in stool samples (Ascaris lumbricoides and Trichiuris trichiura. African ancestry was negatively associated with maternal education and household income and positively associated with infections and variables, indicating poorer housing and living conditions. The self-reported skin colour was associated with infections only. In stratified analyses, the proportion of African ancestry was associated with most of the outcomes investigated, particularly among admixed individuals. In conclusion, BGA was associated with socioenvironmental conditions and infections even in a low-income and highly admixed population, capturing differences that self-reported skin colour miss. Importantly, our findings suggest caution in interpreting significant associations between BGA and diseases

  20. Ancestry informative markers and complete blood count parameters in Brazilian blood donors

    Directory of Open Access Journals (Sweden)

    Gabriela E. S. Felix

    Full Text Available A complete blood count is very useful in clinical diagnoses when reference ranges are well established for the population. Complete blood counts and allele frequencies of Ancestry Informative Markers (AIMs were analyzed in Brazilians with the aim of characterizing the hematological values of an admixed population. Positive associations were observed between gender and neutrophils, monocytes, eosinophils, erythrocytes, hemoglobin, hematocrit, MCV, MCHC and platelet counts. No significant differences were found for age, alcohol consumption, educational status, ethnicity, smoking in respect to the complete blood count values. In general, men had higher red blood cell values, while women had higher values for white blood cells and platelets. The study of the population was highly heterogeneous with mean proportions (± SE of African, European and Amerindian ancestry being 49.0 ± 3.0%, 44.0 ± 9.0% and 7.0 ± 9.0%, respectively. Amerindian ancestry showed limited contribution to the makeup of the population, but estimated ancestral proportions were statistically significant (r = 0.9838; P<0.001. These hematologic values are similar to Afro-Americans, another admixed population.

  1. Forensic genetic analysis of bio-geographical ancestry.

    Science.gov (United States)

    Phillips, Chris

    2015-09-01

    With the great strides made in the last ten years in the understanding of human population variation and the detailed characterization of the genome, it is now possible to identify sets of ancestry informative markers suitable for relatively small-scale PCR-based assays and use them to analyze the ancestry of an individual from forensic DNA. This review outlines some of the current understanding of past human population structure and how it may have influenced the complex distribution of contemporary human diversity. A simplified description of human diversity can provide a suitable basis for choosing the best ancestry-informative markers, which is important given the constraints of multiplex sizes in forensic DNA tests. It is also important to decide the level of geographic resolution that is realistic to ensure the balance between informativeness and an over-simplification of complex human diversity patterns. A detailed comparison is made of the most informative ancestry markers suitable for forensic use and assessments are made of the data analysis regimes that can provide statistical inferences of a DNA donor's bio-geographical ancestry. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Multiparticle correlations and intermittency in high energy collisions

    International Nuclear Information System (INIS)

    Bozek, P.

    1992-01-01

    An analysis of the intermittency signal observed in high energy experiments is presented using multiparticle distributions and correlation functions. The effect of the dimensional projection of the multiparticle distributions on one or two-dimensional subspace is discussed. The structure of the multiparticle cumulants is analyzed for the DELPHI e + e - annihilation data. The model of spatiotemporal intermittency is discussed in details and is shown to reproduce qualitatively the dependence of the intermittency strength on the target and projectile nuclei. A 1-dimensional (lD) cellular-automaton (CA) and a lD forest-fire model is studied. On the example of the noncritical lD Ising model the difficulties of the scaled factorial moment (SFM) method in extracting genuine scaling behaviour are illustrated. The problem of the finite-size effect in connection to the dimensional projection can be easily exemplified in the case of the 2D critical system with conformal symmetry. (R.P.) 122 refs., 38 figs., 3 tabs

  3. Covariance fitting of highly-correlated data in lattice QCD

    Science.gov (United States)

    Yoon, Boram; Jang, Yong-Chull; Jung, Chulwoo; Lee, Weonjong

    2013-07-01

    We address a frequently-asked question on the covariance fitting of highly-correlated data such as our B K data based on the SU(2) staggered chiral perturbation theory. Basically, the essence of the problem is that we do not have a fitting function accurate enough to fit extremely precise data. When eigenvalues of the covariance matrix are small, even a tiny error in the fitting function yields a large chi-square value and spoils the fitting procedure. We have applied a number of prescriptions available in the market, such as the cut-off method, modified covariance matrix method, and Bayesian method. We also propose a brand new method, the eigenmode shift (ES) method, which allows a full covariance fitting without modifying the covariance matrix at all. We provide a pedagogical example of data analysis in which the cut-off method manifestly fails in fitting, but the rest work well. In our case of the B K fitting, the diagonal approximation, the cut-off method, the ES method, and the Bayesian method work reasonably well in an engineering sense. However, interpreting the meaning of χ 2 is easier in the case of the ES method and the Bayesian method in a theoretical sense aesthetically. Hence, the ES method can be a useful alternative optional tool to check the systematic error caused by the covariance fitting procedure.

  4. Electron correlation in highly-charged-ion collisions

    International Nuclear Information System (INIS)

    Hansen, J.P.; Taulbjerg, K.

    1992-01-01

    We have used the coupled-channel method to study the significance of electron correlation in the reaction mechanism for two-electron capture in C 5+ -He collisions. Two different sets of calculations were performed. While the static correlation energy was generally included in the calculations, further correlation effects were ignored in the first set of calculations. In the second set of calculations the so-called doubly excited symmetry basis (DESB) states were used to model the spatial electron correlation. The difference between the two sets of results is so profound that we can conclude that electron correlation plays an essential role in the reaction mechanism. The results of the DESB-based calculations are in good agreement with experimental data [Holt et al., Phys. Rev. A 43, 607 (1991)

  5. Outlining the Ancestry Landscape of Colombian Admixed Populations.

    Science.gov (United States)

    Ossa, Humberto; Aquino, Juliana; Pereira, Rui; Ibarra, Adriana; Ossa, Rafael H; Pérez, Luz Adriana; Granda, Juan David; Lattig, Maria Claudia; Groot, Helena; Fagundes de Carvalho, Elizeu; Gusmão, Leonor

    2016-01-01

    The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population. Considering the importance of population substructure in both clinical and forensic genetics, we sought to investigate and compare patterns of genetic ancestry in Colombia by studying samples from Native and non-Native populations living in its 5 continental regions: the Andes, Caribe, Amazonia, Orinoquía, and Pacific regions. For this purpose, 46 AIM-Indels were genotyped in 761 non-related individuals from current populations. Previously published genotype data from 214 Colombian Natives from five communities were used for population comparisons. Significant differences were observed between Native and non-Native populations, among non-Native populations from different regions and among Native populations from different ethnic groups. The Pacific was the region with the highest African ancestry, Amazonia harboured the highest Native ancestry and the Andean and Orinoquían regions showed the highest proportion of European ancestry. The Andean region was further sub-divided into 6 sub-regions: North East, Central West, Central East, West, South West and South East. Among these regions, the South West region showed a significantly lower European admixture than the other regions. Hardy-Weinberg equilibrium and variance values of ancestry among individuals within populations showed a potential stratification of the Pacific population.

  6. Immunization coverage among Hispanic ancestry, 2003 National Immunization Survey.

    Science.gov (United States)

    Darling, Natalie J; Barker, Lawrence E; Shefer, Abigail M; Chu, Susan Y

    2005-12-01

    The Hispanic population is increasing and heterogeneous (Hispanic refers to persons of Spanish, Hispanic, or Latino descent). The objective was to examine immunization rates among Hispanic ancestry for the 4:3:1:3:3 series (> or = 4 doses diphtheria, tetanus toxoids, and pertussis vaccine; > or = 3 doses poliovirus vaccine; > or = 1 doses measles-containing vaccine; > or = 3 doses Haemophilus influenzae type b vaccine; and > or = 3 doses hepatitis B vaccine). The National Immunization Survey measures immunization coverage among 19- to 35-month-old U.S. children. Coverage was compared from combined 2001-2003 data among Hispanics and non-Hispanic whites using t-tests, and among Hispanic ancestry using a chi-square test. Hispanics were categorized as Mexican, Mexican American, Central American, South American, Puerto Rican, Cuban, Spanish Caribbean (primarily Dominican Republic), other, and multiple ancestry. Children of Hispanic ancestry increased from 21% in 1999 to 25% in 2003. These Hispanic children were less well immunized than non-Hispanic whites (77.0%, +/-2.1% [95% confidence interval] compared to 82.5%, +/-1.1% (95% CI) > in 2003). Immunization coverage did not vary significantly among Hispanics of varying ancestries (p=0.26); however, there was substantial geographic variability. In some areas, immunization coverage among Hispanics was significantly higher than non-Hispanic whites. Hispanic children were less well immunized than non-Hispanic whites; however, coverage varied notably by geographic area. Although a chi-square test found no significant differences in coverage among Hispanic ancestries, the range of coverage, 79.2%, +/-5.1% for Cuban Americans to 72.1%, +/-2.4% for Mexican descent, may suggest a need for improved and more localized monitoring among Hispanic communities.

  7. Genetic African Ancestry and Markers of Mineral Metabolism in CKD.

    Science.gov (United States)

    Gutiérrez, Orlando M; Parsa, Afshin; Isakova, Tamara; Scialla, Julia J; Chen, Jing; Flack, John M; Nessel, Lisa C; Gupta, Jayanta; Bellovich, Keith A; Steigerwalt, Susan; Sondheimer, James H; Wright, Jackson T; Feldman, Harold I; Kusek, John W; Lash, James P; Wolf, Myles

    2016-04-07

    Disorders of mineral metabolism are more common in African Americans with CKD than in European Americans with CKD. Previous studies have focused on the differences in mineral metabolism by self-reported race, making it difficult to delineate the importance of environmental compared with biologic factors. In a cross-sectional analysis of 3013 participants of the Chronic Renal Insufficiency Cohort study with complete data, we compared markers of mineral metabolism (phosphorus, calcium, alkaline phosphatase, parathyroid hormone, fibroblast growth factor 23, and urine calcium and phosphorus excretion) in European Americans versus African Americans and separately, across quartiles of genetic African ancestry in African Americans (n=1490). Compared with European Americans, African Americans had higher blood concentrations of phosphorus, alkaline phosphatase, fibroblast growth factor 23, and parathyroid hormone, lower 24-hour urinary excretion of calcium and phosphorus, and lower urinary fractional excretion of calcium and phosphorus at baseline (PAfrican Americans, a higher percentage of African ancestry was associated with lower 24-hour urinary excretion of phosphorus (PtrendAfrican ancestry was significantly associated with lower 24-hour urinary phosphorus excretion (each 10% higher African ancestry was associated with 39.6 mg lower 24-hour urinary phosphorus, PAfrican ancestry was associated with an absolute 1.1% lower fractional excretion of phosphorus, P=0.01). A higher percentage of African ancestry was independently associated with lower 24-hour urinary phosphorus excretion and lower fractional excretion of phosphorus among African Americans with CKD. These findings suggest that genetic variability might contribute to racial differences in urinary phosphorus excretion in CKD. Copyright © 2016 by the American Society of Nephrology.

  8. Original Research Correlates of cannabis use among high school ...

    African Journals Online (AJOL)

    Department of Community Medicine, University of Zimbabwe, Harare, Zimbabwe ... A descriptive cross-sectional study focusing on the correlates of cannabis use was .... from: https://www.unodc.org/unodc/secured/wdr/wdr2013/World_.

  9. Warfarin maintenance dose in older patients: higher average dose and wider dose frequency distribution in patients of African ancestry than those of European ancestry.

    Science.gov (United States)

    Garwood, Candice L; Clemente, Jennifer L; Ibe, George N; Kandula, Vijay A; Curtis, Kristy D; Whittaker, Peter

    2010-06-15

    Studies report that warfarin doses required to maintain therapeutic anticoagulation decrease with age; however, these studies almost exclusively enrolled patients of European ancestry. Consequently, universal application of dosing paradigms based on such evidence may be confounded because ethnicity also influences dose. Therefore, we determined if warfarin dose decreased with age in Americans of African ancestry, if older African and European ancestry patients required different doses, and if their daily dose frequency distributions differed. Our chart review examined 170 patients of African ancestry and 49 patients of European ancestry cared for in our anticoagulation clinic. We calculated the average weekly dose required for each stable, anticoagulated patient to maintain an international normalized ratio of 2.0 to 3.0, determined dose averages for groups 80 years of age and plotted dose as a function of age. The maintenance dose in patients of African ancestry decreased with age (PAfrican ancestry required higher average weekly doses than patients of European ancestry: 33% higher in the 70- to 79-year-old group (38.2+/-1.9 vs. 28.8+/-1.7 mg; P=0.006) and 52% in the >80-year-old group (33.2+/-1.7 vs. 21.8+/-3.8 mg; P=0.011). Therefore, 43% of older patients of African ancestry required daily doses >5mg and hence would have been under-dosed using current starting-dose guidelines. The dose frequency distribution was wider for older patients of African ancestry compared to those of European ancestry (PAfrican ancestry indicate that strategies for initiating warfarin therapy based on studies of patients of European ancestry could result in insufficient anticoagulation and thereby potentially increase their thromboembolism risk. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Microstructure and property correlations in high-temperature superconductors

    Science.gov (United States)

    Kalyanaraman, Ramakrishnan

    1998-11-01

    The work in this dissertation is intended at developing high quality device gradefilms of the high temperature (high-Tsbc) superconductor, Yttrium Barium Copper Oxide (YBCO), on MgO(001) substrates. Three approaches have been used to achieve the above goal, (i) The use of a SrTiOsb3 buffer layer, (ii) The use of Ag to enhance the growth of YBCO films and (iii) Investigation of the atomic structure-property correlations of low-angle grain boundaries in these films. Thin film heterostructures of YBCO/MgO and YBCO/SrTiOsb3/MgO were fabricated by pulsed laser deposition (PLD), using a 248 nm KrF excimer laser. Analysis of the structure and measurement of superconducting properties of the films were carried out to optimize the suitable conditions under each approach. The key findings were, (i) Single crystal-like SrTiOsb3 buffer layers can be grown and they give the highest JsbcYBCO films, (ii) An in-depth study of the role of Ag showed that it enhanced film growth of YBCO thereby improving its quality, and (iii) Low-angle boundaries in YBCO/MgO occur with two probable habit planes and the Jsbcs across them differ slightly. A systematic investigation of the crystalline quality of the SrTiOsb3 films deposited by PLD was performed as a function of oxygen partial pressure (pOsb2) and substrate temperature (Tsbc). The highest quality films were grown in the pOsb2 range of 0.1-1 mTorr at 750sp°C. The films had as-deposited x-ray diffraction rocking curve (omega) values of {˜}0.70sp° and Rutherford backscattering channeling yields (chisbmin) of 5% as compared to omega˜1.40sp° and chisbmin˜14% for the film deposited in 100 mTorr of pOsb2. The x-ray phi-scans showed epitaxial cube-on-cube alignment of the SrTiOsb3 films on MgO(001) substrates. Thermal annealing of the SrTiOsb3 films further improved the quality, and the 1 mTorr films gave omega{˜}0.13sp° and chisbmin˜2.0%. Transmission electron microscopy investigations (TEM) of these films showed that the defects in

  11. Variants in DENND1A are associated with polycystic ovary syndrome in women of European ancestry.

    Science.gov (United States)

    Welt, Corrine K; Styrkarsdottir, Unnur; Ehrmann, David A; Thorleifsson, Gudmar; Arason, Gudmundur; Gudmundsson, Jens A; Ober, Carole; Rosenfield, Robert L; Saxena, Richa; Thorsteinsdottir, Unnur; Crowley, William F; Stefansson, Kari

    2012-07-01

    A genome-wide association study has identified three loci (five independent signals) that confer risk for polycystic ovary syndrome (PCOS) in Han Chinese women. Replication is necessary to determine whether the same variants confer risk for PCOS in women of European ancestry. The objective of the study was to test whether these PCOS risk variants in Han Chinese women confer risk for PCOS in women of European ancestry. This was a case-control study. The study was conducted at deCODE Genetics in Iceland and two academic medical centers in the United States. Cases were 376 Icelandic women and 565 and 203 women from Boston, MA, and Chicago, IL, respectively, all diagnosed with PCOS by the National Institutes of Health criteria. Controls were 16,947, 483, and 189 women not known to have PCOS from Iceland, Boston, and Chicago, respectively. There were no interventions. Main outcomes were allele frequencies for seven variants in PCOS cases and controls. Two strongly correlated Han Chinese PCOS risk variants on chromosome 9q33.3, rs10986105[C], and rs10818854[A], were replicated in samples of European ancestry with odds ratio of 1.68 (P = 0.00033) and odds ratio of 1.53 (P = 0.0019), respectively. Other risk variants at 2p16.3 (rs13405728), 2p21 (rs12468394, rs12478601, and rs13429458), and 9q33.3 (rs2479106), or variants correlated with them, did not associate with PCOS. The same allele of rs10986105 that increased the risk of PCOS also increased the risk of hyperandrogenism in women without PCOS from Iceland and demonstrated a stronger risk for PCOS defined by the National Institutes of Health criteria than the Rotterdam criteria. We replicated one of the five Chinese PCOS association signals, represented by rs10986105 and rs10818854 on 9q33, in individuals of European ancestry. Examination of the subjects meeting at least one of the Rotterdam criteria for PCOS suggests that the variant may be involved in the hyperandrogenism and possibly the irregular menses of PCOS.

  12. Case Study on Ancestry Estimation in an Alaskan Native Family: Identity and Safeguards Against Reductionism.

    Science.gov (United States)

    Bader, Alyssa C; Malhi, Ripan S

    2015-10-01

    Understanding the complexities of ancestry-related identity is a necessary component of ethically sound research related to the genetic ancestry of modern-day communities. This is especially true when working with indigenous populations, given the legal and social implications that genetic ancestry interpretations may have in these communities. This study employs a multicomponent approach to explore the intricacies of ancestry-related identity within one extended family with members who identify as Alaskan Native. The seven participants were interviewed about their own self-identity, perceptions regarding genetic ancestry estimation, and their knowledge of oral family history. Additionally, each participant consented to having his or her genetic ancestry estimated. The researchers also surveyed ancestry-related documents, such as census records, birth certificates, and Certificates of Indian Blood. These three different perspectives-oral family history and self-identity, genetic ancestry estimation, historical and legal documentation-illustrate the complex nature of ancestry-related identity within the context of indigenous and colonial interactions in North America. While estimates of genetic ancestry broadly reflected each individual's self-reported biogeographic ancestry and supported all described and historically reported biological relationships, the estimates did not always match federally recorded blood quantum values, nor did they provide any information on relationships at the tribe or clan level. Employing a multicomponent approach and engaging study participants may help to safeguard against genetic essentialism and provide a more nuanced understanding of ancestry-related identity within a larger political, legal, and historical context.

  13. Vortex dynamics and correlated disorder in high-{Tc} superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Vinokur, V.M.

    1993-08-01

    We develop a theory for the vortex motion in the presence of correlated disorder in the form of the twin boundaries and columnar defects. Mapping vortex trajectories onto boson world lines enables us to establish the duality of the vortex transport in the systems with correlated disorder and hopping conductivity of charged particles in 2D systems. A glassy-like dynamics of the vortex lines with zero linear-resistivity and strongly nonlinear current-voltage behavior as V {proportional_to} exp[{minus} const/J{sup {mu}}] in a Bose glass state is predicted.

  14. Pauli correlations in heavy-ion collisions at high energies

    International Nuclear Information System (INIS)

    Franco, V.; Nutt, W.T.

    1977-01-01

    The effects of short-range correlations on the Glauber expansion for nucleus-nucleus collisions are calculated using the Fermi gas model for nuclei. When the Pauli principle is neglected for collisions between heavy nuclei, calculation of the optical phase-shift function leads to non-unitary results and cross sections cannot be obtained. When Pauli correlations are included important cancellations in the optical phase-shift function are found which make possible the calculation of total and differential cross sections for heavy nuclei. (Auth.)

  15. Quark structure of static correlators in high temperature QCD

    Science.gov (United States)

    Bernard, Claude; DeGrand, Thomas A.; DeTar, Carleton; Gottlieb, Steven; Krasnitz, A.; Ogilvie, Michael C.; Sugar, R. L.; Toussaint, D.

    1992-07-01

    We present results of numerical simulations of quantum chromodynamics at finite temperature with two flavors of Kogut-Susskind quarks on the Intel iPSC/860 parallel processor. We investigate the properties of the objects whose exchange gives static screening lengths by reconstructing their correlated quark-antiquark structure.

  16. Quark structure of static correlators in high temperature QCD

    International Nuclear Information System (INIS)

    Bernard, C.; Ogilvie, M.C.; DeGrand, T.A.; DeTar, C.; Gottlieb, S.; Krasnitz, A.; Sugar, R.L.; Toussaint, D.

    1992-01-01

    We present results of numerical simulations of quantum chromodynamics at finite temperature with two flavors of Kogut-Susskind quarks on the Intel iPSC/860 parellel processor. We investigate the properties of the objects whose exhange gives static screening lengths by reconstructing their correlated quark-antiquark structure. (orig.)

  17. Quark structure of static correlators in high temperature QCD

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, C.; Ogilvie, M.C. (Washington Univ., St. Louis, MO (United States). Dept. of Physics); DeGrand, T.A. (Colorado Univ., Boulder, CO (United States). Physics Dept.); DeTar, C. (Utah Univ., Salt Lake City, UT (United States). Physics Dept.); Gottlieb, S.; Krasnitz, A. (Indiana Univ., Bloomington, IN (United States). Dept. of Physics); Sugar, R.L. (California Univ., Santa Barbara, CA (United States). Dept. of Physics); Toussaint, D. (Arizona Univ., Tucson, AZ (United States). Dept. of Physics)

    1992-07-20

    We present results of numerical simulations of quantum chromodynamics at finite temperature with two flavors of Kogut-Susskind quarks on the Intel iPSC/860 parellel processor. We investigate the properties of the objects whose exhange gives static screening lengths by reconstructing their correlated quark-antiquark structure. (orig.).

  18. Building a forensic ancestry panel from the ground up

    DEFF Research Database (Denmark)

    Phillips, C; Parson, W; Lundsberg, Birgitte Møller

    2014-01-01

    Emerging next-generation sequencing technologies will enable DNA analyses to add pigmentation predictive and ancestry informative (AIM) SNPs to the range of markers detectable from a single PCR test. This prompted us to re-appraise current forensic and genomics AIM-SNPs and from the best sets, to...

  19. Assessing Patterns of Admixture and Ancestry in Canadian Honey Bees

    Science.gov (United States)

    Canada has a large beekeeping industry comprised of 8483 beekeepers managing 672094 23 colonies. Canadian honey bees, like all honey bees in the New World, originate from centuries of importation of predominately European honey bees, but their precise ancestry remains unknown. There have been no i...

  20. A simple and optimal ancestry labeling scheme for trees

    DEFF Research Database (Denmark)

    Dahlgaard, Søren; Knudsen, Mathias Bæk Tejs; Rotbart, Noy Galil

    2015-01-01

    We present a lg n + 2 lg lg n + 3 ancestry labeling scheme for trees. The problem was first presented by Kannan et al. [STOC 88’] along with a simple 2 lg n solution. Motivated by applications to XML files, the label size was improved incrementally over the course of more than 20 years by a series...

  1. Fanconi anaemia in South African patients with Afrikaner ancestry ...

    African Journals Online (AJOL)

    Background. Fanconi anaemia (FA) is a rare genetic disorder of impaired DNA repair that results in physical and haematological consequences in affected individuals. In South Africa (SA), individuals with Afrikaner ancestry are at an increased risk of inheriting disease-causing FA mutations, owing to the three common ...

  2. Haemoglobin A1c as a screening tool for type 2 diabetes and prediabetes in populations of Swedish and Middle-East ancestry.

    Science.gov (United States)

    Hellgren, Margareta; Hjörleifsdottir Steiner, Kristin; Bennet, Louise

    2017-08-01

    To explore and compare sensitivity and specificity for HbA1c ≥48mmol/mol as a predictor for type 2 diabetes mellitus (T2DM) in two populations with different ethnicity and to examine the predictive value of two levels of HbA1c (≥42mmol/mol, ≥39mmol/mol) for prediabetes in these populations. Four cohorts were examined with an oral glucose tolerance test. (1) The MEDIM Study (n=1991 individuals of Swedish and Iraqi ancestry); (2) The Skaraborg Project (n=1327 individuals of Swedish ancestry); (3) The 4-D study (n=424 individuals of Swedish, Iraqi and Turkish ancestry); (4) The Flemingsberg study (n=212 participants of Turkish ancestry). HbA1c ≥48mmol/mol had a sensitivity for T2DM of 31% and 25% respectively in individuals of Middle-East and Swedish ancestry. The positive and negative predictive value was high in both populations (70.3, 96.4 and 96.2, 97.6 respectively). Using HbA1c ≥42mmol/mol and ≥39mmol/mol as a predictor for prediabetes gave a sensitivity of 17% and 36% in individuals of Middle-East and 15% and 34% in individuals of Swedish ancestry. Even if HbA1c ≥48mmol/mol is a valuable diagnostic tool, it is a blunt and insensitive tool for screening and would exclude most people with T2DM, independent of ancestry and age. HbA1c is an inefficient way to detect individuals with prediabetes. Copyright © 2017 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.

  3. Does ancestry influence health-related quality of life in type 1 diabetes patients? A nationwide study in Brazil.

    Science.gov (United States)

    Santos, Deborah Conte; Pizarro, Marcela Haas; Barros, Bianca S V; de Melo, Laura G Nunes; Porto, Luis Cristovão; Silva, Dayse A; Gomes, Marilia Brito

    2018-04-01

    The aim of the present study was to evaluate the relationship between self-reported color/race and genomic ancestry with HRQoL of patients with type 1 diabetes in a highly admixed population. This was a nationwide, cross-sectional study conducted with 1760 patients with type 1 diabetes from 2011 to 2014 at public clinics in all five Brazilian geographical regions. Information on HRQoL was obtained from two self-completed questionnaires: Short Form-6 Dimensions (SF-6D) and EuroQol-5 Dimensions (EQ-5D) with a visual analogue scale (EQ-VAS). Genomic ancestry was assessed using a Multiplex PCR methodology. Utility scores generated from the questionnaires were analyzed with multivariate logistic regression models. We included 1698 patients. Those patients who self-reported as black had lower EQ-VAS scores compared to the patients who self-reported as white (67.46 ± 18.45; 72.37 ± 16.44, respectively, p = 0.02). In a linear regression model, each 1% increase in African ancestry resulted in a 9.5 point decrease in EQ-VAS score (p ancestry remained associated with lower EQ-VAS scores. A higher level of African ancestry implicates on lower quality of life even after adjustments for sociodemographic and diabetes-related data. Gender, physical activity and diabetes-related microvascular complications were strongly associated with low HRQoL in all three questionnaires used. This fact highlights the importance of social aspects when assessing quality of life, as well as the need for regular practice of physical activity and prevention of chronic complications to improve patients' quality of life.

  4. OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans.

    Directory of Open Access Journals (Sweden)

    Beatriz Sierra

    2017-02-01

    Full Text Available Ethnic groups can display differential genetic susceptibility to infectious diseases. The arthropod-born viral dengue disease is one such disease, with empirical and limited genetic evidence showing that African ancestry may be protective against the haemorrhagic phenotype. Global ancestry analysis based on high-throughput genotyping in admixed populations can be used to test this hypothesis, while admixture mapping can map candidate protective genes. A Cuban dengue fever cohort was genotyped using a 2.5 million SNP chip. Global ancestry was ascertained through ADMIXTURE and used in a fine-matched corrected association study, while local ancestry was inferred by the RFMix algorithm. The expression of candidate genes was evaluated by RT-PCR in a Cuban dengue patient cohort and gene set enrichment analysis was performed in a Thai dengue transcriptome. OSBPL10 and RXRA candidate genes were identified, with most significant SNPs placed in inferred weak enhancers, promoters and lncRNAs. OSBPL10 had significantly lower expression in Africans than Europeans, while for RXRA several SNPs may differentially regulate its transcription between Africans and Europeans. Their expression was confirmed to change through dengue disease progression in Cuban patients and to vary with disease severity in a Thai transcriptome dataset. These genes interact in the LXR/RXR activation pathway that integrates lipid metabolism and immune functions, being a key player in dengue virus entrance into cells, its replication therein and in cytokine production. Knockdown of OSBPL10 expression in THP-1 cells by two shRNAs followed by DENV2 infection tests led to a significant reduction in DENV replication, being a direct functional proof that the lower OSBPL10 expression profile in Africans protects this ancestry against dengue disease.

  5. Ancestry explains the blunted ventilatory response to sustained hypoxia and lower exercise ventilation of Quechua altitude natives.

    Science.gov (United States)

    Brutsaert, Tom D; Parra, Esteban J; Shriver, Mark D; Gamboa, Alfredo; Rivera-Ch, Maria; León-Velarde, Fabiola

    2005-07-01

    Andean high-altitude (HA) natives have a low (blunted) hypoxic ventilatory response (HVR), lower effective alveolar ventilation, and lower ventilation (VE) at rest and during exercise compared with acclimatized newcomers to HA. Despite blunted chemosensitivity and hypoventilation, Andeans maintain comparable arterial O(2) saturation (Sa(O(2))). This study was designed to evaluate the influence of ancestry on these trait differences. At sea level, we measured the HVR in both acute (HVR-A) and sustained (HVR-S) hypoxia in a sample of 32 male Peruvians of mainly Quechua and Spanish origins who were born and raised at sea level. We also measured resting and exercise VE after 10-12 h of exposure to altitude at 4,338 m. Native American ancestry proportion (NAAP) was assessed for each individual using a panel of 80 ancestry-informative molecular markers (AIMs). NAAP was inversely related to HVR-S after 10 min of isocapnic hypoxia (r = -0.36, P = 0.04) but was not associated with HVR-A. In addition, NAAP was inversely related to exercise VE (r = -0.50, P = 0.005) and ventilatory equivalent (VE/Vo(2), r = -0.51, P = 0.004) measured at 4,338 m. Thus Quechua ancestry may partly explain the well-known blunted HVR (10, 35, 36, 57, 62) at least to sustained hypoxia, and the relative exercise hypoventilation at altitude of Andeans compared with European controls. Lower HVR-S and exercise VE could reflect improved gas exchange and/or attenuated chemoreflex sensitivity with increasing NAAP. On the basis of these ancestry associations and on the fact that developmental effects were completely controlled by study design, we suggest both a genetic basis and an evolutionary origin for these traits in Quechua.

  6. Azimuthal correlations of high--transverse-momentum π0 pairs

    International Nuclear Information System (INIS)

    Cobb, J.H.; Iwata, S.; Palmer, R.B.; Rahm, D.C.; Rehak, R.; Stumer, I.; Fabjan, C.W.; Fowler, E.C.; Mannelli, I.; Mouzourakis, P.; Nakamura, K.; Nappi, A.; Struckzinski, W.; Willis, W.J.; Goldberg, M.; Horwitz, N.; Moneti, G.C.; Kourkoumelis, C.; Resvanis, L.K.; Filippas, T.A.; Lankford, A.J.

    1978-01-01

    We have studied correlations between two π 0 's produced at the CERN intersecting storage rings, utlizing detectors with large azimuthal acceptance. We find that the previously observed enhancement of two π 0 's produced at azimuthal difference near 180 0 can be made to vanish when certain kinematic effects are removed. However, we observe aligned configurations above 8 GeV of transverse energy unexplained by such kinematic effects

  7. Velocity-metallicity correlation for high-z DLA galaxies

    DEFF Research Database (Denmark)

    Ledoux, C.; Petitjean, P.; Fynbo, J.P.U.

    2006-01-01

    Galaxies: halos, galaxies: high-redshift, galaxies: ISM, quasars: absorption lines, cosmology: observations Udgivelsesdato: Oct.......Galaxies: halos, galaxies: high-redshift, galaxies: ISM, quasars: absorption lines, cosmology: observations Udgivelsesdato: Oct....

  8. Investigating relationships between ancestry, lifestyle behaviors and perceptions of heart disease and breast cancer among Canadian women with British and with South Asian ancestry.

    Science.gov (United States)

    Curtin, Kimberley D; Berry, Tanya R; Courneya, Kerry S; McGannon, Kerry R; Norris, Colleen M; Rodgers, Wendy M; Spence, John C

    2018-04-01

    Ethnic minority groups including Asians in Canada have different knowledge and perceptions of heart disease and breast cancer compared with the ethnic majority group. Examine relationships between perceptions of heart disease and breast cancer, and lifestyle behaviors for Canadian women with British and with South Asian ancestry. Women with South Asian ( n = 170) and with British ( n = 373) ancestry ( M age = 33.01, SD = 12.86) reported leisure time physical activity, intended fruit and vegetable consumption, disease perceptions (ability to reduce risk, control over getting the diseases, and influence of family history), and demographic information. Mann-Whitney tests and multiple hierarchical linear regressions were used to examine the relationships between lifestyle behaviors and disease perceptions, with ancestry explored as a possible moderator. Participants with South Asian ancestry believed they had greater ability to reduce their risk and have control over getting breast cancer than participants with British ancestry. Family history influences on getting either disease was perceived as higher for women with British ancestry. Age was positively related to all three perceptions in both diseases. Intended fruit and vegetable consumption was positively related to perceptions of ability to reduce risk and control of both diseases, but was stronger for women with South Asian ancestry regarding perceptions of breast cancer. Leisure time physical activity was positively related to perceptions of control over getting heart disease for women with British ancestry. Women's disease perceptions can vary by ancestry and lifestyle behaviors. Accurate representation of diseases is essential in promoting effective preventative behaviors.

  9. Ancestry informative markers in Amerindians from Brazilian Amazon.

    Science.gov (United States)

    Luizon, Marcelo Rizzatti; Mendes-Junior, Celso Teixeira; De Oliveira, Silviene Fabiana; Simões, Aguinaldo Luiz

    2008-01-01

    Ancestry informative markers (AIMs) are genetic loci with large frequency differences between the major ethnic groups and are very useful in admixture estimation. However, their frequencies are poorly known within South American indigenous populations, making it difficult to use them in admixture studies with Latin American populations, such as the trihybrid Brazilian population. To minimize this problem, the frequencies of the AIMs FY-null, RB2300, LPL, AT3-I/D, Sb19.3, APO, and PV92 were determined via PCR and PCR-RFLP in four tribes from Brazilian Amazon (Tikúna, Kashinawa, Baníwa, and Kanamarí), to evaluate their potential for discriminating indigenous populations from Europeans and Africans, as well as discriminating each tribe from the others. Although capable of differentiating tribes, as evidenced by the exact test of population differentiation, a neighbor-joining tree suggests that the AIMs are useless in obtaining reliable reconstructions of the biological relationships and evolutionary history that characterize the villages and tribes studied. The mean allele frequencies from these AIMs were very similar to those observed for North American natives. They discriminated Amerindians from Africans, but not from Europeans. On the other hand, the neighbor-joining dendrogram separated Africans and Europeans from Amerindians with a high statistical support (bootstrap = 0.989). The relatively low diversity (G(ST) = 0.042) among North American natives and Amerindians from Brazilian Amazon agrees with the lack of intra-ethnic variation previously reported for these markers. Despite genetic drift effects, the mean allelic frequencies herein presented could be used as Amerindian parental frequencies in admixture estimates in urban Brazilian populations. (c) 2007 Wiley-Liss, Inc.

  10. Exploring the Y Chromosomal Ancestry of Modern Panamanians.

    Directory of Open Access Journals (Sweden)

    Viola Grugni

    Full Text Available Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama's population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala. In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but

  11. Multi-particle correlation observables in high energy nucleus-nucleus collisions

    International Nuclear Information System (INIS)

    Stock, R.

    1981-01-01

    Global features of exclusively measured events, including number correlations and vector correlations, and hybrid analysis of measurements of one or two specific fragments like spectator nuclei, high transverse momentum particles, polarization of one particle, etc., are considered

  12. Galaxy correlations at high redshift and the environment of quasars

    International Nuclear Information System (INIS)

    Phillipps, Steven

    1986-01-01

    In close line-of-sight pairs of quasars absorption lines may be seen in the spectrum of the further quasar at a redshift corresponding to that of the nearer quasar. This is indicative of the presence of an intervening galaxy belonging to the same cluster as the (galaxy containing the) nearer quasar. The likelihood of this occurring is calculated in terms of the galaxy correlation function and it is found that present results already suggest that quasars at redshifts above one must be associated with rich clusters. (author)

  13. Embryonic aneuploidy does not differ among genetic ancestry according to continental origin as determined by ancestry informative markers.

    Science.gov (United States)

    Franasiak, Jason M; Olcha, Meir; Shastri, Shefali; Molinaro, Thomas A; Congdon, Haley; Treff, Nathan R; Scott, Richard T

    2016-10-01

    Is embryonic aneuploidy, as determined by comprehensive chromosome screening (CCS), related to genetic ancestry, as determined by ancestry informative markers (AIMs)? In this study, when determining continental ancestry utilizing AIMs, genetic ancestry does not have an impact on embryonic aneuploidy. Aneuploidy is one of the best-characterized barriers to ART success and little information exists regarding ethnicity and whole chromosome aneuploidy in IVF. Classifying continental ancestry utilizing genetic profiles from a selected group of single nucleotide polymorphisms, termed AIMs, can determine ancestral origin with more accuracy than self-reported data. This is a retrospective cohort study of patients undergoing their first cycle of IVF with CCS at a single center from 2008 to 2014. There were 2328 patients identified whom had undergone IVF/CCS and AIM genotyping. All patients underwent IVF/ICSI and CCS after trophectoderm biopsy. Patients' serum was genotyped using 32 custom AIMs to identify continental origin. Admixture proportions were determined using Bayesian clustering algorithms. Patients were assigned to the population (European, African, East Asian or Central/South Asian) corresponding to their greatest admixture proportion. The mean number of embryos tested was 5.3 (range = 1-40) and the mode was 1. Patients' ethnic classifications revealed European (n = 1698), African (n = 103), East Asian (n = 206) or Central/South Asian (n = 321). When controlling for age and BMI, aneuploidy rate did not differ by genetic ancestry (P = 0.28). The study type (retrospective) and the ability to classify patients by continental rather than sub-continental origin as well as the predominantly European patient mix may impact generalizability. Post hoc power calculation revealed power to detect a 16.8% difference in embryonic aneuploidy between the two smallest sample size groups. These data do not support differences in embryonic aneuploidy among various genetic

  14. Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution.

    Science.gov (United States)

    Mägi, Reedik; Horikoshi, Momoko; Sofer, Tamar; Mahajan, Anubha; Kitajima, Hidetoshi; Franceschini, Nora; McCarthy, Mark I; Morris, Andrew P

    2017-09-15

    Trans-ethnic meta-analysis of genome-wide association studies (GWAS) across diverse populations can increase power to detect complex trait loci when the underlying causal variants are shared between ancestry groups. However, heterogeneity in allelic effects between GWAS at these loci can occur that is correlated with ancestry. Here, a novel approach is presented to detect SNP association and quantify the extent of heterogeneity in allelic effects that is correlated with ancestry. We employ trans-ethnic meta-regression to model allelic effects as a function of axes of genetic variation, derived from a matrix of mean pairwise allele frequency differences between GWAS, and implemented in the MR-MEGA software. Through detailed simulations, we demonstrate increased power to detect association for MR-MEGA over fixed- and random-effects meta-analysis across a range of scenarios of heterogeneity in allelic effects between ethnic groups. We also demonstrate improved fine-mapping resolution, in loci containing a single causal variant, compared to these meta-analysis approaches and PAINTOR, and equivalent performance to MANTRA at reduced computational cost. Application of MR-MEGA to trans-ethnic GWAS of kidney function in 71,461 individuals indicates stronger signals of association than fixed-effects meta-analysis when heterogeneity in allelic effects is correlated with ancestry. Application of MR-MEGA to fine-mapping four type 2 diabetes susceptibility loci in 22,086 cases and 42,539 controls highlights: (i) strong evidence for heterogeneity in allelic effects that is correlated with ancestry only at the index SNP for the association signal at the CDKAL1 locus; and (ii) 99% credible sets with six or fewer variants for five distinct association signals. © The Author 2017. Published by Oxford University Press.

  15. Multiscale correlations in highly resolved Large Eddy Simulations

    Science.gov (United States)

    Biferale, Luca; Buzzicotti, Michele; Linkmann, Moritz

    2017-11-01

    Understanding multiscale turbulent statistics is one of the key challenges for many modern applied and fundamental problems in fluid dynamics. One of the main obstacles is the existence of anomalously strong non Gaussian fluctuations, which become more and more important with increasing Reynolds number. In order to assess the performance of LES models in reproducing these extreme events with reasonable accuracy, it is helpful to further understand the statistical properties of the coupling between the resolved and the subgrid scales. We present analytical and numerical results focussing on the multiscale correlations between the subgrid stress and the resolved velocity field obtained both from LES and filtered DNS data. Furthermore, a comparison is carried out between LES and DNS results concerning the scaling behaviour of higher-order structure functions using both Smagorinsky or self-similar Fourier sub-grid models. ERC AdG Grant No 339032 NewTURB.

  16. Serum leptin is correlated to high turnover in osteoporosis.

    Science.gov (United States)

    Hipmair, Gunter; Böhler, Nikolaus; Maschek, Wilma; Soriguer, Federico; Rojo-Martínez, Gemma; Schimetta, Wolfgang; Pichler, Robert

    2010-01-01

    Clinical data have suggested that obesity protects against osteoporosis. Leptin, mainly secreted by white adipose tissue, might be involved by mediating an effect on bone metabolism. This study was conducted to investigate a possible relationship of leptin and bone turn-over in postmenopausal women with osteoporosis. We measured bone mineral density (BMD), serum leptin levels and markers of bone metabolism, including osteocalcin and cross-laps in 44 patients with osteoporosis. The main group consisted of 32 postmenopausal women. Mean serum leptin was 13.1 microg/L and showed no statistically significant difference to the levels measured in a collective of normal persons adjusted for age and BMI. When related to serum cross-laps as markers of bone resorption, a positive correlation (posteoporosis.

  17. Performance correlations for high temperature potassium heat pipes

    International Nuclear Information System (INIS)

    Merrigan, M.A.; Keddy, E.S.; Sena, J.T.

    1987-01-01

    Potassium heat pipes designed for operation at a nominal temperature of 775K have been developed for use in a heat pipe cooled reactor design. The heat pipes operate in a gravity assist mode with a maximum required power throughput of approximately 16 kW per heat pipe. Based on a series of sub-scale experiments with 2.12 and 3.2 cm diameter heat pipes the prototypic heat pipe diameter was set at 5.7 cm with a simple knurled wall wick used in the interests of mechanical simplicity. The performance levels required for this design had been demonstrated in prior work with gutter assisted wicks and emphasis in the present work was on the attainment of similar performance with a simplified wick structure. The wick structure used in the experiment consisted of a pattern of knurled grooves in the internal wall of the heat pipe. The knurl depth required for the planned heat pipe performance was determined by scaling of wick characteristic data from the sub-scale tests. These tests indicated that the maximum performance limits of the test heat pipes did not follow normal entrainment limit predictions for textured wall gravity assist heat pipes. Test data was therefore scaled to the prototype design based on the assumption that the performance was controlled by an entrainment parameter based on the liquid flow depth in the groove structure. This correlation provided a reasonable fit to the sub-scale test data and was used in scale up of the design from the 8.0 cm 2 cross section of the largest sub-scale heat pipe to the 25.5 cm 2 cross section prototype. Correlation of the model predictions with test data from the prototype is discussed

  18. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

    Science.gov (United States)

    Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

    2016-07-01

    The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Genomic Ancestry, Self-Rated Health and Its Association with Mortality in an Admixed Population: 10 Year Follow-Up of the Bambui-Epigen (Brazil) Cohort Study of Ageing.

    Science.gov (United States)

    Lima-Costa, M Fernanda; Macinko, James; Mambrini, Juliana Vaz de Melo; Cesar, Cibele C; Peixoto, Sérgio V; Magalhães, Wagner C S; Horta, Bernardo L; Barreto, Mauricio; Castro-Costa, Erico; Firmo, Josélia O A; Proietti, Fernando A; Leal, Thiago Peixoto; Rodrigues, Maira R; Pereira, Alexandre; Tarazona-Santos, Eduardo

    2015-01-01

    Self-rated health (SRH) has strong predictive value for mortality in different contexts and cultures, but there is inconsistent evidence on ethnoracial disparities in SRH in Latin America, possibly due to the complexity surrounding ethnoracial self-classification. We used 370,539 Single Nucleotide Polymorphisms (SNPs) to examine the association between individual genomic proportions of African, European and Native American ancestry, and ethnoracial self-classification, with baseline and 10-year SRH trajectories in 1,311 community dwelling older Brazilians. We also examined whether genomic ancestry and ethnoracial self-classification affect the predictive value of SRH for subsequent mortality. European ancestry predominated among participants, followed by African and Native American (median = 84.0%, 9.6% and 5.3%, respectively); the prevalence of Non-White (Mixed and Black) was 39.8%. Persons at higher levels of African and Native American genomic ancestry, and those self-identified as Non-White, were more likely to report poor health than other groups, even after controlling for socioeconomic conditions and an array of self-reported and objective physical health measures. Increased risks for mortality associated with worse SRH trajectories were strong and remarkably similar (hazard ratio ~3) across all genomic ancestry and ethno-racial groups. Our results demonstrated for the first time that higher levels of African and Native American genomic ancestry--and the inverse for European ancestry--were strongly correlated with worse SRH in a Latin American admixed population. Both genomic ancestry and ethnoracial self-classification did not modify the strong association between baseline SRH or SRH trajectory, and subsequent mortality.

  20. Quasiparticles of strongly correlated Fermi liquids at high temperatures and in high magnetic fields

    International Nuclear Information System (INIS)

    Shaginyan, V. R.

    2011-01-01

    Strongly correlated Fermi systems are among the most intriguing, best experimentally studied and fundamental systems in physics. There is, however, lack of theoretical understanding in this field of physics. The ideas based on the concepts like Kondo lattice and involving quantum and thermal fluctuations at a quantum critical point have been used to explain the unusual physics. Alas, being suggested to describe one property, these approaches fail to explain the others. This means a real crisis in theory suggesting that there is a hidden fundamental law of nature. It turns out that the hidden fundamental law is well forgotten old one directly related to the Landau-Migdal quasiparticles, while the basic properties and the scaling behavior of the strongly correlated systems can be described within the framework of the fermion condensation quantum phase transition (FCQPT). The phase transition comprises the extended quasiparticle paradigm that allows us to explain the non-Fermi liquid (NFL) behavior observed in these systems. In contrast to the Landau paradigm stating that the quasiparticle effective mass is a constant, the effective mass of new quasiparticles strongly depends on temperature, magnetic field, pressure, and other parameters. Our observations are in good agreement with experimental facts and show that FCQPT is responsible for the observed NFL behavior and quasiparticles survive both high temperatures and high magnetic fields.

  1. Ancestry-Adjusted Vitamin D Metabolite Concentrations in Association With Cytochrome P450 3A Polymorphisms.

    Science.gov (United States)

    Wilson, Robin Taylor; Masters, Loren D; Barnholtz-Sloan, Jill S; Salzberg, Anna C; Hartman, Terryl J

    2018-04-01

    We investigated the association between genetic polymorphisms in cytochrome P450 (CYP2R1, CYP24A1, and the CYP3A family) with nonsummer plasma concentrations of vitamin D metabolites (25-hydroxyvitamin D3 (25(OH)D3) and proportion 24,25-dihydroxyvitamin D3 (24,25(OH)2D3)) among healthy individuals of sub-Saharan African and European ancestry, matched on age (within 5 years; n = 188 in each ancestral group), in central suburban Pennsylvania (2006-2009). Vitamin D metabolites were measured using high-performance liquid chromatography with tandem mass spectrometry. Paired multiple regression and adjusted least-squares mean analyses were used to test for associations between genotype and log-transformed metabolite concentrations, adjusted for age, sex, proportion of West-African genetic ancestry, body mass index, oral contraceptive (OC) use, tanning bed use, vitamin D intake, days from summer solstice, time of day of blood draw, and isoforms of the vitamin D receptor (VDR) and vitamin D binding protein. Polymorphisms in CYP2R1, CYP3A43, vitamin D binding protein, and genetic ancestry proportion remained associated with plasma 25(OH)D3 after adjustment. Only CYP3A43 and VDR polymorphisms were associated with proportion 24,25(OH)2D3. Magnitudes of association with 25(OH)D3 were similar for CYP3A43, tanning bed use, and OC use. Significant least-squares mean interactions (CYP2R1/OC use (P = 0.030) and CYP3A43/VDR (P = 0.013)) were identified. A CYP3A43 genotype, previously implicated in cancer, is strongly associated with biomarkers of vitamin D metabolism. Interactive associations should be further investigated.

  2. Prevalence and Correlates of “High Dose” Antipsychotic Prescribing ...

    African Journals Online (AJOL)

    of 1000 mg/day is considered as high dose prescribing. Furthermore ... genetic variations.[16] ... Annals of Medical and Health Sciences Research | Jan-Mar 2013 | Vol 3 | Issue 1 |. 63 ... the unreliability of the CPZeq criteria in the view of an increasing use of ... We obtained ethical clearance from the Ethics and Research.

  3. Neural Correlates of High Performance in Foreign Language Vocabulary Learning

    Science.gov (United States)

    Macedonia, Manuela; Muller, Karsten; Friederici, Angela D.

    2010-01-01

    Learning vocabulary in a foreign language is a laborious task which people perform with varying levels of success. Here, we investigated the neural underpinning of high performance on this task. In a within-subjects paradigm, participants learned 92 vocabulary items under two multimodal conditions: one condition paired novel words with iconic…

  4. Effect of ancestry on interleukin-10 haplotypes in chronic periodontitis.

    Science.gov (United States)

    Lopes, Camile de Barros; Barroso, Regina Fatima Feio; Burbano, Rommel Mario Rodrigues; Garcia, Patricia Aleixo; Pinto, Pablo Diego do Carmo; Santos, Ney Pereira Carneiro Dos; Santos, Sidney Emanuel Batista; Ribeiro-Dos-Santos, Andrea Kely Campos

    2017-06-01

    Chronic periodontitis is caused by an inflammatory reaction of the periodontal tissues and alveolar bone. This inflammation is caused by periodontopathic bacteria located in the subgingival biofilm, resulting in inflammatory reactions that may lead to loss of attachment. This tissue destruction is a consequence of host immune and inflammatory responses to specific periodontal pathogens and their metabolic products. Cytokines modulate the immune response, altering its efficiency in the competition against pathogens and increasing periodontal susceptibility. This study investigated genetic polymorphisms in Interleukin 10 (A-1082G, C-819T and C-592A) in 205 individuals from an admixed Brazilian population. A significantly increased risk of developing chronic periodontitis was observed in individuals with low IL-10 production and Amerindian ancestry. These results suggest that the polymorphisms A-1082G, C-819T, and C-592A, which are associated with ancestry, are involved in the susceptibility to the development of chronic periodontitis in an admixed northern Brazilian population.

  5. Stealing among High School Students: Prevalence and Clinical Correlates

    OpenAIRE

    Grant, Jon E.; Potenza, Marc N.; Krishnan-Sarin, Suchitra; Cavallo, Dana A.; Desai, Rani A.

    2011-01-01

    Although stealing among adolescents appears to be fairly common, an assessment of adolescent stealing and its relationship to other behaviors and health issues is incompletely understood. A large sample of high school students (n=3999) was examined using a self-report survey with 153 questions concerning demographic characteristics, stealing behaviors, other health behaviors including substance use, and functioning variables such as grades and violent behavior. The overall prevalence of steal...

  6. Two-particle correlations from droplet formation in high multiplicity anti pp events

    International Nuclear Information System (INIS)

    Ruuskanen, P.V.; Seibert, D.

    1988-01-01

    We study the correlations that arise from the formation of plasma droplets in high multiplicity events observed in recent FNAL anti pp collisions at √s=1.8 TeV. We show how the correlation between the final particles depends on the droplet size and density and on correlations between the droplets. We find that the two-particle correlation function R 2 could provide a clear signal for the formation of droplets. (orig.)

  7. Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations.

    Science.gov (United States)

    Martin, Eden R; Tunc, Ilker; Liu, Zhi; Slifer, Susan H; Beecham, Ashley H; Beecham, Gary W

    2018-03-01

    Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations. We show that admixture does not lead to confounding when the trait locus is tested directly in a single admixed population. However, if there is more complex population structure or a marker locus in linkage disequilibrium (LD) with the trait locus is tested, both global and local ancestry can be confounders. Additionally, we show the genotype parameters of adjusted and unadjusted models all provide tests for LD between the marker and trait locus, but in different contexts. The local ancestry adjusted model tests for LD in the ancestral populations, while tests using the unadjusted and the global ancestry adjusted models depend on LD in the admixed population(s), which may be enriched due to different ancestral allele frequencies. Practically, this implies that global-ancestry adjustment should be used for screening, but local-ancestry adjustment may better inform fine mapping and provide better effect estimates at trait loci. © 2017 WILEY PERIODICALS, INC.

  8. Ancestry dynamics in a South American population: The impact of gene flow and preferential mating.

    Science.gov (United States)

    Hedrick, Philip W

    2017-07-01

    European ancestry in many populations in Latin America at autosomal loci is often higher than that from X-linked loci indicating more European male ancestry and more Amerindian female ancestry. Generally, this has been attributed to more European male gene flow but could also result from an advantage to European mating or reproductive success. Population genetic models were developed to investigate the dynamics of gene flow and mating or reproductive success. Using estimates of autosomal and X-chromosome European ancestry, the amount of male gene flow or mating or reproductive advantage for Europeans, or those with European ancestry, was estimated. In a population from Antioquia, Colombia with an estimated 79% European autosomal ancestry and an estimated 69% European X-chromosome ancestry, about 15% male gene flow from Europe or about 20% mating or reproductive advantage of Europeans over Amerindians resulted in these levels of European ancestry in the contemporary population. Combinations of gene flow and mating advantage were nearly additive in their impact. Gene flow, mating advantage, or a combination of both factors, are consistent with observed levels of European ancestry in a Latin American population. This approach provides a general methodology to determine the levels of gene flow and mating differences that can explain the observed contemporary differences in ancestry from autosomes and X-chromosomes. © 2017 Wiley Periodicals, Inc.

  9. Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa.

    Science.gov (United States)

    Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale; Rotimi, Charles N

    2018-03-01

    The Hadza and Sandawe populations in present-day Tanzania speak languages containing click sounds and therefore thought to be distantly related to southern African Khoisan languages. We analyzed genome-wide genotype data for individuals sampled from the Hadza and Sandawe populations in the context of a global data set of 3,528 individuals from 163 ethno-linguistic groups. We found that Hadza and Sandawe individuals share ancestry distinct from and most closely related to Omotic ancestry; share Khoisan ancestry with populations such as ≠Khomani, Karretjie, and Ju/'hoansi in southern Africa; share Niger-Congo ancestry with populations such as Yoruba from Nigeria and Luhya from Kenya, consistent with migration associated with the Bantu Expansion; and share Cushitic ancestry with Somali, multiple Ethiopian populations, the Maasai population in Kenya, and the Nama population in Namibia. We detected evidence for low levels of Arabian, Nilo-Saharan, and Pygmy ancestries in a minority of individuals. Our results indicate that west Eurasian ancestry in eastern Africa is more precisely the Arabian parent of Cushitic ancestry. Relative to the Out-of-Africa migrations, Hadza ancestry emerged early whereas Sandawe ancestry emerged late.

  10. An ancestry-based approach for detecting interactions.

    Science.gov (United States)

    Park, Danny S; Eskin, Itamar; Kang, Eun Yong; Gamazon, Eric R; Eng, Celeste; Gignoux, Christopher R; Galanter, Joshua M; Burchard, Esteban; Ye, Chun J; Aschard, Hugues; Eskin, Eleazar; Halperin, Eran; Zaitlen, Noah

    2018-02-01

    Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies. In this work, we develop a new statistical approach to address these issues that leverages genetic ancestry, defined as the proportion of ancestry derived from each ancestral population (e.g., the fraction of European/African ancestry in African Americans), in admixed populations. We applied our method to gene expression and methylation data from African American and Latino admixed individuals, respectively, identifying nine interactions that were significant at Pancestry can be a useful proxy for unknown and unmeasured covariates in the search for interaction effects. These results have important implications for our understanding of the genetic architecture of complex traits. © 2017 WILEY PERIODICALS, INC.

  11. Stealing among High School Students: Prevalence and Clinical Correlates

    Science.gov (United States)

    Grant, Jon E.; Potenza, Marc N.; Krishnan-Sarin, Suchitra; Cavallo, Dana A.; Desai, Rani A.

    2013-01-01

    Although stealing among adolescents appears to be fairly common, an assessment of adolescent stealing and its relationship to other behaviors and health issues is incompletely understood. A large sample of high school students (n=3999) was examined using a self-report survey with 153 questions concerning demographic characteristics, stealing behaviors, other health behaviors including substance use, and functioning variables such as grades and violent behavior. The overall prevalence of stealing was 15.2% (95%CI: 14.8–17.0). Twenty-nine (0.72%) students endorsed symptoms consistent with a diagnosis of DSM-IV kleptomania. Poor grades, alcohol and drug use, regular smoking, sadness and hopelessness, and other antisocial behaviors were all significantly (p<.05) associated with any stealing behavior. Stealing appears fairly common among high school students and is associated with a range of potentially addictive and antisocial behaviors. Significant distress and loss of control over this behavior suggests that stealing often has significant associated morbidity. PMID:21389165

  12. Stealing among high school students: prevalence and clinical correlates.

    Science.gov (United States)

    Grant, Jon E; Potenza, Marc N; Krishnan-Sarin, Suchitra; Cavallo, Dana A; Desai, Rani A

    2011-01-01

    Although stealing among adolescents appears to be fairly common, an assessment of adolescent stealing and its relationship to other behaviors and health problems is incompletely understood. A large sample of high school students (n = 3,999) was examined by self-report survey with 153 questions concerning demographic characteristics, stealing behaviors, other health behaviors including substance use, and functioning variables, such as grades and violent behavior. The overall prevalence of stealing was 15.2 percent (95% confidence interval (CI), 14.8-17.0). Twenty-nine (0.72%) students endorsed symptoms consistent with a diagnosis of DSM-IV-TR kleptomania. Poor grades, alcohol and drug use, regular smoking, sadness and hopelessness, and other antisocial behaviors were all significantly (p stealing behavior. Stealing appears to be fairly common among high school students and is associated with a range of potentially addictive and antisocial behaviors. Significant distress and loss of control over this behavior suggest that stealing often has significant associated morbidity.

  13. Final Report - X-ray Studies of Highly Correlated Systems

    Energy Technology Data Exchange (ETDEWEB)

    Burns, Clement [Western Michigan Univ., Kalamazoo MI (United States)

    2017-11-27

    The overall goal of the research was to improve the capabilities of x-ray synchrotron instrumentation to enable cutting-edge research in condensed matter physics. The main goal of the current grant cycle was to find a method to measure the polarization of the scattered x-ray in resonant inelastic x-ray scattering. To do this, we developed a polarization analysis apparatus using a thin, toroidally bent single crystal, which could be set to reflect one or the other of the two polarization components in the scattered x-ray beam. Resonant x-ray scattering measurements were also carried out on interfaces and the charge density wave in high temperature superconducting materials.

  14. Correlates of gambling on high-school grounds

    Science.gov (United States)

    Foster, Dawn W.; Hoff, Rani A.; Pilver, Corey E.; Yau, Yvonne H. C.; Steinberg, Marvin A.; Wampler, Jeremy; Krishnan-Sarin, Suchitra; Potenza, Marc N.

    2015-01-01

    Objective This study examined adolescent gambling on school grounds (GS+) and how such behavior was associated with gambling-related attitudes. Further, we examined whether GS+ moderated associations between at-risk problem-gambling (ARPG) and gambling behaviors related to gambling partners. Method Participants were 1988 high-school students who completed survey materials. Demographic, perceptions, attitudes, and gambling variables were stratified by problem-gambling severity (ARPG versus recreational gambling) and GS+ status. Chi-square and adjusted logistic regression models were used to examine relationships among study variables. Results Nearly 40% (39.58%) of students reported past-year GS+, with 12.91% of GS+ students, relative to 2.63% of those who did not report gambling on school grounds (GS), meeting DSM-IV criteria for pathological gambling (pgambling behaviors. Weaker links in GS+ students, in comparison with GS-, students, were observed between problem-gambling severity and gambling with family members (interaction odds ratio (IOR)=0.60; 95%CI=0.39–0.92) and gambling with friends (IOR=0.21; 95%CI=0.11–0.39). Conclusions GS+ is common and associated with pathological gambling and more permissive attitudes towards gambling. The finding that GS+ (relative to GS-) youth show differences in how problem-gambling is related to gambling partners (friends and family) warrants further investigation regarding whether and how peer and familial interactions might be improved to diminish youth problem-gambling severity. The high frequency of GS+ and its relationship with ARPG highlight a need for school administrators and personnel to consider interventions that target school-based gambling. PMID:26232102

  15. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.

    Directory of Open Access Journals (Sweden)

    Simon N Stacey

    2010-07-01

    Full Text Available We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1 genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively. Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3, African (OR = 1.35, P = 0.014, and Asian (OR = 1.23, P = 2.9 x 10(-4 population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7, was without significant heterogeneity between ancestries (P(het = 0.36 and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268, which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.

  16. High-resolution x-ray scattering studies of charge ordering in highly correlated electron systems

    International Nuclear Information System (INIS)

    Ghazi, M.E.

    2002-01-01

    Many important properties of transition metal oxides such as, copper oxide high-temperature superconductivity and colossal magnetoresistance (CMR) in manganites are due to strong electron-electron interactions, and hence these systems are called highly correlated systems. These materials are characterised by the coexistence of different kinds of order, including charge, orbital, and magnetic moment. This thesis contains high-resolution X-ray scattering studies of charge ordering in such systems namely the high-T C copper oxides isostructural system, La 2-x Sr x NiO 4 with various Sr concentrations (x = 0.33 - 0.2), and the CMR manganite system, Nd 1/2 Sr 1/2 MnO 3 . It also includes a review of charge ordering in a large variety of transition metal oxides, such as ferrates, vanadates, cobaltates, nickelates, manganites, and cuprates systems, which have been reported to date in the scientific literature. Using high-resolution synchrotron X-ray scattering, it has been demonstrated that the charge stripes exist in a series of single crystals of La 2-x Sr x NiO 4 with Sr concentrations (x = 0.33 - 0.2) at low temperatures. Satellite reflections due to the charge ordering were found with the wavevector (2ε, 0, 1) below the charge ordering transition temperature, T CO , where 2ε is the amount of separation from the corresponding Bragg peak. The charge stripes are shown to be two-dimensional in nature both by measurements of their correlation lengths and by measurement of the critical exponents of the charge stripe melting transition with an anomaly at x = 0.25. The results show by decreasing the hole concentration from the x = 0.33 to 0.2, the well-correlated charge stripes change to a glassy state at x = 0.25. The electronic transition into the charge stripe phase is second-order without any corresponding structural transition. Above the second-order transition critical scattering was observed due to fluctuations into the charge stripe phase. In a single-crystal of Nd

  17. From Bows to Sound-Chests: Tracing the Ancestry of the Violin

    Directory of Open Access Journals (Sweden)

    Janelle R. Finley

    2016-04-01

    Full Text Available The ancestry of the violin is a subject that has been studied, researched, debated, and written about in great detail. However, despite all of the research and study, the ancestry of the violin is still not certain. This paper presents two schools of thought that propose different theories as to how the ancestry of the violin should be determined and what instruments should be included in the ancestry of the violin. The first school of thought proposes that the violin’s ancestry should be traced through the bow. The second theory proposes that the violin’s ancestry should be traced through the sound-chest of the violin. This paper also presents the different arguments for and against each theory, the importance of this topic, and the paper’s position on this topic. Research for this paper was accomplished through the use of scholarly books on the subject of the history of the violin.

  18. Accuracy Rates of Ancestry Estimation by Forensic Anthropologists Using Identified Forensic Cases.

    Science.gov (United States)

    Thomas, Richard M; Parks, Connie L; Richard, Adam H

    2017-07-01

    A common task in forensic anthropology involves the estimation of the ancestry of a decedent by comparing their skeletal morphology and measurements to skeletons of individuals from known geographic groups. However, the accuracy rates of ancestry estimation methods in actual forensic casework have rarely been studied. This article uses 99 forensic cases with identified skeletal remains to develop accuracy rates for ancestry estimations conducted by forensic anthropologists. The overall rate of correct ancestry estimation from these cases is 90.9%, which is comparable to most research-derived rates and those reported by individual practitioners. Statistical tests showed no significant difference in accuracy rates depending on examiner education level or on the estimated or identified ancestry. More recent cases showed a significantly higher accuracy rate. The incorporation of metric analyses into the ancestry estimate in these cases led to a higher accuracy rate. © 2017 American Academy of Forensic Sciences.

  19. Why do hypertensive patients of African ancestry respond better to calcium blockers and diuretics than to ACE inhibitors and β-adrenergic blockers? A systematic review

    Science.gov (United States)

    2013-01-01

    Background Clinicians are encouraged to take an individualized approach when treating hypertension in patients of African ancestry, but little is known about why the individual patient may respond well to calcium blockers and diuretics, but generally has an attenuated response to drugs inhibiting the renin-angiotensin system and to β-adrenergic blockers. Therefore, we systematically reviewed the factors associated with the differential drug response of patients of African ancestry to antihypertensive drug therapy. Methods Using the methodology of the systematic reviews narrative synthesis approach, we sought for published or unpublished studies that could explain the differential clinical efficacy of antihypertensive drugs in patients of African ancestry. PUBMED, EMBASE, LILACS, African Index Medicus and the Food and Drug Administration and European Medicines Agency databases were searched without language restriction from their inception through June 2012. Results We retrieved 3,763 papers, and included 72 reports that mainly considered the 4 major classes of antihypertensive drugs, calcium blockers, diuretics, drugs that interfere with the renin-angiotensin system and β-adrenergic blockers. Pharmacokinetics, plasma renin and genetic polymorphisms did not well predict the response of patients of African ancestry to antihypertensive drugs. An emerging view that low nitric oxide and high creatine kinase may explain individual responses to antihypertensive drugs unites previous observations, but currently clinical data are very limited. Conclusion Available data are inconclusive regarding why patients of African ancestry display the typical response to antihypertensive drugs. In lieu of biochemical or pharmacogenomic parameters, self-defined African ancestry seems the best available predictor of individual responses to antihypertensive drugs. PMID:23721258

  20. Genomics assisted ancestry deconvolution in grape

    Science.gov (United States)

    The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain i...

  1. High Grazing Angle and High Resolution Sea Clutter: Correlation and Polarisation Analyses

    Science.gov (United States)

    2007-03-01

    the azimuthal correlation. The correlation between the HH and VV sea clutter data is low. A CA-CFAR ( cell average constant false-alarm rate...to calculate the power spectra of correlation profiles. The frequency interval of the traditional Discrete Fourier Transform is NT1 Hz, where N and...sea spikes, the Entropy-Alpha decomposition of sea spikes is shown in Figure 30. The process first locates spikes using a cell -average constant false

  2. Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children

    Science.gov (United States)

    Spector, Stephen A.; Brummel, Sean S.; Nievergelt, Caroline M.; Maihofer, Adam X.; Singh, Kumud K.; Purswani, Murli U.; Williams, Paige L.; Hazra, Rohan; Van Dyke, Russell; Seage, George R.

    2016-01-01

    Abstract The Pediatric HIV/AIDS Cohort Study (PHACS), the largest ongoing longitudinal study of perinatal HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) children in the United States, comprises the Surveillance Monitoring of Antiretroviral Therapy [ART] Toxicities (SMARTT) Study in PHEU children and the Adolescent Master Protocol (AMP) that includes PHIV and PHEU children ≥7 years. Although race/ethnicity is often used to assess health outcomes, this approach remains controversial and may fail to accurately reflect the backgrounds of ancestry-diverse populations as represented in the PHACS participants. In this study, we compared genetically determined ancestry (GDA) and self-reported race/ethnicity (SRR) in the PHACS cohort. GDA was estimated using a highly discriminative panel of 41 single nucleotide polymorphisms and compared to SRR. Because SRR was similar between the PHIV and PHEU, and between the AMP and SMARTT cohorts, data for all unique 1958 participants were combined. According to SRR, 63% of study participants identified as Black/African-American, 27% White, and 34% Hispanic. Using the highest percentage of ancestry/ethnicity to identify GDA, 9.5% of subjects were placed in the incorrect superpopulation based on SRR. When ≥50% or ≥75% GDA of a given superpopulation was required, 12% and 25%, respectively, of subjects were placed in the incorrect superpopulation based on SRR, and the percent of subjects classified as multiracial increased. Of 126 participants with unidentified SRR, 71% were genetically identified as Eurasian. GDA provides a more robust assessment of race/ethnicity when compared to self-report, and study participants with unidentified SRR could be assigned GDA using genetic markers. In addition, identification of continental ancestry removes the taxonomic identification of race as a variable when identifying risk for clinical outcomes. PMID:27603370

  3. Econometric analysis of realised covariation: high frequency covariance, regression and correlation in financial economics

    OpenAIRE

    Ole E. Barndorff-Nielsen; Neil Shephard

    2002-01-01

    This paper analyses multivariate high frequency financial data using realised covariation. We provide a new asymptotic distribution theory for standard methods such as regression, correlation analysis and covariance. It will be based on a fixed interval of time (e.g. a day or week), allowing the number of high frequency returns during this period to go to infinity. Our analysis allows us to study how high frequency correlations, regressions and covariances change through time. In particular w...

  4. Wavelet-space correlation imaging for high-speed MRI without motion monitoring or data segmentation.

    Science.gov (United States)

    Li, Yu; Wang, Hui; Tkach, Jean; Roach, David; Woods, Jason; Dumoulin, Charles

    2015-12-01

    This study aims to (i) develop a new high-speed MRI approach by implementing correlation imaging in wavelet-space, and (ii) demonstrate the ability of wavelet-space correlation imaging to image human anatomy with involuntary or physiological motion. Correlation imaging is a high-speed MRI framework in which image reconstruction relies on quantification of data correlation. The presented work integrates correlation imaging with a wavelet transform technique developed originally in the field of signal and image processing. This provides a new high-speed MRI approach to motion-free data collection without motion monitoring or data segmentation. The new approach, called "wavelet-space correlation imaging", is investigated in brain imaging with involuntary motion and chest imaging with free-breathing. Wavelet-space correlation imaging can exceed the speed limit of conventional parallel imaging methods. Using this approach with high acceleration factors (6 for brain MRI, 16 for cardiac MRI, and 8 for lung MRI), motion-free images can be generated in static brain MRI with involuntary motion and nonsegmented dynamic cardiac/lung MRI with free-breathing. Wavelet-space correlation imaging enables high-speed MRI in the presence of involuntary motion or physiological dynamics without motion monitoring or data segmentation. © 2014 Wiley Periodicals, Inc.

  5. Validation of an Arab name algorithm in the determination of Arab ancestry for use in health research.

    Science.gov (United States)

    El-Sayed, Abdulrahman M; Lauderdale, Diane S; Galea, Sandro

    2010-12-01

    Data about Arab-Americans, a growing ethnic minority, are not routinely collected in vital statistics, registry, or administrative data in the USA. The difficulty in identifying Arab-Americans using publicly available data sources is a barrier to health research about this group. Here, we validate an empirically based probabilistic Arab name algorithm (ANA) for identifying Arab-Americans in health research. We used data from all Michigan birth certificates between 2000 and 2005. Fathers' surnames and mothers' maiden names were coded as Arab or non-Arab according to the ANA. We calculated sensitivity, specificity, and positive (PPV) and negative predictive values (NPV) of Arab ethnicity inferred using the ANA as compared to self-reported Arab ancestry. Statewide, the ANA had a specificity of 98.9%, a sensitivity of 50.3%, a PPV of 57.0%, and an NPV of 98.6%. Both the false-positive and false-negative rates were higher among men than among women. As the concentration of Arab-Americans in a study locality increased, the ANA false-positive rate increased and false-negative rate decreased. The ANA is highly specific but only moderately sensitive as a means of detecting Arab ancestry. Future research should compare health characteristics among Arab-American populations defined by Arab ancestry and those defined by the ANA.

  6. Validation of an Arab names algorithm in the determination of Arab ancestry for use in health research

    Science.gov (United States)

    El-Sayed, Abdulrahman M.; Lauderdale, Diane S.; Galea, Sandro

    2010-01-01

    Objective Data about Arab-Americans, a growing ethnic minority, is not routinely collected in vital statistics, registry, or administrative data in the US. The difficulty in identifying Arab-Americans using publicly available data sources is a barrier to health research about this group. Here, we validate an empirically-based, probabilistic Arab name algorithm (ANA) for identifying Arab-Americans in health research. Design We used data from all Michigan birth certificates between 2000-2005. Fathers’ surnames and mothers’ maiden names were coded as Arab or non-Arab according to the ANA. We calculated sensitivity, specificity, and positive (PPV) and negative predictive values (NPV) of Arab ethnicity inferred using the ANA as compared to self-reported Arab ancestry. Results State-wide, the ANA had a specificity of 98.9%, a sensitivity of 50.3%, a PPV of 57.0%, and a NPV of 98.6%. Both the false positive and false negative rates were higher among men than among women. As the concentration of Arab-Americans in a study locality increased, the ANA false positive rate increased and false-negative rate decreased. Conclusion The ANA is highly specific but only moderately sensitive as a means of detecting Arab ancestry. Future research should compare health characteristics among Arab-American populations defined by Arab ancestry and those defined by the ANA. PMID:20845117

  7. Correlations between high momentum particles in proton-proton collisions at high energies

    International Nuclear Information System (INIS)

    Bobbink, G.J.

    1981-01-01

    This thesis describes an experiment performed at the CERN Intersecting Storage Rings. The experiment studies the reaction p+p→h 1 +h 2 +X at two centre-of-mass energies, √s=44.7 GeV and √s=62.3 GeV. Two of the outgoing particles (h 1 and h 2 ) are detected in opposite c.m.s. hemispheres at small polar angles with respect to the direction of two incident protons. The remaining particles produced (X) are not detected. The hadrons hsub(i) are identified mesons (π + , π - , K + , K - ) or baryons (p, Λ) with relatively large longitudinal psub(L) and small transverse momentum psub(T). The aim of the experiment is twofold. The first aim is to study whether the momentum distributions of the fast particles hsub(i) are correlated and thereby to constrain the possible interaction mechanisms responsible for the production of high psub(L), low psub(T) particles. The second aim is to establish to what extent the production of pions and kaons in inclusive proton-proton collisions (e.g. p+p→π+X, X=all other particles) resembles the production of pions and kaons in diffractive proton-proton collisions (e.g. p+p→p+π+X, in which the final-state proton has a momentum close to its maximum possible value). (Auth.)

  8. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India.

    Science.gov (United States)

    Negi, Neetu; Tamang, Rakesh; Pande, Veena; Sharma, Amrita; Shah, Anish; Reddy, Alla G; Vishnupriya, Satti; Singh, Lalji; Chaubey, Gyaneshwer; Thangaraj, Kumarasamy

    2016-02-01

    Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.

  9. Correlational Study between Teacher Perceived High School Principal Leadership Style and Teacher Self-Efficacy

    Science.gov (United States)

    Riggs, Robert

    2017-01-01

    This quantitative correlational study addressed the concept that teacher-perceived high school principal leadership style correlated with teacher self-efficacy. A relationship existed between teacher self-efficacy and student outcomes and research indicated a relationship between leadership style and teacher self-efficacy. Also, the effect of…

  10. Identifying Affective Domains That Correlate and Predict Mathematics Performance in High-Performing Students in Singapore

    Science.gov (United States)

    Lim, Siew Yee; Chapman, Elaine

    2015-01-01

    Past studies have shown that distinct yet highly correlated sub-constructs of three broad mathematics affective variables: (a) motivation, (b) attitudes and (c) anxiety, have varying degree of correlation with mathematics achievement. The sub-constructs of these three affective constructs are as follows: (a) (i) amotivation, (ii) external…

  11. Disparities in breast cancer and african ancestry: a global perspective.

    Science.gov (United States)

    Newman, Lisa A

    2015-01-01

    Recognition of breast cancer disparities between African-American and White American women has generated exciting research opportunities investigating the biologic and hereditary factors that contribute to the observed outcome differences, leading to international studies of breast cancer in Africa. The study of breast cancer in women with African ancestry has opened the door to unique investigations regarding breast cancer subtypes and the genetics of this disease. International research efforts can advance our understanding of race/ethnicity-associated breast cancer disparities within the USA; the pathogenesis of triple negative breast cancer; and hereditary susceptibility for breast cancer. © 2015 Wiley Periodicals, Inc.

  12. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

    Science.gov (United States)

    Banda, Yambazi; Kvale, Mark N.; Hoffmann, Thomas J.; Hesselson, Stephanie E.; Ranatunga, Dilrini; Tang, Hua; Sabatti, Chiara; Croen, Lisa A.; Dispensa, Brad P.; Henderson, Mary; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H.; Ludwig, Dana; Olberg, Diane; Quesenberry, Charles P.; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C.; Sciortino, Stanley; Shen, Ling; Smethurst, David; Somkin, Carol P.; Van Den Eeden, Stephen K.; Walter, Lawrence; Whitmer, Rachel A.; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil

    2015-01-01

    Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian–European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent–child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent–child pairs was largely due to intermarriage. The parent–child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies. PMID:26092716

  13. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.

    Science.gov (United States)

    Banda, Yambazi; Kvale, Mark N; Hoffmann, Thomas J; Hesselson, Stephanie E; Ranatunga, Dilrini; Tang, Hua; Sabatti, Chiara; Croen, Lisa A; Dispensa, Brad P; Henderson, Mary; Iribarren, Carlos; Jorgenson, Eric; Kushi, Lawrence H; Ludwig, Dana; Olberg, Diane; Quesenberry, Charles P; Rowell, Sarah; Sadler, Marianne; Sakoda, Lori C; Sciortino, Stanley; Shen, Ling; Smethurst, David; Somkin, Carol P; Van Den Eeden, Stephen K; Walter, Lawrence; Whitmer, Rachel A; Kwok, Pui-Yan; Schaefer, Catherine; Risch, Neil

    2015-08-01

    Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies. Copyright © 2015 by the Genetics Society of America.

  14. Differentiation analysis for estimating individual ancestry from the Tibetan Plateau by an archaic altitude adaptation EPAS1 haplotype among East Asian populations.

    Science.gov (United States)

    Jiang, Li; Peng, Jianxiong; Huang, Meisha; Liu, Jing; Wang, Ling; Ma, Quan; Zhao, Hui; Yang, Xin; Ji, Anquan; Li, Caixia

    2018-02-10

    Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions. These data were integrated with the genotypes from the 1000 Genome populations and populations in a previously reported paper for population structure analyses. We found that populations representing highland and lowland groups have different dominant ancestry components. The core Denisovan haplotype (AGGAA) was observed at a frequency of 72.32% in the Tibetan Plateau, with a frequency range from 9.48 to 21.05% in the peripheral regions and Tibetan Plateau carried the archaic haplotype, while < 5% of the Chinese Han people carried the haplotype. Our findings indicate that the 5-SNP haplotype has a special distribution pattern in populations of Tibet and peripheral regions and could be integrated into AISNP (Ancestry Informative Single Nucleotide Polymorphism) panels to enhance ancestry resolution.

  15. Exercise capacity and selected physiological factors by ancestry and residential altitude

    DEFF Research Database (Denmark)

    Bianba; Berntsen, Sveinung; Andersen, Lars Bo

    2014-01-01

    AIM: Several physiological compensatory mechanisms have enabled Tibetans to live and work at high altitude, including increased ventilation and pulmonary diffusion capacity, both of which serve to increase oxygen transport in the blood. The aim of the present study was to compare exercise capacity...... Tibetans vs. Han Chinese may reflect a better adaptation to life at high altitude. Tibetans at the lower residential altitude of 3700 m demonstrated a better exercise capacity than residents at a higher altitude of 4300 m when measured at their respective residential altitudes. Such altitude- or ancestry...... (maximal power output) and selected physiological factors (arterial oxygen saturation and heart rate at rest and during maximal exercise, resting hemoglobin concentration, and forced vital capacity) in groups of native Tibetan children living at different residential altitudes (3700 vs. 4300 m above sea...

  16. CGC/saturation approach for soft interactions at high energy: long range rapidity correlations

    International Nuclear Information System (INIS)

    Gotsman, E.; Maor, U.; Levin, E.

    2015-01-01

    In this paper we continue our program to construct a model for high energy soft interactions that is based on the CGC/saturation approach. The main result of this paper is that we have discovered a mechanism that leads to large long range rapidity correlations and results in large values of the correlation function R(y 1 , y 2 ) ≥ 1, which is independent of y 1 and y 2 . Such a behavior of the correlation function provides strong support for the idea that at high energies the system of partons that is produced is not only dense but also has strong attractive forces acting between the partons. (orig.)

  17. Indices of Paraoxonase and Oxidative Status Do Not Enhance the Prediction of Subclinical Cardiovascular Disease in Mixed-Ancestry South Africans

    Directory of Open Access Journals (Sweden)

    M. Macharia

    2014-01-01

    Full Text Available We evaluated the association of indices of paraoxonase (PON1 and oxidative status with subclinical cardiovascular disease (CVD in mixed-ancestry South Africans. Participants were 491 adults (126 men who were stratified by diabetes status and body mass index (BMI. Carotid intima-media thickness (CIMT was used as a measure of subclinical CVD. Indices of PON1 and oxidative status were determined by measuring levels and activities (paraoxonase and arylesterase of PON1, antioxidant activity (ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers (malondialdehyde and oxidized LDL. Diabetic subjects (28.9% displayed a significant decrease in PON1 status and antioxidant activity as well as increase in oxidized LDL and malondialdehyde. A similar profile was apparent across increasing BMI categories. CIMT was higher in diabetic than nondiabetic subjects (P<0.0001  but showed no variation across BMI categories. Overall, CIMT correlated negatively with indices of antioxidant activity and positively with measures of lipid oxidation. Sex, age, BMI, and diabetes altogether explained 29.2% of CIMT, with no further improvement from adding PON1 and/or antioxidant status indices. Though indices of PON1 and oxidative status correlate with CIMT, their measurements may not be useful for identifying subjects at high CVD risk in this population.

  18. Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing.

    Science.gov (United States)

    Mathias, Patrick C; Turner, Emily H; Scroggins, Sheena M; Salipante, Stephen J; Hoffman, Noah G; Pritchard, Colin C; Shirts, Brian H

    2016-03-01

    To apply techniques for ancestry and sex computation from next-generation sequencing (NGS) data as an approach to confirm sample identity and detect sample processing errors. We combined a principal component analysis method with k-nearest neighbors classification to compute the ancestry of patients undergoing NGS testing. By combining this calculation with X chromosome copy number data, we determined the sex and ancestry of patients for comparison with self-report. We also modeled the sensitivity of this technique in detecting sample processing errors. We applied this technique to 859 patient samples with reliable self-report data. Our k-nearest neighbors ancestry screen had an accuracy of 98.7% for patients reporting a single ancestry. Visual inspection of principal component plots was consistent with self-report in 99.6% of single-ancestry and mixed-ancestry patients. Our model demonstrates that approximately two-thirds of potential sample swaps could be detected in our patient population using this technique. Patient ancestry can be estimated from NGS data incidentally sequenced in targeted panels, enabling an inexpensive quality control method when coupled with patient self-report. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Ancestry variation and footprints of natural selection along the genome in Latin American populations.

    Science.gov (United States)

    Deng, Lian; Ruiz-Linares, Andrés; Xu, Shuhua; Wang, Sijia

    2016-02-18

    Latin American populations stem from the admixture of Europeans, Africans and Native Americans, which started over 400 years ago and had lasted for several centuries. Extreme deviation over the genome-wide average in ancestry estimations at certain genomic locations could reflect recent natural selection. We evaluated the distribution of ancestry estimations using 678 genome-wide microsatellite markers in 249 individuals from 13 admixed populations across Latin America. We found significant deviations in ancestry estimations including three locations with more than 3.5 times standard deviations from the genome-wide average: an excess of European ancestry at 1p36 and 14q32, and an excess of African ancestry at 6p22. Using simulations, we could show that at least the deviation at 6p22 was unlikely to result from genetic drift alone. By applying different linguistic groups as well as the most likely ancestral Native American populations as the ancestry, we showed that the choice of Native American ancestry could affect the local ancestry estimation. However, the signal at 6p22 consistently appeared in most of the analyses using various ancestral groups. This study provided important insights for recent natural selection in the context of the unique history of the New World and implications for disease mapping.

  20. Measurement Uncertainty in Racial and Ethnic Identification among Adolescents of Mixed Ancestry: A Latent Variable Approach

    Science.gov (United States)

    Tracy, Allison J.; Erkut, Sumru; Porche, Michelle V.; Kim, Jo; Charmaraman, Linda; Grossman, Jennifer M.; Ceder, Ineke; Garcia, Heidie Vazquez

    2010-01-01

    In this article, we operationalize identification of mixed racial and ethnic ancestry among adolescents as a latent variable to (a) account for measurement uncertainty, and (b) compare alternative wording formats for racial and ethnic self-categorization in surveys. Two latent variable models were fit to multiple mixed-ancestry indicator data from…

  1. Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup

    Science.gov (United States)

    Emery, Leslie S.; Magnaye, Kevin M.; Bigham, Abigail W.; Akey, Joshua M.; Bamshad, Michael J.

    2015-01-01

    The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual’s place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual’s mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin. PMID:25620206

  2. Weight of the evidence of genetic investigations of ancestry informative markers

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2018-01-01

    Ancestry-informative markers (AIMs) are markers that give information about the ancestry of individuals. They are used in forensic genetics for predicting the geographic origin of the investigated individual in crime and identification cases. In the exploration of the genogeographic origin...

  3. Computation of ancestry scores with mixed families and unrelated individuals.

    Science.gov (United States)

    Zhou, Yi-Hui; Marron, James S; Wright, Fred A

    2018-03-01

    The issue of robustness to family relationships in computing genotype ancestry scores such as eigenvector projections has received increased attention in genetic association, and is particularly challenging when sets of both unrelated individuals and closely related family members are included. The current standard is to compute loadings (left singular vectors) using unrelated individuals and to compute projected scores for remaining family members. However, projected ancestry scores from this approach suffer from shrinkage toward zero. We consider two main novel strategies: (i) matrix substitution based on decomposition of a target family-orthogonalized covariance matrix, and (ii) using family-averaged data to obtain loadings. We illustrate the performance via simulations, including resampling from 1000 Genomes Project data, and analysis of a cystic fibrosis dataset. The matrix substitution approach has similar performance to the current standard, but is simple and uses only a genotype covariance matrix, while the family-average method shows superior performance. Our approaches are accompanied by novel ancillary approaches that provide considerable insight, including individual-specific eigenvalue scree plots. © 2017 The Authors. Biometrics published by Wiley Periodicals, Inc. on behalf of International Biometric Society.

  4. Statistical evidence for common ancestry: Application to primates.

    Science.gov (United States)

    Baum, David A; Ané, Cécile; Larget, Bret; Solís-Lemus, Claudia; Ho, Lam Si Tung; Boone, Peggy; Drummond, Chloe P; Bontrager, Martin; Hunter, Steven J; Saucier, William

    2016-06-01

    Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  5. The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions

    Science.gov (United States)

    Pool, John E.

    2015-01-01

    North American populations of Drosophila melanogaster derive from both European and African source populations, but despite their importance for genetic research, patterns of ancestry along their genomes are largely undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome, which may have implications for reference alignment, association mapping, and population genomic studies in Drosophila. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Combining my estimate of admixture timing with historical records, I provide the first estimate of natural generation time for this species (approximately 15 generations per year). Ancestry levels were found to vary strikingly across the genome, with less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes (e.g., circadian rhythm). An important role for natural selection during the admixture process was further supported by evidence that many unlinked pairs of loci showed a deficiency of Africa–Europe allele combinations between them. Numerous epistatic fitness interactions may therefore exist between African and European genotypes, leading to ongoing selection against incompatible variants. By focusing on hubs in this network of fitness interactions, I identified a set of interacting loci that include genes with roles in sensation and neuropeptide/hormone reception. These findings suggest that admixed D. melanogaster samples could become an important study system for the genetics of early-stage isolation between populations. PMID:26354524

  6. High Correlated Paternity Leads to Negative Effects on Progeny Performance in Two Mediterranean Shrub Species.

    Directory of Open Access Journals (Sweden)

    Sofia Nora

    Full Text Available Anthropogenic habitat deterioration can promote changes in plant mating systems that subsequently may affect progeny performance, thereby conditioning plant recruitment for the next generation. However, very few studies yet tested mating system parameters other than outcrossing rates; and the direct effects of the genetic diversity of the pollen received by maternal plants (i.e. correlated paternity has often been overlooked. In this study, we investigated the relation between correlated paternity and progeny performance in two common Mediterranean shrubs, Myrtus communis and Pistacia lentiscus. To do so, we collected open-pollinated progeny from selected maternal plants, calculated mating system parameters using microsatellite genotyping and conducted sowing experiments under greenhouse and field conditions. Our results showed that some progeny fitness components were negatively affected by the high correlated paternity of maternal plants. In Myrtus communis, high correlated paternity had a negative effect on the proportion and timing of seedling emergence in the natural field conditions and in the greenhouse sowing experiment, respectively. In Pistacia lentiscus, seedling emergence time under field conditions was also negatively influenced by high correlated paternity and a progeny survival analysis in the field experiment showed greater mortality of seedlings from maternal plants with high correlated paternity. Overall, we found effects of correlated paternity on the progeny performance of Myrtus communis, a self-compatible species. Further, we also detected effects of correlated paternity on the progeny emergence time and survival in Pistacia lentiscus, an obligate outcrossed species. This study represents one of the few existing empirical examples which highlight the influence that correlated paternity may exert on progeny performance in multiple stages during early seedling growth.

  7. A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.

    Science.gov (United States)

    Rishishwar, Lavanya; Conley, Andrew B; Vidakovic, Brani; Jordan, I King

    2015-12-15

    Uniparental genetic markers, mitochondrial DNA (mtDNA) and Y chromosomal DNA, are widely used for the inference of human ancestry. However, the resolution of ancestral origins based on mtDNA haplotypes is limited by the fact that such haplotypes are often found to be distributed across wide geographical regions. We have addressed this issue here by combining two sources of ancestry information that have typically been considered separately: historical records regarding population origins and genetic information on mtDNA haplotypes. To combine these distinct data sources, we applied a Bayesian approach that considers historical records, in the form of prior probabilities, together with data on the geographical distribution of mtDNA haplotypes, formulated as likelihoods, to yield ancestry assignments from posterior probabilities. This combined evidence Bayesian approach to ancestry assignment was evaluated for its ability to accurately assign sub-continental African ancestral origins to Afro-Colombians based on their mtDNA haplotypes. We demonstrate that the incorporation of historical prior probabilities via this analytical framework can provide for substantially increased resolution in sub-continental African ancestry assignment for members of this population. In addition, a personalized approach to ancestry assignment that involves the tuning of priors to individual mtDNA haplotypes yields even greater resolution for individual ancestry assignment. Despite the fact that Colombia has a large population of Afro-descendants, the ancestry of this community has been understudied relative to populations with primarily European and Native American ancestry. Thus, the application of the kind of combined evidence approach developed here to the study of ancestry in the Afro-Colombian population has the potential to be impactful. The formal Bayesian analytical framework we propose for combining historical and genetic information also has the potential to be widely applied

  8. A correlation for single phase turbulent mixing in square rod arrays under highly turbulent conditions

    International Nuclear Information System (INIS)

    Jeong, Hae Yong; Ha, Kwi Seok; Kwon, Young Min; Chang, Won Pyo; Lee, Yong Bum

    2006-01-01

    The existing experimental data related to the turbulent mixing factor in rod arrays is examined and a new definition of the turbulent mixing factor is introduced to take into account the turbulent mixing of fluids with various Prandtl numbers. The new definition of the mixing factor is based on the eddy diffusivity of energy. With this definition of the mixing factor, it was found that the geometrical parameter, δ ij /D h , correlates the turbulent mixing data better than S/d, which has been used frequently in existing correlations. Based on the experimental data for a highly turbulent condition in square rod arrays, a correlation describing turbulent mixing dependent on the parameter δ ij /D h has been developed. The correlation is insensitive to the Re number and it takes into account the effect of the turbulent Prandtl number. The proposed correlation predicts a reasonable mixing even at a lower S/d ratio

  9. Associations between male infertility and ancestry in South Americans: a case control study.

    Science.gov (United States)

    Skowronek, Maria Fernanda; Velazquez, Tatiana; Mut, Patricia; Figueiro, Gonzalo; Sans, Monica; Bertoni, Bernardo; Sapiro, Rossana

    2017-07-26

    Infertility affects 15% of human couples, with men being responsible in approximately 50% of cases. Moreover, the aetiology of male factor infertility is poorly understood. The majority of male factor infertility remains idiopathic and potentially genetic in origin. The association of the Y chromosome and mitochondrial haplogroups with male infertility has been previously reported. This association differs between studied populations and their geographical distributions. These effects have been only rarely analysed in mixed populations, such as South Americans. In this study, we analysed the contributions of the Y chromosome and mitochondrial haplogroups to male infertility in a mixed population. A case control study was conducted. Regular PCR and high-resolutionmelting- real-time PCR were performed to type haplogroups from fertile and infertile men. The sperm parameters from infertile men were compared in each haplogroup by logistic regression analysis and ANOVA. The genotyping confirmed the known admixture characteristic of the Uruguayan population. The European paternal contribution was higher than the maternal contribution in both fertile and infertile men. Neither maternal nor paternal ancestry presented differences between the cases and controls. Men belonging to the Y chromosome haplogroup F(xK) more frequently presented with an abnormal sperm morphology than men from other haplogroups. The sperm parameters were not associated with the mitochondrial haplogroups. The data presented in this study showed an association between male infertility and ancestry in the Uruguayan population. Specifically, abnormal sperm morphology was associated with the Y chromosome haplogroup F(xK). Since the Y chromosome lacks recombination, these data suggest that some genes that determine sperm morphology might be inherited in blocks with the region that determines specific haplogroups. However, the possible association between the Y chromosome haplogroup F(xK) and sperm

  10. Stimulus recognition occurs under high perceptual load: Evidence from correlated flankers.

    Science.gov (United States)

    Cosman, Joshua D; Mordkoff, J Toby; Vecera, Shaun P

    2016-12-01

    A dominant account of selective attention, perceptual load theory, proposes that when attentional resources are exhausted, task-irrelevant information receives little attention and goes unrecognized. However, the flanker effect-typically used to assay stimulus identification-requires an arbitrary mapping between a stimulus and a response. We looked for failures of flanker identification by using a more-sensitive measure that does not require arbitrary stimulus-response mappings: the correlated flankers effect. We found that flanking items that were task-irrelevant but that correlated with target identity produced a correlated flanker effect. Participants were faster on trials in which the irrelevant flanker had previously correlated with the target than when it did not. Of importance, this correlated flanker effect appeared regardless of perceptual load, occurring even in high-load displays that should have abolished flanker identification. Findings from a standard flanker task replicated the basic perceptual load effect, with flankers not affecting response times under high perceptual load. Our results indicate that task-irrelevant information can be processed to a high level (identification), even under high perceptual load. This challenges a strong account of high perceptual load effects that hypothesizes complete failures of stimulus identification under high perceptual load. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  11. Econometric analysis of realized covariation: high frequency based covariance, regression, and correlation in financial economics

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2004-01-01

    This paper analyses multivariate high frequency financial data using realized covariation. We provide a new asymptotic distribution theory for standard methods such as regression, correlation analysis, and covariance. It will be based on a fixed interval of time (e.g., a day or week), allowing...... the number of high frequency returns during this period to go to infinity. Our analysis allows us to study how high frequency correlations, regressions, and covariances change through time. In particular we provide confidence intervals for each of these quantities....

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

    Science.gov (United States)

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

    2013-01-01

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

  13. Correlation among High School Senior Students' Test Anxiety, Academic Performance and Points of University Entrance Exam

    Science.gov (United States)

    Karatas, Hakan; Alci, Bulent; Aydin, Hasan

    2013-01-01

    Test anxiety seems like a benign problem to some people, but it can be potentially serious when it leads to high levels of distress and academic failure. The aim of this study is to define the correlation among high school senior students' test anxiety, academic performance (GPA) and points of university entrance exam (UEE). The study group of…

  14. Matrix correlations for high-dimensional data: The modified RV-coefficient

    NARCIS (Netherlands)

    Smilde, A.K.; Kiers, H.A.L.; Bijlsma, S.; Rubingh, C.M.; Erk, M.J. van

    2009-01-01

    Motivation: Modern functional genomics generates high-dimensional datasets. It is often convenient to have a single simple number characterizing the relationship between pairs of such high-dimensional datasets in a comprehensive way. Matrix correlations are such numbers and are appealing since they

  15. Correlation Function Approach for Estimating Thermal Conductivity in Highly Porous Fibrous Materials

    Science.gov (United States)

    Martinez-Garcia, Jorge; Braginsky, Leonid; Shklover, Valery; Lawson, John W.

    2011-01-01

    Heat transport in highly porous fiber networks is analyzed via two-point correlation functions. Fibers are assumed to be long and thin to allow a large number of crossing points per fiber. The network is characterized by three parameters: the fiber aspect ratio, the porosity and the anisotropy of the structure. We show that the effective thermal conductivity of the system can be estimated from knowledge of the porosity and the correlation lengths of the correlation functions obtained from a fiber structure image. As an application, the effects of the fiber aspect ratio and the network anisotropy on the thermal conductivity is studied.

  16. Correlation between the pionization region and the fragmentation region in high energy proton-proton collisions

    CERN Document Server

    Albrow, M G; Barber, D P; Bogaerts, A; Bosnjakovic, B; Brooks, J R; Clegg, A B; Erné, F C; Gee, C N P; Locke, D H; Loebinger, F K; Murphy, P G; Rudge, A; Sens, Johannes C

    1973-01-01

    Measurements are reported of two-particle correlations in high energy proton-proton collisions with one particle in the pionization region and the other a proton in the fragmentation region. The correlation function is independent of x of the fragmentation proton for 0.55correlation is an energy-independent function of x. The measurements for two values of the rapidity of the pionization particle give similar results. (11 refs).

  17. A serach for moderate- and high-energy neturino emission correlated with gamma-ray bursts

    Science.gov (United States)

    Becker-Szendy, R.; Bratton, C. B.; Breault, J.; Casper, D.; Dye, S. T.; Gajewski, W.; Goldhaber, M.; Haines, T. J.; Halverson, P. G.; Kielczewska, D.

    1995-01-01

    A temporal correlation analysis between moderate- (60 Mev less than or equal to E(sub nu)greater than or equal to 2500 MeV) and high-energy (E(sub nu) greater than or equal to 2000 MeV) neutrino interactions consist of two types: the moderate-energy interactions that are contained within the volume of IMB-3 and the upward-going muons produced by high-energy nu(sub mu) interactions in the rock around the detector. No evidence is found for moderate- or high-energy neutrino emission from GRBs nor for any neutrino/neutrino correlation. The nonobservation of nu/GRB correlations allows upper limits to be placed on the neutrino flux associated with GRBs.

  18. Deep ancestry of programmed genome rearrangement in lampreys.

    Science.gov (United States)

    Timoshevskiy, Vladimir A; Lampman, Ralph T; Hess, Jon E; Porter, Laurie L; Smith, Jeramiah J

    2017-09-01

    In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Ancient genomes revisit the ancestry of domestic and Przewalski's horses.

    Science.gov (United States)

    Gaunitz, Charleen; Fages, Antoine; Hanghøj, Kristian; Albrechtsen, Anders; Khan, Naveed; Schubert, Mikkel; Seguin-Orlando, Andaine; Owens, Ivy J; Felkel, Sabine; Bignon-Lau, Olivier; de Barros Damgaard, Peter; Mittnik, Alissa; Mohaseb, Azadeh F; Davoudi, Hossein; Alquraishi, Saleh; Alfarhan, Ahmed H; Al-Rasheid, Khaled A S; Crubézy, Eric; Benecke, Norbert; Olsen, Sandra; Brown, Dorcas; Anthony, David; Massy, Ken; Pitulko, Vladimir; Kasparov, Aleksei; Brem, Gottfried; Hofreiter, Michael; Mukhtarova, Gulmira; Baimukhanov, Nurbol; Lõugas, Lembi; Onar, Vedat; Stockhammer, Philipp W; Krause, Johannes; Boldgiv, Bazartseren; Undrakhbold, Sainbileg; Erdenebaatar, Diimaajav; Lepetz, Sébastien; Mashkour, Marjan; Ludwig, Arne; Wallner, Barbara; Merz, Victor; Merz, Ilja; Zaibert, Viktor; Willerslev, Eske; Librado, Pablo; Outram, Alan K; Orlando, Ludovic

    2018-04-06

    The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  20. Prediction of breast cancer risk based on common genetic variants in women of East Asian ancestry.

    Science.gov (United States)

    Wen, Wanqing; Shu, Xiao-Ou; Guo, Xingyi; Cai, Qiuyin; Long, Jirong; Bolla, Manjeet K; Michailidou, Kyriaki; Dennis, Joe; Wang, Qin; Gao, Yu-Tang; Zheng, Ying; Dunning, Alison M; García-Closas, Montserrat; Brennan, Paul; Chen, Shou-Tung; Choi, Ji-Yeob; Hartman, Mikael; Ito, Hidemi; Lophatananon, Artitaya; Matsuo, Keitaro; Miao, Hui; Muir, Kenneth; Sangrajrang, Suleeporn; Shen, Chen-Yang; Teo, Soo H; Tseng, Chiu-Chen; Wu, Anna H; Yip, Cheng Har; Simard, Jacques; Pharoah, Paul D P; Hall, Per; Kang, Daehee; Xiang, Yongbing; Easton, Douglas F; Zheng, Wei

    2016-12-08

    Approximately 100 common breast cancer susceptibility alleles have been identified in genome-wide association studies (GWAS). The utility of these variants in breast cancer risk prediction models has not been evaluated adequately in women of Asian ancestry. We evaluated 88 breast cancer risk variants that were identified previously by GWAS in 11,760 cases and 11,612 controls of Asian ancestry. SNPs confirmed to be associated with breast cancer risk in Asian women were used to construct a polygenic risk score (PRS). The relative and absolute risks of breast cancer by the PRS percentiles were estimated based on the PRS distribution, and were used to stratify women into different levels of breast cancer risk. We confirmed significant associations with breast cancer risk for SNPs in 44 of the 78 previously reported loci at P women in the middle quintile of the PRS, women in the top 1% group had a 2.70-fold elevated risk of breast cancer (95% CI: 2.15-3.40). The risk prediction model with the PRS had an area under the receiver operating characteristic curve of 0.606. The lifetime risk of breast cancer for Shanghai Chinese women in the lowest and highest 1% of the PRS was 1.35% and 10.06%, respectively. Approximately one-half of GWAS-identified breast cancer risk variants can be directly replicated in East Asian women. Collectively, common genetic variants are important predictors for breast cancer risk. Using common genetic variants for breast cancer could help identify women at high risk of breast cancer.

  1. The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States

    Science.gov (United States)

    Bryc, Katarzyna; Durand, Eric Y.; Macpherson, J. Michael; Reich, David; Mountain, Joanna L.

    2015-01-01

    Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry. PMID:25529636

  2. The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand.

    Science.gov (United States)

    Veale, Andrew J; Russell, James C; King, Carolyn M

    2018-01-01

    The house mouse ( Mus musculus ) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus . We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city-Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2-3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7-8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry-though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.

  3. Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

    Science.gov (United States)

    Decker, Jared E.; McKay, Stephanie D.; Rolf, Megan M.; Kim, JaeWoo; Molina Alcalá, Antonio; Sonstegard, Tad S.; Hanotte, Olivier; Götherström, Anders; Seabury, Christopher M.; Praharani, Lisa; Babar, Masroor Ellahi; Correia de Almeida Regitano, Luciana; Yildiz, Mehmet Ali; Heaton, Michael P.; Liu, Wan-Sheng; Lei, Chu-Zhao; Reecy, James M.; Saif-Ur-Rehman, Muhammad; Schnabel, Robert D.; Taylor, Jeremy F.

    2014-01-01

    The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation. PMID:24675901

  4. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

    Energy Technology Data Exchange (ETDEWEB)

    Schellenberger, Pascale [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Kaufmann, Rainer [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Siebert, C. Alistair; Hagen, Christoph [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Wodrich, Harald [Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux (France); Grünewald, Kay, E-mail: kay@strubi.ox.ac.uk [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2014-08-01

    Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm.

  5. Correlation of diffusion and perfusion MRI with Ki-67 in high-grade meningiomas.

    Science.gov (United States)

    Ginat, Daniel T; Mangla, Rajiv; Yeaney, Gabrielle; Wang, Henry Z

    2010-12-01

    Atypical and anaplastic meningiomas have a greater likelihood of recurrence than benign meningiomas. The risk for recurrence is often estimated using the Ki-67 labeling index. The purpose of this study was to determine the correlation between Ki-67 and regional cerebral blood volume (rCBV) and between Ki-67 and apparent diffusion coefficient (ADC) in atypical and anaplastic meningiomas. A retrospective review of the advanced imaging and immunohistochemical characteristics of atypical and anaplastic meningiomas was performed. The relative minimum ADC, relative maximum rCBV, and specimen Ki-67 index were measured. Pearson's correlation was used to compare these parameters. There were 23 cases with available ADC maps and 20 cases with available rCBV maps. The average Ki-67 among the cases with ADC maps and rCBV maps was 17.6% (range, 5-38%) and 16.7% (range, 3-38%), respectively. The mean minimum ADC ratio was 0.91 (SD, 0.26) and the mean maximum rCBV ratio was 22.5 (SD, 7.9). There was a significant positive correlation between maximum rCBV and Ki-67 (Pearson's correlation, 0.69; p = 0.00038). However, there was no significant correlation between minimum ADC and Ki-67 (Pearson's correlation, -0.051; p = 0.70). Maximum rCBV correlated significantly with Ki-67 in high-grade meningiomas.

  6. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

    International Nuclear Information System (INIS)

    Schellenberger, Pascale; Kaufmann, Rainer; Siebert, C. Alistair; Hagen, Christoph; Wodrich, Harald; Grünewald, Kay

    2014-01-01

    Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm

  7. Effect of Genetic African Ancestry on eGFR and Kidney Disease

    Science.gov (United States)

    Nadkarni, Girish N.; Belbin, Gillian; Lotay, Vaneet; Wyatt, Christina; Gottesman, Omri; Bottinger, Erwin P.; Kenny, Eimear E.; Peter, Inga

    2015-01-01

    Self-reported ancestry, genetically determined ancestry, and APOL1 polymorphisms are associated with variation in kidney function and related disease risk, but the relative importance of these factors remains unclear. We estimated the global proportion of African ancestry for 9048 individuals at Mount Sinai Medical Center in Manhattan (3189 African Americans, 1721 European Americans, and 4138 Hispanic/Latino Americans by self-report) using genome-wide genotype data. CKD-EPI eGFR and genotypes of three APOL1 coding variants were available. In admixed African Americans and Hispanic/Latino Americans, serum creatinine values increased as African ancestry increased (per 10% increase in African ancestry, creatinine values increased 1% in African Americans and 0.9% in Hispanic/Latino Americans; P≤1x10−7). eGFR was likewise significantly associated with African genetic ancestry in both populations. In contrast, APOL1 risk haplotypes were significantly associated with CKD, eGFRblack on the basis of ≥50% African ancestry resulted in higher eGFR for 14.7% of Hispanic/Latino Americans and lower eGFR for 4.1% of African Americans, affecting CKD staging in 4.3% and 1% of participants, respectively. Reclassified individuals had electrolyte values consistent with their newly assigned CKD stage. In summary, proportion of African ancestry was significantly associated with normal-range creatinine and eGFR, whereas APOL1 risk haplotypes drove the associations with CKD. Recalculation of eGFR on the basis of genetic ancestry affected CKD staging and warrants additional investigation. PMID:25349204

  8. High-speed holographic correlation system for video identification on the internet

    Science.gov (United States)

    Watanabe, Eriko; Ikeda, Kanami; Kodate, Kashiko

    2013-12-01

    Automatic video identification is important for indexing, search purposes, and removing illegal material on the Internet. By combining a high-speed correlation engine and web-scanning technology, we developed the Fast Recognition Correlation system (FReCs), a video identification system for the Internet. FReCs is an application thatsearches through a number of websites with user-generated content (UGC) and detects video content that violates copyright law. In this paper, we describe the FReCs configuration and an approach to investigating UGC websites using FReCs. The paper also illustrates the combination of FReCs with an optical correlation system, which is capable of easily replacing a digital authorization sever in FReCs with optical correlation.

  9. High correlation between performance on a virtual-reality simulator and real-life cataract surgery

    DEFF Research Database (Denmark)

    Thomsen, Ann Sofia Skou; Smith, Phillip; Subhi, Yousif

    2017-01-01

    -tracking software of cataract surgical videos with a Pearson correlation coefficient of -0.70 (p = 0.017). CONCLUSION: Performance on the EyeSi simulator is significantly and highly correlated to real-life surgical performance. However, it is recommended that performance assessments are made using multiple data......PURPOSE: To investigate the correlation in performance of cataract surgery between a virtual-reality simulator and real-life surgery using two objective assessment tools with evidence of validity. METHODS: Cataract surgeons with varying levels of experience were included in the study. All...... antitremor training, forceps training, bimanual training, capsulorhexis and phaco divide and conquer. RESULTS: Eleven surgeons were enrolled. After a designated warm-up period, the proficiency-based test on the EyeSi simulator was strongly correlated to real-life performance measured by motion...

  10. Correlation between Substance Use and Anxiety-Depression Spectrum among Senior High School Students in Bandung

    Directory of Open Access Journals (Sweden)

    Achmad Samjunanto

    2016-12-01

    Full Text Available Background: Both substance use and anxiety-depression spectrum are the problem that currently faced by adolescents especially among Senior High School students. Moreover, there is a high comorbidity between both problems. This study was conducted to discover the substance use’s prevalence and to find out anxiety-depression spectrum proportion among adolescent, and more importantly to determine whether there is correlation between both variables. Methods: During October–November 2013, four hundred and fifty two students from five Senior High Schools located in Karees Sub-District, Bandung were included in this cross-sectional analytic study. Among whom, only 425 students filled the questionnaire properly. Data were collected using Kessler-10 (K10 to explore anxiety-depression spectrum and addiction severity index lite version (ASI-Lite to identify substance use. The correlation between both variables was analyzed by Gamma correlation test. Results: The study revealed that there were 93 (21.9% students that used substance. In addition, there were 244 students (57.4% that screened as having anxiety-depression spectrum. Statistical analysis, according to Gamma correlation test, showed that there was a weak correlation between alcohol use and anxiety-depression spectrum (p=0.041; r=0.316. The remaining substances gave no statistically significant result (p>0.05. Conclusions: There is a high prevalence in substance use and psychological distress in anxiety-depression spectrum among high school student. In addition, alcohol is the only substances that correlated with anxiety-depression spectrum.

  11. Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity

    International Nuclear Information System (INIS)

    Schorb, Martin; Briggs, John A.G.

    2014-01-01

    Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals. - Highlights: • Workflow for correlated cryo-fluorescence and cryo-electron microscopy. • Cryo-fluorescence microscopy setup incorporating a high numerical aperture objective. • Fluorescent signals located in cryo-electron micrographs with 50 nm spatial precision

  12. Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Schorb, Martin [Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany); Briggs, John A.G., E-mail: john.briggs@embl.de [Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany); Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany)

    2014-08-01

    Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals. - Highlights: • Workflow for correlated cryo-fluorescence and cryo-electron microscopy. • Cryo-fluorescence microscopy setup incorporating a high numerical aperture objective. • Fluorescent signals located in cryo-electron micrographs with 50 nm spatial precision.

  13. Analysis of potential protein-modifying variants in 9000 endometriosis patients and 150000 controls of European ancestry

    DEFF Research Database (Denmark)

    Sapkota, Yadav; Vivo, Immaculata De; Steinthorsdottir, Valgerdur

    2017-01-01

    -modifying variants in endometriosis using exome-array genotyping in 7164 cases and 21005 controls, and a replication set of 1840 cases and 129016 controls of European ancestry. Results in the discovery sample identified significant evidence for association with coding variants in single-variant (rs1801232-CUBN...... sufficient power, our results did not identify any protein-modifying variants (MAF > 0.01) with moderate or large effect sizes in endometriosis, although these variants may exist in non-European populations or in high-risk families. The results suggest continued discovery efforts should focus on genotyping...

  14. CGC/saturation approach for soft interactions at high energy: long range rapidity correlations

    Energy Technology Data Exchange (ETDEWEB)

    Gotsman, E.; Maor, U. [Tel Aviv University, Department of Particle Physics, School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv (Israel); Levin, E. [Tel Aviv University, Department of Particle Physics, School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv (Israel); Universidad Tecnica Federico Santa Maria and Centro Cientifico- Tecnologico de Valparaiso, Departemento de Fisica, Valparaiso (Chile)

    2015-11-15

    In this paper we continue our program to construct a model for high energy soft interactions that is based on the CGC/saturation approach. The main result of this paper is that we have discovered a mechanism that leads to large long range rapidity correlations and results in large values of the correlation function R(y{sub 1}, y{sub 2}) ≥ 1, which is independent of y{sub 1} and y{sub 2}. Such a behavior of the correlation function provides strong support for the idea that at high energies the system of partons that is produced is not only dense but also has strong attractive forces acting between the partons. (orig.)

  15. Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

    Science.gov (United States)

    Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Zaitlen, Noah; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Chen, Gary K.; Le Marchand, Loic; Henderson, Brian; Reich, David; Haiman, Christopher A.; Gonzàlez Burchard, Esteban; Halperin, Eran

    2013-01-01

    Motivation: Local ancestry analysis of genotype data from recently admixed populations (e.g. Latinos, African Americans) provides key insights into population history and disease genetics. Although methods for local ancestry inference have been extensively validated in simulations (under many unrealistic assumptions), no empirical study of local ancestry accuracy in Latinos exists to date. Hence, interpreting findings that rely on local ancestry in Latinos is challenging. Results: Here, we use 489 nuclear families from the mainland USA, Puerto Rico and Mexico in conjunction with 3204 unrelated Latinos from the Multiethnic Cohort study to provide the first empirical characterization of local ancestry inference accuracy in Latinos. Our approach for identifying errors does not rely on simulations but on the observation that local ancestry in families follows Mendelian inheritance. We measure the rate of local ancestry assignments that lead to Mendelian inconsistencies in local ancestry in trios (MILANC), which provides a lower bound on errors in the local ancestry estimates. We show that MILANC rates observed in simulations underestimate the rate observed in real data, and that MILANC varies substantially across the genome. Second, across a wide range of methods, we observe that loci with large deviations in local ancestry also show enrichment in MILANC rates. Therefore, local ancestry estimates at such loci should be interpreted with caution. Finally, we reconstruct ancestral haplotype panels to be used as reference panels in local ancestry inference and show that ancestry inference is significantly improved by incoroprating these reference panels. Availability and implementation: We provide the reconstructed reference panels together with the maps of MILANC rates as a public resource for researchers analyzing local ancestry in Latinos at http://bogdanlab.pathology.ucla.edu. Contact: bpasaniuc@mednet.ucla.edu Supplementary information: Supplementary data are

  16. What Aspects of Principal Leadership Are Most Highly Correlated with School Outcomes in China?

    Science.gov (United States)

    Zheng, Qiao; Li, Lingyan; Chen, Huijuan; Loeb, Susanna

    2017-01-01

    Purpose: The purpose of this study is to build a broader framework for Chinese principal leadership and to determine what aspects of principal leadership correlate most highly with school outcomes from the perspectives of both principals and teachers. Method: The data come from a 2013 national student achievement assessment in China comprising…

  17. Correlation between X-ray and high energy gamma-ray emission form Cygnus X-3

    International Nuclear Information System (INIS)

    Weekes, T.C.; Danaher, S.; Fegan, D.J.; Porter, N.A.

    1981-01-01

    In May-June 1980, the 4.8 hour modulated X-ray flux from Cygnus X-3 underwent a significant change in the shape of the light curve; this change correlates with the peak in the high-energy (E > 2 x 10 12 eV) gamma ray emission at the same epoch. (orig.)

  18. High temperature limit of the order parameter correlation functions in the quantum Ising model

    Science.gov (United States)

    Reyes, S. A.; Tsvelik, A. M.

    2006-06-01

    In this paper we use the exact results for the anisotropic two-dimensional Ising model obtained by Bugrii and Lisovyy [A.I. Bugrii, O.O. Lisovyy, Theor. Math. Phys. 140 (2004) 987] to derive the expressions for dynamical correlation functions for the quantum Ising model in one dimension at high temperatures.

  19. High temperature limit of the order parameter correlation functions in the quantum Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Reyes, S.A. [Department of Physics and Astronomy, SUNY at Stony Brook, Stony Brook, NY 11794-3840 (United States); Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Tsvelik, A.M. [Department of Physics and Astronomy, SUNY at Stony Brook, Stony Brook, NY 11794-3840 (United States) and Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)]. E-mail tsvelik@bnl.gov

    2006-06-12

    In this paper we use the exact results for the anisotropic two-dimensional Ising model obtained by Bugrii and Lisovyy [A.I. Bugrii, O.O. Lisovyy, Theor. Math. Phys. 140 (2004) 987] to derive the expressions for dynamical correlation functions for the quantum Ising model in one dimension at high temperatures.

  20. Bronchiectasis: correlation of high-resolution CT findings with health-related quality of life

    Energy Technology Data Exchange (ETDEWEB)

    Eshed, I. [Department of Diagnostic Radiology, E. Wolfson Medical Center, Holon (Israel)]. E-mail: iriseshed@gmail.com; Minski, I. [Department of Diagnostic Radiology, E. Wolfson Medical Center, Holon (Israel); Katz, R. [Department of Diagnostic Radiology, E. Wolfson Medical Center, Holon (Israel); Jones, P.W. [Department of Respiratory Medicine, St George' s Hospital Medical School, University of London (United Kingdom); Priel, I.E. [Department of Pulmonary Medicine, E. Wolfson Medical Center, Holon, Israel, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University (Israel)

    2007-02-15

    Aim: To evaluate the relationship between the severity of bronchiectatic diseases, as evident on high-resolution computed tomography (HRCT) and the patient's quality of life measured using the St George's Respiratory Questionnaire (SGRQ). Methods and materials: Forty-six patients (25 women, 21 men, mean age: 63 years) with bronchiectatic disease as evident on recent HRCT examinations were recruited. Each patient completed the SGRQ and underwent respiratory function tests. HRCT findings were blindly and independently scored by two radiologists, using the modified Bhalla scoring system. The relationships between HRCT scores, SGRQ scores and pulmonary function tests were evaluated. Results: The patients' total CT score did not correlate with the SGRQ scores. However, patients with more advanced disease on HRCT, significantly differed in their SGRQ scores from patients with milder bronchiectatic disease. A significant correlation was found between the CT scores for the middle and distal lung zones and the activity, impacts and total SGRQ scores. No correlation was found between CT scores and respiratory function test indices. However, a significant correlation was found between the SGRQ scores and most of the respiratory function test indices. Conclusion: A correlation between the severity of bronchiectatic disease as expressed in HRCT and the health-related quality of life exists in patients with a more severe bronchiectatic disease but not in patients with mild disease. Such correlation depends on the location of the bronchiectasis in the pulmonary tree.

  1. Correlation between Substance Use and Anxiety-Depression Spectrum among Senior High School Students in Bandung

    OpenAIRE

    Achmad Samjunanto; Lucky Saputra; RA. Retno Ekowati

    2016-01-01

    Background: Both substance use and anxiety-depression spectrum are the problem that currently faced by adolescents especially among Senior High School students. Moreover, there is a high comorbidity between both problems. This study was conducted to discover the substance use’s prevalence and to find out anxiety-depression spectrum proportion among adolescent, and more importantly to determine whether there is correlation between both variables. Methods: During October–November 2013, four...

  2. Electron-$\\gamma$ - perturbed angular correlation studies on high-T$_{C}$ superconductors

    CERN Document Server

    Correia, J G; Marques, J G; Ramos, A R; Lourenço, A A; Amaral, V S; Galindo, V; Senateur, J P; Weiss, F; Wahl, U; Melo, A A; Soares, J C; Sousa, J B

    2000-01-01

    Recent results on the study of high-T$_{c}$ superconductors using the e$^-\\!-\\gamma$ perturbed angular correlation technique are presented. The basic features of the experimental equipment and its installation at the ISOLDE facility are briefly described. Results obtained from $^{197m}$Hg implanted into high quality Y$_{1}$Ba$_{2}$Cu$_{3}$O$_{6+\\delta}$ epitaxy thin films are presented and discussed.

  3. Electron-gamma perturbed angular correlation studies on high-TC superconductors

    International Nuclear Information System (INIS)

    Correia, J.G.; Araujo, J.P.; Marques, J.G.; Ramos, A.R.; Lourenco, A.A.; Amaral, V.; Galindo, V.; Senateur, J.P.; Weiss, F.; Wahl, U.; Melo, A.A.; Soares, J.C.; Sousa, J.B.

    2000-01-01

    Recent results on the study of high-T C superconductors using the e - -γperturbed angular correlation technique are presented. The basic features of the experimental equipment and its installation at the ISOLDE facility are briefly described. Results obtained from 197m Hg implanted into high quality Y 1 Ba 2 Cu 3 O 6+δ epitaxy thin films are presented and discussed

  4. Cognitive Changes during Prolonged Stay at High Altitude and Its Correlation with C-Reactive Protein.

    Directory of Open Access Journals (Sweden)

    Sheng Li Hu

    Full Text Available Hypersensitive C-reaction protein (hsCRP may be a risk factor for cognitive impairment resulting from Alzheimer's disease (AD, stroke, and vascular dementia. This study explored the correlation of peripheral blood hsCRP level with cognitive decline due to high altitude exposure. The study was conducted on 100 male military participants who had never been to high altitude. Cerebral oxygen saturation monitoring, event related potentials (P300, N200 detection, and neurocognitive assessment was performed and total hsCRP, interleukin-6 (IL-6, and homocysteine was estimated at 500 m altitude, 3650 m altitude, 3 day, 1, and 3 month post arriving at the base camp (4400 m, and 1 month after coming back to the 500 m altitude. High altitude increased brain oxygen saturation, prolonged P300 and N200 latencies, injured cognitive functions, and raised plasma hsCRP levels. But they all recovered in varying degrees at 1 and 3 month post arriving at the base camp (4400 m. P300 latencies and hsCRP levels were strongly correlated to cognitive performances. These results suggested that cognitive deterioration occurred during the acute period of exposure to high altitude and may recover probably owning to acclimatization after extended stay at high altitude. Plasma hsCRP is inversely correlated to neurological cognition and it may be a potential biomarker for the prediction of high altitude induced cognitive dysfunction.

  5. From Coherently Excited Highly Correlated States to Incoherent Relaxation Processes in Semiconductors

    International Nuclear Information System (INIS)

    Scha''fer, W.; Lo''venich, R.; Fromer, N. A.; Chemla, D. S.

    2001-01-01

    Recent theories of highly excited semiconductors are based on two formalisms, referring to complementary experimental conditions, the real-time nonequilibrium Green's function techniques and the coherently controlled truncation of the many-particle problem. We present a novel many-particle theory containing both of these methods as limiting cases. As a first example of its application, we investigate four-particle correlations in a strong magnetic field including dephasing resulting from the growth of incoherent one-particle distribution functions. Our results are the first rigorous solution concerning formation and decay of four-particle correlations in semiconductors. They are in excellent agreement with experimental data

  6. Correlated double electron capture in slow, highly charged ion-atom collisions

    Energy Technology Data Exchange (ETDEWEB)

    Stolterfoht, N.; Havener, C.C.; Phaneuf, R.A.; Swenson, J.K.; Shafroth, S.M.; Meyer, F.W.

    1986-01-01

    Recent measurements of autoionization electrons produced in slow, highly charged ion-atom collisions are reviewed. Mechanisms for double electron capture into equivalent and nonequivalent configurations are analyzed by comparing the probabilities for the creation of L/sub 1/L/sub 23/X Coster Kronig electrons and L-Auger electrons. It is shown that the production of the Coster-Kronig electrons is due to electron correlation effects whose analysis leads beyond the independent-particle model. The importance of correlation effects on different capture mechanisms is discussed. 28 refs., 6 figs.

  7. Correlated double electron capture in slow, highly charged ion-atom collisions

    International Nuclear Information System (INIS)

    Stolterfoht, N.; Havener, C.C.; Phaneuf, R.A.; Swenson, J.K.; Shafroth, S.M.; Meyer, F.W.

    1986-01-01

    Recent measurements of autoionization electrons produced in slow, highly charged ion-atom collisions are reviewed. Mechanisms for double electron capture into equivalent and nonequivalent configurations are analyzed by comparing the probabilities for the creation of L 1 L 23 X Coster Kronig electrons and L-Auger electrons. It is shown that the production of the Coster-Kronig electrons is due to electron correlation effects whose analysis leads beyond the independent-particle model. The importance of correlation effects on different capture mechanisms is discussed. 28 refs., 6 figs

  8. Searching for squeezed particle-antiparticle correlations in high-energy heavy-ion collisions

    International Nuclear Information System (INIS)

    Padula, Sandra S.; Socolowski, O. Jr.

    2010-01-01

    Squeezed correlations of particle-antiparticle pairs were predicted to exist if the hadron masses were modified in the hot and dense medium formed in high-energy heavy-ion collisions. Although well-established theoretically, they have not yet been observed experimentally. We suggest here a clear method to search for such a signal by analyzing the squeezed correlation functions in terms of measurable quantities. We illustrate this suggestion for simulated φφ pairs at the Relativistic Heavy Ion Collider (RHIC) energies.

  9. High $p_T$ particle correlations in pp collisions at LHC/ALICE

    CERN Document Server

    Mao, Yaxian

    2011-01-01

    Two-particle correlation triggered by high-\\pt{} particles allows us to study hard scattering phenomena when full jet reconstruction is challenging. An analysis of the first ALICE pp data where charged and neutral particles isolated or not are used as trigger particles is presented. The two-particle correlation between the trigger ($t$) and the associate ($a$) particles is studied as a function of the imbalance parameter \\xe=-$\\vec{p}_{T_{a}} \\cdot \\vec{p}_{T_{t}}/\\mid \\vec{p}_{T_{t}}\\mid ^{2}$ and interpreted in terms of jet fragmentation function.

  10. Native American Ancestry Affects the Risk for Gene Methylation in the Lungs of Hispanic Smokers from New Mexico

    Science.gov (United States)

    Liu, Yushi; Thomas, Cynthia L.; Gauderman, W. James; Picchi, Maria A.; Bruse, Shannon E.; Zhang, Xiequn; Flores, Kristina G.; Van Den Berg, David; Stidley, Christine A.; Gilliland, Frank D.

    2013-01-01

    Rationale: Gene promoter methylation detected in sputum predicts lung cancer risk in smokers. Compared with non-Hispanic whites (NHW), Hispanics have a lower age-standardized incidence for lung cancer. Objectives: This study compared the methylation prevalence in sputum of NHWs with Hispanics using the Lovelace Smokers cohort (n = 1998) and evaluated the effect of Native American ancestry (NAA) and diet on biomarkers for lung cancer risk. Methods: Genetic ancestry was estimated using 48 ancestry markers. Diet was assessed by the Harvard University Dietary Assessment questionnaire. Methylation of 12 genes was measured in sputum using methylation-specific polymerase chain reaction. The association between NAA and risk for methylation was assessed using generalized estimating equations. The ethnic difference in the association between pack-years and risk for lung cancer was assessed in the New Mexico lung cancer study. Measurements and Main Results: Overall Hispanics had a significantly increased risk for methylation across the 12 genes analyzed (odds ratio, 1.18; P = 0.007). However, the risk was reduced by 32% (P = 0.032) in Hispanics with high versus low NAA. In the New Mexico lung cancer study, Hispanic non–small cell lung cancer cases have significantly lower pack-years than NHW counterparts (P = 0.007). Furthermore, compared with NHW smokers, Hispanic smokers had a more rapidly increasing risk for lung cancer as a function of pack-years (P = 0.058). Conclusions: NAA may be an important risk modifier for methylation in Hispanic smokers. Smoking intensity may have a greater impact on risk for lung cancer in Hispanics compared with NHWs. PMID:24032348

  11. What role does African ancestry play in how hypertensive patients respond to certain antihypertensive drug therapy?

    Science.gov (United States)

    Seedat, Yackoob K; Brewster, Lizzy M

    2014-02-01

    This article is a summary of the response of the four commonly used antihypertensive agents in African ancestry patients. They are thiazide like diuretics or indapamide, calcium channel blockers (CCB), angiotensin converting enzyme inhibitors (ACEI) or angiotensin receptor blockers, and β-adrenergic blockers (ARB). Response was superior in African ancestry patients on a thiazide like diuretic or indapamide and CCB, while the response to β-adrenergic blockers and ACEI are attenuated. Available data are very limited but self-defined ancestry seems to be the best predictor of individual responses to antihypertensive drugs. Knowledge of the factors like economic and social consideration affect the lower rate of detection, treatment and control of hypertension in the African ancestry population of the USA. For regions in which health care resources are particularly scarce, investment in population-based primary prevention strategies may yield the largest benefit.

  12. Impact of ancestry and body size on sonographic ulnar nerve dimensions

    International Nuclear Information System (INIS)

    Childs, Jessie T.; Phillips, Maureen; Thoirs, Kerry A.

    2012-01-01

    Introduction: The purpose of this study was to investigate the impact that geographic ancestry and body size have on ultrasonographic measurements of the ulnar nerve size measured at the elbow. Materials and methods: We performed anthropometric measurements of body size and ultrasonographic measurements of the ulnar nerve at the elbow on 13 Vietnamese and 24 European participants. Regression analysis was used to determine the effect of body size and geographic ancestry on ulnar nerve size. Results: BMI had the greatest impact on ulnar nerve size. The short axis diameter was least resilient, and the long axis diameter was the most resilient to the effects of body size and geographic ancestry. Discussion: The long axis diameter has an apparent immunity to the influences of overall body size, arm size, or geographic ancestry and has the most potential as a sensitive discriminator between normal nerves and nerves affected by ulnar neuropathy at the elbow.

  13. Genetic ancestry analysis in non-alcoholic fatty liver disease patients from Brazil and Portugal.

    Science.gov (United States)

    Cavalcante, Lourianne Nascimento; Stefano, Jose Tadeu; Machado, Mariana V; Mazo, Daniel F; Rabelo, Fabiola; Sandes, Kiyoko Abe; Carrilho, Flair José; Cortez-Pinto, Helena; Lyra, Andre Castro; de Oliveira, Claudia P

    2015-06-08

    To study the association between genetic ancestry, non-alcoholic fatty liver disease (NAFLD) metabolic characteristics in two cohorts of patients, from Brazil and Portugal. We included 131 subjects from Brazil [(n = 45 with simple steatosis (S. Steatosis) and n = 86 with nonalcoholic steatohepatitis (NASH)] and 90 patients from Portugal (n = 66, S. Steatosis; n = 24, NASH). All patients had biopsy-proven NAFLD. In histologic evaluation NAFLD activity score was used to assess histology and more than 5 points defined NASH in this study. Patients were divided into two groups according to histology diagnosis: simple steatosis or non-alcoholic statohepatitis. Genetic ancestry was assessed using real-time polymerase chain reaction. Seven ancestry informative markers (AT3-I/D, LPL, Sb19.3, APO, FY-Null, PV92, and CKMM) with the greatest ethnic-geographical differential frequencies (≥ 48%) were used to define genetic ancestry. Data were analyzed using R PROJECTS software. Ancestry allele frequencies between groups were analyzed by GENEPOP online and the estimation of genetic ancestry contribution was evaluated by ADMIX-95 software. The 5% alpha-error was considered as significant (P 2.5 [NASH 5.3 (70.8%) vs S. Steatosis 4.6 (29.2%) P = 0.04]. In the Portuguese study population, dyslipidemia was present in all patients with NASH (P = 0.03) and hypertension was present in a larger percentage of subjects in the S. Steatosis group (P = 0.003, respectively). The genetic ancestry contribution among Brazilian and Portuguese individuals with NASH was similar to those with S. Steatosis from each cohort (Brazilian cohort: P = 0.75; Portuguese cohort: P = 0.97). Nonetheless, the genetic ancestry contribution of the Brazilian and Portuguese population were different, and a greater European and Amerindian ancestry contribution was detected in the Portuguese population while a higher African genetic ancestry contribution was observed in Brazilian population of both NASH and S

  14. Genetic ancestry analysis in non-alcoholic fatty liver disease patients from Brazil and Portugal

    Science.gov (United States)

    Cavalcante, Lourianne Nascimento; Stefano, Jose Tadeu; Machado, Mariana V; Mazo, Daniel F; Rabelo, Fabiola; Sandes, Kiyoko Abe; Carrilho, Flair José; Cortez-Pinto, Helena; Lyra, Andre Castro; de Oliveira, Claudia P

    2015-01-01

    AIM: To study the association between genetic ancestry, non-alcoholic fatty liver disease (NAFLD) metabolic characteristics in two cohorts of patients, from Brazil and Portugal. METHODS: We included 131 subjects from Brazil [(n = 45 with simple steatosis (S. Steatosis) and n = 86 with nonalcoholic steatohepatitis (NASH)] and 90 patients from Portugal (n = 66, S. Steatosis; n = 24, NASH). All patients had biopsy-proven NAFLD. In histologic evaluation NAFLD activity score was used to assess histology and more than 5 points defined NASH in this study. Patients were divided into two groups according to histology diagnosis: simple steatosis or non-alcoholic statohepatitis. Genetic ancestry was assessed using real-time polymerase chain reaction. Seven ancestry informative markers (AT3-I/D, LPL, Sb19.3, APO, FY-Null, PV92, and CKMM) with the greatest ethnic-geographical differential frequencies (≥ 48%) were used to define genetic ancestry. Data were analyzed using R PROJECTS software. Ancestry allele frequencies between groups were analyzed by GENEPOP online and the estimation of genetic ancestry contribution was evaluated by ADMIX-95 software. The 5% alpha-error was considered as significant (P 2.5 [NASH 5.3 (70.8%) vs S. Steatosis 4.6 (29.2%) P = 0.04]. In the Portuguese study population, dyslipidemia was present in all patients with NASH (P = 0.03) and hypertension was present in a larger percentage of subjects in the S. Steatosis group (P = 0.003, respectively). The genetic ancestry contribution among Brazilian and Portuguese individuals with NASH was similar to those with S. Steatosis from each cohort (Brazilian cohort: P = 0.75; Portuguese cohort: P = 0.97). Nonetheless, the genetic ancestry contribution of the Brazilian and Portuguese population were different, and a greater European and Amerindian ancestry contribution was detected in the Portuguese population while a higher African genetic ancestry contribution was observed in Brazilian population of both NASH

  15. Rate-adaptive BCH coding for Slepian-Wolf coding of highly correlated sources

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Salmistraro, Matteo; Larsen, Knud J.

    2012-01-01

    This paper considers using BCH codes for distributed source coding using feedback. The focus is on coding using short block lengths for a binary source, X, having a high correlation between each symbol to be coded and a side information, Y, such that the marginal probability of each symbol, Xi in X......, given Y is highly skewed. In the analysis, noiseless feedback and noiseless communication are assumed. A rate-adaptive BCH code is presented and applied to distributed source coding. Simulation results for a fixed error probability show that rate-adaptive BCH achieves better performance than LDPCA (Low......-Density Parity-Check Accumulate) codes for high correlation between source symbols and the side information....

  16. Does Chicago Classification address Symptom Correlation with High-resolution Esophageal Manometry?

    Science.gov (United States)

    Jain, Mayank; Srinivas, Melpakkam; Bawane, Piyush; Venkataraman, Jayanthi

    2017-01-01

    To assess the correlation of symptoms with findings on esophageal high-resolution manometry (HRM) in Indian patients. Prospective data collection of all patients undergoing esophageal manometry was done at two centers in India-Indore and Chennai-over a period of 18 months. Symptom profile of the study group was divided into four: Motor dysphagia, noncardiac chest pain (NCCP), gastroesophageal reflux (GER), and esophageal belchers. The symptoms were correlated with manometric findings. Of the study group (154), 35.71% patients had a normal study, while major and minor peristaltic disorders were noted in 31.16 and 33.76% respectively. In patients with symptoms of dysphagia, achalasia cardia was the commonest cause (45.1%), followed by ineffective esophageal motility (IEM) (22.53%) and normal study (19.71%). In patients with NCCP, normal peristalsis (50%) and ineffective motility (31.25%) formed the major diagnosis. Of the 56 patients with GER symptoms, 26 (46.4%) had normal manometry. An equal number had ineffective motility. Of the 11 esophageal belchers, 7 (63.6%) of these had a normal study and 3 had major motility disorder. Dysphagia was the only symptom to have a high likelihood ratio and positive predictive value to pick up major motility disorder. Dysphagia correlates with high chance to pick up a major peristaltic abnormality in motor dysphagia. The role of manometry in other symptoms in Indian setting needs to be ascertained by larger studies. The present study highlights lack of symptom correlation with manometry findings in Indian patients. How to cite this article: Jain M, Srinivas M, Bawane P, Venkataraman J. Does Chicago Classification address Symptom Correlation with High-resolution Esophageal Manometry? Euroasian J Hepato-Gastroenterol 2017;7(2):122-125.

  17. Correlating the Ancient Maya and Modern European Calendars with High-Precision AMS 14C Dating

    Science.gov (United States)

    Kennett, Douglas J.; Hajdas, Irka; Culleton, Brendan J.; Belmecheri, Soumaya; Martin, Simon; Neff, Hector; Awe, Jaime; Graham, Heather V.; Freeman, Katherine H.; Newsom, Lee; Lentz, David L.; Anselmetti, Flavio S.; Robinson, Mark; Marwan, Norbert; Southon, John; Hodell, David A.; Haug, Gerald H.

    2013-04-01

    The reasons for the development and collapse of Maya civilization remain controversial and historical events carved on stone monuments throughout this region provide a remarkable source of data about the rise and fall of these complex polities. Use of these records depends on correlating the Maya and European calendars so that they can be compared with climate and environmental datasets. Correlation constants can vary up to 1000 years and remain controversial. We report a series of high-resolution AMS 14C dates on a wooden lintel collected from the Classic Period city of Tikal bearing Maya calendar dates. The radiocarbon dates were calibrated using a Bayesian statistical model and indicate that the dates were carved on the lintel between AD 658-696. This strongly supports the Goodman-Martínez-Thompson (GMT) correlation and the hypothesis that climate change played an important role in the development and demise of this complex civilization.

  18. Static correlation lengths in QCD at high temperatures and finite densities

    CERN Document Server

    Hart, A; Philipsen, O

    2000-01-01

    We use a perturbatively derived effective field theory and three-dimensional lattice simulations to determine the longest static correlation lengths in the deconfined QCD plasma phase at high temperatures (T\\gsim 2 Tc) and finite densities (\\mu\\lsim 4 T). For vanishing chemical potential, we refine a previous determination of the Debye screening length, and determine the dependence of different correlation lengths on the number of massless flavours as well as on the number of colours. For non-vanishing but small chemical potential, the existence of Debye screening allows us to carry out simulations corresponding to the full QCD with two (or three) massless dynamical flavours, in spite of a complex action. We investigate how the correlation lengths in the different quantum number channels change as the chemical potential is switched on.

  19. Charge- and transverse momentum dependence of correlations in proton-proton interactions at very high energies

    International Nuclear Information System (INIS)

    Hofmann, W.

    1977-07-01

    The charge- and momentum dependence of correlations between secondaries emitted in pp-collisions at √s = 52 GeV was investigated using the Split-Field-Magnet spectrometer at the CERN Intersecting Storage Rings (ISR). For nondiffractive inelastic events the central particle production is characterized by local conservation of charge and global compensation of transverse momenta. Strong short range correlations due to cluster decay and Bose-Einstein effects are observed. A consistent description of the correlations is given in the framework of cluster models. Local conservation of charge is also detected in events, where a particle of high transverse momentum is produced. The observations are in good agreement with the predictions of a simple quark parton model. (orig.) [de

  20. High plasma triglyceride levels strongly correlate with low kisspeptin in the arcuate nucleus of male rats

    DEFF Research Database (Denmark)

    Overgaard, A; Axel, A M; Lie, M E

    2015-01-01

    OBJECTIVE: It is well known that reproductive capacity is lower in obese individuals, but what mediators and signals are involved is unclear. Kisspeptin is a potent stimulator of GnRH release, and it has been suggested that kisspeptin neurons located in the arcuate nucleus transmit metabolic...... signals to the GnRH neurons. METHODS: In this study, we measured body weight and plasma concentrations of leptin, insulin, testosterone, and triglycerides after high fat diet exposure and correlated these parameters with the number of kisspeptin-immunoreactive neurons in the arcuate nucleus of male rats...... with increased fat in the diet. Kisspeptin-immunoreactive cells are not correlated with body weight, testosterone, leptin or insulin. However, we find that the number of kisspeptin-immunoreactive cells is strongly and negatively correlated with the level of plasma triglycerides (R2=0.49, p=0.004). CONCLUSION: We...

  1. Relative Skeletal Maturation and Population Ancestry in Nonobese Children and Adolescents.

    Science.gov (United States)

    McCormack, Shana E; Chesi, Alessandra; Mitchell, Jonathan A; Roy, Sani M; Cousminer, Diana L; Kalkwarf, Heidi J; Lappe, Joan M; Gilsanz, Vicente; Oberfield, Sharon E; Shepherd, John A; Mahboubi, Soroosh; Winer, Karen K; Kelly, Andrea; Grant, Struan Fa; Zemel, Babette S

    2017-01-01

    More rapid skeletal maturation in African-American (AA) children is recognized and generally attributed to an increased prevalence of obesity. The objective of the present study was to evaluate the effects of population ancestry on relative skeletal maturation in healthy, non-obese children and adolescents, accounting for body composition and sexual maturation. To do this, we leveraged a multiethnic, mixed-longitudinal study with annual assessments for up to 7 years (The Bone Mineral Density in Childhood Study and its ancillary cohort) conducted at five US clinical centers. Participants included 1592 children, skeletally immature (45% females, 19% AA) who were aged 5 to 17 years at study entry. The primary outcome measure was relative skeletal maturation as assessed by hand-wrist radiograph. Additional covariates measured included anthropometrics, body composition by dual-energy X-ray absorptiometry (DXA), and Tanner stage of sexual maturation. Using mixed effects longitudinal models, without covariates, advancement in relative skeletal maturation was noted in self-reported AA girls (∼0.33 years, p ancestry groups showed independent positive associations of height, lean mass, fat mass, and puberty with relative skeletal maturation. The effect of ancestry was attenuated but persistent after accounting for covariates: for girls, 0.19 years (ancestry by self-report, p = 0.02) or 0.29 years (ancestry by admixture, p = 0.004); and for boys, 0.20 years (ancestry by self-report, p = 0.004), or 0.29 years (ancestry by admixture, p = 0.004). In summary, we conclude that advancement in relative skeletal maturation was associated with AA ancestry in healthy, non-obese children, independent of growth, body composition, and puberty. Further research into the mechanisms underlying this observation may provide insights into the regulation of skeletal maturation. © 2016 American Society for Bone and Mineral Research. © 2016 American Society for Bone and

  2. Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data.

    Science.gov (United States)

    Serra, Angela; Coretto, Pietro; Fratello, Michele; Tagliaferri, Roberto; Stegle, Oliver

    2018-02-15

    Microarray technology can be used to study the expression of thousands of genes across a number of different experimental conditions, usually hundreds. The underlying principle is that genes sharing similar expression patterns, across different samples, can be part of the same co-expression system, or they may share the same biological functions. Groups of genes are usually identified based on cluster analysis. Clustering methods rely on the similarity matrix between genes. A common choice to measure similarity is to compute the sample correlation matrix. Dimensionality reduction is another popular data analysis task which is also based on covariance/correlation matrix estimates. Unfortunately, covariance/correlation matrix estimation suffers from the intrinsic noise present in high-dimensional data. Sources of noise are: sampling variations, presents of outlying sample units, and the fact that in most cases the number of units is much larger than the number of genes. In this paper, we propose a robust correlation matrix estimator that is regularized based on adaptive thresholding. The resulting method jointly tames the effects of the high-dimensionality, and data contamination. Computations are easy to implement and do not require hand tunings. Both simulated and real data are analyzed. A Monte Carlo experiment shows that the proposed method is capable of remarkable performances. Our correlation metric is more robust to outliers compared with the existing alternatives in two gene expression datasets. It is also shown how the regularization allows to automatically detect and filter spurious correlations. The same regularization is also extended to other less robust correlation measures. Finally, we apply the ARACNE algorithm on the SyNTreN gene expression data. Sensitivity and specificity of the reconstructed network is compared with the gold standard. We show that ARACNE performs better when it takes the proposed correlation matrix estimator as input. The R

  3. Evolution of pressures and correlations in the glasma produced in high energy nuclear collisions

    Science.gov (United States)

    Ruggieri, M.; Liu, J. H.; Oliva, L.; Peng, G. X.; Greco, V.

    2018-04-01

    We consider the SU(2) glasma with Gaussian fluctuations and study its evolution by means of classical Yang-Mills equations solved numerically on a lattice. Neglecting in this first study the longitudinal expansion, we follow the evolution of the pressures of the system and compute the effect of the fluctuations in the early stage up to t ≈2 fm /c , that is the time range in which the glasma is relevant for high energy collisions. We measure the ratio of the longitudinal over the transverse pressure, PL/PT, and we find that unless the fluctuations carry a substantial amount of the energy density at the initial time, they do not change significantly the evolution of PL/PT in the early stage and that the system remains quite anisotropic. We also measure the longitudinal fields correlators both in the transverse plane and along the longitudinal direction: while at initial time fields appear to be anticorrelated in the transverse plane, this anticorrelation disappears in the very early stage, and the correlation length in the transverse plane increases. On the other hand, we find a dependence of the gauge invariant correlator on the longitudinal coordinate, which we interpret as a partial loss of correlation induced by the dynamics that we dub the gauge invariant string breaking. We finally study the effect of fluctuations on the longitudinal correlations: we find that string breaking is accelerated by the fluctuations and waiting for a sufficiently long time fluctuations lead to the complete breaking of the color strings.

  4. Minijet thermalization and diffusion of transverse momentum correlation in high-energy heavy-ion collisions

    International Nuclear Information System (INIS)

    Pang Longgang; Wang Qun; Wang Xinnian; Xu Rong

    2010-01-01

    Transverse momentum correlations in the azimuthal angle of hadrons produced owing to minijets are first studied within the HIJING Monte Carlo model in high-energy heavy-ion collisions. Quenching of minijets during thermalization is shown to lead to significant diffusion (broadening) of the correlation. Evolution of the transverse momentum density fluctuation that gives rise to this correlation in azimuthal angle in the later stage of heavy-ion collisions is further investigated within a linearized diffusion-like equation and is shown to be determined by the shear viscosity of the evolving dense matter. This diffusion equation for the transverse momentum fluctuation is solved with initial values given by HIJING and together with the hydrodynamic equation for the bulk medium. The final transverse momentum correlation in azimuthal angle is calculated along the freeze-out hypersurface and is found to be further diffused for higher values of the shear viscosity to entropy density ratio, η/s∼0.2-0.4. Therefore the final transverse momentum correlation in azimuthal angle can be used to study the thermalization of minijets in the early stage of heavy-ion collisions and the viscous effect in the hydrodynamic evolution of strongly coupled quark-gluon plasma.

  5. Degree of European Genetic Ancestry is Associated with Serum Vitamin D Levelsin African Americans.

    Science.gov (United States)

    Haddad, Stephen A; Ruiz-Narváez, Edward A; Cozier, Yvette C; Gerlovin, Hanna; Rosenberg, Lynn; Palmer, Julie R

    2018-01-30

    Circulating levels of vitamin D are generally lower in African Americans compared to U.S. whites, and one prior analysis in a small number of African Americans suggested that, within this population, vitamin D levels may be related to the degree of genetic admixture. We assessed the association of percent European ancestry with serum vitamin D levels in 2183 African American women from the Black Women's Health Study in 2013-2015, whose DNA had been genotyped for ancestry informative markers. ADMIXMAP software was used to estimate percent European versus African ancestry in each individual. In linear regression analyses with adjustment for genotype batch, age, body mass index, supplemental vitamin D use, UVB flux in state of residence, and season of blood draw, each 10% increase in European ancestry was associated with a 0.672 ng/mL increase in serum vitamin D concentration (95% confidence interval 0.173, 1.170). The association was statistically significant only among women who were not taking vitamin D supplements (beta coefficient for 10% increase in European ancestry 0.855, 95% confidence interval 0.139, 1.571). Among African Americans, use of vitamin D supplementation may help to reduce vitamin D deficiency due to genetic ancestry. © The Author(s) 2018. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia.

    Science.gov (United States)

    Li, Cai-Xia; Pakstis, Andrew J; Jiang, Li; Wei, Yi-Liang; Sun, Qi-Fan; Wu, Hong; Bulbul, Ozlem; Wang, Ping; Kang, Long-Li; Kidd, Judith R; Kidd, Kenneth K

    2016-07-01

    Many ancestry informative SNP (AISNP) panels have been published. Ancestry resolution in them varies from three to eight continental clusters of populations depending on the panel used. However, none of these panels differentiates well among East Asian populations. To meet this need, we have developed a 74 AISNP panel after analyzing a much larger number of SNPs for Fst and allele frequency differences between two geographically close population groups within East Asia. The 74 AISNP panel can now distinguish at least 10 biogeographic groups of populations globally: Sub-Saharan Africa, North Africa, Europe, Southwest Asia, South Asia, North Asia, East Asia, Southeast Asia, Pacific and Americas. Compared with our previous 55-AISNP panel, Southeast Asia and North Asia are two newly assignable clusters. For individual ancestry assignment, the likelihood ratio and ancestry components were analyzed on a different set of 500 test individuals from 11 populations. All individuals from five of the test populations - Yoruba (YRI), European (CEU), Han Chinese in Henan (CHNH), Rondonian Surui (SUR) and Ticuna (TIC) - were assigned to their appropriate geographical regions unambiguously. For the other test populations, most of the individuals were assigned to their self-identified geographical regions with a certain degree of overlap with adjacent populations. These alternative ancestry components for each individual thus help give a clearer picture of the possible group origins of the individual. We have demonstrated that the new AISNP panel can achieve a deeper resolution of global ancestry. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations.

    Directory of Open Access Journals (Sweden)

    Alkes L Price

    2009-06-01

    Full Text Available Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history. Most methods require the use of unlinked markers; but, using all markers from genome-wide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite accuracy. We describe a method, HAPMIX, which employs an explicit population genetic model to perform such local ancestry inference based on fine-scale variation data. We show that HAPMIX outperforms other methods, and we explore its utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate the method empirically by applying it to populations that have experienced recent and ancient admixture: 935 African Americans from the United States and 29 Mozabites from North Africa. HAPMIX will be of particular utility for mapping disease genes in recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association signals to be combined, enabling more powerful tests of association than with either signal alone.

  8. The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand

    Science.gov (United States)

    Russell, James C.; King, Carolyn M.

    2018-01-01

    The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city—Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2–3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7–8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry—though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice. PMID:29410804

  9. Correlation between Health Perception, Body Image, and Eating Habits in High School Students

    Directory of Open Access Journals (Sweden)

    Abdullah Ichsan

    2016-06-01

    Full Text Available Background: Mental disorders, including eating disorders, mostly begin during youth. Moreover, negative body image is found to cause unhealthy eating habits in the context of several cross-cultural settings. This study aimed to examine the correlation between health perception and body image with eating habits among high school students. Methods: A structured, anonymous questionnaire was distributed to students of a private high school in Bandung, Indonesia in June-October 2014. The questionnaire included questions about health perception, body image, eating habits, body weight and height, and also other demographic parameters. The school was selected as the study object through purposive sampling, and 140 high school students (72 male and 68 female were ramdomly selected. Results: Male and female did not show considerable differences in health perceptions. Out of 13 statements, 12 statements of male respondents showed better body image than female. While in eating habits statements, female respondents seemed to maintain healthier eating habits than male respondents. No significant correlation was observed between body image and eating habits (r=-0.015, p=0.858. There was significant correlation between health perception and eating habits (r=0.374, p<0.001. Correlation between sex and eating habits was found (p=0.020, there was not significant relationship between eating habits and Body Mass Index (BMI (p=0.368. Conclusions: The negative relationship between body image and eating habits is not significant. However there was a significant positive relationship between health perception and eating habits. Furthermore, there was correlation between sex and eating habits, while the positive relationship between eating habits and BMI was still not found.

  10. Angular correlation between IceCube high-energy starting events and starburst sources

    Energy Technology Data Exchange (ETDEWEB)

    Moharana, Reetanjali; Razzaque, Soebur, E-mail: moharana.reetanjali@mail.huji.ac.il, E-mail: srazzaque@uj.ac.za [Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa)

    2016-12-01

    Starburst galaxies and star-forming regions in the Milkyway, with high rate of supernova activities, are candidate sources of high-energy neutrinos. Using a gamma-ray selected sample of these sources we perform statistical analysis of their angular correlation with the four-year sample of high-energy starting events (HESE), detected by the IceCube Neutrino Observatory. We find that the two samples (starburst galaxies and local star-forming regions) are correlated with cosmic neutrinos at ∼ (2–3)σ (pre-trial) significance level, when the full HESE sample with deposited energy ∼> 20 TeV is considered. However when we consider the HESE sample with deposited energy ∼> 60 TeV, which is almost free of atmospheric neutrino and muon backgrounds, the significance of correlation decreased drastically. We perform a similar study for Galactic sources in the 2nd Catalog of Hard Fermi -LAT Sources (2FHL, >50 GeV) catalog as well, obtaining ∼ (2–3)σ (pre-trial) correlation, however the significance of correlation increases with higher cutoff energy in the HESE sample for this case. We also fit available gamma-ray data from these sources using a pp interaction model and calculate expected neutrino fluxes. We find that the expected neutrino fluxes for most of the sources are at least an order of magnitude lower than the fluxes required to produce the HESE neutrinos from these sources. This puts the starburst sources being the origin of the IceCube HESE neutrinos in question.

  11. Air pollution forecast in cities by an air pollution index highly correlated with meteorological variables

    International Nuclear Information System (INIS)

    Cogliani, E.

    2001-01-01

    There are many different air pollution indexes which represent the global urban air pollution situation. The daily index studied here is also highly correlated with meteorological variables and this index is capable of identifying those variables that significantly affect the air pollution. The index is connected with attention levels of NO 2 , CO and O 3 concentrations. The attention levels are fixed by a law proposed by the Italian Ministries of Health and Environment. The relation of that index with some meteorological variables is analysed by the linear multiple partial correlation statistical method. Florence, Milan and Vicence were selected to show the correlation among the air pollution index and the daily thermic excursion, the previous day's air pollution index and the wind speed. During the January-March period the correlation coefficient reaches 0.85 at Milan. The deterministic methods of forecasting air pollution concentrations show very high evaluation errors and are applied on limited areas around the observation stations, as opposed to the whole urban areas. The global air pollution, instead of the concentrations at specific observation stations, allows the evaluation of the level of the sanitary risk regarding the whole urban population. (Author)

  12. Relevance of the ancestry for the variability of the Drug-Metabolizing Enzymes CYP2C9, CYP2C19 and CYP2D6 polymorphisms in a multiethnic Costa Rican population.

    Science.gov (United States)

    Céspedes-Garro, Carolina; Rodrigues-Soares, Fernanda; Jiménez-Arce, Gerardo; Naranjo, María-Eugenia G; Tarazona-Santos, Eduardo; Fariñas, Humberto; Barrantes, Ramiro; Llerena, Adrián

    2016-09-01

    CYP2C9, CYP2C19 and CYP2D6 metabolize around 40% of drugs and their genes vary across populations. The Costa Rican population has a trihybrid ancestry and its key geographic location turns it into a suitable scenario to evaluate interethnic differences across populations. This study aims to describe the diversity of CYP2C9, CYP2C19 and CYP2D6 polymorphisms in Costa Rican populations in the context of their ancestry. A total of 448 healthy individuals were included in the study: Bribri (n= 47), Cabécar (n= 27), Maleku (n= 16), Guaymí (n= 30), Huetar (n= 48), Chorotega (n= 41), Admixed/Mestizos from the Central Valley/Guanacaste (n= 189), and Afro-Caribbeans (n= 50) from Limón. CYP2C9 (alleles *2, *3, *6) and CYP2C19 (*2, *3, *4, *5, *17) genotypes were determined by Real-Time PCR. African, European and Native American ancestry were inferred using 87 ancestry informative markers. The frequency of the decreased activity allele CYP2C9*2 is lower in the self-reported Amerindian groups compared to the admixed population, and the highest frequencies of CYP2C19*2 (null activity) and the CYP2C19*17 (increased activity) were found in the self-reported Afro-Caribbean population. Moreover, a frequency of 0.7 % CYP2C9 gPMs in the Admixed population and a variable frequency of CYP2C19 gUMs (0.0-32.6 %, more prevalent in Afro-Caribbeans) in Costa Rican populations, was found. Finally, the following alleles were positively correlated with genomic African ancestry and negatively correlated with genomic Native American ancestry: CYP2D6*5 (null activity), CYP2D6*17 (decreased activity), CYP2D6*29 (decreased activity) and CYP2C19*17 (increased activity). No correlation for CYP2C9 polymorphisms and genomic ancestry was found. Further studies assessing the CYP2C9 and CYP2C19 sequence in these populations, preferentially by sequencing these genes, are warranted.

  13. Paraoxonase1 Genetic Polymorphisms in a Mixed Ancestry African Population

    Directory of Open Access Journals (Sweden)

    M. Macharia

    2014-01-01

    Full Text Available Paraoxonase 1 (PON1 activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4% and 55M (82.6%. The Q192 was significantly associated with 5.8 units’ increase in PON1 concentration and 15.4 units’ decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes.

  14. Highly ordered FEPT and FePd magnetic nano-structures: Correlated structural and magnetic studies

    International Nuclear Information System (INIS)

    Lukaszew, Rosa Alejandra; Cebollada, Alfonso; Clavero, Cesar; Garcia-Martin, Jose Miguel

    2006-01-01

    The micro-structure of epitaxial FePt and FePd films grown on MgO (0 0 1) substrates is correlated to their magnetic behavior. The FePd films exhibit high chemical ordering and perpendicular magnetic anisotropy. On the other hand FePt films exhibit low chemical ordering, with nano-grains oriented in two orthogonal directions, forcing the magnetization to remain in the plane of the films

  15. Video Game Addiction among High School Students in Hordaland; Prevalence and Correlates

    OpenAIRE

    Bjordal, Sunniva Alsvik; Skumsnes, Toril; Ørland, Anette

    2011-01-01

    The aim of this study was to estimate the prevalence and correlates of video game addiction among high school students (N = 531) in Hordaland county, Norway. Video game addiction measured by the Game Addiction Scale for Adolescents was estimated both by a monothetic and a polythetic format. The prevalence was found to be 2.5% and 12.5%, respectively. Regression analyses were conducted where video game addiction comprised the dependent variable. Demographic variables, depression, anxiety, lone...

  16. Correlations between the simulated military tasks performance and physical fitness tests at high altitude

    Directory of Open Access Journals (Sweden)

    Eduardo Borba Neves

    2017-11-01

    Full Text Available The aim of this study was to investigate the Correlations between the Simulated Military Tasks Performance and Physical Fitness Tests at high altitude. This research is part of a project to modernize the physical fitness test of the Colombian Army. Data collection was performed at the 13th Battalion of Instruction and Training, located 30km south of Bogota D.C., with a temperature range from 1ºC to 23ºC during the study period, and at 3100m above sea level. The sample was composed by 60 volunteers from three different platoons. The volunteers start the data collection protocol after 2 weeks of acclimation at this altitude. The main results were the identification of a high positive correlation between the 3 Assault wall in succession and the Simulated Military Tasks performance (r = 0.764, p<0.001, and a moderate negative correlation between pull-ups and the Simulated Military Tasks performance (r = -0.535, p<0.001. It can be recommended the use of the 20-consecutive overtaking of the 3 Assault wall in succession as a good way to estimate the performance in operational tasks which involve: assault walls, network of wires, military Climbing Nets, Tarzan jump among others, at high altitude.

  17. Mass transfer in wetted-wall columns: correlations at high Reynolds numbers

    DEFF Research Database (Denmark)

    Nielsen, Christian H.E.; Kiil, Søren; Thomsen, Henrik W.

    1998-01-01

    (G)) were determined. In dimensionless form, the correlations are given by Sh(L) = 0.01613 Re-G(0.664) Re-L(0.426) Sc-L(0.5) Sh(G) = 0.00031 Re-G(1.05) Re-L(0.207) Sc-G(0.5) and are valid at gas-phase Reynolds numbers from 7500 to 18,300 and liquid-phase Reynolds numbers from 4000 to 12,000, conditions...... of industrial relevance. To our knowledge, no correlations for Sh(G) have been reported in the literature which are valid at such high Reynolds numbers. The wetted-wall column was equipped with six intermediate measuring positions for gas and two for liquid samples, giving rise to a high accuracy...... of the obtained correlations. Our data showed that Sh(L) and Sh(G) both depend on Re-G and Re-L due to changes in the interfacial area at the high Reynolds numbers employed. The presence of inert particles in the liquid-phase may influence the rate of mass transport, and experimental work was initiated to study...

  18. Bronchial asthma: correlation of high resolution computerized tomography findings with clinical data

    International Nuclear Information System (INIS)

    Mogami, Roberto; Marchiori, Edson; Kirk, Kennedy; Capone, Domenico; Daltro, Pedro

    1999-01-01

    In this work we did a sectional study of 31 asthmatic patients with several levels of disease severity, which were submitted to high resolution computed tomography of the thorax and spirometry, between the months of July, 1995 and August, 1997. The tomographic findings were correlated with the clinical classification of the patients and the most frequent tomographic findings were bronchial wall thickening, bronchial dilatation, air trapping, centrilobular opacities, cicatricial linear shadows, mucoid impaction, emphysema and atelectasis. In asthmatic patients of long duration we observed small airway disease and irreversible lesions as the predominant findings. In smoking patients there was no high frequency of emphysema. (author)

  19. Nuclear material enrichment identification method based on cross-correlation and high order spectra

    International Nuclear Information System (INIS)

    Yang Fan; Wei Biao; Feng Peng; Mi Deling; Ren Yong

    2013-01-01

    In order to enhance the sensitivity of nuclear material identification system (NMIS) against the change of nuclear material enrichment, the principle of high order statistic feature is introduced and applied to traditional NMIS. We present a new enrichment identification method based on cross-correlation and high order spectrum algorithm. By applying the identification method to NMIS, the 3D graphs with nuclear material character are presented and can be used as new signatures to identify the enrichment of nuclear materials. The simulation result shows that the identification method could suppress the background noises, electronic system noises, and improve the sensitivity against enrichment change to exponential order with no system structure modification. (authors)

  20. Palate Shape and Depth: A Shape-Matching and Machine Learning Method for Estimating Ancestry from Human Skeletal Remains.

    Science.gov (United States)

    Maier, Christopher A; Zhang, Kang; Manhein, Mary H; Li, Xin

    2015-09-01

    In the past, assessing ancestry relied on the naked eye and observer experience; however, replicability has become an important aspect of such analysis through the application of metric techniques. This study examines palate shape and assesses ancestry quantitatively using a 3D digitizer and shape-matching and machine learning methods. Palate curves and depths were recorded, processed, and tested for 376 individuals. Palate shape was an accurate indicator of ancestry in 58% of cases. Cluster analysis revealed that the parabolic, hyperbolic, and elliptical shapes are discrete from one another. Preliminary results indicate that palate depth in Hispanic individuals is greatest. Palate shape appears to be a useful indicator of ancestry, particularly when assessed by a computer. However, these data suggest that palate shape is not useful for assessing ancestry in Hispanic individuals. Although ancestry may be determined from palate shape, the use of multiple features is recommended and more reliable. © 2015 American Academy of Forensic Sciences.

  1. Ethnicity, desirable responding, and self-reports of abuse: a comparison of European- and Asian-ancestry undergraduates.

    Science.gov (United States)

    Meston, C M; Heiman, J R; Trapnell, P D; Carlin, A S

    1999-02-01

    One thousand fifty-two (582 non-Asian, 470 Asian) university students were assessed regarding levels of physical abuse, emotional abuse, sexual abuse, neglect, and socially desirable responding. Differences between Asian-ancestry and European-ancestry students in self-reported incidence and expression of abuse were evaluated, as was gender and the relation between self-reported abuse and socially desirable responding. Asian-ancestry men and women reported higher levels of physical abuse, emotional abuse, and neglect than did their Euro-ancestry counterparts, and Euro-ancestry women reported a higher incidence of sexual abuse than did Asian-ancestry women. Across ethnicity, men reported higher levels of physical abuse and neglect but lower levels of sexual abuse than did women. Socially desirable responding was not related to measures of abuse. Findings are discussed in terms of cultural influences on child-rearing and disciplinary practices.

  2. Positive Correlation Between Academic Library Services and High-Impact Practices for

    Directory of Open Access Journals (Sweden)

    Saori Wendy Herman, MLIS, AHIP

    2016-03-01

    Full Text Available Objective – To investigate the perceived alignment between academic library services and high-impact practices (HIPs that affect student retention. Design – Survey questionnaire. Setting – Public comprehensive universities in the United States of America with a Carnegie classification of master’s level as of January 2013. Subjects – 68 library deans or directors out of the 271 who were originally contacted. Methods – The author used Qualtrics software to create a survey based on the HIPs, tested the survey for reliability, and then distributed it to 271 universities. Library services were grouped into 1 of 3 library scales: library collection, library instruction, or library facilities. The survey consisted of a matrix of 10 Likert-style questions addressing the perceived level of alignment between the library scales and the HIPs. Each question provided an opportunity for the respondent to enter a “brief description of support practices” (p 477. Additional demographic questions addressed the years of experience of the respondent, undergraduate student enrollment of the university, and whether librarians held faculty rank. Main Results – The author measured Pearson correlation coefficients and found a positive correlation between the library scales and the HIPs. All three library scales displayed a moderately strong positive correlation between first-year seminars and experiences (HIP 1, common intellectual experiences (HIP 2, writing-intensive courses (HIP 4, undergraduate research (HIP 6, diversity and global learning (HIP 7, service learning and community-based learning (HIP 8, internships (HIP 9, and capstone courses and projects (HIP 10. The library collections scale and library facilities scale displayed a moderately strong correlation with learning communities (HIP 3 and collaborative assignments and projects (HIP 5. The library instruction scale displayed a strong positive correlation with HIP 3 and a very strong

  3. Strong correlations and the search for high-Tc superconductivity in chromium pnictides and chalcogenides

    Science.gov (United States)

    Pizarro, J. M.; Calderón, M. J.; Liu, J.; Muñoz, M. C.; Bascones, E.

    2017-02-01

    Undoped iron superconductors accommodate n =6 electrons in five d orbitals. Experimental and theoretical evidence shows that the strength of correlations increases with hole doping, as the electronic filling approaches half filling with n =5 electrons. This evidence delineates a scenario in which the parent compound of iron superconductors is the half-filled system, in analogy to cuprate superconductors. In cuprates the superconductivity can be induced upon electron or hole doping. In this work we propose to search for high-Tc superconductivity and strong correlations in chromium pnictides and chalcogenides with n slave-spin and multiorbital random-phase-approximation calculations we analyze the strength of the correlations and the superconducting and magnetic instabilities in these systems with the main focus on LaCrAsO. We find that electron-doped LaCrAsO is a strongly correlated system with competing magnetic interactions, with (π ,π ) antiferromagnetism and nodal d -wave pairing being the most plausible magnetic and superconducting instabilities, respectively.

  4. An examination of sociodemographic correlates of ecstasy use among high school seniors in the United States.

    Science.gov (United States)

    Palamar, Joseph J; Kamboukos, Dimitra

    2014-11-01

    Although ecstasy (MDMA) use is not as prevalent in the United States (US) as it was in the early 2000s, use remains popular among adolescents and young adults. Few recent studies have examined ecstasy use in national samples among those at particularly high risk for use-adolescents approaching adulthood. Research is needed to delineate sociodemographic correlates of use in this group. Data were examined from a nationally representative sample of high school seniors in the US (modal age = 18) from the Monitoring the Future study (years 2007-2012; weighted N = 26,504). Data from all cohorts were aggregated and correlates of recent (last 12-month) use of ecstasy were examined. Roughly 4.4% of high school seniors reported use of ecstasy within the last year. Females and religious students were consistently at lower odds for use. Black and Hispanic students, and students residing with two parents, were at lower odds for ecstasy use, until controlling for other drug use. Odds of use were consistently increased for those residing in a city, students with weekly income of >$50 from a job, and students earning >$10 weekly from other sources. Lifetime use of alcohol, cigarettes, marijuana, and other illicit drugs each robustly increased odds of ecstasy use. Subgroups of high school seniors, defined by specific sociodemographic factors, and those who have used other drugs, are currently at high risk for ecstasy initiation and use. Since ecstasy is regaining popularity in the US, prevention efforts should consider these factors.

  5. Strongly correlated electrons at high pressure: an approach by inelastic X-Ray scattering

    International Nuclear Information System (INIS)

    Rueff, J.P.

    2007-06-01

    Inelastic X-ray scattering (IXS) and associated methods has turn out to be a powerful alternative for high-pressure physics. It is an all-photon technique fully compatible with high-pressure environments and applicable to a vast range of materials. Standard focalization of X-ray in the range of 100 microns is typical of the sample size in the pressure cell. Our main aim is to provide an overview of experimental results obtained by IXS under high pressure in 2 classes of materials which have been at the origin of the renewal of condensed matter physics: strongly correlated transition metal oxides and rare-earth compounds. Under pressure, d and f-electron materials show behaviors far more complex that what would be expected from a simplistic band picture of electron delocalization. These spectroscopic studies have revealed unusual phenomena in the electronic degrees of freedom, brought up by the increased density, the changes in the charge-carrier concentration, the over-lapping between orbitals, and hybridization under high pressure conditions. Particularly we discuss about pressure induced magnetic collapse and metal-insulator transitions in 3d compounds and valence fluctuations phenomena in 4f and 5f compounds. Thanks to its superior penetration depth, chemical selectivity and resonant enhancement, resonant inelastic X-ray scattering has appeared extremely well suited to high pressure physics in strongly correlated materials. (A.C.)

  6. High-resolution CT with histopathological correlates of the classic metaphyseal lesion of infant abuse

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Andy; Kleinman, Paul K. [Boston Children' s Hospital, Department of Radiology, Boston, MA (United States); McDonald, Anna G. [Office of the Chief Medical Examiner, Boston, MA (United States); Rosenberg, Andrew E. [University of Miami Hospital, Department of Pathology, Miami, FL (United States); Gupta, Rajiv [Massachusetts General Hospital, Department of Radiology, Boston, MA (United States)

    2014-02-15

    The classic metaphyseal lesion (CML) is a common high specificity indicator of infant abuse and its imaging features have been correlated histopathologically in infant fatalities. High-resolution CT imaging and histologic correlates were employed to (1) characterize the normal infant anatomy surrounding the chondro-osseous junction, and (2) confirm the 3-D model of the CML previously inferred from planar radiography and histopathology. Long bone specimens from 5 fatally abused infants, whose skeletal survey showed definite or suspected CMLs, were studied postmortem. After skeletal survey, selected specimens were resected and imaged with high-resolution digital radiography. They were then scanned with micro-CT (isotropic resolution of 45 μm{sup 3}) or with high-resolution flat-panel CT (isotropic resolutions of 200 μm{sup 3}). Visualization of the bony structures was carried out using image enhancement, segmentation and isosurface extraction, together with volume rendering and multiplanar reformatting. These findings were then correlated with histopathology. Study of normal infant bone clarifies the 3-D morphology of the subperiosteal bone collar (SPBC) and the radiographic zone of provisional calcification (ZPC). Studies on specimens with CML confirm that this lesion is a fracture extending in a planar fashion through the metaphysis, separating a mineralized fragment. This disk-like mineralized fragment has two components: (1) a thick peripheral component encompassing the SPBC; and (2) a thin central component comprised predominantly of the radiologic ZPC. By manipulating the 3-D model, the varying appearances of the CML are displayed. High-resolution CT coupled with histopathology provides elucidation of the morphology of the CML, a strong indicator of infant abuse. This new information may prove useful in assessing the biomechanical factors that produce this strong indicator of abusive assaults in infants. (orig.)

  7. High-resolution CT with histopathological correlates of the classic metaphyseal lesion of infant abuse

    International Nuclear Information System (INIS)

    Tsai, Andy; Kleinman, Paul K.; McDonald, Anna G.; Rosenberg, Andrew E.; Gupta, Rajiv

    2014-01-01

    The classic metaphyseal lesion (CML) is a common high specificity indicator of infant abuse and its imaging features have been correlated histopathologically in infant fatalities. High-resolution CT imaging and histologic correlates were employed to (1) characterize the normal infant anatomy surrounding the chondro-osseous junction, and (2) confirm the 3-D model of the CML previously inferred from planar radiography and histopathology. Long bone specimens from 5 fatally abused infants, whose skeletal survey showed definite or suspected CMLs, were studied postmortem. After skeletal survey, selected specimens were resected and imaged with high-resolution digital radiography. They were then scanned with micro-CT (isotropic resolution of 45 μm 3 ) or with high-resolution flat-panel CT (isotropic resolutions of 200 μm 3 ). Visualization of the bony structures was carried out using image enhancement, segmentation and isosurface extraction, together with volume rendering and multiplanar reformatting. These findings were then correlated with histopathology. Study of normal infant bone clarifies the 3-D morphology of the subperiosteal bone collar (SPBC) and the radiographic zone of provisional calcification (ZPC). Studies on specimens with CML confirm that this lesion is a fracture extending in a planar fashion through the metaphysis, separating a mineralized fragment. This disk-like mineralized fragment has two components: (1) a thick peripheral component encompassing the SPBC; and (2) a thin central component comprised predominantly of the radiologic ZPC. By manipulating the 3-D model, the varying appearances of the CML are displayed. High-resolution CT coupled with histopathology provides elucidation of the morphology of the CML, a strong indicator of infant abuse. This new information may prove useful in assessing the biomechanical factors that produce this strong indicator of abusive assaults in infants. (orig.)

  8. Genetic Ancestry and Asthma and Rhinitis Occurrence in Hispanic Children: Findings from the Southern California Children's Health Study.

    Directory of Open Access Journals (Sweden)

    Muhammad T Salam

    Full Text Available Asthma and rhinitis are common childhood health conditions. Being an understudied and rapidly growing population in the US, Hispanic children have a varying risk for these conditions that may result from sociocultural (including acculturative factors, exposure and genetic diversities. Hispanic populations have varying contributions from European, Amerindian and African ancestries. While previous literature separately reported associations between genetic ancestry and acculturation factors with asthma, whether Amerindian ancestry and acculturative factors have independent associations with development of early-life asthma and rhinitis in Hispanic children remains unknown. We hypothesized that genetic ancestry is an important determinant of early-life asthma and rhinitis occurrence in Hispanic children independent of sociodemographic, acculturation and environmental factors.Subjects were Hispanic children (5-7 years who participated in the southern California Children's Health Study. Data from birth certificates and questionnaire provided information on acculturation, sociodemographic and environmental factors. Genetic ancestries (Amerindian, European, African and Asian were estimated based on 233 ancestry informative markers. Asthma was defined by parental report of doctor-diagnosed asthma. Rhinitis was defined by parental report of a history of chronic sneezing or runny or blocked nose without a cold or flu. Sample sizes were 1,719 and 1,788 for investigating the role of genetic ancestry on asthma and rhinitis, respectively.Children had major contributions from Amerindian and European ancestries. After accounting for potential confounders, per 25% increase in Amerindian ancestry was associated with 17.6% (95% confidence interval [CI]: 0.74-0.99 and 13.6% (95% CI: 0.79-0.98 lower odds of asthma and rhinitis, respectively. Acculturation was not associated with either outcome.Earlier work documented that Hispanic children with significant

  9. Towards high velocity deformation characterisation of metals and composites using Digital Image Correlation

    DEFF Research Database (Denmark)

    Eriksen, Rasmus Normann Wilken; Berggreen, Christian; Boyd, S.W

    2010-01-01

    images and then extracting deformation data using Digital Image Correlation (DIC) from tensile testing in the intermediate strain rate regime available with the test machines. Three different materials, aluminium alloy 1050, S235 steel and glass fibre reinforced plastic (GFRP) were tested at different......Characterisation of materials subject to high velocity deformation is necessary as many materials behave differently under such conditions. It is particularly important for accurate numerical simulation of high strain rate events. High velocity servo-hydraulic test machines have enabled material...... testing in the strain rate regime from 1 – 500 ε/s. The range is much lower than that experienced under ballistic, shock or impact loads, nevertheless it is a useful starting point for the application of optical techniques. The present study examines the possibility of using high speed cameras to capture...

  10. Inverse correlation between quasiparticle mass and T c in a cuprate high-T c superconductor.

    Science.gov (United States)

    Putzke, Carsten; Malone, Liam; Badoux, Sven; Vignolle, Baptiste; Vignolles, David; Tabis, Wojciech; Walmsley, Philip; Bird, Matthew; Hussey, Nigel E; Proust, Cyril; Carrington, Antony

    2016-03-01

    Close to a zero-temperature transition between ordered and disordered electronic phases, quantum fluctuations can lead to a strong enhancement of electron mass and to the emergence of competing phases such as superconductivity. A correlation between the existence of such a quantum phase transition and superconductivity is quite well established in some heavy fermion and iron-based superconductors, and there have been suggestions that high-temperature superconductivity in copper-oxide materials (cuprates) may also be driven by the same mechanism. Close to optimal doping, where the superconducting transition temperature T c is maximal in cuprates, two different phases are known to compete with superconductivity: a poorly understood pseudogap phase and a charge-ordered phase. Recent experiments have shown a strong increase in quasiparticle mass m* in the cuprate YBa2Cu3O7-δ as optimal doping is approached, suggesting that quantum fluctuations of the charge-ordered phase may be responsible for the high-T c superconductivity. We have tested the robustness of this correlation between m* and T c by performing quantum oscillation studies on the stoichiometric compound YBa2Cu4O8 under hydrostatic pressure. In contrast to the results for YBa2Cu3O7-δ, we find that in YBa2Cu4O8, the mass decreases as T c increases under pressure. This inverse correlation between m* and T c suggests that quantum fluctuations of the charge order enhance m* but do not enhance T c.

  11. Genomic Insights into the Ancestry and Demographic History of South America

    Science.gov (United States)

    Homburger, Julian R.; Moreno-Estrada, Andrés; Gignoux, Christopher R.; Nelson, Dominic; Sanchez, Elena; Ortiz-Tello, Patricia; Pons-Estel, Bernardo A.; Acevedo-Vasquez, Eduardo; Miranda, Pedro; Langefeld, Carl D.; Gravel, Simon; Alarcón-Riquelme, Marta E.; Bustamante, Carlos D.

    2015-01-01

    South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9–14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical

  12. Genomic Insights into the Ancestry and Demographic History of South America.

    Science.gov (United States)

    Homburger, Julian R; Moreno-Estrada, Andrés; Gignoux, Christopher R; Nelson, Dominic; Sanchez, Elena; Ortiz-Tello, Patricia; Pons-Estel, Bernardo A; Acevedo-Vasquez, Eduardo; Miranda, Pedro; Langefeld, Carl D; Gravel, Simon; Alarcón-Riquelme, Marta E; Bustamante, Carlos D

    2015-12-01

    South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9-14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical

  13. Genomic Insights into the Ancestry and Demographic History of South America.

    Directory of Open Access Journals (Sweden)

    Julian R Homburger

    2015-12-01

    Full Text Available South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9-14 generations ago, with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform

  14. Race, Genetic Ancestry and Response to Antidepressant Treatment for Major Depression

    Science.gov (United States)

    Murphy, Eleanor; Hou, Liping; Maher, Brion S; Woldehawariat, Girma; Kassem, Layla; Akula, Nirmala; Laje, Gonzalo; McMahon, Francis J

    2013-01-01

    The Sequenced Treatment Alternatives to Relieve Depression (STAR*D) Study revealed poorer antidepressant treatment response among black compared with white participants. This racial disparity persisted even after socioeconomic and baseline clinical factors were taken into account. Some studies have suggested genetic contributions to this disparity, but none have attempted to disentangle race and genetic ancestry. Here we used genome-wide single-nucleotide polymorphism (SNP) data to examine independent contributions of race and genetic ancestry to citalopram response. Secondary data analyses included 1877 STAR*D participants who completed an average of 10 weeks of citalopram treatment and provided DNA samples. Participants reported their race as White (n=1464), black (n=299) or other/mixed (n=114). Genetic ancestry was estimated by multidimensional scaling (MDS) analyses of about 500 000 SNPs. Ancestry proportions were estimated by STRUCTURE. Structural equation modeling was used to examine the direct and indirect effects of observed and latent predictors of response, defined as change in the Quick Inventory of Depressive Symptomatology (QIDS) score from baseline to exit. Socioeconomic and baseline clinical factors, race, and anxiety significantly predicted response, as previously reported. However, direct effects of race disappeared in all models that included genetic ancestry. Genetic African ancestry predicted lower treatment response in all models. Although socioeconomic and baseline clinical factors drive racial differences in antidepressant response, genetic ancestry, rather than self-reported race, explains a significant fraction of the residual differences. Larger samples would be needed to identify the specific genetic mechanisms that may be involved, but these findings underscore the importance of including more African-American patients in drug trials. PMID:23827886

  15. A novel test for gene-ancestry interactions in genome-wide association data.

    Directory of Open Access Journals (Sweden)

    Joanna L Davies

    Full Text Available Genome-wide association study (GWAS data on a disease are increasingly available from multiple related populations. In this scenario, meta-analyses can improve power to detect homogeneous genetic associations, but if there exist ancestry-specific effects, via interactions on genetic background or with a causal effect that co-varies with genetic background, then these will typically be obscured. To address this issue, we have developed a robust statistical method for detecting susceptibility gene-ancestry interactions in multi-cohort GWAS based on closely-related populations. We use the leading principal components of the empirical genotype matrix to cluster individuals into "ancestry groups" and then look for evidence of heterogeneous genetic associations with disease or other trait across these clusters. Robustness is improved when there are multiple cohorts, as the signal from true gene-ancestry interactions can then be distinguished from gene-collection artefacts by comparing the observed interaction effect sizes in collection groups relative to ancestry groups. When applied to colorectal cancer, we identified a missense polymorphism in iron-absorption gene CYBRD1 that associated with disease in individuals of English, but not Scottish, ancestry. The association replicated in two additional, independently-collected data sets. Our method can be used to detect associations between genetic variants and disease that have been obscured by population genetic heterogeneity. It can be readily extended to the identification of genetic interactions on other covariates such as measured environmental exposures. We envisage our methodology being of particular interest to researchers with existing GWAS data, as ancestry groups can be easily defined and thus tested for interactions.

  16. Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings.

    Directory of Open Access Journals (Sweden)

    Tailce K M Leite

    Full Text Available A current concern in genetic epidemiology studies in admixed populations is that population stratification can lead to spurious results. The Brazilian census classifies individuals according to self-reported "color", but several studies have demonstrated that stratifying according to "color" is not a useful strategy to control for population structure, due to the dissociation between self-reported "color" and genomic ancestry. We report the results of a study in a group of Brazilian siblings in which we measured skin pigmentation using a reflectometer, and estimated genomic ancestry using 21 Ancestry Informative Markers (AIMs. Self-reported "color", according to the Brazilian census, was also available for each participant. This made it possible to evaluate the relationship between self-reported "color" and skin pigmentation, self-reported "color" and genomic ancestry, and skin pigmentation and genomic ancestry. We observed that, although there were significant differences between the three "color" groups in genomic ancestry and skin pigmentation, there was considerable dispersion within each group and substantial overlap between groups. We also saw that there was no good agreement between the "color" categories reported by each member of the sibling pair: 30 out of 86 sibling pairs reported different "color", and in some cases, the sibling reporting the darker "color" category had lighter skin pigmentation. Socioeconomic status was significantly associated with self-reported "color" and genomic ancestry in this sample. This and other studies show that subjective classifications based on self-reported "color", such as the one that is used in the Brazilian census, are inadequate to describe the population structure present in recently admixed populations. Finally, we observed that one of the AIMs included in the panel (rs1426654, which is located in the known pigmentation gene SLC24A5, was strongly associated with skin pigmentation in this sample.

  17. Associations among ancestry, geography and breast cancer incidence, mortality, and survival in Trinidad and Tobago.

    Science.gov (United States)

    Warner, Wayne A; Morrison, Robert L; Lee, Tammy Y; Williams, Tanisha M; Ramnarine, Shelina; Roach, Veronica; Slovacek, Simeon; Maharaj, Ravi; Bascombe, Nigel; Bondy, Melissa L; Ellis, Matthew J; Toriola, Adetunji T; Roach, Allana; Llanos, Adana A M

    2015-11-01

    Breast cancer (BC) is the most common newly diagnosed cancer among women in Trinidad and Tobago (TT) and BC mortality rates are among the highest in the world. Globally, racial/ethnic trends in BC incidence, mortality and survival have been reported. However, such investigations have not been conducted in TT, which has been noted for its rich diversity. In this study, we investigated associations among ancestry, geography and BC incidence, mortality and survival in TT. Data on 3767 incident BC cases, reported to the National Cancer Registry of TT, from 1995 to 2007, were analyzed in this study. Women of African ancestry had significantly higher BC incidence and mortality rates ( 66.96; 30.82 per 100,000) compared to women of East Indian ( 41.04, MORTALITY: 14.19 per 100,000) or mixed ancestry ( 36.72, MORTALITY: 13.80 per 100,000). Geographically, women residing in the North West Regional Health Authority (RHA) catchment area followed by the North Central RHA exhibited the highest incidence and mortality rates. Notable ancestral differences in survival were also observed. Women of East Indian and mixed ancestry experienced significantly longer survival than those of African ancestry. Differences in survival by geography were not observed. In TT, ancestry and geographical residence seem to be strong predictors of BC incidence and mortality rates. Additionally, disparities in survival by ancestry were found. These data should be considered in the design and implementation of strategies to reduce BC incidence and mortality rates in TT. © 2015 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  18. Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings.

    Science.gov (United States)

    Leite, Tailce K M; Fonseca, Rômulo M C; de França, Nanci M; Parra, Esteban J; Pereira, Rinaldo W

    2011-01-01

    A current concern in genetic epidemiology studies in admixed populations is that population stratification can lead to spurious results. The Brazilian census classifies individuals according to self-reported "color", but several studies have demonstrated that stratifying according to "color" is not a useful strategy to control for population structure, due to the dissociation between self-reported "color" and genomic ancestry. We report the results of a study in a group of Brazilian siblings in which we measured skin pigmentation using a reflectometer, and estimated genomic ancestry using 21 Ancestry Informative Markers (AIMs). Self-reported "color", according to the Brazilian census, was also available for each participant. This made it possible to evaluate the relationship between self-reported "color" and skin pigmentation, self-reported "color" and genomic ancestry, and skin pigmentation and genomic ancestry. We observed that, although there were significant differences between the three "color" groups in genomic ancestry and skin pigmentation, there was considerable dispersion within each group and substantial overlap between groups. We also saw that there was no good agreement between the "color" categories reported by each member of the sibling pair: 30 out of 86 sibling pairs reported different "color", and in some cases, the sibling reporting the darker "color" category had lighter skin pigmentation. Socioeconomic status was significantly associated with self-reported "color" and genomic ancestry in this sample. This and other studies show that subjective classifications based on self-reported "color", such as the one that is used in the Brazilian census, are inadequate to describe the population structure present in recently admixed populations. Finally, we observed that one of the AIMs included in the panel (rs1426654), which is located in the known pigmentation gene SLC24A5, was strongly associated with skin pigmentation in this sample.

  19. High values of disorder-generated multifractals and logarithmically correlated processes

    International Nuclear Information System (INIS)

    Fyodorov, Yan V.; Giraud, Olivier

    2015-01-01

    In the introductory section of the article we give a brief account of recent insights into statistics of high and extreme values of disorder-generated multifractals following a recent work by the first author with P. Le Doussal and A. Rosso (FLR) employing a close relation between multifractality and logarithmically correlated random fields. We then substantiate some aspects of the FLR approach analytically for multifractal eigenvectors in the Ruijsenaars–Schneider ensemble (RSE) of random matrices introduced by E. Bogomolny and the second author by providing an ab initio calculation that reveals hidden logarithmic correlations at the background of the disorder-generated multifractality. In the rest we investigate numerically a few representative models of that class, including the study of the highest component of multifractal eigenvectors in the Ruijsenaars–Schneider ensemble

  20. High Degree Cubature Federated Filter for Multisensor Information Fusion with Correlated Noises

    Directory of Open Access Journals (Sweden)

    Lijun Wang

    2016-01-01

    Full Text Available This paper proposes an improved high degree cubature federated filter for the nonlinear fusion system with cross-correlation between process and measurement noises at the same time using the fifth-degree cubature rule and the decorrelated principle in its local filters. The master filter of the federated filter adopts the no-reset mode to fuse local estimates of local filters to generate a global estimate according to the scalar weighted rule. The air-traffic maneuvering target tracking simulations are performed between the proposed filter and the fifth-degree cubature federated filter. Simulations results demonstrate that the proposed filter not only can achieve almost the same accuracy as the fifth-degree cubature federated filter with independent white noises, but also has superior performance to the fifth-degree cubature federated filter while the noises are cross-correlated at the same time.

  1. Prevalence of IFNL3 gene polymorphism among blood donors and its relation to genomic profile of ancestry in Brazil.

    Science.gov (United States)

    Rizzo, Silvia Renata Cornelio Parolin; Gazito, Diana; Pott-Junior, Henrique; Latini, Flavia Roche Moreira; Castelo, Adauto

    The recent development of interferon-free regimens based on direct-acting antivirals for the treatment of chronic hepatitis C virus infection has benefited many but not all patients. Some patients still experience treatment failure, possibly attributed to unknown host and viral factors, such as IFNL3 gene polymorphism. The present study assessed the prevalence of rs12979860-CC, rs12979860-CT, and rs12979860-TT genotypes of the IFNL3 gene, and its relationship with ancestry informative markers in 949 adult Brazilian healthy blood donors. Race was analyzed using ancestry informative markers as a surrogate for ancestry. IFNL3 gene was genotyped using the ABI TaqMan single nucleotide polymorphisms genotyping assays. The overall frequency of rs12979860-CC genotype was 36.9%. The contribution of African ancestry was significantly higher among donors from the northeast region in relation to southeast donors, whereas the influence of European ancestry was significantly higher in southeast donors. Donors with rs12979860-CC and rs12979860-CT genotypes had similar ancestry background. The contribution of African ancestry was higher among rs12979860-TT genotype donors in comparison to both rs12979860-CC and rs12979860-CT genotypes. The prevalence of rs12979860-CC genotype is similar to that found in the US, despite the Brazilian ancestry informative markers admixture. However, in terms of ancestry, rs12979860-CT genotype was much closer to rs12979860-CC individuals than to rs12979860-TT. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

  2. Positive Correlation between Serum Osteocalcin and Testosterone in Male Hyperthyroidism Patients with High Bone Turnover.

    Science.gov (United States)

    Zhong, N; Xu, B; Cui, R; Xu, M; Su, J; Zhang, Z; Liu, Y; Li, L; Sheng, C; Sheng, H; Qu, S

    2016-07-01

    Animal studies suggested that there is an independent bone-osteocalcin-gonadal axis, except of the hypothalamic-pituitary-gonadal axis. Based on this hypothesis, the higher osteocalcin during the high bone turnover should be followed by higher testosterone formation. Yet such clinical evidence is limited. The patients with uncontrolled hyperthyroidism are proper model with high bone turnover. If this hypothesis is true, there should be high testosterone level in patients with uncontrolled hyperthyroidism. Therefore, Graves' disease patients were recruited to study the correlation between osteocalcin and testosterone. 50 male hyperthyroidism patients with Graves' disease and 50 health persons matched by age and gender were enrolled in our cross-section study. Serum markers for thyroid hormone, sex hormone and bone metabolic markers including free triiodothyronine (FT3), free thyroxine (FT4), thyroid-stimulating hormone (TSH), testosterone, luteinizing hormone (LH), follicle-stimulating hormone (FSH) and osteocalcin (OC), C-terminal telopeptide fragments of type I collagen (CTX) were examined. The demographic parameters such as duration of disease were also collected. All data was analyzed by SPSS 20.0. High testosterone and osteocalcin level was observed in the hyperthyroidism patients (T 36.35±10.72 nmol/l and OC 46.79±26.83 ng/ml). In simple Pearson correlation, testosterone was positively associated with OC (r=0.486, Phyperthyroidism patients, osteocalcin was positively correlated with serum testosterone, which indirectly supports the hypothesis that serum osteocalcin participates in the regulation of sex hormone. © Georg Thieme Verlag KG Stuttgart · New York.

  3. Directly patching high-level exchange-correlation potential based on fully determined optimized effective potentials

    Science.gov (United States)

    Huang, Chen; Chi, Yu-Chieh

    2017-12-01

    The key element in Kohn-Sham (KS) density functional theory is the exchange-correlation (XC) potential. We recently proposed the exchange-correlation potential patching (XCPP) method with the aim of directly constructing high-level XC potential in a large system by patching the locally computed, high-level XC potentials throughout the system. In this work, we investigate the patching of the exact exchange (EXX) and the random phase approximation (RPA) correlation potentials. A major challenge of XCPP is that a cluster's XC potential, obtained by solving the optimized effective potential equation, is only determined up to an unknown constant. Without fully determining the clusters' XC potentials, the patched system's XC potential is "uneven" in the real space and may cause non-physical results. Here, we developed a simple method to determine this unknown constant. The performance of XCPP-RPA is investigated on three one-dimensional systems: H20, H10Li8, and the stretching of the H19-H bond. We investigated two definitions of EXX: (i) the definition based on the adiabatic connection and fluctuation dissipation theorem (ACFDT) and (ii) the Hartree-Fock (HF) definition. With ACFDT-type EXX, effective error cancellations were observed between the patched EXX and the patched RPA correlation potentials. Such error cancellations were absent for the HF-type EXX, which was attributed to the fact that for systems with fractional occupation numbers, the integral of the HF-type EXX hole is not -1. The KS spectra and band gaps from XCPP agree reasonably well with the benchmarks as we make the clusters large.

  4. Effect of strong correlations on the high energy anomaly in hole- and electron-doped high-Tc superconductors

    International Nuclear Information System (INIS)

    Moritz, B; Johnston, S; Greven, M; Shen, Z-X; Devereaux, T P; Schmitt, F; Meevasana, W; Motoyama, E M; Lu, D H; Kim, C; Scalettar, R T

    2009-01-01

    Recently, angle-resolved photoemission spectroscopy (ARPES) has been used to highlight an anomalously large band renormalization at high binding energies in cuprate superconductors: the high energy 'waterfall' or high energy anomaly (HEA). This paper demonstrates, using a combination of new ARPES measurements and quantum Monte Carlo simulations, that the HEA is not simply the by-product of matrix element effects, but rather represents a cross-over from a quasi-particle band at low binding energies near the Fermi level to valence bands at higher binding energy, assumed to be of strong oxygen character, in both hole- and electron-doped cuprates. While photoemission matrix elements clearly play a role in changing the aesthetic appearance of the band dispersion, i.e. the 'waterfall'-like behavior, they provide an inadequate description for the physics that underlies the strong band renormalization giving rise to the HEA. Model calculations of the single-band Hubbard Hamiltonian showcase the role played by correlations in the formation of the HEA and uncover significant differences in the HEA energy scale for hole- and electron-doped cuprates. In addition, this approach properly captures the transfer of spectral weight accompanying both hole and electron doping in a correlated material and provides a unifying description of the HEA across both sides of the cuprate phase diagram.

  5. Distribution and correlates of non-high-density lipoprotein cholesterol and triglycerides in Lebanese school children.

    Science.gov (United States)

    Gannagé-Yared, Marie-Hélène; Farah, Vanessa; Chahine, Elise; Balech, Nicole; Ibrahim, Toni; Asmar, Nadia; Barakett-Hamadé, Vanda; Jambart, Selim

    2016-01-01

    The prevalence of dyslipidelmia in pediatric Middle-Eastern populations is unknown. Our study aims to investigate the distribution and correlates of non-high-density lipoprotein cholesterol (non-HDL-C) and triglycerides among Lebanese school children. A total of 969 subjects aged 8-18 years were included in the study (505 boys and 464 girls). Recruitment was done from 10 schools located in the Great Beirut and Mount-Lebanon areas. Non-fasting total cholesterol, triglycerides, and HDL-cholesterol (HDL-C) were measured. Non-HDL-C was calculated. Schools were categorized into 3 socioeconomic statuses (SESs; low, middle, and high). In the overall population, the prevalence of high non-HDL-C (>3.8 mmol/L), very high non-HDL-C (>4.9 mmol/L), and high triglycerides (>1.5 mmol/l) are respectively 9.2%, 1.24%, and 26.6%. There is no significant gender difference for non-HDL-C or triglycerides. Non-HDL-C and triglycerides are inversely correlated with age in girls (P triglycerides are higher in children from lower SES schools. After adjustment for age and body mass index (BMI), testosterone is inversely associated with triglycerides in boys (P triglycerides are independently associated with BMI and schools' SES in both girls and boys. This study confirms, in our population, the association between obesity and both high non-HDL-C and triglycerides, and between high triglycerides and low SES. Copyright © 2016 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  6. High daily doses of benzodiazepines among Quebec seniors: prevalence and correlates

    Directory of Open Access Journals (Sweden)

    Moride Yola

    2001-11-01

    Full Text Available Abstract Background Use of high daily doses of benzodiazepines is generally contraindicated for seniors. While both patient and physician factors may influence the use of high daily doses, previous research on the effect of patient factors has been extremely limited. The objectives of this study were to determine the one year prevalence of use of high daily doses of benzodiazepines, and examine physician and patient correlates of such use among Quebec community-dwelling seniors. Methods Patient information for 1423 community-dwelling Quebec seniors who participated in the Canadian Study of Health and Aging was linked to provincial health insurance administrative data bases containing detailed information on prescriptions received and prescribers. Results The standardized one year period prevalence of use of high daily doses of benzodiazepines was 7.9%. Use of high daily doses was more frequent among younger seniors and those who had reported anxiety during the previous year. Patients without cognitive impairment were more likely to receive high dose prescriptions from general practitioners, while those with cognitive impairment were more likely to receive high dose prescriptions from specialists. Conclusion High dose prescribing appears to be related to both patient and physician factors.

  7. A Genealogical Look at Shared Ancestry on the X Chromosome.

    Science.gov (United States)

    Buffalo, Vince; Mount, Stephen M; Coop, Graham

    2016-09-01

    Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism data sets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We hope to learn additional information about recent ancestry through shared IBD segments on the X chromosome, but currently lack the theoretical framework to use this information fully. Here, we fill this gap by developing probability distributions for the number and length of X chromosome segments shared IBD between an individual and an ancestor k generations back, as well as between half- and full-cousin relationships. Due to the inheritance pattern of the X and the fact that X homologous recombination occurs only in females (outside of the pseudoautosomal regions), the number of females along a genealogical lineage is a key quantity for understanding the number and length of the IBD segments shared among relatives. When inferring relationships among individuals, the number of female ancestors along a genealogical lineage will often be unknown. Therefore, our IBD segment length and number distributions marginalize over this unknown number of recombinational meioses through a distribution of recombinational meioses we derive. By using Bayes' theorem to invert these distributions, we can estimate the number of female ancestors between two relatives, giving us details about the genealogical relations between individuals not possible with autosomal data alone. Copyright © 2016 by the Genetics Society of America.

  8. The relationship of family history and risk of type 2 diabetes differs by ancestry.

    Science.gov (United States)

    Kral, B G; Becker, D M; Yanek, L R; Vaidya, D; Mathias, R A; Becker, L C; Kalyani, R R

    2018-05-21

    Type 2 diabetes (T2DM) in a first-degree relative is a risk factor for incident diabetes. Americans of African ancestry (AA) have higher rates of T2DM than Americans of European ancestry (EA). Thus, we aimed to determine whether the presence, number and kinship of affected relatives are associated with race-specific T2DM incidence in a prospective study of participants from the Genetic Study of Atherosclerosis Risk (GeneSTAR), who underwent baseline screening including a detailed family history. Nondiabetic healthy siblings (n=1405) of patients with early-onset coronary artery disease (18-59 years) were enrolled (861 EA and 544 AA) and followed for incident T2DM (mean 14±6 years). Baseline age was 46.2±7.3 years and 56% were female. T2DM occurred in 12.3% of EA and 19.1% of AA. Among EA, 32.6% had ≥1 affected first-degree relatives versus 53.1% in AA, Phistory was related to incident T2DM in EA (HR=2.53, 95% CI: 1.58-4.06) but not in AA (HR=1.01, 0.67-1.53). The number of affected relatives conferred incremental risk of T2DM in EA with HR=1.82 (1.08-3.06), 4.83 (2.15-10.85) and 8.46 (3.09-23.91) for 1, 2, and ≥3 affected, respectively. In AA only ≥3 affected increased risk (HR=2.45, 1.44-4.19). Specific kinship patterns were associated with incident T2DM in EA but not in AA. The presence of any first-degree relative with T2DM does not discriminate risk in AA given the high race-specific prevalence of diabetes. Accounting for the number of affected relatives may more appropriately estimate risk for incident diabetes in both races. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  9. The Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome Reveals a Network of Epistatic Fitness Interactions.

    Science.gov (United States)

    Pool, John E

    2015-12-01

    North American populations of Drosophila melanogaster derive from both European and African source populations, but despite their importance for genetic research, patterns of ancestry along their genomes are largely undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome, which may have implications for reference alignment, association mapping, and population genomic studies in Drosophila. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Combining my estimate of admixture timing with historical records, I provide the first estimate of natural generation time for this species (approximately 15 generations per year). Ancestry levels were found to vary strikingly across the genome, with less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes (e.g., circadian rhythm). An important role for natural selection during the admixture process was further supported by evidence that many unlinked pairs of loci showed a deficiency of Africa-Europe allele combinations between them. Numerous epistatic fitness interactions may therefore exist between African and European genotypes, leading to ongoing selection against incompatible variants. By focusing on hubs in this network of fitness interactions, I identified a set of interacting loci that include genes with roles in sensation and neuropeptide/hormone reception. These findings suggest that admixed D. melanogaster samples could become an important study system for the genetics of early-stage isolation between populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Gene-by-Psychosocial Factor Interactions Influence Diastolic Blood Pressure in European and African Ancestry Populations: Meta-Analysis of Four Cohort Studies

    Directory of Open Access Journals (Sweden)

    Jennifer A. Smith

    2017-12-01

    Full Text Available Inter-individual variability in blood pressure (BP is influenced by both genetic and non-genetic factors including socioeconomic and psychosocial stressors. A deeper understanding of the gene-by-socioeconomic/psychosocial factor interactions on BP may help to identify individuals that are genetically susceptible to high BP in specific social contexts. In this study, we used a genomic region-based method for longitudinal analysis, Longitudinal Gene-Environment-Wide Interaction Studies (LGEWIS, to evaluate the effects of interactions between known socioeconomic/psychosocial and genetic risk factors on systolic and diastolic BP in four large epidemiologic cohorts of European and/or African ancestry. After correction for multiple testing, two interactions were significantly associated with diastolic BP. In European ancestry participants, outward/trait anger score had a significant interaction with the C10orf107 genomic region (p = 0.0019. In African ancestry participants, depressive symptom score had a significant interaction with the HFE genomic region (p = 0.0048. This study provides a foundation for using genomic region-based longitudinal analysis to identify subgroups of the population that may be at greater risk of elevated BP due to the combined influence of genetic and socioeconomic/psychosocial risk factors.

  11. Herschel-ATLAS: The Angular Correlation Function of Submillimetre Galaxies at High and Low Redshift

    Science.gov (United States)

    Maddox, S. J.; Dunne, L.; Rigby, E.; Eales, S.; Cooray, A.; Scott, D.; Peacock, J. A.; Negrello, M.; Smith, D. J. B.; Benford, D.; hide

    2010-01-01

    We present measurements of the angular correlation function of galaxies selected from the first field of the H-ATLAS survey. Careful removal of the background from galactic cirrus is essential, and currently dominates the uncertainty in our measurements. For our 250 micrometer-selected sample we detect no significant clustering, consistent with the expectation that the 250 pm-selected sources are mostly normal galaxies at z high redshift galaxies at z approx. 2-3 we detect significant strong clustering, leading to an estimate of r(0) approx. 7-11/h Mpc. The slope of our clustering measurements is very steep. delta approx. 2. The measurements are consistent with the idea that sub-mm sources consist of a low redshift population of normal galaxies and a high redshift population of highly clustered star-bursting galaxies.

  12. High-resolution CT of the lungs: Anatomic-pathologic correlation

    International Nuclear Information System (INIS)

    Stein, M.G.; Webb, W.R.; Finkbeiner, W.; Gamsu, G.

    1986-01-01

    The interpretation of thin-section (1.5-mm), high-resolution CT scans of the lungs has been limited by lack of direct radiologic and pathologic correlation. The author scanned fresh inflated isolated lungs from ten healthy and five diseased subjects using thin-section, high-resolution techniques. The lungs were then fixed by inflation with endobronchial Formalin. Gough sections (1 mm thick) were obtained at the same levels as the CT scans. In healthy subjects, secondary lobules were identified by the presence of visible interlobular septa and central arterioles. In some patients with disease, septal thickening was visible. In patients with honeycombing cystic areas of destroyed lung were seen, along with areas of fibrosis. Emphysema was well evaluated. Thin-section, high-resolution CT can define lung architecture and may resolve mild changes of the interstitium

  13. CORRELATION BETWEEN FAMILY COMMUNICATION PATTERNS AND JUVENILE DELINQUENCY IN JUNIOR HIGH SCHOOL

    Directory of Open Access Journals (Sweden)

    Zurriyatun Thoyibah

    2017-08-01

    Full Text Available Background: Adolescents who are in transition period have high risk behavior of juvenile delinquency. Communication between parents and adolescents effectively and openly could help adolescents to avoid delinquency behavior. Objective: This study aims to examine the relationship between family communication patterns and juvenile delinquency in Junior High School. Methods: This research employed a cross-sectional design with correlation description approach. There were 243 students selected using simple random sampling from the 7th and 8th grade students of Junior High School. A questionnaire of juvenile delinquency and family communication pattern were used in this study. Data were analyzed using Chi Square test. Result: The research showed that the majority juvenile delinquency category was low (65% and the majority of communication pattern was in functional category (73.3%. There was a significant relationship between family communication pattern and juvenile delinquency (p<0.05. Conclusion: Communication pattern within family have significant association with juvenile delinquency.

  14. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

    Directory of Open Access Journals (Sweden)

    Geiger Dan

    2010-10-01

    Full Text Available Abstract Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD among African Americans (AA remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1 Assembly of the sample dataset (ESKD AA; 2 Design of the estimated mutual information ancestry informative markers (n = 2016 screening panel 3; Genotyping the sample set whose size was determined by a power analysis (n = 576 appropriate for the initial screening panel; 4 Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5 Enrichment of the initial screening panel; 6 Power analysis of the enriched panel 7 Genotyping of additional samples. 8 Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non

  15. The effect of high correlated colour temperature office lighting on employee wellbeing and work performance

    Directory of Open Access Journals (Sweden)

    Tomkins Susannah C

    2007-01-01

    Full Text Available Abstract Background The effects of lighting on the human circadian system are well-established. The recent discovery of 'non-visual' retinal receptors has confirmed an anatomical basis for the non-image forming, biological effects of light and has stimulated interest in the use of light to enhance wellbeing in the corporate setting. Methods A prospective controlled intervention study was conducted within a shift-working call centre to investigate the effect of newly developed fluorescent light sources with a high correlated colour temperature (17000 K upon the wellbeing, functioning and work performance of employees. Five items of the SF-36 questionnaire and a modification of the Columbia Jet Lag scale, were used to evaluate employees on two different floors of the call centre between February and May 2005. Questionnaire completion occurred at baseline and after a three month intervention period, during which time one floor was exposed to new high correlated colour temperature lighting and the other remained exposed to usual office lighting. Two sided t-tests with Bonferroni correction for type I errors were used to compare the characteristics of the two groups at baseline and to evaluate changes in the intervention and control groups over the period of the study. Results Individuals in the intervention arm of the study showed a significant improvement in self-reported ability to concentrate at study end as compared to those within the control arm (p Conclusion High correlated colour temperature fluorescent lights could provide a useful intervention to improve wellbeing and productivity in the corporate setting, although further work is necessary in quantifying the magnitude of likely benefits.

  16. High energy x-ray scattering studies of strongly correlated oxides

    International Nuclear Information System (INIS)

    Hatton, Peter D; Wilkins, S B; Spencer, P D; Zimmermann, M v; D'Almeida, T

    2003-01-01

    Many transition metal oxides display strongly correlated charge, spin, or orbital ordering resulting in varied phenomena such as colossal magnetoresistance, high temperature superconductivity, metal-insulator transitions etc. X-ray scattering is one of the principle techniques for probing the structural response to such effects. In this paper, we discuss and review the use of synchrotron radiation high energy x-rays (50-200 keV) for the study of transition metal oxides such as nickelates (La 2-x Sr x NiO 4 ) and manganites (La 2-2x Sr 1+2x Mn 2 O 7 ). High energy x-rays have sufficient penetration to allow us to study large flux-grown single crystals. The huge increase in sample scattering volume means that extremely weak peaks can be observed. This allows us to study very weak charge ordering. Measurements of the intensity, width and position of the charge ordering satellites as a function of temperature provide us with quantitative measures of the charge amplitude, inverse correlation length and wavevector of the charge ordering

  17. Meta-Analysis of Correlations Between Marginal Bone Resorption and High Insertion Torque of Dental Implants.

    Science.gov (United States)

    Li, Haoyan; Liang, Yongqiang; Zheng, Qiang

    2015-01-01

    To evaluate correlations between marginal bone resorption and high insertion torque value (> 50 Ncm) of dental implants and to assess the significance of immediate and early/conventional loading of implants under a certain range torque value. Specific inclusion and exclusion criteria were used to retrieve eligible articles from Ovid, PubMed, and EBSCO up to December 2013. Screening of eligible studies, quality assessment, and data extraction were conducted in duplicate. The results were expressed as random/fixed-effects models using weighted mean differences for continuous outcomes with 95% confidence intervals. Initially, 154 articles were selected (11 from Ovid, 112 from PubMed, and 31 from EBSCO). After exclusion of duplicate articles and articles that did not meet the inclusion criteria, six clinical studies were selected. Assessment of P values revealed that correlations between marginal bone resorption and high insertion torque were not statistically significant and that there was no difference between immediately versus early/conventionally loaded implants under a certain range of torque. None of the meta-analyses revealed any statistically significant differences between high insertion torque and conventional insertion torque in terms of effects on marginal bone resorption.

  18. Measurement and correlation of high frequency behaviors of a very flexible beam undergoing large deformation

    International Nuclear Information System (INIS)

    Lee, Jae Wook; Kim, Hyun Woo; Ku, Hi Chun; Yoo, Wan Suk

    2009-01-01

    A correlation method of high frequency behaviors of a very flexible beam undergoing large displacement is presented. The suggested method based on the experimental modal analysis leads to more accurate correlation results because it directly uses the modal parameters of each mode achieved from experiment. First, the modal testing and the parameter identification method are suggested for flexible multibody dynamics. Due to the flexibility of a very thin beam, traditional testing methods such as impact hammer or contact type accelerometer are not working well. The suggested measurement with high speed camera, even though the test beam is very flexible, is working well. Using measurements with a high speed camera, modal properties until the 5th mode are measured. And After measuring each damping ratio until the 5th mode, a generic damping model is constructed using inverse modal transformation technique. It's very interesting that the modal transformation technique can be also applied even in the ANCF simulation which uses the global displacement and finite slope as the nodal coordinates. The results of experiment and simulation are compared until the 5th mode frequency, respectively, by using ANCF forced vibration analysis. Through comparison between numerical simulation and experiment, this study showed that the proposed generic damping matrix, modal testing and parameter identification method is very proper in flexible multibody dynamic problems undergoing large deformation

  19. Predicting freeboard heat transfer by using empirical correlations in high temperature fluidized beds

    Energy Technology Data Exchange (ETDEWEB)

    Biyikli, Suleyman [Okan University Tuzla Kampusu, Faculty of Engineering and Architecture (Turkey)], email: suleyman.biyikli@okan.edu.tr

    2011-07-01

    This article investigates the heat transfer characteristics for horizontal tubes in a freeboard region of high temperature fluidized beds. The freeboard entrainment heights are calculated by using empirical correlations described in detail and used in estimating the heat transfer coefficients from a horizontal tube occurring by radiation, gas convection, and particle contact mechanisms in high temperature a fluidized bed combustor. The total average of these coefficients around a horizontal tube carrying water in high temperature fluidized beds can be written as the sum of convective, radiative, and fluidized-particle contact heat transfer coefficients and these correlations are tested against certain published experimental measurements. In full agreement with this data, it was observed that the calculated heat transfer coefficients increased with increasing gas velocity at a given tube elevation and they decreased and approached the values of single-phase gas convection and radiation with increasing tube elevation in the freeboard region while the relative contribution of radiation increases and approaches a constant fraction of total heat transfer.

  20. High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria.

    Directory of Open Access Journals (Sweden)

    Yeung Lo Tutterrow

    Full Text Available VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2. Thus, the purpose of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low transmission areas in Cameroon were evaluated for Ab to FV2 and the proportion of high avidity Ab (i.e., Ab that remain bound in the presence of 3M NH(4SCN was assessed. Ab levels and proportion of high avidity Ab were compared between women with placental malaria (PM(+ and those without (PM(- at delivery. Results showed that PM(- women had significantly higher Ab levels (p = 0.0047 and proportion of high avidity Ab (p = 0.0009 than PM(+ women throughout pregnancy. Specifically, women with moderate to high Ab levels (>5,000 MFI and those with ≥ 35% high avidity Ab at 5-6 months were found to have 2.3 (95% CI, 1.0-4.9 and 7.6-fold (p = 0.0013, 95% CI: 1.2-50.0 reduced risk of placental malaria, respectively. These data show that high levels of Ab to FV2, particularly those with high avidity for FV2, produced by mid-pregnancy are important in clearing parasites from the placenta. Both high Ab levels and proportion of high avidity Ab to FV2 may serve as correlates of protection for assessing immunity against placental malaria.

  1. Race/ethnicity, genetic ancestry, and breast cancer-related lymphedema in the Pathways Study.

    Science.gov (United States)

    Kwan, Marilyn L; Yao, Song; Lee, Valerie S; Roh, Janise M; Zhu, Qianqian; Ergas, Isaac J; Liu, Qian; Zhang, Yali; Kutner, Susan E; Quesenberry, Charles P; Ambrosone, Christine B; Kushi, Lawrence H

    2016-08-01

    Breast cancer-related lymphedema (BCRL) is a serious chronic condition after breast cancer (BC) surgery and treatment. It is unclear if BCRL risk varies by race/ethnicity. In a multiethnic prospective cohort study of 2953 BC patients, we examined the association of self-reported BCRL status with self-reported race/ethnicity and estimated genetic ancestry. Hazard ratios (HR) and 95 % confidence intervals (CI) were calculated by multivariable Cox proportional hazards models, with follow-up starting 6 months post-BC diagnosis. Estimates were further stratified by body mass index (BMI). By 48 months of follow-up, 342 (11.6 %) women reported having BCRL. Younger age at BC diagnosis, higher BMI at baseline, and lower physical activity were associated with greater BCRL risk. African American (AA) women had a 2-fold increased risk of BCRL compared with White women (HR = 2.04; 95 % CI 1.35-3.08). African genetic ancestry was also associated with an increased risk (HR = 2.50; 95 % CI 1.43, 4.36). Both risks were attenuated but remained elevated after adjusting for known risk factors and became more pronounced when restricted to the nonobese women (adjusted HR = 2.31 for AA and HR = 3.70 for African ancestry, both p ancestry data, with a potential ancestry-obesity interaction.

  2. Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors.

    Science.gov (United States)

    Sandoval, Jose R; Salazar-Granara, Alberto; Acosta, Oscar; Castillo-Herrera, Wilder; Fujita, Ricardo; Pena, Sergio D J; Santos, Fabricio R

    2013-09-01

    In order to investigate the underlying genetic structure and genomic ancestry proportions of Peruvian subpopulations, we analyzed 551 human samples of 25 localities from the Andean, Amazonian, and Coastal regions of Peru with a set of 40 ancestry informative insertion-deletion polymorphisms. Using genotypes of reference populations from different continents for comparison, our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry. Among populations from the Titicaca Lake islands of Taquile, Amantani, Anapia, and Uros, and the Yanque locality from the southern Peruvian Andes, there was no significant proportion of non-autochthonous genomes, indicating that their genetic background is effectively derived from the first settlers of South America. However, the Andean populations from San Marcos, Cajamarca, Characato and Chogo, and coastal populations from Lambayeque and Lima displayed a low but significant European ancestry proportion. Furthermore, Amazonian localities of Pucallpa, Lamas, Chachapoyas, and Andean localities of Ayacucho and Huancayo displayed intermediate levels of non-autochthonous ancestry, mostly from Europe. These results are in close agreement with the documented history of post-Columbian immigrations in Peru and with several reports suggesting a larger effective size of indigenous inhabitants during the formation of the current country's population.

  3. Quantification of Maxillary Dental Arcade Curvature and the Estimation of Biological Ancestry in Forensic Anthropology.

    Science.gov (United States)

    Clark, Melissa A; Guatelli-Steinberg, Debbie; Hubbe, Mark; Stout, Sam

    2016-01-01

    Previous studies suggest that palate shape is a useful indicator of biological ancestry in human remains. This study evaluates interobserver error in ancestry estimation using palate shape and explores palate shape variation in Gullah (descendants of West Africans) and Seminole (Indigenous American) population samples using geometric morphometric analysis. Ten participants were asked to ascribe biological ancestry and shape to 28 dental casts based on a classification scheme employed in previous studies. The mean correct classification was 42.0%, indicating that the likelihood of assigning the correct ancestry is very poor and not significantly different from random assignment (p = 0.12). The accuracy analysis based on categorical classification of the casts was complemented by geometric morphometric analysis of nine 3D landmarks reflecting palate shape of 158 casts. Principal component analysis results show no difference between populations regarding palate shape, and cross-validated discriminant function analysis correctly classified only 62.0% of the specimens. Combined, these results show that previous methods to estimate ancestry are inaccurate and that this inaccuracy is probably due to a lack of palate shape differences between groups, rather than limitation of the analytical method per se. Therefore, we recommend caution should be used when choosing to apply the analysis of palate shape in forensically relevant contexts. © 2015 American Academy of Forensic Sciences.

  4. High-resolution computed tomography in silicosis: correlation with chest radiography and pulmonary function tests

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, Agnaldo Jose [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Pedro Ernesto Univ. Hospital. Dept. of Respiratory Function]. E-mail: phel.lop@uol.com.br; Mogami, Roberto; Capone, Domenico; Jansen, Jose Manoel [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). School of Medical Sciences; Tessarollo, Bernardo [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Dept. of Radiology and Diagnostic Image; Melo, Pedro Lopes de [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Inst. of Biology

    2008-05-15

    Objective: To correlate tomographic findings with pulmonary function findings, as well as to compare chest X-ray findings with high-resolution computed tomography (HRCT) findings, in patients with silicosis. Methods: A cross-sectional study was conducted in 44 non-smoking patients without a history of tuberculosis. Chest X-ray findings were classified according to the International Labour Organization recommendations. Using a semiquantitative system, the following HRCT findings were measured: the full extent of pulmonary involvement; parenchymal opacities; and emphysema. Spirometry and forced oscillation were performed. Pulmonary volumes were evaluated using the helium dilution method, and diffusing capacity of the lung for carbon monoxide was assessed. Results: Of the 44 patients studied, 41 were male. The mean age was 48.4 years. There were 4 patients who were classified as category 0 based on X-ray findings and as category 1 based on HRCT findings. Using HRCT scans, we identified progressive massive fibrosis in 33 patients, compared with only 23 patients when X-rays were used. Opacity score was found to correlate most closely with airflow, DLCO and compliance. Emphysema score correlated inversely with volume, DLCO and airflow. In this sample of patients presenting a predominance of large opacities (75% of the individuals), the deterioration of pulmonary function was associated with the extent of structural changes. Conclusions: In the early detection of silicosis and the identification of progressive massive fibrosis, HRCT scans are superior to X-rays. (author)

  5. High-resolution computed tomography in silicosis: correlation with chest radiography and pulmonary function tests

    International Nuclear Information System (INIS)

    Lopes, Agnaldo Jose; Mogami, Roberto; Capone, Domenico; Jansen, Jose Manoel; Tessarollo, Bernardo; Melo, Pedro Lopes de

    2008-01-01

    Objective: To correlate tomographic findings with pulmonary function findings, as well as to compare chest X-ray findings with high-resolution computed tomography (HRCT) findings, in patients with silicosis. Methods: A cross-sectional study was conducted in 44 non-smoking patients without a history of tuberculosis. Chest X-ray findings were classified according to the International Labour Organization recommendations. Using a semiquantitative system, the following HRCT findings were measured: the full extent of pulmonary involvement; parenchymal opacities; and emphysema. Spirometry and forced oscillation were performed. Pulmonary volumes were evaluated using the helium dilution method, and diffusing capacity of the lung for carbon monoxide was assessed. Results: Of the 44 patients studied, 41 were male. The mean age was 48.4 years. There were 4 patients who were classified as category 0 based on X-ray findings and as category 1 based on HRCT findings. Using HRCT scans, we identified progressive massive fibrosis in 33 patients, compared with only 23 patients when X-rays were used. Opacity score was found to correlate most closely with airflow, DLCO and compliance. Emphysema score correlated inversely with volume, DLCO and airflow. In this sample of patients presenting a predominance of large opacities (75% of the individuals), the deterioration of pulmonary function was associated with the extent of structural changes. Conclusions: In the early detection of silicosis and the identification of progressive massive fibrosis, HRCT scans are superior to X-rays. (author)

  6. Serum leptin levels correlation with high blood pressure in adult females

    International Nuclear Information System (INIS)

    Haque, Z.; Shahid, K.U.; Mazahir, I.; Lakho, G.R.; Nafees, M.

    2006-01-01

    To measure serum leptin levels and compare them in lean and obese subjects and to identify correlation between serum leptin levels, heart rate and hypertension in lean and obese subjects among adult females. Seventy female subjects with different body mass indices were selected from OPD of Jinnah Medical and Dental College Hospital (OPD), Karachi. Heart rate was counted manually; blood pressure was measured by mercury sphygmomanometer while serum leptin was measured using enzyme-linked immunoassay. The outcomes hypertension and heart rate were correlated to risk factor leptin. Mean heart rate, systolic and diastolic blood pressure and serum leptin levels of obese people were 90+-1, 142+-2, 89+-1 and 24.13+-1.7 respectively, which were significantly higher as compared to lean subjects (p<0.05). All the parameters correlated positively and significantly with increasing BMI. There was a relationship of tachycardia and hypertension with high serum leptin levels in obesity. Serum leptin levels increase with the level of obesity. Hyper-leptinemia is associated with tachycardia and increases in both systolic and diastolic blood pressure in obesity via complex mechanisms. (author)

  7. Breast MR imaging: correlation of high resolution dynamic MR findings with prognostic factors

    International Nuclear Information System (INIS)

    Lee, Shin Ho; Cho, Nariya; Chung, Hye Kyung; Kim, Seung Ja; Cho, Kyung Soo; Moon, Woo Kyung; Cho, Joo Hee

    2005-01-01

    We wanted to correlate the kinetic and morphologic MR findings of invasive breast cancer with the classical and molecular prognostic factors. Eighty-seven patients with invasive ductal carcinoma NOS underwent dynamic MR imaging at 1.5 T, and with using the T1-weighted 3D FLASH technique. The morphologic findings (shape, margin, internal enhancement of the mass or the enhancement distribution and the internal enhancement of any non-mass lesion) and the kinetic findings (the initial phase and the delayed phase of the time-signal. Intensity curve) were interpreted using a ACR BI-RADS-MRI lexicon. We correlate MR findings with histopathologic prognostic factors (tumor size, lymph node status and tumor grade) and the immunohistochemically detected biomarkers (ER, PR, ρ 53, c-erbB-2, EGFR and Ki-67). Univariate and multivariate statistical analyses were than performed. Among the MR findings, a spiculated margin, rim enhancement and washout were significantly correlated with the prognostic factors. A spiculated margin was independently associated with the established predictors of a good prognosis (a lower histologic and nuclear grade, positive ER and PR) and rim enhancement was associated with a poor prognosis (a higher histologic and nuclear grade, negative ER and PR). Wash out was a independent predictor of Ki-67 activity. Some of the findings of high resolution dynamic MR imaging were associated with the prognostic factors, and these findings may predict the prognosis of breast cancer

  8. Study of Isospin Correlation in High Energy Heavy Ion Interactions with the RHIC PHENIX. Final Report

    International Nuclear Information System (INIS)

    Takahashi, Y.

    2003-01-01

    This report describes the research work performed under the support of the DOE research grant E-FG02-97ER4108. The work is composed of three parts: (1) Visual analysis and quality control of the Micro Vertex Detector (MVD) of the PHENIX experiments carried out of Brookhaven National Laboratory. (2) Continuation of the data analysis of the EMU05/09/16 experiments for the study of the inclusive particle production spectra and multi-particle correlation. (3) Exploration of a new statistical means to study very high-multiplicity of nuclear-particle ensembles and its perspectives to apply to the higher energy experiments

  9. ANALYZING THE MATHEMATICAL DISPOSITION AND ITS CORRELATION WITH MATHEMATICS ACHIEVEMENT OF ABSTRACT SENIOR HIGH SCHOOL STUDENTS

    Directory of Open Access Journals (Sweden)

    Louise M. Saija

    2012-09-01

    Full Text Available Salah satu standar yang diberikan oleh National Council of Teachers of Mathematics (NCTM adalah disposisi matematik. Disposisi  bukan sekedar merujuk pada sikap tetapi suatu kecenderungan untuk berpikir dan bersikap dalam cara yang positif. Penelitian ini bertujuan untuk menganalisa disposisi matematik dan hubungannya dengan hasil belajar matematika siswa-siswa sekolah menengah atas (SMA. Sampel pada penelitian ini adalah 149 siswa SMA di Bandung. Analisa statistik didasarkan pada korelasi peringkat Spearman dan uji-t. Ditemukan bahwa secara rata-rata,  disposisi matematik dari siswa-siswa SMA dikategorikan rendah. Selanjutnya, terdapat korelasi positif dan signifikan antara disposisi matematik dan hasil belajar matematika siswa-siswa SMA, walaupun nilai koefisien korelasinya tidak tinggi. Suatu observasi juga dilakukan untuk menganalisa hubungan ini, dan didapati bahwa walaupun beberapa siswa memiliki disposisi matematik yang baik, kadang kala mereka tidak dapat menyelesaikan ujian dengan baik, karena padatnya kurikulum, dan juga aktifitas sosial mereka, yang membuat hasil belajar matematika mereka lebih rendah. Temuan lainnya adalah bahwa siswa-siswa SMA memerlukan guru-guru matematika dengan lebih banyak strategi mengajar  agar mereka dapat memiliki disposisi matematik yang lebih baik.   Kata Kunci: Disposisi Matematik, Hasil Belajar Matematika       One of the evaluation standards given by the National Council of Teachers of Mathematics (NCTM was mathematical disposition. Disposition refers not simply to attitudes but to a tendency to think and to act in positive ways. This study aimed to analyze the mathematical disposition and its correlation with mathematics achievement of senior high school (SMA students. A total of 149 SMA students in Bandung were procured as samples. Statistical analysis was based on the Spearman rank correlation and on the t-test. The findings showed that at average, the mathematical disposition of the SMA

  10. Paraquat-poisoning in the rabbit lungs: high resolution computed tomographic findings and pathologic correlation

    International Nuclear Information System (INIS)

    Lee, Kyung Soo; Kim, Eui Han; Lee, Byoung Ho; Kim, Kun Sang

    1992-01-01

    The authors evaluated high resolution computed tomographic (HRCT) findings of the isolated rabbit lungs with paraquat poisoning, and the findings were correlated with pathologic specimens. The purposes of this study are 1) to obtain the HRCT findings of the normal rabbit lung. 2) to find out if pulmonary pathology can be induced in rabbits by paraquat, and 3) to correlate the HRCT findings to those of pathology. Thirty rabbits were divided into three groups: group I included four control rabbits; group II included 16 rabbits given paraquat intraperitoneally (IP group); and group III included 10 rabbits given paraquat intravenously (IV group). The rabbits were sacrificed seven, 10, and 14 days after injection of various amount of paraquat, and then the lungs were isolated for HRCT and pathologic studies. Gross and microscopic findings of the three groups of control and paraquat-injected rabbit lungs were correlated with HRCT findings. Pulmonary congestion, mild thickening of alveolar walls and septae, and multifocal micro-atelectasis were the man pathologic findings of the lungs in both groups of the rabbits. Pulmonary hemorrhage was noted in five (31%) of 16 rabbits of IP group and three (30%) of 10 IV group. Pulmonary edema was seen in one rabbits (6%) of IP and four (40%) of IV group. Typical pulmonary fibrosis was seen in one rabbit of IP (6%) and IV (10%) group, respectively. There was no correlation between the amount of paraquat and frequency of the pulmonary pathology. Pulmonary fibrosis was seen at least one week after the paraquat injection. On HRCT, pulmonary hemorrhage and edema appeared as diffuse air-space consolidation and pulmonary fibrosis as linear or band-like opacities. However, minimal changes such as mild congestion

  11. High correlation between quantitative ultrasound and DXA during 7 years of follow-up

    Energy Technology Data Exchange (ETDEWEB)

    Trimpou, Penelope [Section for Endocrinology, Department of Internal Medicine, Sahlgrenska University Hospital at Sahlgrenska Academy, University of Gothenburg, SE-41345 Goeteborg (Sweden)], E-mail: pinelopi.trimpou@vgregion.se; Bosaeus, Ingvar [Department for Clinical Nutrition, Sahlgrenska University Hospital, Goeteborg (Sweden)], E-mail: ingvar.bosaeus@nutrition.gu.se; Bengtsson, Bengt-Ake [Section for Endocrinology, Department of Internal Medicine, Sahlgrenska University Hospital at Sahlgrenska Academy, University of Gothenburg, SE-41345 Goeteborg (Sweden)], E-mail: bengt-ake.bengtsson@medic.gu.se; Landin-Wilhelmsen, Kerstin [Section for Endocrinology, Department of Internal Medicine, Sahlgrenska University Hospital at Sahlgrenska Academy, University of Gothenburg, SE-41345 Goeteborg (Sweden)], E-mail: kerstin.landin@sahlgrenska.se

    2010-02-15

    Ultrasound is a quick, cheap and non-radiating device for assessing bone quality. We wanted to validate the method for clinical and epidemiological use. Eighty women, aged 53-73 years, with osteoporosis and/or fractures were followed repeatedly during 7 years. Quantitative ultrasound (QUS) measurements (LUNAR Achilles) were compared with bone mineral density (BMD) and bone mineral content (BMC) estimated by DXA (LUNAR) in regions of interest. Changes in the speed of sound, broadband ultrasound attenuation and stiffness were positively correlated with changes in BMD and BMC in all regions measured with DXA (r = 0.20-0.53; p = 0.09 to <0.0001). The QUS t-score at the left heel was positively correlated with the t-score at the right heel (r = 0.90, p < 0.0001). The DXA t-score of the left vs. the right femur was also positively correlated (r = 0.72-0.86; p < 0.0001). A t-score < -2.5 S.D. was found in 70% and 56% at baseline, and 74% and 65% at follow-up measured with QUS and DXA, respectively. The mean sensitivity of QUS vs. DXA was 79% and the mean specificity 45% over a 7-year period. A QUS t-score of <-3.65 S.D. was consistent with a DXA t-score of <-2.5 S.D. In conclusion, QUS was well correlated with DXA in all regions over the 7-year period. QUS can be used in settings without access to DXA and in epidemiological studies. The sensitivity was high but the specificity was low, implicating that DXA, if available, is recommended before treatment for osteoporosis. However, treatment can be started without DXA at a QUS t-score < -3.65 S.D., and especially in the presence of fractures.

  12. ICE-Based Custom Full-Mesh Network for the CHIME High Bandwidth Radio Astronomy Correlator

    Science.gov (United States)

    Bandura, K.; Cliche, J. F.; Dobbs, M. A.; Gilbert, A. J.; Ittah, D.; Mena Parra, J.; Smecher, G.

    2016-03-01

    New generation radio interferometers encode signals from thousands of antenna feeds across large bandwidth. Channelizing and correlating this data requires networking capabilities that can handle unprecedented data rates with reasonable cost. The Canadian Hydrogen Intensity Mapping Experiment (CHIME) correlator processes 8-bits from N=2,048 digitizer inputs across 400MHz of bandwidth. Measured in N2× bandwidth, it is the largest radio correlator that is currently commissioning. Its digital back-end must exchange and reorganize the 6.6terabit/s produced by its 128 digitizing and channelizing nodes, and feed it to the 256 graphics processing unit (GPU) node spatial correlator in a way that each node obtains data from all digitizer inputs but across a small fraction of the bandwidth (i.e. ‘corner-turn’). In order to maximize performance and reliability of the corner-turn system while minimizing cost, a custom networking solution has been implemented. The system makes use of Field Programmable Gate Array (FPGA) transceivers to implement direct, passive copper, full-mesh, high speed serial connections between sixteen circuit boards in a crate, to exchange data between crates, and to offload the data to a cluster of 256 GPU nodes using standard 10Gbit/s Ethernet links. The GPU nodes complete the corner-turn by combining data from all crates and then computing visibilities. Eye diagrams and frame error counters confirm error-free operation of the corner-turn network in both the currently operating CHIME Pathfinder telescope (a prototype for the full CHIME telescope) and a representative fraction of the full CHIME hardware providing an end-to-end system validation. An analysis of an equivalent corner-turn system built with Ethernet switches instead of custom passive data links is provided.

  13. Correlative degree and collective side ward flow of final state particles in high energy heavy ion collisions

    International Nuclear Information System (INIS)

    Zhang Weigang

    1999-01-01

    A concept of correlative degree is proposed. Using the method of particle-group correlation's function, the effects of the particles with different correlative degrees on collective side ward flow are studied for 1.2A GeV Ar + Bal 2 collisions at the Bevalac stream chamber. The studies indicate that correlative degree is an important parameter on describing collective side ward flow properties. The minority of correlative particles (or fragments) with larger correlative degrees can produce the effect arising from the collective side ward flow, but the effect arising from high-order collective flow correlations can not be dominated by these minority of particles (or fragments). It is results from the collective contribution of the majority of collective particles (or fragments) with various correlative degrees

  14. Bio science: genetic genealogy testing and the pursuit of African ancestry.

    Science.gov (United States)

    Nelson, Alondra

    2008-10-01

    This paper considers the extent to which the geneticization of 'race' and ethnicity is the prevailing outcome of genetic testing for genealogical purposes. The decoding of the human genome precipitated a change of paradigms in genetics research, from an emphasis on genetic similarity to a focus on molecular-level differences among individuals and groups. This shift from lumping to splitting spurred ongoing disagreements among scholars about the significance of 'race' and ethnicity in the genetics era. I characterize these divergent perspectives as 'pragmatism' and 'naturalism'. Drawing upon ethnographic fieldwork and interviews, I argue that neither position fully accounts for how understandings of 'race' and ethnicity are being transformed with genetic genealogy testing. While there is some acquiescence to genetic thinking about ancestry, and by implication, 'race', among African-American and black British consumers of genetic genealogy testing, test-takers also adjudicate between sources of genealogical information and from these construct meaningful biographical narratives. Consumers engage in highly situated 'objective' and 'affiliative' self-fashioning, interpreting genetic test results in the context of their 'genealogical aspirations'. I conclude that issues of site, scale, and subjectification must be attended to if scholars are to understand whether and to what extent social identities are being transformed by recent developments in genetic science.

  15. Photo-Realistic Statistical Skull Morphotypes: New Exemplars for Ancestry and Sex Estimation in Forensic Anthropology.

    Science.gov (United States)

    Caple, Jodi; Stephan, Carl N

    2017-05-01

    Graphic exemplars of cranial sex and ancestry are essential to forensic anthropology for standardizing casework, training analysts, and communicating group trends. To date, graphic exemplars have comprised hand-drawn sketches, or photographs of individual specimens, which risks bias/subjectivity. Here, we performed quantitative analysis of photographic data to generate new photo-realistic and objective exemplars of skull form. Standardized anterior and left lateral photographs of skulls for each sex were analyzed in the computer graphics program Psychomorph for the following groups: South African Blacks, South African Whites, American Blacks, American Whites, and Japanese. The average cranial form was calculated for each photographic view, before the color information for every individual was warped to the average form and combined to produce statistical averages. These mathematically derived exemplars-and their statistical exaggerations or extremes-retain the high-resolution detail of the original photographic dataset, making them the ideal casework and training reference standards. © 2016 American Academy of Forensic Sciences.

  16. Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico.

    Science.gov (United States)

    Martínez-Cruzado, J C; Toro-Labrador, G; Ho-Fung, V; Estévez-Montero, M A; Lobaina-Manzanet, A; Padovani-Claudio, D A; Sánchez-Cruz, H; Ortiz-Bermúdez, P; Sánchez-Crespo, A

    2001-08-01

    To estimate the maternal contribution of Native Americans to the human gene pool of Puerto Ricans--a population of mixed African, European, and Amerindian ancestry--the mtDNAs of two sample sets were screened for restriction fragment length polymorphisms (RFLPs) defining the four major Native American haplogroups. The sample set collected from people who claimed to have a maternal ancestor with Native American physiognomic traits had a statistically significant higher frequency of Native American mtDNAs (69.6%) than did the unbiased sample set (52.6%). This higher frequency suggests that, despite the fact that the native Taíno culture has been extinct for centuries, the Taíno contribution to the current population is considerable and some of the Taíno physiognomic traits are still present. Native American haplogroup frequency analysis shows a highly structured distribution, suggesting that the contribution of Native Americans foreign to Puerto Rico is minimal. Haplogroups A and C cover 56.0% and 35.6% of the Native American mtDNAs, respectively. No haplogroup D mtDNAs were found. Most of the linguistic, biological, and cultural evidence suggests that the Ceramic culture of the Taínos originated in or close to the Yanomama territory in the Amazon. However, the absence of haplogroup A in the Yanomami suggests that the Yanomami are not the only Taíno ancestors.

  17. Race, Ethnicity and Ancestry in Unrelated Transplant Matching for the National Marrow Donor Program: A Comparison of Multiple Forms of Self-Identification with Genetics

    Science.gov (United States)

    Hollenbach, Jill A.; Saperstein, Aliya; Albrecht, Mark; Vierra-Green, Cynthia; Parham, Peter; Norman, Paul J.; Maiers, Martin

    2015-01-01

    We conducted a nationwide study comparing self-identification to genetic ancestry classifications in a large cohort (n = 1752) from the National Marrow Donor Program. We sought to determine how various measures of self-identification intersect with genetic ancestry, with the aim of improving matching algorithms for unrelated bone marrow transplant. Multiple dimensions of self-identification, including race/ethnicity and geographic ancestry were compared to classifications based on ancestry informative markers (AIMs), and the human leukocyte antigen (HLA) genes, which are required for transplant matching. Nearly 20% of responses were inconsistent between reporting race/ethnicity versus geographic ancestry. Despite strong concordance between AIMs and HLA, no measure of self-identification shows complete correspondence with genetic ancestry. In certain cases geographic ancestry reporting matches genetic ancestry not reflected in race/ethnicity identification, but in other cases geographic ancestries show little correspondence to genetic measures, with important differences by gender. However, when respondents assign ancestry to grandparents, we observe sub-groups of individuals with well- defined genetic ancestries, including important differences in HLA frequencies, with implications for transplant matching. While we advocate for tailored questioning to improve accuracy of ancestry ascertainment, collection of donor grandparents’ information will improve the chances of finding matches for many patients, particularly for mixed-ancestry individuals. PMID:26287376

  18. Race, Ethnicity and Ancestry in Unrelated Transplant Matching for the National Marrow Donor Program: A Comparison of Multiple Forms of Self-Identification with Genetics.

    Directory of Open Access Journals (Sweden)

    Jill A Hollenbach

    Full Text Available We conducted a nationwide study comparing self-identification to genetic ancestry classifications in a large cohort (n = 1752 from the National Marrow Donor Program. We sought to determine how various measures of self-identification intersect with genetic ancestry, with the aim of improving matching algorithms for unrelated bone marrow transplant. Multiple dimensions of self-identification, including race/ethnicity and geographic ancestry were compared to classifications based on ancestry informative markers (AIMs, and the human leukocyte antigen (HLA genes, which are required for transplant matching. Nearly 20% of responses were inconsistent between reporting race/ethnicity versus geographic ancestry. Despite strong concordance between AIMs and HLA, no measure of self-identification shows complete correspondence with genetic ancestry. In certain cases geographic ancestry reporting matches genetic ancestry not reflected in race/ethnicity identification, but in other cases geographic ancestries show little correspondence to genetic measures, with important differences by gender. However, when respondents assign ancestry to grandparents, we observe sub-groups of individuals with well- defined genetic ancestries, including important differences in HLA frequencies, with implications for transplant matching. While we advocate for tailored questioning to improve accuracy of ancestry ascertainment, collection of donor grandparents' information will improve the chances of finding matches for many patients, particularly for mixed-ancestry individuals.

  19. The effect of high correlated colour temperature office lighting on employee wellbeing and work performance.

    Science.gov (United States)

    Mills, Peter R; Tomkins, Susannah C; Schlangen, Luc J M

    2007-01-11

    The effects of lighting on the human circadian system are well-established. The recent discovery of 'non-visual' retinal receptors has confirmed an anatomical basis for the non-image forming, biological effects of light and has stimulated interest in the use of light to enhance wellbeing in the corporate setting. A prospective controlled intervention study was conducted within a shift-working call centre to investigate the effect of newly developed fluorescent light sources with a high correlated colour temperature (17000 K) upon the wellbeing, functioning and work performance of employees. Five items of the SF-36 questionnaire and a modification of the Columbia Jet Lag scale, were used to evaluate employees on two different floors of the call centre between February and May 2005. Questionnaire completion occurred at baseline and after a three month intervention period, during which time one floor was exposed to new high correlated colour temperature lighting and the other remained exposed to usual office lighting. Two sided t-tests with Bonferroni correction for type I errors were used to compare the characteristics of the two groups at baseline and to evaluate changes in the intervention and control groups over the period of the study. Individuals in the intervention arm of the study showed a significant improvement in self-reported ability to concentrate at study end as compared to those within the control arm (p wellbeing and productivity in the corporate setting, although further work is necessary in quantifying the magnitude of likely benefits.

  20. High avidity antibodies to full-length VAR2CSA correlate with absence of placental malaria

    DEFF Research Database (Denmark)

    Tutterrow, Yeung Lo; Salanti, Ali; Avril, Marion

    2012-01-01

    VAR2CSA mediates sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, increasing the risk of poor pregnancy outcomes. Naturally acquired antibodies (Ab) to placental parasites at delivery have been associated with improved pregnancy outcomes, but Ab levels and how early...... in pregnancy Ab must be present in order to eliminate placental parasites before delivery remains unknown. Antibodies to individual Duffy-binding like domains of VAR2CSA have been studied, but the domains lack many of the conformational epitopes present in full-length VAR2CSA (FV2). Thus, the purpose...... of this study was to describe the acquisition of Ab to FV2 in women residing in high and low transmission areas and determine how Ab levels during pregnancy correlate with clearance of placental parasites. Plasma samples collected monthly throughout pregnancy from pregnant women living in high and low...

  1. High precision Cross-correlated imaging in Few-mode fibers

    DEFF Research Database (Denmark)

    Muliar, Olena; Usuga Castaneda, Mario A.; Kristensen, Torben

    2017-01-01

    us to distinguishing differential time delays between HOMs in the picosecond timescale. Broad wavelength scanning in combination with spectral shaping, allows us to estimate the modal behavior of FMF without prior knowledge of the fiber parameters. We performed our demonstration at wavelengths from...... existing approaches for modal content analysis, several methods as S2, C2 in time and frequency domain are available. In this contribution we will present an improved time-domain cross-correlated (C2) imaging technique for the experimental evaluation of modal properties in HOM fibers over a broad range......) in a few-mode fiber (FMF) are used as multiple spatial communication channels, comes in this context as a viable approach to enable the optimization of high-capacity links. From this perspective, it becomes highly necessary to possess a diagnostic tool for the precise modal characterization of FMFs. Among...

  2. VOLUME STUDY WITH HIGH DENSITY OF PARTICLES BASED ON CONTOUR AND CORRELATION IMAGE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Tatyana Yu. Nikolaeva

    2014-11-01

    Full Text Available The subject of study is the techniques of particle statistics evaluation, in particular, processing methods of particle images obtained by coherent illumination. This paper considers the problem of recognition and statistical accounting for individual images of small scattering particles in an arbitrary section of the volume in case of high concentrations. For automatic recognition of focused particles images, a special algorithm for statistical analysis based on contouring and thresholding was used. By means of the mathematical formalism of the scalar diffraction theory, coherent images of the particles formed by the optical system with high numerical aperture were simulated. Numerical testing of the method proposed for the cases of different concentrations and distributions of particles in the volume was performed. As a result, distributions of density and mass fraction of the particles were obtained, and the efficiency of the method in case of different concentrations of particles was evaluated. At high concentrations, the effect of coherent superposition of the particles from the adjacent planes strengthens, which makes it difficult to recognize images of particles using the algorithm considered in the paper. In this case, we propose to supplement the method with calculating the cross-correlation function of particle images from adjacent segments of the volume, and evaluating the ratio between the height of the correlation peak and the height of the function pedestal in the case of different distribution characters. The method of statistical accounting of particles considered in this paper is of practical importance in the study of volume with particles of different nature, for example, in problems of biology and oceanography. Effective work in the regime of high concentrations expands the limits of applicability of these methods for practically important cases and helps to optimize determination time of the distribution character and

  3. Correlation of Pc5 wave power inside and outside themagnetosphere during high speed streams

    Directory of Open Access Journals (Sweden)

    R. L. Kessel

    2004-01-01

    Full Text Available We show a clear correlation between the ULF wave power (Pc5 range inside and outside the Earth's magnetosphere during high speed streams in 1995. We trace fluctuations beginning 200RE upstream using Wind data, to fluctuations just upstream from Earth's bow shock and in the magnetosheath using Geotail data and compare to pulsations on the ground at the Kilpisjarvi ground station. With our 5-month data set we draw the following conclusions. ULF fluctuations in the Pc5 range are found in high speed streams; they are non-Alfvénic at the leading edge and Alfvénic in the central region. Compressional and Alfvénic fluctuations are modulated at the bow shock, some features of the waveforms are preserved in the magnetosheath, but overall turbulence and wave power is enhanced by about a factor of 10. Parallel (compressional and perpendicular (transverse power are at comparable levels in the solar wind and magnetosheath, both in the compression region and in the central region of high speed streams. Both the total parallel and perpendicular Pc5 power in the solar wind (and to a lesser extent in the magnetosheath correlate well with the total Pc5 power of the ground-based H-component magnetic field. ULF fluctuations in the magnetosheath during high speed streams are common at frequencies from 1–4mHz and can coincide with the cavity eigenfrequencies of 1.3, 1.9, 2.6, and 3.4mHz, though other discrete frequencies are also often seen.

    Key words. Interplanetary physics (MHD waves and turbulence – Magnetospheric physics (solar wind-magnetosphere interactions; MHD waves and instabilities

  4. Evaluation of the Precision ID Ancestry Panel for crime case work

    DEFF Research Database (Denmark)

    Pereira, Vania; Mogensen, Helle S; Børsting, Claus

    2017-01-01

    The application of massive parallel sequencing (MPS) methodologies in forensic genetics is promising and it is gradually being implemented in forensic genetic case work. One of the major advantages of these technologies is that several traditional electrophoresis assays can be combined into one...... single MPS assay. This reduces both the amount of sample used and the time of the investigations. This study assessed the utility of the Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) in forensic genetics. This assay was developed for the Ion Torrent PGM™ System and genotypes 165...... ancestry informative SNPs. The performance of the assay and the accompanying software solution for ancestry inference was assessed by typing 142 Danes and 98 Somalis. Locus balance, heterozygote balance, and noise levels were calculated and future analysis criteria for crime case work were estimated...

  5. Strong selection during the last millennium for African ancestry in the admixed population of Madagascar.

    Science.gov (United States)

    Pierron, Denis; Heiske, Margit; Razafindrazaka, Harilanto; Pereda-Loth, Veronica; Sanchez, Jazmin; Alva, Omar; Arachiche, Amal; Boland, Anne; Olaso, Robert; Deleuze, Jean-Francois; Ricaut, Francois-Xavier; Rakotoarisoa, Jean-Aimé; Radimilahy, Chantal; Stoneking, Mark; Letellier, Thierry

    2018-03-02

    While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

  6. Do High School Students in India Gamble? A Study of Problem Gambling and Its Correlates.

    Science.gov (United States)

    Jaisoorya, T S; Beena, K V; Beena, M; Ellangovan, K; Thennarassu, K; Bowden-Jones, Henrietta; Benegal, Vivek; George, Sanju

    2017-06-01

    Studies from the West suggest that significant numbers of high school students gamble, despite it being illegal in this age group. To date, there have been no studies on the prevalence of gambling among senior high school and higher secondary school students in India. This study reports point prevalence of gambling and its psychosocial correlates among high school students in the State of Kerala, India. 5043 high school students in the age group 15-19 years, from 73 schools, were selected by cluster random sampling from the district of Ernakulam, Kerala, South India. They completed questionnaires that assessed gambling, substance use, psychological distress, suicidality, and symptoms of Attention Deficit Hyperactivity Disorder (ADHD). Of a total of 4989 completed questionnaires, 1400 (27.9 %) high school students reported to have ever gambled and 353 (7.1 %) were problem gamblers. Of those who had ever gambled, 25.2 % were problem gamblers. Sports betting (betting on cricket and football) was the most popular form of gambling followed by the lottery. Problem gamblers when compared with non-problem gamblers and non-gamblers were significantly more likely to be male, have academic failures, have higher rates of lifetime alcohol and tobacco use, psychological distress, suicidality, history of sexual abuse and higher ADHD symptom scores. Gambling among adolescents in India deserves greater attention, as one in four students who ever gambled was a problem gambler and because of its association with a range of psychosocial variables.

  7. Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities.

    Science.gov (United States)

    Wang, Zheng; He, Guanglin; Luo, Tao; Zhao, Xueying; Liu, Jing; Wang, Mengge; Zhou, Di; Chen, Xu; Li, Chengtao; Hou, Yiping

    2018-05-01

    The Tibeto-Burman language, one subfamily of the Sino-Tibetan languages, is spoken by over 60 million people all over East Asia. Yet the ethnic origin and genetic architecture of Tibeto-Burman speaking populations remain largely unexplored. In the present study, 169 Chinese individuals from Tibeto-Burman speaking populations (two ethnic groups: Tibetan and Yi) in four different geographic regions in western China were analyzed using the Precision ID Ancestry Panel (165 AISNPs) and the Ion PGM System. The performance and corresponding forensic statistical parameters of this AISNPs panel were investigated. Comprehensive population genetic comparisons (143 populations based on Kidd' SNPs, 92 populations on the basis of Seldin' SNPs and 31 populations based on the Precision ID Ancestry Panel) and ancestry inference were further performed. Sequencing performance demonstrated that the Precision ID Ancestry Panel is effective and robust. Forensic characteristics suggested that this panel not only can be used for ancestry estimation of Tibeto-Burman populations but also for individual identification. Tibetan and Yi shared a common genetic ancestry origin but experienced the complex history of gene flow, local adaptation, and isolation, and constructed the specific genetic landscape of human genetic diversity of Highlander and Lowlander populations. Tibetan-Burman populations and other East Asian populations showed sufficient genetic difference and could be distinguished into three distinct groups. Furthermore, analysis of population structure revealed that significant genetic difference was existed inter-continent populations and strong genetic affinity was observed within-continent populations. Additional population-specific AISNPs and a relatively more comprehensive database with sufficient reference population data remain necessary to get better-scale resolution within a geographically proximate populations in East Asia. Copyright © 2018 Elsevier B.V. All rights

  8. Genetic Ancestry and Susceptibility to Late-Onset Alzheimer Disease (LOAD) in the Admixed Colombian Population.

    Science.gov (United States)

    Moreno, Diana J; Pino, Sebastián; Ríos, Ángela; Lopera, Francisco; Ostos, Henry; Via, Marc; Bedoya, Gabriel

    2017-01-01

    Differences in the prevalence of dementia among populations and in the effect of apolipoprotein E (APOE) on the emergence of Alzheimer disease (AD), which is the main type of dementia, have been reported. This study estimated the ancestry of a group of individuals with late-onset Alzheimer disease (LOAD) (N=280) and established whether there were any differences when compared with a control group (N=357) in a sample of the Colombian population. When the analyses were adjusted for known risk factors such as age, sex, presence of APOE[Latin Small Letter Open E]4, socioeconomic status, educational attainment, and place of birth, African ancestry was associated with an increased LOAD risk (odds ratio: 1.55; 95% confidence interval, 1.09-2.03; P=0.029), whereas Native American ancestry was associated with lower risk (odds ratio: 0.75; 95% confidence interval, 0.61-0.98; P=0.046), for every 10% increase in ancestry. In addition, there were significant differences in the proportion of Native American ancestry between carriers and noncarriers of the APOE[Latin Small Letter Open E]4 allele (Mann-Whitney U test, P=0.047), with noncarriers having higher mean Native American ancestry when compared with carriers. Our results are consistent with the presence of variants of African origin in the genome of the Colombian population and different from APOE[Latin Small Letter Open E]4 that represents a risk factor for the development of LOAD, whereas variants of Native American origin may be conferring protection. However, unknown environmental factors or epigenetic differences among continental groups could also explain the observed associations.

  9. Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

    Science.gov (United States)

    Gravel, Simon; Wang, Wei; Brisbin, Abra; Byrnes, Jake K.; Fadhlaoui-Zid, Karima; Zalloua, Pierre A.; Moreno-Estrada, Andres; Bertranpetit, Jaume; Bustamante, Carlos D.; Comas, David

    2012-01-01

    North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa. PMID:22253600

  10. Genomic ancestry of North Africans supports back-to-Africa migrations.

    Directory of Open Access Journals (Sweden)

    Brenna M Henn

    2012-01-01

    Full Text Available North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from "back-to-Africa" gene flow more than 12,000 years ago (ya, prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya; a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya. Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

  11. Ancestry and Language in the United States: November 1979. Current Population Reports, Special Studies. Series P-23. No. 116.

    Science.gov (United States)

    Levin, Michael J.; Sweet, Nancy S.

    Information on the ancestry, languages, and literacy of the U.S. population based on data collected by the Bureau of the Census in 1979 is reported. Items surveyed include ancestry, country of birth of the individual and parents, citizenship, year of immigration, native language, language spoken in the home, ability to speak English, and ability…

  12. Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA

    NARCIS (Netherlands)

    O. Lao Grueso (Oscar); P.M. Vallone (Peter); M.D. Coble (Michael); T.M. Diegoli (Toni); M. van Oven (Mannis); K. van der Gaag (Kristiaan); J. Pijpe (Jeroen); P. de Knijff (Peter); M.H. Kayser (Manfred)

    2010-01-01

    textabstractThe current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with self-declared ancestry we have analyzed paternally, maternally and bi-parentally inherited

  13. Considering the significance of ancestry through the prism of mixed-race identity.

    Science.gov (United States)

    Tashiro, Cathy J

    2002-12-01

    People of mixed ancestry promise to be a significant percentage of the population of the United States in the 21st century. This article describes a qualitative study of 20 older mixed-race adults of African-American-white and Asian-American-white ancestries and focuses on how the participants construct identity. Using grounded theory methodology, racial identity did not emerge as a singular, distinct entity in this study, and five dimensions of racial identity were observed. Significant differences in patterns of identity dimensions were noted for the two mixed groups. Implications for nursing practice are discussed.

  14. A high performance cost-effective digital complex correlator for an X-band polarimetry survey.

    Science.gov (United States)

    Bergano, Miguel; Rocha, Armando; Cupido, Luís; Barbosa, Domingos; Villela, Thyrso; Boas, José Vilas; Rocha, Graça; Smoot, George F

    2016-01-01

    The detailed knowledge of the Milky Way radio emission is important to characterize galactic foregrounds masking extragalactic and cosmological signals. The update of the global sky models describing radio emissions over a very large spectral band requires high sensitivity experiments capable of observing large sky areas with long integration times. Here, we present the design of a new 10 GHz (X-band) polarimeter digital back-end to map the polarization components of the galactic synchrotron radiation field of the Northern Hemisphere sky. The design follows the digital processing trends in radio astronomy and implements a large bandwidth (1 GHz) digital complex cross-correlator to extract the Stokes parameters of the incoming synchrotron radiation field. The hardware constraints cover the implemented VLSI hardware description language code and the preliminary results. The implementation is based on the simultaneous digitized acquisition of the Cartesian components of the two linear receiver polarization channels. The design strategy involves a double data rate acquisition of the ADC interleaved parallel bus, and field programmable gate array device programming at the register transfer mode. The digital core of the back-end is capable of processing 32 Gbps and is built around an Altera field programmable gate array clocked at 250 MHz, 1 GSps analog to digital converters and a clock generator. The control of the field programmable gate array internal signal delays and a convenient use of its phase locked loops provide the timing requirements to achieve the target bandwidths and sensitivity. This solution is convenient for radio astronomy experiments requiring large bandwidth, high functionality, high volume availability and low cost. Of particular interest, this correlator was developed for the Galactic Emission Mapping project and is suitable for large sky area polarization continuum surveys. The solutions may also be adapted to be used at signal processing

  15. High blood pressure in children and its correlation with three definitions of obesity in childhood.

    Science.gov (United States)

    Moraes, Leonardo Iezzi de; Nicola, Thaís Coutinho; Jesus, Julyanna Silva Araújo de; Alves, Eduardo Roberty Badiani; Giovaninni, Nayara Paula Bernurdes; Marcato, Daniele Gasparini; Sampaio, Jéssica Dutra; Fuly, Jeanne Teixeira Bessa; Costalonga, Everlayny Fiorot

    2014-02-01

    Several authors have correlated the increase of cardiovascular risk with the nutritional status, however there are different criteria for the classification of overweight and obesity in children. To evaluate the performance of three nutritional classification criteria in children, as definers of the presence of obesity and predictors of high blood pressure in schoolchildren. Eight hundred and seventeen children ranging 6 to 13 years old, enrolled in public schools in the municipality of Vila Velha (ES) were submitted to anthropometric evaluation and blood pressure measurement. The classification of the nutritional status was established by two international criteria (CDC/NCHS 2000 and IOTF 2000) and one Brazilian criterion (Conde e Monteiro 2006). The prevalence of overweight was higher when the criterion of Conde e Monteiro (27%) was used, and inferior by the IOTF (15%) criteria. High blood pressure was observed in 7.3% of children. It was identified a strong association between the presence of overweight and the occurrence of high blood pressure, regardless of the test used (p<0.001). The test showing the highest sensitivity in predicting elevated BP was the Conde e Monteiro (44%), while the highest specificity (94%) and greater overall accuracy (63%), was the CDC criterion. The prevalence of overweight in Brazilian children is higher when using the classification criterion of Conde e Monteiro, and lower when the criterion used is IOTF. The Brazilian classification criterion proved to be the most sensitive predictor of high BP risk in this sample.

  16. The correlates of urinary albumin to creatinine ratio (ACR) in a high risk Australian aboriginal community.

    Science.gov (United States)

    Wang, Zaimin; Hoy, Wendy E; Wang, Zhiqiang

    2013-08-16

    Albuminuria marks renal disease and cardiovascular risk. It was estimated to contribute 75% of the risk of all-cause natural death in one Aboriginal group. The urine albumin/creatinine ratio (ACR) is commonly used as an index of albuminuria. This study aims to examine the associations between demographic factors, anthropometric index, blood pressure, lipid-protein measurements and other biomarkers and albuminuria in a cross-sectional study in a high-risk Australian Aboriginal population. The models will be evaluated for albuminuria at or above the microalbuminuria threshold, and at or above the "overt albuminuria" threshold with the potential to distinguish associations they have in common and those that differ. This was a cross-sectional study of 598 adults aged 18-76 years. All participants were grouped into quartiles by age. Logistic regression models were used to explore the correlates of ACR categories. The significant correlates were systolic blood pressure (SBP), C-reactive protein (CRP), uric acid, diabetes, gamma-glutamyl transferase (GGT) (marginally significant, p=0.054) and serum albumin (negative association) for ACR 17+ (mg/g) for men and 25+ for women. Independent correlates were SBP, uric acid, diabetes, total cholesterol, alanine amino transferase (ALT), Cystatin C and serum albumin (negative association) for overt albuminuria; and SBP, CRP and serum albumin only for microalbuminuria. This is the most detailed modelling of pathologic albuminuria in this setting to date. The somewhat variable association with risk factors suggests that microalbuminuria and overt albuminuria might reflect different as well as shared phenomena.

  17. Radiation propagation in random media: From positive to negative correlations in high-frequency fluctuations

    International Nuclear Information System (INIS)

    Davis, Anthony B.; Mineev-Weinstein, Mark B.

    2011-01-01

    We survey research on radiation propagation or ballistic particle motion through media with randomly variable material density, and we investigate the topic with an emphasis on very high spatial frequencies. Our new results are based on a specific variability model consisting of a zero-mean Gaussian scaling noise riding on a constant value that is large enough with respect to the amplitude of the noise to yield overwhelmingly non-negative density. We first generalize known results about sub-exponential transmission from regular functions, which are almost everywhere continuous, to merely 'measurable' ones, which are almost everywhere discontinuous (akin to statistically stationary noises), with positively correlated fluctuations. We then use the generalized measure-theoretic formulation to address negatively correlated stochastic media without leaving the framework of conventional (continuum-limit) transport theory. We thus resolve a controversy about recent claims that only discrete-point process approaches can accommodate negative correlations, i.e., anti-clustering of the material particles. We obtain in this case the predicted super-exponential behavior, but it is rather weak. Physically, and much like the alternative discrete-point process approach, the new model applies most naturally to scales commensurate with the inter-particle distance in the material, i.e., when the notion of particle density breaks down due to Poissonian-or maybe not-so-Poissonian-number-count fluctuations occur in the sample volume. At the same time, the noisy structure must prevail up to scales commensurate with the mean-free-path to be of practical significance. Possible applications are discussed.

  18. Pore volume is most highly correlated with the visual assessment of skin pores.

    Science.gov (United States)

    Kim, S J; Shin, M K; Back, J H; Koh, J S

    2014-11-01

    Many studies have been focused on evaluating assessment techniques for facial pores amid growing attention on skin care. Ubiquitous techniques used to assess the size of facial pores include visual assessment, cross-section images of the skin surface, and profilometric analysis of silicone replica of the facial skin. In addition, there are indirect assessment methods, including observation of pores based on confocal laser scanning microscopy and the analysis of sebum secretion and skin elasticity. The aim of this study was to identify parameters useful in estimating pore of surface in normal skin. The severity of pores on the cheek area by frontal optical images was divided on a 0-6 scale with '0' being faint and small pore and '6' being obvious and large pore. After the photos of the frontal cheek of 32 women aged between 35 and 49 were taken, the size of their pores was measured on a 0-6 scale; and the correlation between visual grading of pore and various evaluations (pore volume by 3-D image, pore area and number by Optical Image Analyzer) contributing to pore severity investigated using direct, objective, and noninvasive evaluations. The visual score revealed that the size of pores was graded on a 1-6 scale. Visual grading of pore was highly correlated with pore volume measured from 3-D images and pore area measured from 2-D optical images in the order (P pore was also slightly correlated with the number of pores in size of over 0.04 mm(2) (P pore score and pore volume can be explained by 3-D structural characteristics of pores. It is concluded that pore volume and area serve as useful parameters in estimating pore of skin surface. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. Nonspecific interstitial pneumonia: Histologic correlation with high-resolution CT in 29 patients

    Energy Technology Data Exchange (ETDEWEB)

    Sumikawa, Hiromitsu [Department of Radiology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0825 (Japan)], E-mail: h-sumikawa@radiol.med.osaka-u.ac.jp; Johkoh, Takeshi [Department of Radiology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0825 (Japan); Department of Medical Physics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0825 (Japan); Ichikado, Kazuya [Division of Respiratory Medicine, Saiseikai Kumamoto Hospital, 5-3-1 Tikami, Kumamoto 861-4193 (Japan); Taniguchi, Hiroyuki; Kondoh, Yasuhiro [Department of Respiratory Medicine and Allergy, Tosei General Hospital, 160 Nishioiwake-cho, Seto City, Aichi (Japan); Fujimoto, Kiminori [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan); Yanagawa, Masahiro; Inoue, Atsuo; Mihara, Naoki; Honda, Osamu; Tomiyama, Noriyuki; Nakamura, Hironobu [Department of Radiology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0825 (Japan); Colby, Thomas V. [Department of Pathology, Mayo Clinic, Scottsdale, AZ (United States)

    2009-04-15

    Purpose: To determine the pathological correlation with various high-resolution CT (HRCT) findings in cases with nonspecific interstitial pneumonia (NSIP), paying special attention to pathological subgroups. Material and methods: The study involved 29 patients diagnosed with NSIP by surgical lung biopsy. A total of 54 specimens were obtained and grouped according to Katzenstein's classification (groups 1-3) for NSIP. Two observers then evaluated the HRCT findings for every biopsy site and classified the findings according to the main pattern evident into the following four radiologic pattern groups: A, ground-glass attenuation and fine reticulation; B, ground-glass and coarse reticulation; C, consolidation and D, ground-glass attenuation and consolidation. Results: The pathological pattern was NSIP group 1 in 6 patients, group 2 in 22 and group 3 in 25, while 1 specimen was normal. The main HRCT pattern was pattern A in 15 specimens, B in 8, C in 9 and D in 21. Although there were no significant correlation between HRCT patterns and histological subgroups (Chi-square test, p = 0.07), pattern C was more frequently seen in group 2 (7 of 9) and pattern A was more common in group 3 (11 of 15). HRCT pattern A corresponded pathologically to areas of thickened alveolar septa with temporal uniformity. Pattern B correlated with areas with airspace enlargement/emphysema or dilation of small airways superimposed on thickened alveolar septa. Pattern C was pathologically associated with areas of severe thickened alveolar septa, mucin stasis in the small airways and intraluminal organization. Conclusion: The pathological backgrounds of the same CT findings in patients with NSIP varied among all pathological subgroups. Areas of ground-glass attenuation and air-space consolidation did not always correspond to reversible pathological findings.

  20. A new procedure of modal parameter estimation for high-speed digital image correlation

    Science.gov (United States)

    Huňady, Róbert; Hagara, Martin

    2017-09-01

    The paper deals with the use of 3D digital image correlation in determining modal parameters of mechanical systems. It is a non-contact optical method, which for the measurement of full-field spatial displacements and strains of bodies uses precise digital cameras with high image resolution. Most often this method is utilized for testing of components or determination of material properties of various specimens. In the case of using high-speed cameras for measurement, the correlation system is capable of capturing various dynamic behaviors, including vibration. This enables the potential use of the mentioned method in experimental modal analysis. For that purpose, the authors proposed a measuring chain for the correlation system Q-450 and developed a software application called DICMAN 3D, which allows the direct use of this system in the area of modal testing. The created application provides the post-processing of measured data and the estimation of modal parameters. It has its own graphical user interface, in which several algorithms for the determination of natural frequencies, mode shapes and damping of particular modes of vibration are implemented. The paper describes the basic principle of the new estimation procedure which is crucial in the light of post-processing. Since the FRF matrix resulting from the measurement is usually relatively large, the estimation of modal parameters directly from the FRF matrix may be time-consuming and may occupy a large part of computer memory. The procedure implemented in DICMAN 3D provides a significant reduction in memory requirements and computational time while achieving a high accuracy of modal parameters. Its computational efficiency is particularly evident when the FRF matrix consists of thousands of measurement DOFs. The functionality of the created software application is presented on a practical example in which the modal parameters of a composite plate excited by an impact hammer were determined. For the

  1. Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of chinese, Japanese, and European ancestry.

    Science.gov (United States)

    Cai, Qiuyin; Wen, Wanqing; Qu, Shimian; Li, Guoliang; Egan, Kathleen M; Chen, Kexin; Deming, Sandra L; Shen, Hongbing; Shen, Chen-Yang; Gammon, Marilie D; Blot, William J; Matsuo, Keitaro; Haiman, Christopher A; Khoo, Ui Soon; Iwasaki, Motoki; Santella, Regina M; Zhang, Lina; Fair, Alecia Malin; Hu, Zhibin; Wu, Pei-Ei; Signorello, Lisa B; Titus-Ernstoff, Linda; Tajima, Kazuo; Henderson, Brian E; Chan, Kelvin Y K; Kasuga, Yoshio; Newcomb, Polly A; Zheng, Hong; Cui, Yong; Wang, Furu; Shieh, Ya-Lan; Iwata, Hiroji; Le Marchand, Loic; Chan, Sum Yin; Shrubsole, Martha J; Trentham-Dietz, Amy; Tsugane, Shoichiro; Garcia-Closas, Montserrat; Long, Jirong; Li, Chun; Shi, Jiajun; Huang, Bo; Xiang, Yong-Bing; Gao, Yu-Tang; Lu, Wei; Shu, Xiao-Ou; Zheng, Wei

    2011-02-15

    We evaluated the generalizability of a single nucleotide polymorphism (SNP), rs2046210 (A/G allele), associated with breast cancer risk that was initially identified at 6q25.1 in a genome-wide association study conducted among Chinese women. In a pooled analysis of more than 31,000 women of East-Asian, European, and African ancestry, we found a positive association for rs2046210 and breast cancer risk in Chinese women [ORs (95% CI) = 1.30 (1.22-1.38) and 1.64 (1.50-1.80) for the AG and AA genotypes, respectively, P for trend = 1.54 × 10⁻³⁰], Japanese women [ORs (95% CI) = 1.31 (1.13-1.52) and 1.37 (1.06-1.76), P for trend = 2.51 × 10⁻⁴], and European-ancestry American women [ORs (95% CI) = 1.07 (0.99-1.16) and 1.18 (1.04-1.34), P for trend = 0.0069]. No association with this SNP, however, was observed in African American women [ORs (95% CI) = 0.81 (0.63-1.06) and 0.85 (0.65-1.11) for the AG and AA genotypes, respectively, P for trend = 0.4027]. In vitro functional genomic studies identified a putative functional variant, rs6913578. This SNP is 1,440 bp downstream of rs2046210 and is in high linkage disequilibrium with rs2046210 in Chinese (r(2) = 0.91) and European-ancestry (r² = 0.83) populations, but not in Africans (r² = 0.57). SNP rs6913578 was found to be associated with breast cancer risk in Chinese and European-ancestry American women. After adjusting for rs2046210, the association of rs6913578 with breast cancer risk in African Americans approached borderline significance. Results from this large consortium study confirmed the association of rs2046210 with breast cancer risk among women of Chinese, Japanese, and European ancestry. This association may be explained in part by a putatively functional variant (rs6913578) identified in the region. ©2011 AACR.

  2. High resolution CT in children with cystic fibrosis: correlation with pulmonary functions and radiographic scores

    Energy Technology Data Exchange (ETDEWEB)

    Demirkazik, Figen Basaran E-mail: demirkaz@dialup.ankara.edu.tr; Ariyuerek, O. Macit; Oezcelik, Ugur; Goecmen, Ayhan; Hassanabad, Hossein K.; Kiper, Nural

    2001-01-01

    Objective: To compare the high resolution CT (HRCT) scores of the Bhalla system with pulmonary function tests and radiographic and clinical points of the Shwachman-Kulczycki clinical scoring system. Methods: HRCT of the chest was obtained in 40 children to assess the role of HRCT in evaluating bronchopulmonary pathology in children with cystic fibrosis (CF). The HRCT severity scores of the Bhalla system were compared with chest radiographic and clinical points of the Shwachman-Kulczycki scoring system and pulmonary function tests. Only 14 of the patients older than 6 years cooperated with spirometry. Results: HRCT scores correlated well with radiographic points (r=0.80, P<0.0001) and clinical points (r=0.67, P<0.0001) of the Shwachman-Kulczycki system, FVC (r=0.71 P=0.004) and FEV{sub 1} (r=0.66, P=0.01). Although radiographic points correlated significantly with FVC (r=0.61, P=0.02) and FEV{sub 1} (r=0.56, P=0.04), HRCT provides a more precise scoring than the chest X-ray. Conclusion: The HRCT scoring system may provide a sensitive method of monitoring pulmonary disease status and may replace the radiographic scoring in the Shwachman-Kulczycki system. It may be helpful especially in follow-up of small children too young to cooperate with spirometry.

  3. Thalamo-Sensorimotor Functional Connectivity Correlates with World Ranking of Olympic, Elite, and High Performance Athletes

    Directory of Open Access Journals (Sweden)

    Zirui Huang

    2017-01-01

    Full Text Available Brain plasticity studies have shown functional reorganization in participants with outstanding motor expertise. Little is known about neural plasticity associated with exceptionally long motor training or of its predictive value for motor performance excellence. The present study utilised resting-state functional magnetic resonance imaging (rs-fMRI in a unique sample of world-class athletes: Olympic, elite, and internationally ranked swimmers (n=30. Their world ranking ranged from 1st to 250th: each had prepared for participation in the Olympic Games. Combining rs-fMRI graph-theoretical and seed-based functional connectivity analyses, it was discovered that the thalamus has its strongest connections with the sensorimotor network in elite swimmers with the highest world rankings (career best rank: 1–35. Strikingly, thalamo-sensorimotor functional connections were highly correlated with the swimmers’ motor performance excellence, that is, accounting for 41% of the individual variance in best world ranking. Our findings shed light on neural correlates of long-term athletic performance involving thalamo-sensorimotor functional circuits.

  4. Internet addiction and its correlates among high school students: a preliminary study from Ahmedabad, India.

    Science.gov (United States)

    Yadav, Priyanka; Banwari, Girish; Parmar, Chirag; Maniar, Rajesh

    2013-12-01

    Internet addiction (IA) is an upcoming and less researched entity in psychiatry, especially in low and middle income countries. This is the first such effort to study IA amongst Indian school students of class 11th and 12th and to find its correlation with socio-educational characteristics, internet use patterns and psychological variables, namely depression, anxiety and stress. Six hundred and twenty one students of six English medium schools of Ahmedabad participated, of which 552 (88.9%) who completed forms were analyzed. Young's Internet Addiction Test and 21 item Depression Anxiety and Stress Scale were used to measure IA and psychological variables respectively. Logistic regression analysis was applied to find the predictors of IA. Sixty-five (11.8%) students had IA; it was predicted by time spent online, usage of social networking sites and chat rooms, and also by presence of anxiety and stress. Age, gender and self-rated academic performance did not predict IA. There was a strong positive correlation between IA and depression, anxiety and stress. IA may be a relevant clinical construct, and needs extensive research even in developing nations. All high school students suffering from depression, anxiety and stress must be screened for IA, and vice versa. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Ground-glass opacity in diffuse lung diseases: high-resolution computed tomography-pathology correlation

    International Nuclear Information System (INIS)

    Santos, Maria Lucia de Oliveira; Vianna, Alberto Domingues; Marchiori, Edson; Souza Junior, Arthur Soares; Moraes, Heleno Pinto de

    2003-01-01

    Ground-glass opacity is a finding frequently seen in high-resolution computed tomography examinations of the chest and is characterized by hazy increased attenuation of lung, however without blurring of bronchial and vascular margins. Due to its un specificity, association with other radiological, clinical and pathological findings must be considered for an accurate diagnostic interpretation. In this paper were reviewed 62 computed tomography examinations of patients with diffuse pulmonary diseases of 14 different etiologies in which ground-glass opacity was the only or the most remarkable finding, and correlated this findings with pathology abnormalities seen on specimens obtained from biopsies or necropsies. In pneumocystosis, ground-glass opacities correlated histologically with alveolar occupation by a foaming material containing parasites, in bronchiole alveolar cell carcinoma with thickening of the alveolar septa and occupation of the lumen by mucus and tumoral cells, in paracoccidioidomycosis with thickening of the alveolar septa, areas of fibrosis and alveolar bronchopneumonia exudate, in sarcoidosis with fibrosis or clustering of granulomas and in idiopathic pulmonary fibrosis with alveolar septa thickening due to fibrosis. Alveolar occupation by blood was found in cases of leptospirosis, idiopathic hemo siderosis, metastatic kidney tumor and invasive aspergillosis whereas oily vacuole were seen in lipoid pneumonia, proteinaceous and lipo proteinaceous material in silico proteinosis and pulmonary alveolar proteinosis, and edematous fluid in cardiac failure. (author)

  6. High resolution CT in children with cystic fibrosis: correlation with pulmonary functions and radiographic scores

    International Nuclear Information System (INIS)

    Demirkazik, Figen Basaran; Ariyuerek, O. Macit; Oezcelik, Ugur; Goecmen, Ayhan; Hassanabad, Hossein K.; Kiper, Nural

    2001-01-01

    Objective: To compare the high resolution CT (HRCT) scores of the Bhalla system with pulmonary function tests and radiographic and clinical points of the Shwachman-Kulczycki clinical scoring system. Methods: HRCT of the chest was obtained in 40 children to assess the role of HRCT in evaluating bronchopulmonary pathology in children with cystic fibrosis (CF). The HRCT severity scores of the Bhalla system were compared with chest radiographic and clinical points of the Shwachman-Kulczycki scoring system and pulmonary function tests. Only 14 of the patients older than 6 years cooperated with spirometry. Results: HRCT scores correlated well with radiographic points (r=0.80, P 1 (r=0.66, P=0.01). Although radiographic points correlated significantly with FVC (r=0.61, P=0.02) and FEV 1 (r=0.56, P=0.04), HRCT provides a more precise scoring than the chest X-ray. Conclusion: The HRCT scoring system may provide a sensitive method of monitoring pulmonary disease status and may replace the radiographic scoring in the Shwachman-Kulczycki system. It may be helpful especially in follow-up of small children too young to cooperate with spirometry

  7. Irreducible Greens' Functions method in the theory of highly correlated systems

    International Nuclear Information System (INIS)

    Kuzemsky, A.L.

    1994-09-01

    The self-consistent theory of the correlation effects in Highly Correlated Systems (HCS) is presented. The novel Irreducible Green's Function (IGF) method is discussed in detail for the Hubbard model and random Hubbard model. The interpolation solution for the quasiparticle spectrum, which is valid for both the atomic and band limit is obtained. The (IGF) method permits to calculate the quasiparticle spectra of many-particle systems with the complicated spectra and strong interaction in a very natural and compact way. The essence of the method deeply related to the notion of the Generalized Mean Fields (GMF), which determine the elastic scattering corrections. The inelastic scattering corrections leads to the damping of the quasiparticles and are the main topic of the present consideration. The calculation of the damping has been done in a self-consistent way for both limits. For the random Hubbard model the weak coupling case has been considered and the self-energy operator has been calculated using the combination of the IGF method and Coherent Potential Approximation (CPA). The other applications of the method to the s-f model, Anderson model, Heisenberg antiferromagnet, electron-phonon interaction models and quasiparticle tunneling are discussed briefly. (author). 79 refs

  8. Capillary sieving electrophoresis and micellar electrokinetic capillary chromatography produce highly correlated separation of tryptic digests

    Science.gov (United States)

    Dickerson, Jane A.; Dovichi, Norman J.

    2011-01-01

    We perform two-dimensional capillary electrophoresis on fluorescently labeled proteins and peptides. Capillary sieving electrophoresis was performed in the first dimension and micellar electrokinetic capillary chromatography was performed in the second. A cellular homogenate was labeled with the fluorogenic reagent FQ and separated using the system. This homogenate generated a pair of ridges; the first had essentially constant migration time in the CSE dimension, while the second had essentially constant migration time in the MEKC dimension. In addition a few spots were scattered through the electropherogram. The same homogenate was digested using trypsin, and then labeled and subjected to the two dimensional separation. In this case, the two ridges observed from the original two-dimensional separation disappeared, and were replaced by a set of spots that fell along the diagonal. Those spots were identified using a local-maximum algorithm and each was fit using a two-dimensional Gaussian surface by an unsupervised nonlinear least squares regression algorithm. The migration times of the tryptic digest components were highly correlated (r = 0.862). When the slowest migrating components were eliminated from the analysis, the correlation coefficient improved to r = 0.956. PMID:20564272

  9. Correlation of understanding of physics and psychological symptoms among high-school students in Greece

    Science.gov (United States)

    Aggeliki, Anagnostopoulou; Miltiades, Kyprianou; Antigoni-Elisavet, Rota; Evangelia, Pavlatou; Loizos, Zaphiris

    2017-09-01

    Depression may essentially influence cognitive function contributing to poor school performance. The present study undertakes to determine the existence and strength of correlation between depressive symptomatology and other mental conditions with the acquired level of understanding of Newtonian physics taught in schools. The current study recruited 490 students (262 girls, 228 boys) attending the first semester of the Greek Second Grade of General Lyceum School. Force Concept Inventory (FCI) tested the depth of the students’ understanding of Newtonian Physics. Symptom Checklist-90-R assessed general mental status. The tests took place in the classroom during a 1 h session. Low FCI scores significantly correlated with mental conditions, with depression ranking first. Girls had higher scores in all nine symptoms scales of SCL-90 and lower FCI scores. Stepwise regression models proved that the gender effect on FCI could be effectively explained through the significant effect of depression. An understanding of Newtonian physics among high school students may be restricted by common problematic mental conditions, with depression being the greatest among all. Further research, using a more systematic approach to measure depression among adolescents with poor understanding of physics, would help to elucidate the nature of the effect.

  10. A high-accuracy image registration algorithm using phase-only correlation for dental radiographs

    International Nuclear Information System (INIS)

    Ito, Koichi; Nikaido, Akira; Aoki, Takafumi; Kosuge, Eiko; Kawamata, Ryota; Kashima, Isamu

    2008-01-01

    Dental radiographs have been used for the accurate assessment and treatment of dental diseases. The nonlinear deformation between two dental radiographs may be observed, even if they are taken from the same oral regions of the subject. For an accurate diagnosis, the complete geometric registration between radiographs is required. This paper presents an efficient dental radiograph registration algorithm using Phase-Only Correlation (POC) function. The use of phase components in 2D (two-dimensional) discrete Fourier transforms of dental radiograph images makes possible to achieve highly robust image registration and recognition. Experimental evaluation using a dental radiograph database indicates that the proposed algorithm exhibits efficient recognition performance even for distorted radiographs. (author)

  11. Initial root length in wheat is highly correlated with acid soil tolerance in the field

    Directory of Open Access Journals (Sweden)

    Jorge Fernando Pereira

    Full Text Available ABSTRACT: In acid soils, toxic aluminum ions inhibit plant root growth. In order to discriminate aluminum (Al tolerance, trustful screening techniques are required. In this study, 20 wheat cultivars, showing different levels of Al tolerance, were evaluated in a short-term soil experiment to access their relative root length (RRL. Moreover, the alleles of two important genes (TaALMT1 and TaMATE1B for Al tolerance in wheat were discriminated. Both of these genes encode membrane transporters responsible for the efflux of organic acids by the root apices that are thought to confer tolerance by chelating Al. Genotypes showing TaALMT1 alleles V and VI and an insertion at the TaMATE1B promoter were among the ones showing greater RRL. Mechanisms of Al tolerance, which are not associated with organic acid efflux, can be potentially present in two cultivars showing greater RRL among the ones carrying inferior TaALMT1 and TaMATE1B alleles. The RRL data were highly correlated with wheat performance in acid soil at three developmental stages, tillering (r = −0.93, p < 0.001, silking (r = −0.91, p < 0.001 and maturation (r = −0.90, p < 0.001, as well as with the classification index of aluminum toxicity in the field (r = −0.92, p < 0.001. Since the RRL was obtained after only six days of growth and it is highly correlated with plant performance in acid soil under field conditions, the short-term experiment detailed here is an efficient and rapid method for reliable screening of wheat Al tolerance.

  12. Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure.

    Science.gov (United States)

    Byun, Jinyoung; Han, Younghun; Gorlov, Ivan P; Busam, Jonathan A; Seldin, Michael F; Amos, Christopher I

    2017-10-16

    Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome association study, failing to account for differences in genetic ancestry between cases and controls may also lead to false-positive results. Although a number of strategies for inferring and taking into account the confounding effects of genetic ancestry are available, applying them to large studies (tens thousands samples) is challenging. The goal of this study is to develop an approach for inferring genetic ancestry of samples with unknown ancestry among closely related populations and to provide accurate estimates of ancestry for application to large-scale studies. In this study we developed a novel distance-based approach, Ancestry Inference using Principal component analysis and Spatial analysis (AIPS) that incorporates an Inverse Distance Weighted (IDW) interpolation method from spatial analysis to assign individuals to population memberships. We demonstrate the benefits of AIPS in analyzing population substructure, specifically related to the four most commonly used tools EIGENSTRAT, STRUCTURE, fastSTRUCTURE, and ADMIXTURE using genotype data from various intra-European panels and European-Americans. While the aforementioned commonly used tools performed poorly in inferring ancestry from a large number of subpopulations, AIPS accurately distinguished variations between and within subpopulations. Our results show that AIPS can be applied to large-scale data sets to discriminate the modest variability among intra-continental populations as well as for characterizing inter-continental variation. The method we developed will protect against spurious associations when mapping the genetic basis of a disease. Our approach is more accurate and computationally efficient method for inferring genetic ancestry in the large-scale genetic studies.

  13. Ultrasonic attenuation measurements at very high SNR: Correlation, information theory and performance

    International Nuclear Information System (INIS)

    Challis, Richard; Ivchenko, Vladimir; Al-Lashi, Raied

    2013-01-01

    This paper describes a system for ultrasonic wave attenuation measurements which is based on pseudo-random binary codes as transmission signals combined with on-the-fly correlation for received signal detection. The apparatus can receive signals in the nanovolt range against a noise background in the order of hundreds of microvolts and an analogue to digital convertor (ADC) bit-step also in the order of hundreds of microvolts. Very high signal to noise ratios (SNRs) are achieved without recourse to coherent averaging with its associated requirement for high sampling times. The system works by a process of dithering – in which very low amplitude received signals enter the dynamic range of the ADC by 'riding' on electronic noise at the system input. The amplitude of this 'useful noise' has to be chosen with care for an optimised design. The process of optimisation is explained on the basis of classical information theory and is achieved through a simple noise model. The performance of the system is examined for different transmitted code lengths and gain settings in the receiver chain. Experimental results are shown to verify the expected operation when the system is applied to a very highly attenuating material – an aerated slurry

  14. Canine classical seminoma: a specific malignant type with human classifications is highly correlated with tumor angiogenesis

    International Nuclear Information System (INIS)

    Kim, Jong-Hyuk; Yu, Chi-Ho; Yhee, Ji-Young; Im, Keum-Soon; Kim, Na-Hyun; Sur, Jung-Hyang

    2010-01-01

    Human seminoma is classified as classical seminoma (SE) and spermatocytic seminoma (SS). Human SE is known to be more malignant and metastasizing more frequently than SS. Tumor angiogenesis is highly related with tumor progression and metastasis, with microvessel density (MVD) being an important parameter of metastatic potential. Canine seminoma is not yet well-established as SE or SS type including correlation with angiogenesis. We classified canine SE and SS, and then compared them to tumor associated vessels. Twenty-three cases of canine seminomas (2 intratubular, 9 diffuse, and 12 intratubular/diffuse seminomas showing both intratubular and diffuse patterns) were classified as SE or SS by immunohistochemistry (IHC) using monoclonal antibody against PLAP and by PAS stain. The histopathological data were then compared to see if there was a correlation with SE or SS. Angiogenesis of seminomas were evaluated by immunohistochemical assay using polyclonal antibody against Von Willebrand factor (vWF) and by calculating the means of MVD, vessels area and perimeters using computerized image analysis. Statistical Package for Social Sciences (SPSS) program was used for various statistical analyses. The numbers of PLAP+/PAS+ canine SEs were 8/23 (34.8%) and PLAP-/PAS- SSs were 15/23 (61.2%). All SE cases (8/8, 100%) were intratubular/diffuse types. SS types included 2 intratubular (2/15, 13.3%), 9 diffuse (9/15, 60%), and 4 intratubular/diffuse (4/15, 26.7%) types. MVD and vascular parameters in SEs were significantly higher than in SSs, showing the highest value in the intratubular/diffuse type. Seminomas observed with neoplastic cells invasion of vessels presented higher perimeter and area values than seminomas without conformed neoplastic cells invasion. In this study, we demonstrated a positive relationship between canine SE and tumor angiogenesis. Furthermore, we also showed that a tumor cells invasion of vessels were a correlated vascular parameter. Although

  15. Canine classical seminoma: a specific malignant type with human classifications is highly correlated with tumor angiogenesis

    Directory of Open Access Journals (Sweden)

    Kim Jong-Hyuk

    2010-05-01

    Full Text Available Abstract Background Human seminoma is classified as classical seminoma (SE and spermatocytic seminoma (SS. Human SE is known to be more malignant and metastasizing more frequently than SS. Tumor angiogenesis is highly related with tumor progression and metastasis, with microvessel density (MVD being an important parameter of metastatic potential. Canine seminoma is not yet well-established as SE or SS type including correlation with angiogenesis. We classified canine SE and SS, and then compared them to tumor associated vessels. Methods Twenty-three cases of canine seminomas (2 intratubular, 9 diffuse, and 12 intratubular/diffuse seminomas showing both intratubular and diffuse patterns were classified as SE or SS by immunohistochemistry (IHC using monoclonal antibody against PLAP and by PAS stain. The histopathological data were then compared to see if there was a correlation with SE or SS. Angiogenesis of seminomas were evaluated by immunohistochemical assay using polyclonal antibody against Von Willebrand factor (vWF and by calculating the means of MVD, vessels area and perimeters using computerized image analysis. Statistical Package for Social Sciences (SPSS program was used for various statistical analyses. Results The numbers of PLAP+/PAS+ canine SEs were 8/23 (34.8% and PLAP-/PAS- SSs were 15/23 (61.2%. All SE cases (8/8, 100% were intratubular/diffuse types. SS types included 2 intratubular (2/15, 13.3%, 9 diffuse (9/15, 60%, and 4 intratubular/diffuse (4/15, 26.7% types. MVD and vascular parameters in SEs were significantly higher than in SSs, showing the highest value in the intratubular/diffuse type. Seminomas observed with neoplastic cells invasion of vessels presented higher perimeter and area values than seminomas without conformed neoplastic cells invasion. Conclusion In this study, we demonstrated a positive relationship between canine SE and tumor angiogenesis. Furthermore, we also showed that a tumor cells invasion of vessels

  16. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora.

    Science.gov (United States)

    Behar, Doron M; Metspalu, Ene; Kivisild, Toomas; Rosset, Saharon; Tzur, Shay; Hadid, Yarin; Yudkovsky, Guennady; Rosengarten, Dror; Pereira, Luisa; Amorim, Antonio; Kutuev, Ildus; Gurwitz, David; Bonne-Tamir, Batsheva; Villems, Richard; Skorecki, Karl

    2008-04-30

    The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.

  17. Endotoxin levels correlate positively with a sedentary lifestyle and negatively with highly trained subjects.

    Science.gov (United States)

    Lira, Fabio S; Rosa, Jose C; Pimentel, Gustavo D; Souza, Hélio A; Caperuto, Erico C; Carnevali, Luiz C; Seelaender, Marília; Damaso, Ana R; Oyama, Lila M; de Mello, Marco T; Santos, Ronaldo V

    2010-08-04

    A sedentary lifestyle increases the risk of developing cardiovascular disease, obesity, and diabetes. This phenomenon is supported by recent studies suggesting a chronic, low-grade inflammation status. Endotoxin derived from gut flora may be key to the development of inflammation by stimulating the secretion of inflammatory factors. This study aimed to examine plasma inflammatory markers and endotoxin levels in individuals with a sedentary lifestyle and/or in highly trained subjects at rest. Fourteen male subjects (sedentary lifestyle n = 7; highly trained subjects n = 7) were recruited. Blood samples were collected after an overnight fast (approximately 12 h). The plasmatic endotoxin, plasminogen activator inhibitor type-1 (PAI-1), monocyte chemotactic protein-1 (MCP1), ICAM/CD54, VCAM/CD106 and lipid profile levels were determined. Endotoxinemia was lower in the highly trained subject group relative to the sedentary subjects (p < 0.002). In addition, we observed a positive correlation between endotoxin and PAI-1 (r = 0.85, p < 0.0001), endotoxin and total cholesterol (r = 0.65; p < 0.01), endotoxin and LDL-c (r = 0.55; p < 0.049) and endotoxin and TG levels (r = 0.90; p < 0.0001). The plasma levels of MCP-1, ICAM/CD54 and VCAM/CD106 did not differ. These results indicate that a lifestyle associated with high-intensity and high-volume exercise induces favorable changes in chronic low-grade inflammation markers and may reduce the risk for diseases such as obesity, diabetes and cardiovascular diseases.

  18. Aminostratigraphic correlations and paleotemperature implications, Pliocene-Pleistocene high-sea-level deposits, northwestern Alaska

    Science.gov (United States)

    Kaufman, Darrell S.; Brigham-Grette, Julie

    Multiple periods of Late Pliocene and Pleistocene high sea level are recorded by surficial deposits along the coastal plains of northwestern Alaska. Analyses of the extent of amino acid epimerization in fossil molluscan shells from the Nome coastal plain of the northern Bering Sea coast, and from the Alaskan Arctic Coastal Plain of the Chukchi and Beaufort Sea coasts, allow recognition of at least five intervals of higher-than-present relative sea level. Three Late Pliocene transgressions are represented at Nome by the complex and protracted Beringian transgression, and on the Arctic Coastal Plain by the Colvillian, Bigbendian, and Fishcreekian transgressions. These were followed by a lengthy period of non-marine deposition during the Early Pleistocene when sea level did not reach above its present position. A Middle Pleistocene high-sea-level event is represented at Nome by the Anvilian transgression, and on the Arctic Coastal Plain by the Wainwrightian transgression. Anvilian deposits at the type locality are considerably younger than previously thought, perhaps as young as Oxygen-Isotope Stage 11 (˜410,000 BP). Finally, the last interglacial Pelukian transgression is represented discontinuously along the shores of northwestern Alaska. Amino acid epimerization data, together with previous paleomagnetic measurements, radiometric-age determinations, and paleontologic evidence provide geochronological constraints on the sequence of marine deposits. They form the basis of regional correlations and offer a means of evaluating the post-depositional thermal history of the high-sea-level deposits. Provisional correlations between marine units at Nome and the Artic Coastal Plain indicate that the temperature difference that separates the two sites today had existed by about 3.0 Ma. Since that time, the effective diagenetic temperature was lowered by about 3-4°C at both sites, and the mean annual temperature was lowered considerably more. This temperature decrease was

  19. An abbreviated SNP panel for ancestry assignment of honeybees (Apis mellifera)

    Science.gov (United States)

    This paper examines whether an abbreviated panel of 37 single nucleotide polymorphisms (SNPs) has the same power as a larger and more expensive panel of 95 SNPs to assign ancestry of honeybees (Apis mellifera) to three ancestral lineages. We selected 37 SNPs from the original 95 SNP panel using alle...

  20. Typing of two Middle Eastern populations with the Precision ID Ancestry Panel

    DEFF Research Database (Denmark)

    Truelsen, Ditte Mikkelsen; Farzad, Maryam Sharafi; Mogensen, Helle Smidt

    2017-01-01

    , Turkish and Iranian individuals were SNP typed with Massively Parallel Sequencing with the Precision ID Ancestry Panel (Thermo Fisher Scientific) to assess whether it was possible to differentiate geographically proximate populations in the Middle East using this kit. Analyses showed that it were...

  1. Significant others and the importance of ancestry for Czech national identity

    Czech Academy of Sciences Publication Activity Database

    Plecitá, Klára

    (2018) ISSN 1460-8944 R&D Projects: GA MŠk(CZ) LG12023 Institutional support: RVO:68378025 Keywords : national identity * ancestry * immigration Subject RIV: AO - Sociology, Demography OBOR OECD: Sociology http://www.tandfonline.com/doi/full/10.1080/14608944.2017.1362378

  2. What role does African ancestry play in how hypertensive patients respond to certain antihypertensive drug therapy?

    NARCIS (Netherlands)

    Seedat, Yackoob K.; Brewster, Lizzy M.

    2014-01-01

    This article is a summary of the response of the four commonly used antihypertensive agents in African ancestry patients. They are thiazide like diuretics or indapamide, calcium channel blockers (CCB), angiotensin converting enzyme inhibitors (ACEI) or angiotensin receptor blockers, and β-adrenergic

  3. Inequalities in asthma treatment among children by country of birth and ancestry:

    DEFF Research Database (Denmark)

    Cantarero Arevalo, Lourdes; Holstein, Bjørn Evald; Andersen, Anette

    2013-01-01

    Investigations in several Western countries have reported ethnic differences in asthma prevalence and treatment among children and in some countries these differences are increasing. The aim of this study was to analyse whether there are inequalities in asthma treatment by country of birth...... and ancestry among children residing in Denmark, and whether this potential association may vary between different household income groups....

  4. Assessing the risk for suicide in schizophrenia according to migration, ethnicity and geographical ancestry.

    Science.gov (United States)

    Hettige, Nuwan C; Bani-Fatemi, Ali; Kennedy, James L; De Luca, Vincenzo

    2017-02-09

    Suicide is a leading cause of mortality among those afflicted by schizophrenia. Previous studies demonstrated that the stressors associated with immigration may lead to an onset of schizophrenia and suicide separately in susceptible individuals. However, no studies have shown whether immigration may lead to suicidal behaviour for individuals with schizophrenia. Our study proposes that an individual's geographical ancestry, ethnicity or migration status may be predictive of suicide risk in schizophrenia. In a sample of 276 participants with schizophrenia spectrum disorders, we conducted cross-sectional assessments to collect clinical information. Self-identified ethnicity and suicide history were collected through self-report questionnaires and interview-based scales. Ancestry was identified using 292 genetic markers from HapMap. Migrants were classified as those who immigrated to Canada during their lifetime. Using a regression analysis, we tested whether a history of migration, ethnicity or geographical ancestry were predictive of a history of suicide attempts. Our analysis failed to demonstrate a significant relationship between suicide history and migration, ethnicity or ancestry. However, ethnicity appears to be significantly associated with the number of psychiatric hospitalizations in our sample. Ethnicity and migration history are not predictive of previous suicide attempts. Ethnicity may be an important demographic factor affecting access to mental health resources and frequency of hospitalizations.

  5. Measurement and analysis of quadruple (αγγ) angular correlations for high spin states of 24Mg

    International Nuclear Information System (INIS)

    Wiedenhoever, I.; Wuosmaa, A. H.; Lister, C. J.; Carpenter, M. P.; Janssens, R. V. F.; Amro, H.; Caggiano, J.; Heinz, A.; Kondev, F. G.; Lauritsen, T.; Siem, S.; Sonzogni, A.; Bhattacharyya, P.; Devlin, M.; Sarantites, D. G.; Sobotka, L. G.

    2000-01-01

    The high-lying, α-decaying states in 24 Mg have been studied by measuring the complete decay path of α and γ emissions using five segmented Silicon detectors in conjunction with GAMMASPHERE. The authors analyzed the (αγ) triple angular correlations and, for the first time, (αγγ) quadruple correlations. The data analysis is based on a new Fourier transformation technique. The power of the technique is demonstrated

  6. A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

    Science.gov (United States)

    Pan, Bing; Wang, Bo

    2017-10-01

    Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

  7. Reverse Correlating Love: Highly Passionate Women Idealize Their Partner’s Facial Appearance

    Science.gov (United States)

    Gunaydin, Gul; DeLong, Jordan E.

    2015-01-01

    A defining feature of passionate love is idealization—evaluating romantic partners in an overly favorable light. Although passionate love can be expected to color how favorably individuals represent their partner in their mind, little is known about how passionate love is linked with visual representations of the partner. Using reverse correlation techniques for the first time to study partner representations, the present study investigated whether women who are passionately in love represent their partner’s facial appearance more favorably than individuals who are less passionately in love. In a within-participants design, heterosexual women completed two forced-choice classification tasks, one for their romantic partner and one for a male acquaintance, and a measure of passionate love. In each classification task, participants saw two faces superimposed with noise and selected the face that most resembled their partner (or an acquaintance). Classification images for each of high passion and low passion groups were calculated by averaging across noise patterns selected as resembling the partner or the acquaintance and superimposing the averaged noise on an average male face. A separate group of women evaluated the classification images on attractiveness, trustworthiness, and competence. Results showed that women who feel high (vs. low) passionate love toward their partner tend to represent his face as more attractive and trustworthy, even when controlling for familiarity effects using the acquaintance representation. Using an innovative method to study partner representations, these findings extend our understanding of cognitive processes in romantic relationships. PMID:25806540

  8. Correlation effects in high-Tc superconductors and heavy fermion compounds

    International Nuclear Information System (INIS)

    Kuzemsky, A.L.

    1993-10-01

    This paper describes certain aspects of Highly Correlated Systems (HCS) such as high Tc superconductors (HTSC) and some new class of Heavy Fermion (HF) systems which have been studied recently. The problem is discussed on how the charge and spin degrees of freedom participate in the specific character of superconductivity in the copper oxides and competition of the magnetism and Kondo screening in heavy fermions. The electronic structure and possible superconducting mechanisms of HTSC compounds are discussed. The similarity and dissimilarity with HF compounds is pointed out. It is shown that the spins and carriers in the copper oxides are coupled in a very nontrivial way in order to introduce the discussion and the comparison of the Emery model, the t - J-model and the Kondo-Heisenberg model. It concerns attempts to derive from fundamental multi-band Hamiltonian the reduced effective Hamiltonians to extract and separate the relevant low-energy physics. A short review of the arguments which seem to support the spin-polaron pairing mechanism in HTSC are presented. Many other topics like the idea of mixed valence states in oxides, the role of charge transfer (CT) excitations, phase separation, self-consistent nonperturbative technique, etc. are also discussed. (author). 161 refs

  9. Profumo di SUSY: Suggestive Correlations in the ATLAS and CMS High Jet Multiplicity Data

    CERN Document Server

    Li, Tianjun; Nanopoulos, Dimitri V; Walker, Joel W

    2011-01-01

    We present persistently amassing evidence that the CMS and ATLAS Collaborations may indeed be already registering supersymmetry events at the Large Hadron Collider (LHC). Our analysis is performed in the context of a highly phenomenologically favorable model named No-Scale F-SU(5), which represents the unification of the F-lipped SU(5) Grand Unified Theory (GUT), two pairs of hypothetical TeV-scale vector-like supersymmetric multiplets derived out of F-Theory, and the dynamically established boundary conditions of No-Scale supergravity. We document highly suggestive correlations between the first inverse femtobarn of observations by CMS and ATLAS, where seductive excesses in multijet events, particularly those with nine or more jets, are unambiguously accounted for by a precision Monte-Carlo simulation of the F-SU(5) model space. This intimate correspondence is optimized by a unified gaugino mass in the neighborhood of M_{1/2}=518 GeV. We supplement this analysis by extrapolating for the expected data profile...

  10. Reverse correlating love: highly passionate women idealize their partner's facial appearance.

    Science.gov (United States)

    Gunaydin, Gul; DeLong, Jordan E

    2015-01-01

    A defining feature of passionate love is idealization--evaluating romantic partners in an overly favorable light. Although passionate love can be expected to color how favorably individuals represent their partner in their mind, little is known about how passionate love is linked with visual representations of the partner. Using reverse correlation techniques for the first time to study partner representations, the present study investigated whether women who are passionately in love represent their partner's facial appearance more favorably than individuals who are less passionately in love. In a within-participants design, heterosexual women completed two forced-choice classification tasks, one for their romantic partner and one for a male acquaintance, and a measure of passionate love. In each classification task, participants saw two faces superimposed with noise and selected the face that most resembled their partner (or an acquaintance). Classification images for each of high passion and low passion groups were calculated by averaging across noise patterns selected as resembling the partner or the acquaintance and superimposing the averaged noise on an average male face. A separate group of women evaluated the classification images on attractiveness, trustworthiness, and competence. Results showed that women who feel high (vs. low) passionate love toward their partner tend to represent his face as more attractive and trustworthy, even when controlling for familiarity effects using the acquaintance representation. Using an innovative method to study partner representations, these findings extend our understanding of cognitive processes in romantic relationships.

  11. Prevalence and correlates of delayed sleep phase in high school students.

    Science.gov (United States)

    Saxvig, Ingvild W; Pallesen, Ståle; Wilhelmsen-Langeland, Ane; Molde, Helge; Bjorvatn, Bjørn

    2012-02-01

    To investigate prevalence and correlates of delayed sleep phase, characterized by problems falling asleep in the evening and rising at adequate times in the morning, in a large sample of Norwegian high school students. A randomized sample of 1285 high school students (aged 16-19 years) participated in an internet based study answering questions about sleep habits, height, weight, smoking, alcohol use, school grades, and anxiety and depression symptoms. Delayed sleep phase was operationalized as difficulties falling asleep before 2 a.m. at least three nights per week together with much or very much difficulty waking up in the morning. The results show a prevalence of delayed sleep phase of 8.4%. In all, 68% of these students (5.7% of the total sample) also reported problems advancing their sleep period as well as one daytime consequence (oversleeping at least two days a week or experiencing much/very much sleepiness at school). Delayed sleep phase was associated with lower average school grades, smoking, alcohol usage, and elevated anxiety and depression scores. Delayed sleep phase appears to be common amongst Norwegian adolescents and is associated with negative outcomes such as lower average school grades, smoking, alcohol usage, and elevated anxiety and depression scores. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Changes in Physical Activity Domains During the Transition Out of High School: Psychosocial and Environmental Correlates.

    Science.gov (United States)

    Molina-García, Javier; Queralt, Ana; Castillo, Isabel; Sallis, James F

    2015-10-01

    This study examined changes in multiple physical activity domains during the transition out of high school and psychosocial and environmental determinants of these changes. A 1-year prospective study was designed. The baseline sample was composed of 244 last-year high school students (58.6% female) from Valencia, Spain. Follow-up rate was 46%. Physical activity and potential determinants were measured by the Global Physical Activity Questionnaire and other evaluated scales in 2 waves. Total physical activity and active commuting (AC) decreased, respectively, by 21% and 36%, only in males. At time 1, access to car/motorbike (inverse), planning/psychosocial barriers (inverse), street connectivity (positive) and parental education (inverse) were significantly associated with AC (P genders, there was a decrease in leisure-time physical activity (LTPA; -35% in males, -43% in females). At time 1, self-efficacy and social support were positive correlates of LTPA (P physical activity change were identified, and these are promising targets for interventions.

  13. Correlates of bullying in Quebec high school students: The vulnerability of sexual-minority youth.

    Science.gov (United States)

    Cénat, Jude Mary; Blais, Martin; Hébert, Martine; Lavoie, Francine; Guerrier, Mireille

    2015-09-01

    Bullying has become a significant public health issue, particularly among youth. This study documents cyberbullying, homophobic bullying and bullying at school or elsewhere and their correlates among both heterosexual and sexual-minority high school students in Quebec (Canada). A representative sample of 8194 students aged 14-20 years was recruited in Quebec (Canada) high schools. We assessed cyberbullying, homophobic bullying and bullying at school or elsewhere in the past 12 months and their association with current self-esteem and psychological distress as well as suicidal ideations. Bullying at school or elsewhere was the most common form of bullying (26.1%), followed by cyberbullying (22.9%) and homophobic bullying (3.6%). Overall, girls and sexual-minority youth were more likely to experience cyberbullying and other forms of bullying as well as psychological distress, low self-esteem and suicidal ideations. The three forms of bullying were significantly and independently associated with all mental health outcomes. The results underscore the relevance of taking into account gender and sexual orientation variations in efforts to prevent bullying experience and its consequences. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

  14. Correlation of waterside corrosion and cladding microstructure in high-burnup fuel and gadolinia rods

    International Nuclear Information System (INIS)

    Chung, H.M.

    1989-09-01

    Waterside corrosion of the Zircaloy cladding has been examined in high-burnup fuel rods from several BWRs and PWRs, as well as in 3 wt % gadolinia burnable poison rods obtained from a BWR. The corrosion behavior of the high-burnup rods was then correlated with results from a microstructural characterization of the cladding by optical, scanning-electron, and transmission-electron microscopy (OM, SEM, and TEM). OM and SEM examination of the BWR fuel cladding showed both uniform and nodular oxide layers 2 to 45 μm in thickness after burnups of 11 to 30 MWd/kgU. For one of the BWRs, which was operated at 307 degree C rather than the normal 288 degree C, a relatively thick (50 to 70 μm) uniform oxide, rather than nodular oxides, was observed after a burnup of 27 to 30 MWd/kgU. TEM characterization revealed a number of microstructural features that occurred in association with the intermetallic precipitates in the cladding metal, apparently as a result of irradiation-induced or -enhanced processes. The BWR rods that exhibited white nodular oxides contained large precipitates (300 to 700 nm in size) that were partially amorphized during service, indicating that a distribution of the large intermetallic precipitates is conductive to nodular oxidation. 23 refs., 9 figs

  15. Idiopathic pulmonary fibrosis with coexisting emphysema : high-resolution CT and clinical correlation

    International Nuclear Information System (INIS)

    Kang, Eun Young; Kim, Kyeong Ah; Oh, Yu Whan; Shim, Jae Jeong; Kang, Kyung Ho

    1997-01-01

    To correlate high-resolution CT (HRCT) findings with smoking history and pulmonary function test (PFT) in patients with idiopathic pulmonary fibrosis (IPF) with or without coexisting emphsema. The study included 24 patients who had undergone HRCT and in whom IPF had been confirmed pathologically (n=7) and clinically (n=17). The patients included 19 men and 5 women aged between from 44 and 78(mean 59) years. HRCT findings were reviewed by two radiologists and assessed for the presence and extent of emphysema (CT emphysema score;CES) and honeycombing (CT honeycombing score;CHS). CES and CHS were retrospectively correlated with smoking status and pulmonary function test. Evidence of emphysema was seen on HRCT in 20 fo 24 patients with IPF (83%). CES was 14.3 and CHS was 18.1 in smokers with IPF, as compared with 1.8 and 6.7 in nonsmokers (p<0.01). Pulmonary function tests showed lower percent predicted FEVI (69.3%), FVC (64.7%), TLC (73.7%), and RV (77.3%), a lower percent predicted diffusing capacity of carbon monoxide (58.2%), and normal FEVI/FVC (99.1%). The pulmonary function test in smokers showed higher TLC and RV than in nonsmokers. Eight of nine patients whose CES was higher than their CHS, an seen on HRCT, were smokers and had a smoking history of 33.1 pack-years. Seven of 15 whose CHS was higher than their CES were smokers and had a smoking history of 16.8 pack-years. In patients with a higher CES than CHS pulmonary function test results showed normal TLC(85%) and RV(100.7%); this contrasted with decreased TLC(72%) and RV (68%) in patients whose CHS was higher than their CES. Emphysema is a frequently associated finding in patients with IPF, as seen on HRCT, and emphysema is more frequent and extensive in smokers with IPF than non-smokers. HRCT is useful for detecting emphysema in patients with IPF, and the extent of emphysema on HRCT correlates with the results of the pulmonary function test and smoking status

  16. Idiopathic pulmonary fibrosis with coexisting emphysema : high-resolution CT and clinical correlation

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Eun Young; Kim, Kyeong Ah; Oh, Yu Whan; Shim, Jae Jeong; Kang, Kyung Ho [Korea Univ. College of Medicine, Seoul (Korea, Republic of)

    1997-05-01

    To correlate high-resolution CT (HRCT) findings with smoking history and pulmonary function test (PFT) in patients with idiopathic pulmonary fibrosis (IPF) with or without coexisting emphsema. The study included 24 patients who had undergone HRCT and in whom IPF had been confirmed pathologically (n=7) and clinically (n=17). The patients included 19 men and 5 women aged between from 44 and 78(mean 59) years. HRCT findings were reviewed by two radiologists and assessed for the presence and extent of emphysema (CT emphysema score;CES) and honeycombing (CT honeycombing score;CHS). CES and CHS were retrospectively correlated with smoking status and pulmonary function test. Evidence of emphysema was seen on HRCT in 20 fo 24 patients with IPF (83%). CES was 14.3 and CHS was 18.1 in smokers with IPF, as compared with 1.8 and 6.7 in nonsmokers (p<0.01). Pulmonary function tests showed lower percent predicted FEVI (69.3%), FVC (64.7%), TLC (73.7%), and RV (77.3%), a lower percent predicted diffusing capacity of carbon monoxide (58.2%), and normal FEVI/FVC (99.1%). The pulmonary function test in smokers showed higher TLC and RV than in nonsmokers. Eight of nine patients whose CES was higher than their CHS, an seen on HRCT, were smokers and had a smoking history of 33.1 pack-years. Seven of 15 whose CHS was higher than their CES were smokers and had a smoking history of 16.8 pack-years. In patients with a higher CES than CHS pulmonary function test results showed normal TLC(85%) and RV(100.7%); this contrasted with decreased TLC(72%) and RV (68%) in patients whose CHS was higher than their CES. Emphysema is a frequently associated finding in patients with IPF, as seen on HRCT, and emphysema is more frequent and extensive in smokers with IPF than non-smokers. HRCT is useful for detecting emphysema in patients with IPF, and the extent of emphysema on HRCT correlates with the results of the pulmonary function test and smoking status.

  17. Nonvolcanic Tremor Activity is Highly Correlated With Slow Slip Events, Mexico

    Science.gov (United States)

    Kostoglodov, V.; Shapiro, N.; Larson, K. M.; Payero, J. S.; Husker, A.; Santiago, L. A.; Clayton, R. W.

    2008-12-01

    Significant activity of nonvolcanic tremor (NVT) has been observed in the central Mexico (Guerrero) subduction zone since 2001 when continuous seismic records became available. Although the quality of these records is poor, it is possible to estimate a temporal variation of energy in the range of 1-2Hz (best signal/noise ratio for the NVT). These clearly indicate a maximum of NVT energy release (En) during the 2001-2002 and 2006 large aseismic slow slip events (SSE) registered by the Guerrero GPS network. In particular En is higher for the 2001-2002 SSE which had larger surface displacements and extension than the 2006 SSE. A more detailed and accurate study of NVT activity was carried out using the data collected during the MASE experiment in Mexico. MASE consisted of 100 broad band seismometers in operation for ~2.5 years (2005-2007) along the profile oriented SSW-NNE from Acapulco, and crossing over the subduction zone for a distance of ~500 km. Epicenters and depths of individual tremor events determined using the envelope cross-correlation technique have rather large uncertainties, partly originated from the essentially 2D geometry of the network. The 'energy' approach is more efficient in this case because it provides an average NVT activity evolution in time and space. The data processing consists of a band pass (1-2Hz) filter of the raw 100 Hz sampled N-S component records, application a 10 min-width median filter to eliminate the effect of local seismic events and noise, and integration of the energy and normalization of daily En using an average coda amplitude from several regional earthquakes of M~5. A time-space distribution of En reveals a strong correlation between NVT energy release and the 2006 SSE, which also replicates the two-phase character of this slow event and a migration of the slow slip maximum from North to South. There are also a few clear episodes of relatively high NVT energy release that do not correspond to any significant geodetic

  18. Correlation between High Resolution Dynamic MR Features and Prognostic Factors in Breast Cancer

    International Nuclear Information System (INIS)

    Lee, Shin Ho; Cho, Nariya; Kim, Seung Ja; Cho, Kyung Soo; Ko, Eun Sook; Moon, Woo Kyung; Cha, Joo Hee

    2008-01-01

    To correlate high resolution dynamic MR features with prognostic factors in breast cancer. One hundred and ninety-four women with invasive ductal carcinomas underwent dynamic MR imaging using T1-weighted three dimensional fast low-angle shot (3D-FLASH) sequence within two weeks prior to surgery. Morphological and kinetic MR features were determined based on the breast imaging and reporting data system (BI-RADS) MR imaging lexicon. Histological specimens were analyzed for tumor size, axillary lymph node status, histological grade, expression of estrogen receptor (ER), expression of progesterone receptor (PR), and expression of p53, c-erbB-2, and Ki-67. Correlations between the MR features and prognostic factors were determined using the Pearson x 2 test, linear-by-linear association, and logistic regression analysis. By multivariate analysis, a spiculated margin was a significant, independent predictor of a lower histological grade (p < 0.001), and lower expression of Ki-67 (p = 0.007). Rim enhancement was significant, independent predictor of a higher histological grade (p < 0.001), negative expression of ER (p 0.001), negative expression of PR (p < 0.001) and a larger tumor size (p = 0.006). A washout curve may predict a higher level of Ki-67 (p = 0.05). Most of the parameters of the initial enhancement phase cannot predict the status of the prognostic factors. Only the enhancement ratio may predict a larger tumor size (p 0.05). Of the BI-RADS-MR features, a spiculated margin may predict favorable prognosis, whereas rim enhancement or washout may predict unfavorable prognosis of breast cancer

  19. Strongly correlated electrons at high pressure: an approach by inelastic X-Ray scattering; Electrons correles sous haute pression: une approche par diffusion inelastique des rayons X

    Energy Technology Data Exchange (ETDEWEB)

    Rueff, J.P

    2007-06-15

    Inelastic X-ray scattering (IXS) and associated methods has turn out to be a powerful alternative for high-pressure physics. It is an all-photon technique fully compatible with high-pressure environments and applicable to a vast range of materials. Standard focalization of X-ray in the range of 100 microns is typical of the sample size in the pressure cell. Our main aim is to provide an overview of experimental results obtained by IXS under high pressure in 2 classes of materials which have been at the origin of the renewal of condensed matter physics: strongly correlated transition metal oxides and rare-earth compounds. Under pressure, d and f-electron materials show behaviors far more complex that what would be expected from a simplistic band picture of electron delocalization. These spectroscopic studies have revealed unusual phenomena in the electronic degrees of freedom, brought up by the increased density, the changes in the charge-carrier concentration, the over-lapping between orbitals, and hybridization under high pressure conditions. Particularly we discuss about pressure induced magnetic collapse and metal-insulator transitions in 3d compounds and valence fluctuations phenomena in 4f and 5f compounds. Thanks to its superior penetration depth, chemical selectivity and resonant enhancement, resonant inelastic X-ray scattering has appeared extremely well suited to high pressure physics in strongly correlated materials. (A.C.)

  20. Association of genetic ancestry with breast cancer in ethnically diverse women from Chicago.

    Directory of Open Access Journals (Sweden)

    Umaima Al-Alem

    Full Text Available Non-Hispanic (nH Black and Hispanic women are disproportionately affected by early onset disease, later stage, and with more aggressive, higher grade and ER/PR negative breast cancers. The purpose of this analysis was to examine whether genetic ancestry could account for these variation in breast cancer characteristics, once data were stratified by self-reported race/ethnicity and adjusted for potential confounding by social and behavioral factors.We used a panel of 100 ancestry informative markers (AIMs to estimate individual genetic ancestry in 656 women from the "Breast Cancer Care in Chicago" study, a multi-ethnic cohort of breast cancer patients to examine the association between individual genetic ancestry and breast cancer characteristics. In addition we examined the association of individual AIMs and breast cancer to identify genes/regions that may potentially play a role in breast cancer disease disparities.As expected, nH Black and Hispanic patients were more likely than nH White patients to be diagnosed at later stages, with higher grade, and with ER/PR negative tumors. Higher European genetic ancestry was protective against later stage at diagnosis (OR 0.7 95%CI: 0.54-0.92 among Hispanic patients, and higher grade (OR 0.73, 95%CI: 0.56-0.95 among nH Black patients. After adjustment for multiple social and behavioral risk factors, the association with later stage remained, while the association with grade was not significant. We also found that the AIM SNP rs10954631 on chromosome 7 was associated with later stage (p = 0.02 and higher grade (p = 0.012 in nH Whites and later stage (p = 0.03 in nH Blacks.Non-European genetic ancestry was associated with later stage at diagnosis in ethnic minorities. The relation between genetic ancestry and stage at diagnosis may be due to genetic factors and/or unmeasured environmental factors that are overrepresented within certain racial/ethnic groups.

  1. African genetic ancestry interacts with body mass index to modify risk for uterine fibroids.

    Science.gov (United States)

    Giri, Ayush; Edwards, Todd L; Hartmann, Katherine E; Torstenson, Eric S; Wellons, Melissa; Schreiner, Pamela J; Velez Edwards, Digna R

    2017-07-01

    Race, specifically African ancestry, and obesity are important risk factors for uterine fibroids, and likely interact to provide the right conditions for fibroid growth. However, existing studies largely focus on the main-effects rather than their interaction. Here, we firstly provide evidence for interaction between categories of body mass index (BMI) and reported-race in relation to uterine fibroids. We then investigate whether the association between inferred local European ancestry and fibroid risk is modified by BMI in African American (AA) women in the Vanderbilt University Medical Center bio-repository (BioVU) (539 cases and 794 controls) and the Coronary Artery Risk Development in Young Adults study (CARDIA, 264 cases and 173 controls). We used multiple logistic regression to evaluate interactions between local European ancestry and BMI in relation to fibroid risk, then performed fixed effects meta-analysis. Statistical significance threshold for local-ancestry and BMI interactions was empirically estimated with 10,000 permutations (p-value = 1.18x10-4). Admixture mapping detected an association between European ancestry and fibroid risk which was modified by BMI (continuous-interaction p-value = 3.75x10-5) around ADTRP (chromosome 6p24); the strongest association was found in the obese category (ancestry odds ratio (AOR) = 0.51, p-value = 2.23x10-5). Evaluation of interaction between genotyped/imputed variants and BMI in this targeted region suggested race-specific interaction, present in AAs only; strongest evidence was found for insertion/deletion variant (6:11946435), again in the obese category (OR = 1.66, p-value = 1.72x10-6). We found nominal evidence for interaction between local ancestry and BMI at a previously reported region in chromosome 2q31-32, which includes COL5A2, and TFPI, an immediate downstream target of ADTRP. Interactions between BMI and SNPs (single nucleotide polymorphisms) found in this region in AA women were also detected in an

  2. Association between Plasma 25-Hydroxyvitamin D, Ancestry and Aggressive Prostate Cancer among African Americans and European Americans in PCaP.

    Directory of Open Access Journals (Sweden)

    Susan E Steck

    Full Text Available African Americans (AAs have lower circulating 25-hydroxyvitamin D3 [25(OHD3] concentrations and higher prostate cancer (CaP aggressiveness than other racial/ethnic groups. The purpose of the current study was to examine the relationship between plasma 25(OHD3, African ancestry and CaP aggressiveness among AAs and European Americans (EAs.Plasma 25(OHD3 was measured using LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometry in 537 AA and 663 EA newly-diagnosed CaP patients from the North Carolina-Louisiana Prostate Cancer Project (PCaP classified as having either 'high' or 'low' aggressive disease based on clinical stage, Gleason grade and prostate specific antigen at diagnosis. Mean plasma 25(OHD3 concentrations were compared by proportion of African ancestry. Logistic regression was used to calculate multivariable adjusted odds ratios (OR and 95% confidence intervals (95%CI for high aggressive CaP by tertile of plasma 25(OHD3.AAs with highest percent African ancestry (>95% had the lowest mean plasma 25(OHD3 concentrations. Overall, plasma 25(OHD3 was associated positively with aggressiveness among AA men, an association that was modified by calcium intake (ORT 3vs.T1: 2.23, 95%CI: 1.26-3.95 among men with low calcium intake, and ORT 3vs.T1: 0.19, 95%CI: 0.05-0.70 among men with high calcium intake. Among EAs, the point estimates of the ORs were <1.0 for the upper tertiles with CIs that included the null.Among AAs, plasma 25(OHD3 was associated positively with CaP aggressiveness among men with low calcium intake and inversely among men with high calcium intake. The clinical significance of circulating concentrations of 25(OHD3 and interactions with calcium intake in the AA population warrants further study.

  3. High Avidity dsDNA Autoantibodies in Brazilian Women with Systemic Lupus Erythematosus: Correlation with Active Disease and Renal Dysfunction

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    Rodrigo C. Oliveira

    2015-01-01

    Full Text Available We investigated in Brazilian women with SLE the prevalence and levels of high avidity (HA dsDNA antibodies and tested their correlation with lupus activity and biomarkers of renal disease. We also compared these correlations to those observed with total dsDNA antibodies and antibodies against nucleosome (ANuA. Autoantibodies were detected by ELISA, while C3 and C4 levels were determined by nephelometry. Urine protein/creatinine ratio was determined, and lupus activity was measured by SLEDAI-2K. The prevalence of total and HA dsDNA antibodies was similar to but lower than that verified for ANuA. The levels of the three types of antibodies were correlated, but the correlation was more significant between HA dsDNA antibodies and ANuA. High avidity dsDNA antibodies correlated positively with ESR and SLEDAI and inversely with C3 and C4. Similar correlations were observed for ANuA levels, whereas total dsDNA antibodies only correlated with SLEDAI and C3. The levels of HA dsDNA antibodies were higher in patients with proteinuria, but their levels of total dsDNA antibodies and ANuA were unaltered. High avidity dsDNA antibodies can be found in high prevalence in Brazilian women with SLE and are important biomarkers of active disease and kidney dysfunction.

  4. Microwave Imaging Sensor Using Compact Metamaterial UWB Antenna with a High Correlation Factor

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    Md. Moinul Islam

    2015-07-01

    Full Text Available The design of a compact metamaterial ultra-wideband (UWB antenna with a goal towards application in microwave imaging systems for detecting unwanted cells in human tissue, such as in cases of breast cancer, heart failure and brain stroke detection is proposed. This proposed UWB antenna is made of four metamaterial unit cells, where each cell is an integration of a modified split ring resonator (SRR, capacitive loaded strip (CLS and wire, to attain a design layout that simultaneously exhibits both a negative magnetic permeability and a negative electrical permittivity. This design results in an astonishing negative refractive index that enables amplification of the radiated power of this reported antenna, and therefore, high antenna performance. A low-cost FR4 substrate material is used to design and print this reported antenna, and has the following characteristics: thickness of 1.6 mm, relative permeability of one, relative permittivity of 4.60 and loss tangent of 0.02. The overall antenna size is 19.36 mm × 27.72 mm × 1.6 mm where the electrical dimension is 0.20 λ × 0.28 λ × 0.016 λ at the 3.05 GHz lower frequency band. Voltage Standing Wave Ratio (VSWR measurements have illustrated that this antenna exhibits an impedance bandwidth from 3.05 GHz to more than 15 GHz for VSWR < 2 with an average gain of 4.38 dBi throughout the operating frequency band. The simulations (both HFSS and computer simulation technology (CST and the measurements are in high agreement. A high correlation factor and the capability of detecting tumour simulants confirm that this reported UWB antenna can be used as an imaging sensor.

  5. Disordered Eating Attitudes and Their Correlates among Iranian High School Girls

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    Mahdiyeh Hamed Behzad

    2011-07-01

    Full Text Available Background: Disordered eating attitudes are contributing factors to the development of eatingdisorders. Adolescent girls are at high risk for eating diseases. In Iran, there is few data onthe subject, especially in Azarian adolescent girls, so we did this study for assessing disorderedeating attitudes and their correlates among Iranian Azarbaijani high school girls.Methods: In a cross-sectional study, 1887 high school girls were selected. Eating AttitudeTest-26 (EAT-26 and socio economical questionnaires were used. The EAT-26 score of 20or higher defined as disordered eating attitudes. Data were analyzed using the Statistical Programfor Social Sciences, by using from descriptive and analytical statistics.Results: Reliability and validity of the translated EAT-26 were 0.80, 0.76, respectively. Instudied subjects, mean (SD of EAT-26 was 11.71(8.48. Totally, 16.7% (C.I with 95%: 15.1-18.3% of students had disordered eating attitudes. About half of the participants were unhappywith their body weight and considered themselves as obese. Mean of EAT-26 washigher in this group. Groups, who intent to weight loss, were smoker, and who had age ofmenarche less than 11 years, also had higher EAT-26 scores. Parent’s literacy or job, birthorder, family size or income and house ownership had not any significant effect on EAT-26score.Conclusions: Persian version of EAT-26 has good reliability and validity for assessing disorderedeating attitudes in Azarian girl adolescents. Prevalence of disordered eating attitudesamong Azarian adolescent girls are in the range of some studies, but are less than Arabiancountries, and some European ones. In adolescent girls, body weight dissatisfaction, smokingand early menarche has important role in eating attitudes.

  6. Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant.

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    Tobias Ahsendorf

    Full Text Available The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs, coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1, was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified.

  7. Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

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    Sergio eTofanelli

    2014-11-01

    Full Text Available Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA and the non-recombining portion of the Y chromosome (NRY to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their classical 6 STR marker format or in the extended 12 STR format, as well as four founder mtDNA lineages (HVS-I segments accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same haplotype signatures. Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.

  8. Associations between Common Variants in Iron-Related Genes with Haematological Traits in Populations of African Ancestry.

    Science.gov (United States)

    Gichohi-Wainaina, Wanjiku N; Tanaka, Toshiko; Towers, G Wayne; Verhoef, Hans; Veenemans, Jacobien; Talsma, Elise F; Harryvan, Jan; Boekschoten, Mark V; Feskens, Edith J; Melse-Boonstra, Alida

    2016-01-01

    Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations.

  9. Components of ongoing EEG with high correlation point to emotionally-laden attention -- a possible marker of engagement?

    Directory of Open Access Journals (Sweden)

    Jacek P Dmochowski

    2012-05-01

    Full Text Available Recent evidence from functional magnetic resonance imaging suggests that cortical hemodynamic responses coincide in different subjects experiencing a common naturalistic stimulus. Here we utilize neural responses in the electroencephalogram (EEG evoked by multiple presentations of short film clips to index brain states marked by high levels of correlation within and across subjects. We formulate a novel signal decomposition method which extracts maximally correlated signal components from multiple EEG records. The resulting components capture correlations down to a one-second time resolution, thus revealing that peak correlations of neural activity across viewings can occur in remarkable correspondence with arousing moments of the film. Moreover, a significant reduction in neural correlation occurs upon a second viewing of the film or when the narrative is disrupted by presenting its scenes scrambled in time. We also probe oscillatory brain activity during periods of heightened correlation, and observe during such times a significant increase in the theta-band for a frontal component and reductions in the alpha and beta frequency bands for parietal and occipital components. Low-resolution EEG tomography of these components suggests that the correlated neural activity is consistent with sources in the cingulate and orbitofrontal cortices. Put together, these results suggest that the observed synchrony reflects attention- and emotion-modulated cortical processing, and that naturalistic brain states such as engagement may be decoded with high temporal resolution by extracting maximally correlated components of neural activity.

  10. An Investigation of the Correlation among Sources of Stress, Perceived Stress, and Coping styles in High School Students

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    Farhadh Asghari

    2016-07-01

    Full Text Available Background and Objectives: Coping with stress is an important issue, especially in regard to source of stress and perceived stress in adolescence period. In this research, the correlation among stress sources, perceived stress, and coping styles was investigated in high school students. Methods: The present research was a descriptive correlational study. The research sample consisted of 575 high school students from the families of personnel of Bushehr University of Medical Sciences in education year 2014-15 who were selected by multistage cluster sampling method. Stress source scale, perceived stress scale and Tehran coping styles scale, were used for data collection. The data were analyzed using statistical methods, including Pearson correlation coefficient and multivariate regression analysis. Results: In this study, 50% of students had perceived stress higher than cut-off point. Stress sources of students were related to school and maturity. There was a positive correlation between problem-oriented coping style and perceived stress, and there was a negative and inverse correlation between problem-oriented coping style and stress related to school and maturity. There was a positive correlation between positive emotion-oriented coping style and perceived stress, but there was a negative and inverse correlation between problem-oriented coping style and stress related to school and maturity. There was no significant correlation between emotion-oriented coping style and stress related to school, maturity, family, and peers. There was a positive correlation between negative emotion-oriented coping style and stress related to school, maturity, and peers. Conclusion: According to the findings of this study, the level of correlation was not significant and no significant relationship could be found between the variables with this level of correlation. Therefore, it is suggested that more extensive researches be conducted on the relationship between

  11. Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation.

    Science.gov (United States)

    Narang, Ankita; Jha, Pankaj; Kumar, Dhirendra; Kutum, Rintu; Mondal, Anupam Kumar; Dash, Debasis; Mukerji, Mitali

    2014-11-13

    Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. Genome-wide analysis of the diversity and ancestry of Korean dogs.

    Science.gov (United States)

    Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

    2017-01-01

    There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

  13. Pharmacogenomic diversity among Brazilians: Influence of ancestry, self-reported Color and geographical origin

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    Guilherme eSuarez-Kurtz

    2012-11-01

    Full Text Available By virtue of being the product of the genetic admixture of three ancestral roots: Europeans, Africans and Amerindians, the present day Brazilian population displays very high levels of genomic diversity, which have important pharmacogenetic/-genomic (PGx implications. Recognition of this fact has prompted the creation of the Brazilian Pharmacogenomics Network (Refargen, a nationwide consortium of research groups, with the mission to provide leadership in PGx research and education in Brazil, with a population heath impact. Here, we present original data and review published results from a Refargen comprehensive study of the distribution of PGx polymorphisms in a representative cohort of the Brazilian people, comprising 1,034 healthy, unrelated adults, self-identified as white, brown or black, according to the Color categories adopted by the Brazilian Census. Multinomial log-linear regression analysis was applied to infer the statistical association between allele, genotype and haplotype distributions among Brazilians (response variables and self-reported Color, geographical region and biogeographical ancestry (explanatory variables, whereas Wright´s FST statistics was used to assess the extent of PGx divergence among different strata of the Brazilian population. Major PGx implications of these findings are: first, extrapolation of data from relatively well-defined ethnic groups is clearly not applicable to the majority of Brazilians; second, the frequency distribution of polymorphisms in several pharmacogenes of clinical relevance (e.g. ABCB1, CYP3A5, CYP2C9, VKORC varies continuously among Brazilians and is not captured by race/Color self-identification; third, the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of PGx studies in order to avoid spurious conclusions based on improper matching of study cohorts.

  14. Genome-wide analysis of the diversity and ancestry of Korean dogs.

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    Bong Hwan Choi

    Full Text Available There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves, ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485 and Korean Donggyeong White (109, respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

  15. Mosaic maternal ancestry in the Great Lakes region of East Africa.

    Science.gov (United States)

    Gomes, Verónica; Pala, Maria; Salas, Antonio; Álvarez-Iglesias, Vanesa; Amorim, António; Gómez-Carballa, Alberto; Carracedo, Ángel; Clarke, Douglas J; Hill, Catherine; Mormina, Maru; Shaw, Marie-Anne; Dunne, David W; Pereira, Rui; Pereira, Vânia; Prata, Maria João; Sánchez-Diz, Paula; Rito, Teresa; Soares, Pedro; Gusmão, Leonor; Richards, Martin B

    2015-09-01

    The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

  16. Correlation of analysis with high level vibration test results for primary coolant piping

    International Nuclear Information System (INIS)

    Park, Y.J.; Hofmayer, C.H.; Costello, J.F.

    1992-01-01

    Dynamic tests on a modified 1/2.5-scale model of pressurized water reactor (PWR) primary coolant piping were performed using a large shaking table at Tadotsu, Japan. The High Level Vibration Test (HLVT) program was part of a cooperative study between the United States (Nuclear Regulatory Commission/Brookhaven National Laboratory, NRC/BNL) and Japan (Ministry of International Trade and Industry/Nuclear Power Engineering Center). During the test program, the excitation level of each test run was gradually increased up to the limit of the shaking table and significant plastic strains, as well as cracking, were induced in the piping. To fully utilize the test results, NRC/BNL sponsored a project to develop corresponding analytical predictions for the nonlinear dynamic response of the piping for selected test runs. The analyses were performed using both simplified and detailed approaches. The simplified approaches utilize a linear solution and an approximate formulation for nonlinear dynamic effects such as the use of a deamplification factor. The detailed analyses were performed using available nonlinear finite element computer codes, including the MARC, ABAQUS, ADINA and WECAN codes. A comparison of various analysis techniques with the test results shows a higher prediction error in the detailed strain values in the overall response values. A summary of the correlation analyses was presented before the BNL. This paper presents a detailed description of the various analysis results and additional comparisons with test results

  17. High correlation of the response of upper and lower lobe small airway epithelium to smoking.

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    Ben-Gary Harvey

    Full Text Available The distribution of lung disease induced by inhaled cigarette smoke is complex, depending on many factors. With the knowledge that the small airway epithelium (SAE is the earliest site of smoking-induced lung disease, and that the SAE gene expression is likely sensitive to inhaled cigarette smoke, we compared upper vs. lower lobe gene expression in the SAE within the same cigarette smokers to determine if the gene expression patterns were similar or different. Active smokers (n = 11 with early evidence of smoking-induced lung disease (normal spirometry but low diffusing capacity underwent bronchoscopy and brushing of the upper and lower lobe SAE in order to compare upper vs lower lobe genome-wide and smoking-responsive gene expression by microarray. Cluster and principal component analysis demonstrated that, for each individual, the expression of the known SAE smoking-responsive genes were highly correlated in upper and lower lobe pairs, although, as expected, there were differences in the smoking-induced changes in gene expression from individual to individual. These observations support the concept that the heterogeneity observed among smokers in the anatomic distribution of smoking-induced disease are not secondary to the topographic differences in the effects of cigarette smoke on the airway epithelium.

  18. A Hybrid Feature Subset Selection Algorithm for Analysis of High