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Sample records for ancestry highly correlated

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

    PubMed Central

    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.

    PubMed

    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

  3. The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

    PubMed Central

    Magalhães da Silva, Thiago; Sandhya Rani, M R; de Oliveira Costa, Gustavo Nunes; Figueiredo, Maria A; Melo, Paulo S; Nascimento, João F; Molyneaux, Neil D; Barreto, Maurício L; Reis, Mitermayer G; Teixeira, M Glória; Blanton, Ronald E

    2015-01-01

    The degree of admixture in Brazil between historically isolated populations is complex and geographically variable. Studies differ as to what the genetic and phenotypic consequences of this mixing have been. In Northeastern Brazil, we enrolled 522 residents of Salvador and 620 of Fortaleza whose distributions of self-declared color were comparable to those in the national census. Using the program Structure and principal components analysis there was a clear correlation between biogeographic ancestry and categories of skin color. This correlation with African ancestry was stronger in Salvador (r=0.585; P<0.001) than in Fortaleza (r=0.236; P<0.001). In Fortaleza, although self-declared blacks had a greater proportion of European ancestry, they had more African ancestry than the other categories. When the populations were analyzed without pseudoancestors, as in some studies, the relationship of ‘race' to genetic ancestry tended to diffuse or disappear. The inclusion of different African populations also influenced ancestry estimates. The percentage of unlinked ancestry informative markers in linkage disequilibrium, a measure of population structure, was 3–5 times higher in both Brazilian populations than expected by chance. We propose that certain methods, ascertainment bias and population history of the specific populations surveyed can result in failure to demonstrate a correlation between skin color and genetic ancestry. Population structure in Brazil has important implications for genetic studies, but genetic ancestry is irrelevant for how individuals are treated in society, their health, their income or their inclusion. These track more closely with perceived skin color than genetic ancestry. PMID:25293718

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

    PubMed Central

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    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…

  6. Genomic ancestry and somatic alterations correlate with age at diagnosis in Hispanic children with B-cell acute lymphoblastic leukemia.

    PubMed

    Walsh, Kyle M; de Smith, Adam J; Welch, Tara C; Smirnov, Ivan; Cunningham, Marc J; Ma, Xiaomei; Chokkalingam, Anand P; Dahl, Gary V; Roberts, William; Barcellos, Lisa F; Buffler, Patricia A; Metayer, Catherine; Wiemels, Joseph L

    2014-07-01

    Hispanic children have a higher incidence of acute lymphoblastic leukemia (ALL) than non-Hispanic whites but tend to be diagnosed at older ages. In genome-wide association studies, Native American ancestry and polymorphisms in six genes have been associated with ALL risk. In multivariable regression models, we investigated whether genomic ancestry, inherited risk SNPs, or acquired somatic alterations were associated with differences in age at diagnosis in Hispanic children with B-cell ALL. Genome-wide array data were used to estimate each participant's percent membership in the three Hispanic ancestral populations: Native American, African, and European. Each 20% increase in European ancestry was associated with a six month younger age at diagnosis (95% CI = 0.36-11.6 months, P = 0.037). Correspondingly, each 20% increase in Native American ancestry was associated with a six-month older age at diagnosis (P = 0.037). Both the TEL-AML1 translocation and high-hyperdiploidy were associated with younger age at diagnosis (24.4 months, P = 2.0 x 10(-4) and 12.4 months, P = 0.011, respectively), while CDKN2A and IKZF1 deletions were associated with older age at diagnosis (19.7 months, P = 7.0 x 10(-4) and 18.1 months, P = 0.012, respectively). No associations with age at diagnosis were observed for RAS mutation, PAX5 deletion or for known heritable risk alleles in IKZF1, CDKN2A, PIP4K2A, GATA3, ARID5B, or CEBPE. Because younger age at diagnosis is associated with improved treatment outcomes for children with ALL, the effect of European ancestry on ALL survival may be mediated by its effect on age at diagnosis, or by proxy, its association with more treatable molecular subtypes of ALL.

  7. African Ancestry is a Risk Factor for Asthma and High Total IgE Levels in African Admixed Populations

    PubMed Central

    Vergara, Candelaria; Murray, Tanda; Rafaels, Nicholas; Lewis, Rachel; Campbell, Monica; Foster, Cassandra; Gao, Li; Faruque, Mezbah; Oliveira, Ricardo Riccio; Carvalho, Edgar; Araujo, Maria Ilma; Cruz, Alvaro A.; Watson, Harold; Mercado, Dilia; Knight-Madden, Jennifer; Ruczinski, Ingo; Dunston, Georgia; Ford, Jean; Caraballo, Luis; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.

    2014-01-01

    Characterization of genetic admixture of populations in the Americas and the Caribbean is of interest for anthropological, epidemiological, and historical reasons. Asthma has a higher prevalence and is more severe in populations with a high African component. Association of African ancestry with asthma has been demonstrated. We estimated admixture proportions of samples from six trihybrid populations of African descent and determined the relationship between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 237 ancestry informative markers in asthmatics and nonasthmatic controls from Barbados (190/277), Jamaica (177/529), Brazil (40/220), Colombia (508/625), African Americans from New York (207/171), and African Americans from Baltimore/Washington, D.C. (625/757). We estimated individual ancestries and evaluated genetic stratification using Structure and principal component analysis. Association of African ancestry and asthma and tIgE was evaluated by regression analysis. Mean SD African ancestry ranged from 0.76 ± 0.10 among Barbadians to 0.33 ± 0.13 in Colombians. The European component varied from 0.14 ± 0.05 among Jamaicans and Barbadians to 0.26 ± 0.08 among Colombians. African ancestry was associated with risk for asthma in Colombians (odds ratio (OR) = 4.5, P = 0.001) Brazilians (OR = 136.5, P = 0.003), and African Americans of New York (OR: 4.7; P = 0.040). African ancestry was also associated with higher tIgE levels among Colombians (β = 1.3, P = 0.04), Barbadians (β = 3.8, P = 0.03), and Brazilians (β = 1.6, P = 0.03). Our findings indicate that African ancestry can account for, at least in part, the association between asthma and its associated trait, tIgE levels. PMID:23554133

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

    PubMed

    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.

  9. Correlation of E-selectin concentrations with carotid intima-media thickness and cardio-metabolic profile of mixed ancestry South Africans: a cross-sectional study.

    PubMed

    Zemlin, Annalise E; Matsha, Tandi E; Kengne, Andre P; Hon, Gloudina M; Erasmus, Rajiv T

    2017-01-01

    Background E-selectin, an adhesion molecule, is a specific marker of endothelial dysfunction. High concentrations have been reported in type 2 diabetes and disorders with high risk of cardiovascular disease (CVD). Measurement of carotid intima-media thickness (CIMT) is a surrogate marker of early atherosclerosis. We examined the relationship between E-selectin concentrations, CIMT and cardio-metabolic traits in normo- and hyperglycaemic mixed ancestry South Africans. Methods E-selectin concentrations were determined in 308 subjects from the Cape Town Bellville South Community-based study on a mixed ancestry population. Their correlation with CIMT and cardio-metabolic profile used robust correlations and linear regression models. Results E-selectin concentrations were significantly higher in the hyperglycaemic (median 139.8 µg/L) compared to the normoglycaemic group (median 118.8 µg/L), ( p = 0.0007). Significant differences between the two groups were found for markers of glycaemia and adiposity, but not for CIMT. Significant correlations were found between E-selectin and age, markers of glycaemia and inflammation, central obesity and lipid variables. Associations remained significant only with age, hyperglycaemia and C-reactive protein in robust linear regression models. In similar regressions models, age and gender were the main predictors of CIMT, which was not associated with E-selectin. Conclusions E-selectin concentrations in this study were associated with hyperglycaemia, possibly reflecting early endothelial damage. However, E-selectin was not useful to assess CIMT, a marker of subclinical atherosclerosis, which appeared to be determined by ageing and male gender.

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

    PubMed

    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.

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

    PubMed

    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 <20% Native American 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.

  12. Breast cancer disparities: high-risk breast cancer and African ancestry.

    PubMed

    Newman, Lisa A

    2014-07-01

    African American women have a lower lifetime incidence of breast cancer than white/Caucasian Americans yet have a higher risk of breast cancer mortality. African American women are also more likely to be diagnosed with breast cancer at young ages, and they have higher risk for the biologically more aggressive triple-negative breast cancers. These features are also more common among women from western, sub-Saharan Africa who share ancestry with African Americans, and this prompts questions regarding an association between African ancestry and inherited susceptibility for certain patterns of mammary carcinogenesis.

  13. Surname‐Inferred andean ancestry is associated with child stature and limb lengths at high altitude in Peru, but not at sea level

    PubMed Central

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

    2015-01-01

    Abstract Objectives 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. Methods 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]). Results 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. Conclusions 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. Am. J. Hum. Biol. 27:798–806, 2015. © 2015 The Authors American Journal of Human Biology Published by Wiley Periodicals, Inc. PMID:25960137

  14. Race, genetic West African ancestry, and prostate cancer prediction by prostate-specific antigen in prospectively screened high-risk men.

    PubMed

    Giri, Veda N; Egleston, Brian; Ruth, Karen; Uzzo, Robert G; Chen, David Y T; Buyyounouski, Mark; Raysor, Susan; Hooker, Stanley; Torres, Jada Benn; Ramike, Teniel; Mastalski, Kathleen; Kim, Taylor Y; Kittles, Rick

    2009-03-01

    "Race-specific" prostate-specific antigen (PSA) needs evaluation in men at high risk for prostate cancer for optimizing early detection. Baseline PSA and longitudinal prediction for prostate cancer were examined by self-reported race and genetic West African (WA) ancestry in the Prostate Cancer Risk Assessment Program, a prospective high-risk cohort. Eligibility criteria were age 35 to 69 years, family history of prostate cancer, African American race, or BRCA1/2 mutations. Biopsies were done at low PSA values (<4.0 ng/mL). WA ancestry was discerned by genotyping 100 ancestry informative markers. Cox proportional hazards models evaluated baseline PSA, self-reported race, and genetic WA ancestry. Cox models were used for 3-year predictions for prostate cancer. Six hundred forty-six men (63% African American) were analyzed. Individual WA ancestry estimates varied widely among self-reported African American men. Race-specific differences in baseline PSA were not found by self-reported race or genetic WA ancestry. Among men with > or =1 follow-up visit (405 total, 54% African American), 3-year prediction for prostate cancer with a PSA of 1.5 to 4.0 ng/mL was higher in African American men with age in the model (P = 0.025) compared with European American men. Hazard ratios of PSA for prostate cancer were also higher by self-reported race (1.59 for African American versus 1.32 for European American, P = 0.04). There was a trend for increasing prediction for prostate cancer with increasing genetic WA ancestry. "Race-specific" PSA may need to be redefined as higher prediction for prostate cancer at any given PSA in African American men. Large-scale studies are needed to confirm if genetic WA ancestry explains these findings to make progress in personalizing prostate cancer early detection.

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

    PubMed

    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.

  16. High interpopulation homogeneity in Central Argentina as assessed by Ancestry Informative Markers (AIMs).

    PubMed

    García, Angelina; Dermarchi, Darío A; Tovo-Rodrigues, Luciana; Pauro, Maia; Callegari-Jacques, Sidia M; Salzano, Francisco M; Hutz, Mara H

    2015-01-01

    The population of Argentina has already been studied with regard to several genetic markers, but much more data are needed for the appropriate definition of its genetic profile. This study aimed at investigating the admixture patterns and genetic structure in Central Argentina, using biparental markers and comparing the results with those previously obtained by us with mitochondrial DNA (mtDNA) in the same samples. A total of 521 healthy unrelated individuals living in 13 villages of the Córdoba and San Luis provinces were tested. The individuals were genotyped for ten autosomal ancestry informative markers (AIMs). Allele frequencies were compared with those of African, European and Native American populations, chosen to represent parental contributions. The AIM estimates indicated a greater influence of the Native American ancestry as compared to previous studies in the same or other Argentinean regions, but smaller than that observed with the mtDNA tests. These differences can be explained, respectively, by different genetic contributions between rural and urban areas, and asymmetric gene flow occurred in the past. But a most unexpected finding was the marked interpopulation genetic homogeneity found in villages located in diverse geographic environments across a wide territory, suggesting considerable gene flow.

  17. High interpopulation homogeneity in Central Argentina as assessed by Ancestry Informative Markers (AIMs)

    PubMed Central

    García, Angelina; Dermarchi, Darío A.; Tovo-Rodrigues, Luciana; Pauro, Maia; Callegari-Jacques, Sidia M.; Salzano, Francisco M.; Hutz, Mara H.

    2015-01-01

    The population of Argentina has already been studied with regard to several genetic markers, but much more data are needed for the appropriate definition of its genetic profile. This study aimed at investigating the admixture patterns and genetic structure in Central Argentina, using biparental markers and comparing the results with those previously obtained by us with mitochondrial DNA (mtDNA) in the same samples. A total of 521 healthy unrelated individuals living in 13 villages of the Córdoba and San Luis provinces were tested. The individuals were genotyped for ten autosomal ancestry informative markers (AIMs). Allele frequencies were compared with those of African, European and Native American populations, chosen to represent parental contributions. The AIM estimates indicated a greater influence of the Native American ancestry as compared to previous studies in the same or other Argentinean regions, but smaller than that observed with the mtDNA tests. These differences can be explained, respectively, by different genetic contributions between rural and urban areas, and asymmetric gene flow occurred in the past. But a most unexpected finding was the marked interpopulation genetic homogeneity found in villages located in diverse geographic environments across a wide territory, suggesting considerable gene flow. PMID:26500436

  18. What Is Genetic Ancestry Testing?

    MedlinePlus

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

  19. Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine.

    PubMed

    Yang, Nan; Li, Hongzhe; Criswell, Lindsey A; Gregersen, Peter K; Alarcon-Riquelme, Marta E; Kittles, Rick; Shigeta, Russell; Silva, Gabriel; Patel, Pragna I; Belmont, John W; Seldin, Michael F

    2005-12-01

    We and others have identified several hundred ancestry informative markers (AIMs) with large allele frequency differences between different major ancestral groups. For this study, a panel of 199 widely distributed AIMs was used to examine a diverse set of 796 DNA samples including self-identified European Americans, West Africans, East Asians, Amerindians, African Americans, Mexicans, Mexican Americans, Puerto Ricans and South Asians. Analysis using a Bayesian clustering algorithm (STRUCTURE) showed grouping of individuals with similar ethnic identity without any identifier other than the AIMs genotyping and showed admixture proportions that clearly distinguished different individuals of mixed ancestry. Additional analyses showed that, for the majority of samples, the predicted ethnic identity corresponded with the self-identified ethnicity at high probability (P > 0.99). Overall, the study demonstrates that AIMs can provide a useful adjunct to forensic medicine, pharmacogenomics and disease studies in which major ancestry or ethnic affiliation might be linked to specific outcomes.

  20. High-altitude ancestry and hypoxia acclimation have distinct effects on exercise capacity and muscle phenotype in deer mice.

    PubMed

    Lui, Mikaela A; Mahalingam, Sajeni; Patel, Paras; Connaty, Alex D; Ivy, Catherine M; Cheviron, Zachary A; Storz, Jay F; McClelland, Grant B; Scott, Graham R

    2015-05-01

    The hypoxic and cold environment at high altitudes requires that small mammals sustain high rates of O2 transport for exercise and thermogenesis while facing a diminished O2 availability. We used laboratory-born and -raised deer mice (Peromyscus maniculatus) from highland and lowland populations to determine the interactive effects of ancestry and hypoxia acclimation on exercise performance. Maximal O₂consumption (V̇o(2max)) during exercise in hypoxia increased after hypoxia acclimation (equivalent to the hypoxia at ∼4,300 m elevation for 6-8 wk) and was consistently greater in highlanders than in lowlanders. V̇o(2max) during exercise in normoxia was not affected by ancestry or acclimation. Highlanders also had consistently greater capillarity, oxidative fiber density, and maximal activities of oxidative enzymes (cytochrome c oxidase and citrate synthase) in the gastrocnemius muscle, lower lactate dehydrogenase activity in the gastrocnemius, and greater cytochrome c oxidase activity in the diaphragm. Hypoxia acclimation did not affect any of these muscle traits. The unique gastrocnemius phenotype of highlanders was associated with higher mRNA and protein abundances of peroxisome proliferator-activated receptor γ (PPARγ). Vascular endothelial growth factor (VEGFA) transcript abundance was lower in highlanders, and hypoxia acclimation reduced the expression of numerous genes that regulate angiogenesis and energy metabolism, in contrast to the observed population differences in muscle phenotype. Lowlanders exhibited greater increases in blood hemoglobin content, hematocrit, and wet lung mass (but not dry lung mass) than highlanders after hypoxia acclimation. Genotypic adaptation to high altitude, therefore, improves exercise performance in hypoxia by mechanisms that are at least partially distinct from those underlying hypoxia acclimation.

  1. High-altitude ancestry and hypoxia acclimation have distinct effects on exercise capacity and muscle phenotype in deer mice

    PubMed Central

    Lui, Mikaela A.; Mahalingam, Sajeni; Patel, Paras; Connaty, Alex D.; Ivy, Catherine M.; Cheviron, Zachary A.; Storz, Jay F.; McClelland, Grant B.

    2015-01-01

    The hypoxic and cold environment at high altitudes requires that small mammals sustain high rates of O2 transport for exercise and thermogenesis while facing a diminished O2 availability. We used laboratory-born and -raised deer mice (Peromyscus maniculatus) from highland and lowland populations to determine the interactive effects of ancestry and hypoxia acclimation on exercise performance. Maximal O2 consumption (V̇o2max) during exercise in hypoxia increased after hypoxia acclimation (equivalent to the hypoxia at ∼4,300 m elevation for 6–8 wk) and was consistently greater in highlanders than in lowlanders. V̇o2max during exercise in normoxia was not affected by ancestry or acclimation. Highlanders also had consistently greater capillarity, oxidative fiber density, and maximal activities of oxidative enzymes (cytochrome c oxidase and citrate synthase) in the gastrocnemius muscle, lower lactate dehydrogenase activity in the gastrocnemius, and greater cytochrome c oxidase activity in the diaphragm. Hypoxia acclimation did not affect any of these muscle traits. The unique gastrocnemius phenotype of highlanders was associated with higher mRNA and protein abundances of peroxisome proliferator-activated receptor γ (PPARγ). Vascular endothelial growth factor (VEGFA) transcript abundance was lower in highlanders, and hypoxia acclimation reduced the expression of numerous genes that regulate angiogenesis and energy metabolism, in contrast to the observed population differences in muscle phenotype. Lowlanders exhibited greater increases in blood hemoglobin content, hematocrit, and wet lung mass (but not dry lung mass) than highlanders after hypoxia acclimation. Genotypic adaptation to high altitude, therefore, improves exercise performance in hypoxia by mechanisms that are at least partially distinct from those underlying hypoxia acclimation. PMID:25695288

  2. African ancestry is associated with risk of asthma and high total serum IgE in a population from the Caribbean Coast of Colombia.

    PubMed

    Vergara, Candelaria; Caraballo, Luis; Mercado, Dilia; Jimenez, Silvia; Rojas, Winston; Rafaels, Nicholas; Hand, Tracey; Campbell, Monica; Tsai, Yuhjung J; Gao, Li; Duque, Constanza; Lopez, Sergio; Bedoya, Gabriel; Ruiz-Linares, Andrés; Barnes, Kathleen C

    2009-06-01

    African descended populations exhibit an increased prevalence of asthma and allergies compared to Europeans. One approach to distinguish between environmental and genetic explanations for this difference is to study relationships of asthma risk to individual admixture. We aimed to determine the admixture proportions of a case-control sample from the Caribbean Coast of Colombia currently participating in genetic studies for asthma, and to test for population stratification and association between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 368 asthmatics and 365 non-asthmatics for 52 autosomal ancestry informative markers, six mtDNA haplogroups and nine haplogroups and five microsatellites in Y chromosome. Autosomal admixture proportions, population stratification, and associations between ancestry and the phenotypes were estimated by ADMIXMAP. The average admixture proportions among asthmatics were 42.8% European, 39.9% African and 17.2% Native American and among non-asthmatics they were 44.2% (P = 0.068), 37.6% (P = 0.007) and 18.1% (P = 0.050), respectively. In the total sample, the paternal contributions were 71% European, 25% African and 4.0% Native American and the maternal lineages were 56.8% Native American, and 20.2% African; 22.9% of the individuals carried other non-Native American mtDNA haplogroups. African ancestry was significantly associated with asthma (OR: 2.97; 95% CI: 1.08-8.08), high tIgE (OR: 1.9; 95% CI: 1.17-3.12) and socioeconomic status (OR = 0.64; 95% CI: 0.47-0.87). Significant population stratification was observed in this sample. Our findings indicate that genetic factors can explain the association between asthma and African ancestry and suggest that this sample is a useful resource for performing admixture mapping for asthma.

  3. Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

    PubMed

    Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

    2014-12-12

    Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P < 0.0001). Sampled demes sites (1- 7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (Rxy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

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

    PubMed

    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.

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

    PubMed Central

    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

  6. Cattle ancestry in bison: explanations for higher mtDNA than autosomal ancestry.

    PubMed

    Hedrick, Philip W

    2010-08-01

    Understanding and documenting the process of hybridization and introgression between related species is a major focus of recent evolutionary research using molecular techniques. Many North American bison herds have cattle ancestry introduced by crossbreeding over a century ago. Molecular estimates of this ancestry have shown much higher levels for cattle mtDNA than for autosomal cattle genes. A large part of this difference appears to be the result of partial reproductive isolation between the two species where only bison bull x domestic cow crosses are successful, and all the surviving progeny are females. In addition, selection against autosomal cattle genes in bison may have contributed to differential levels of cattle ancestry. The impact of selection against cattle mtDNA and gene flow of bison mtDNA are examined to explain particular combinations of mtDNA and autosomal cattle ancestry. A bottleneck, after the level of cattle ancestry in bison was reduced to a low level, is consistent with the high variance over autosomal loci observed for cattle ancestry, and differential selection among cattle loci in bison does not need to be invoked. Further examination of the cattle genome in bison may shed light on whether these markers, or their associated regions, are indeed neutral.

  7. Exploring iris colour prediction and ancestry inference in admixed populations of South America.

    PubMed

    Freire-Aradas, A; Ruiz, Y; Phillips, C; Maroñas, O; Söchtig, J; Tato, A Gómez; Dios, J Álvarez; de Cal, M Casares; Silbiger, V N; Luchessi, A D; Luchessi, A D; Chiurillo, M A; Carracedo, Á; Lareu, M V

    2014-11-01

    New DNA-based predictive tests for physical characteristics and inference of ancestry are highly informative tools that are being increasingly used in forensic genetic analysis. Two eye colour prediction models: a Bayesian classifier - Snipper and a multinomial logistic regression (MLR) system for the Irisplex assay, have been described for the analysis of unadmixed European populations. Since multiple SNPs in combination contribute in varying degrees to eye colour predictability in Europeans, it is likely that these predictive tests will perform in different ways amongst admixed populations that have European co-ancestry, compared to unadmixed Europeans. In this study we examined 99 individuals from two admixed South American populations comparing eye colour versus ancestry in order to reveal a direct correlation of light eye colour phenotypes with European co-ancestry in admixed individuals. Additionally, eye colour prediction following six prediction models, using varying numbers of SNPs and based on Snipper and MLR, were applied to the study populations. Furthermore, patterns of eye colour prediction have been inferred for a set of publicly available admixed and globally distributed populations from the HGDP-CEPH panel and 1000 Genomes databases with a special emphasis on admixed American populations similar to those of the study samples.

  8. Pairing Correlations at High Spins

    NASA Astrophysics Data System (ADS)

    Ma, Hai-Liang; Dong, Bao-Guo; Zhang, Yan; Fan, Ping; Yuan, Da-Qing; Zhu, Shen-Yun; Zhang, Huan-Qiao; Petrache, C. M.; Ragnarsson, I.; Carlsson, B. G.

    The pairing correcting energies at high spins in 161Lu and 138Nd are studied by comparing the results of the cranked-Nilsson-Strutinsky (CNS) and cranked-Nilsson-Strutinsky-Bogoliubov (CNSB) models. It is concluded that the Coriolis effect rather than the rotational alignment effect plays a major role in the reduction of the pairing correlations in the high spin region. Then we proposed an average pairing correction method which not only better reproduces the experimental data comparing with the CNS model but also enables a clean-cut tracing of the configurations thus the full-spin-range discussion on the various rotating bands.

  9. Biogeographical ancestry and race.

    PubMed

    Gannett, Lisa

    2014-09-01

    The use of racial and ethnic categories in biological and biomedical research is controversial-for example, in the comparison of disease risk in different groups or as a means of making use of or controlling for population structure in the mapping of genes to chromosomes. Biogeographical ancestry (BGA) has been recommended as a more accurate and appropriate category. BGA is a product of the collaboration between biological anthropologist Mark Shriver from Pennsylvania State University and molecular biologist Tony Frudakis from the now-defunct biotechnology start-up company DNAPrint genomics, Inc. Shriver and Frudakis portray BGA as a measure of the 'biological', 'genetic', 'natural', and 'objective' components of race and ethnicity, what philosophers of science would call a natural kind. This paper argues that BGA is not a natural kind that escapes social and political connotations of race and ethnicity, as Shriver and Frudakis and other proponents believe, but a construction that is built upon race-as race has been socially constructed in the European scientific and philosophical traditions. More specifically, BGA is not a global category of biological and anthropological classification but a local category shaped by the U.S. context of its production, especially the forensic aim of being able to predict the race or ethnicity of an unknown suspect based on DNA found at the crime scene. Therefore, caution needs to be exercised in the embrace of BGA as an alternative to the use of racial and ethnic categories in biological and biomedical research.

  10. Ancestry, Temporality, and Potentiality

    PubMed Central

    Gibbon, Sahra

    2014-01-01

    In this paper I examine the variety of ways potential is articulated, entailed, and produced in how the field of cancer genetics is being constituted as a domain of transnational research and an emerging site of health-care intervention in southern Brazil. Drawing on analysis of fieldwork in Brazilian cancer-genetics clinics, I explore how different expressions of potential come to inform dynamically the pursuit of prevention, care, and research as diversely scaled investments for those working and living with cancer-genetics knowledge and technologies. It illustrates how specific temporalities help to constitute and “abductively” frame the meaning of these different potentials particularly as this relates to a focus on ancestry. Colonial histories of migration, the embodied effects of dietary habits, or the moral failings of near and distant ancestors as well as promissory futures and the contingency of lived lives become at different times templates for identifying, materializing, and transforming how the potential of cancer genetics in Brazil is articulated. Potential is also expressed through an idiom of “choice” in different efforts to situate participation in cancer-genetics research as prevention or to negotiate access to basic public health. I explore how these expressions of cancer genetics as potential powerfully yet unevenly work to sustain knowledge practices as well as propel patients and their families into fledgling domains of clinical practice and scientific research. At the same time there is always an “excess of meaning” in these endeavors that make visible lines of fracture and disjuncture in collective efforts to make future histories of and from the pursuit of cancer genetics in southern Brazil. PMID:25018561

  11. Maternal oxygen delivery is not related to altitude- and ancestry-associated differences in human fetal growth

    PubMed Central

    Zamudio, Stacy; Postigo, Lucrecia; Illsley, Nicholas P; Rodriguez, Carmelo; Heredia, Gladys; Brimacombe, Michael; Echalar, Lourdes; Torricos, Tatiana; Tellez, Wilma; Maldonado, Ivan; Balanza, Elfride; Alvarez, Tatiana; Ameller, Julio; Vargas, Enrique

    2007-01-01

    Fetal growth is reduced at high altitude, but the decrease is less among long-resident populations. We hypothesized that greater maternal uteroplacental O2 delivery would explain increased fetal growth in Andean natives versus European migrants to high altitude. O2 delivery was measured with ultrasound, Doppler and haematological techniques. Participants (n= 180) were pregnant women of self-professed European or Andean ancestry living at 3600 m or 400 m in Bolivia. Ancestry was quantified using ancestry-informative single nucleotide polymorphims. The altitude-associated decrement in birth weight was 418 g in European versus 236 g in Andean women (P < 0.005). Altitude was associated with decreased uterine artery diameter, volumetric blood flow and O2 delivery regardless of ancestry. But the hypothesis was rejected as O2 delivery was similar between ancestry groups at their respective altitudes of residence. Instead, Andean neonates were larger and heavier per unit of O2 delivery, regardless of altitude (P < 0.001). European admixture among Andeans was negatively correlated with birth weight at both altitudes (P < 0.01), but admixture was not related to any of the O2 transport variables. Genetically mediated differences in maternal O2 delivery are thus unlikely to explain the Andean advantage in fetal growth. Of the other independent variables, only placental weight and gestational age explained significant variation in birth weight. Thus greater placental efficiency in O2 and nutrient transport, and/or greater fetal efficiency in substrate utilization may contribute to ancestry- and altitude-related differences in fetal growth. Uterine artery O2 delivery in these pregnancies was 99 ± 3 ml min−1, ∼5-fold greater than near-term fetal O2 consumption. Deficits in maternal O2 transport in third trimester normal pregnancy are unlikely to be causally associated with variation in fetal growth. PMID:17510190

  12. Structural reconstruction of protein ancestry.

    PubMed

    Rouet, Romain; Langley, David B; Schofield, Peter; Christie, Mary; Roome, Brendan; Porebski, Benjamin T; Buckle, Ashley M; Clifton, Ben E; Jackson, Colin J; Stock, Daniela; Christ, Daniel

    2017-03-29

    Ancestral protein reconstruction allows the resurrection and characterization of ancient proteins based on computational analyses of sequences of modern-day proteins. Unfortunately, many protein families are highly divergent and not suitable for sequence-based reconstruction approaches. This limitation is exemplified by the antigen receptors of jawed vertebrates (B- and T-cell receptors), heterodimers formed by pairs of Ig domains. These receptors are believed to have evolved from an extinct homodimeric ancestor through a process of gene duplication and diversification; however molecular evidence has so far remained elusive. Here, we use a structural approach and laboratory evolution to reconstruct such molecules and characterize their interaction with antigen. High-resolution crystal structures of reconstructed homodimeric receptors in complex with hen-egg white lysozyme demonstrate how nanomolar affinity binding of asymmetrical antigen is enabled through selective recruitment and structural plasticity within the receptor-binding site. Our results provide structural evidence in support of long-held theories concerning the evolution of antigen receptors, and provide a blueprint for the experimental reconstruction of protein ancestry in the absence of phylogenetic evidence.

  13. Selecting SNPs to Identify Ancestry

    PubMed Central

    Sampson, Joshua; Kidd, Kenneth K; Kidd, Judith R; Zhao, Hongyu

    2011-01-01

    Background/Aims An individual’s genotypes at a group of Single Nucleotide Polymorphisms (SNPs) can be used to predict that individual’s ethnicity, or ancestry. In medical studies, knowledge of a subject’s ancestry can minimize possible confounding, and in forensic applications, such knowledge can help direct investigations. Our goal is to select a small subset of SNPs, from the millions already identified in the human genome, that can predict ancestry with a minimal error rate. Methods The general form for this variable selection procedure is to estimate the expected error rates for sets of SNPs using a training dataset and consider those sets with the lowest error rates given their size. The quality of the estimate for the error rate determines the quality of the resulting SNPs. As the apparent error rate performs poorly when either the number of SNPs or the number of populations is large, we propose a new estimate, the Improved Bayesian Estimate. Conclusions We demonstrate that selection procedures based on this estimate produce small sets of SNPs that can accurately predict ancestry. We also provide a list of the 100 optimal SNPs for identifying ancestry. R functions are available at http://bioinformatics.med.yale.edu/group/josh/index.html. PMID:21668909

  14. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.

    PubMed

    Pereira, Rui; Phillips, Christopher; Pinto, Nádia; Santos, Carla; dos Santos, Sidney Emanuel Batista; Amorim, António; Carracedo, Ángel; Gusmão, Leonor

    2012-01-01

    Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.

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

    PubMed

    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.

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

    USGS Publications Warehouse

    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. Ethnic characterization of a population of children exposed to high doses of arsenic via drinking water and a possible correlation with metabolic processes.

    PubMed

    Bobillo, Cecilia; Navoni, Julio A; Olmos, Valentina; Merini, Luciano J; Villaamil Lepori, Edda; Corach, Daniel

    2014-01-01

    Because the ratio between the two major arsenic metabolites is related to the adverse health effects of arsenic, numerous studies have been performed to establish a relationship between the ability to metabolically detoxify arsenic and other variables, including exposure level, gender, age and ethnicity. Because ethnicity may play a key role and provide relevant information for heterogeneous populations, we characterized a group of 70 children from rural schools in the Argentinean provinces of Chaco and Santiago del Estero who were exposed to high levels of arsenic. We used genetic markers for maternal, paternal and bi-parental ancestry to achieve this goal. Our results demonstrate that the Amerindian maternal linages are present in 100% of the samples, whereas the Amerindian component transmitted through the paternal line is less than 10%. Informative markers for autosomal ancestry show a predominantly European ancestry, in which 37% of the samples contained between 90 and 99% European ancestry. The native American component ranged from 50 to 80% in 15.7% of the samples, and in all but four samples, the African component was less than 10%. Correlation analysis demonstrated that the ethnicity and the ratio of the excreted arsenic metabolites monomethyl arsenic and dimethyl arsenic are not associated, dismissing a relationship between ethnic origin and differential metabolism.

  18. Ethnic characterization of a population of children exposed to high doses of arsenic via drinking water and a possible correlation with metabolic processes

    PubMed Central

    Bobillo, Cecilia; Navoni, Julio A; Olmos, Valentina; Merini, Luciano J; Villaamil Lepori, Edda; Corach, Daniel

    2014-01-01

    Because the ratio between the two major arsenic metabolites is related to the adverse health effects of arsenic, numerous studies have been performed to establish a relationship between the ability to metabolically detoxify arsenic and other variables, including exposure level, gender, age and ethnicity. Because ethnicity may play a key role and provide relevant information for heterogeneous populations, we characterized a group of 70 children from rural schools in the Argentinean provinces of Chaco and Santiago del Estero who were exposed to high levels of arsenic. We used genetic markers for maternal, paternal and bi-parental ancestry to achieve this goal. Our results demonstrate that the Amerindian maternal linages are present in 100% of the samples, whereas the Amerindian component transmitted through the paternal line is less than 10%. Informative markers for autosomal ancestry show a predominantly European ancestry, in which 37% of the samples contained between 90 and 99% European ancestry. The native American component ranged from 50 to 80% in 15.7% of the samples, and in all but four samples, the African component was less than 10%. Correlation analysis demonstrated that the ethnicity and the ratio of the excreted arsenic metabolites monomethyl arsenic and dimethyl arsenic are not associated, dismissing a relationship between ethnic origin and differential metabolism. PMID:24596592

  19. The role of ancestry in TB susceptibility of an admixed South African population.

    PubMed

    Daya, Michelle; van der Merwe, Lize; van Helden, Paul D; Möller, Marlo; Hoal, Eileen G

    2014-07-01

    Genetic susceptibility to tuberculosis (TB) has been well established and this, taken together with variation in susceptibility observed between different geographic and ethnic populations, implies that susceptibility to TB may in part be affected by ethnicity. In a previous genome-wide TB case-control study (642 cases and 91 controls) of the admixed South African Coloured (SAC) population, we found a positive correlation between African San ancestry and TB susceptibility, and negative correlations with European and Asian ancestries. Since genome-wide data was available for only a small number of controls in the previous study, we endeavored to validate this finding by genotyping a panel of ancestry informative markers (AIMs) in additional individuals, yielding a data set of 918 cases and 507 controls. Ancestry proportions were estimated using the AIMs for each of the source populations of the SAC (African San, African non-San, European, South Asian and East Asian). Using logistic regression models to test for association between TB and ancestry, we confirmed the substantial effect of ancestry on TB susceptibility. We also investigated the effect of adjusting for ancestry in candidate gene TB association studies of the SAC. We report a polymorphism that is no longer significantly associated with TB after adjustment for ancestry, a polymorphism that is significantly associated with TB only after adjustment for ancestry, and a polymorphism where the association significance remains unchanged. By comparing the allele frequencies of these polymorphisms in the source populations of the SAC, we demonstrate that association results are likely to be affected by adjustment for ancestry if allele frequencies differ markedly in the source populations of the SAC.

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

    PubMed Central

    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 do we validate inferences about ancestry in genetic research? What are the data that demonstrate our ability to do this correctly? What can we say and what can we not say from our research findings and the test results that we generate? This white paper from the American Society of Human Genetics (ASHG) Ancestry and Ancestry Testing Task Force builds upon the 2008 ASHG Ancestry Testing Summary Statement in providing a more in-depth analysis of key scientific and non-scientific aspects of genetic ancestry inference in academia and industry. It culminates with recommendations for advancing the current debate and facilitating the development of scientifically based, ethically sound, and socially attentive guidelines concerning the use of these continually evolving technologies. PMID:20466090

  1. Uniparental ancestry markers in Chilean populations

    PubMed Central

    Vieira-Machado, Camilla Dutra; Tostes, Maluah; Alves, Gabrielle; Nazer, Julio; Martinez, Liliana; Wettig, Elisabeth; Pizarro Rivadeneira, Oscar; Diaz Caamaño, Marcela; Larenas Ascui, Jessica; Pavez, Pedro; Dutra, Maria da Graça; Castilla, Eduardo Enrique; Orioli, Ieda Maria

    2016-01-01

    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. PMID:27561109

  2. HGDP and HapMap analysis by Ancestry Mapper reveals local and global population relationships.

    PubMed

    Magalhães, Tiago R; Casey, Jillian P; Conroy, Judith; Regan, Regina; Fitzpatrick, Darren J; Shah, Naisha; Sobral, João; Ennis, Sean

    2012-01-01

    Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set.

  3. HGDP and HapMap Analysis by Ancestry Mapper Reveals Local and Global Population Relationships

    PubMed Central

    Magalhães, Tiago R.; Casey, Jillian P.; Conroy, Judith; Regan, Regina; Fitzpatrick, Darren J.; Shah, Naisha; Sobral, João; Ennis, Sean

    2012-01-01

    Knowledge of human origins, migrations, and expansions is greatly enhanced by the availability of large datasets of genetic information from different populations and by the development of bioinformatic tools used to analyze the data. We present Ancestry Mapper, which we believe improves on existing methods, for the assignment of genetic ancestry to an individual and to study the relationships between local and global populations. The principle function of the method, named Ancestry Mapper, is to give each individual analyzed a genetic identifier, made up of just 51 genetic coordinates, that corresponds to its relationship to the HGDP reference population. As a consequence, the Ancestry Mapper Id (AMid) has intrinsic biological meaning and provides a tool to measure similarity between world populations. We applied Ancestry Mapper to a dataset comprised of the HGDP and HapMap data. The results show distinctions at the continental level, while simultaneously giving details at the population level. We clustered AMids of HGDP/HapMap and observe a recapitulation of human migrations: for a small number of clusters, individuals are grouped according to continental origins; for a larger number of clusters, regional and population distinctions are evident. Calculating distances between AMids allows us to infer ancestry. The number of coordinates is expandable, increasing the power of Ancestry Mapper. An R package called Ancestry Mapper is available to apply this method to any high density genomic data set. PMID:23189146

  4. Angular correlations and high energy evolution

    SciTech Connect

    Kovner, Alex; Lublinsky, Michael

    2011-11-01

    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{sub 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.

  5. Population genetics models of local ancestry.

    PubMed

    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.

  6. Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation

    PubMed Central

    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.

    2012-01-01

    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. PMID:23040495

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

    PubMed Central

    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

    Objective 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). Methods 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). Results 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, p<0.05). The thoracic fluid content index (r=0.124. p<0.05), E wave peak (r=0.127. p<0.05) and E/e′ ratio (r=0.197. p<0.01) were correlated positively with African ancestry. In multiple linear regression, African ancestry remained associated with the E/e′ ratio, even after adjustment to risk factors. Conclusions 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. Trials registration number NTC02043431. PMID:27547430

  8. Association of serum lipid components and obesity with genetic ancestry in an admixed population of elderly women

    PubMed Central

    Lins, Tulio C.; Pires, Alause S.; Paula, Roberta S.; Moraes, Clayton F.; Vieira, Rodrigo G.; Vianna, Lucy G.; Nobrega, Otávio T.; Pereira, Rinaldo W.

    2012-01-01

    The prevalence of metabolic disorders varies among ethnic populations and these disorders represent a critical health care issue for elderly women. This study investigated the correlation between genetic ancestry and body composition, metabolic traits and clinical status in a sample of elderly women. Clinical, nutritional and anthropometric data were collected from 176 volunteers. Genetic ancestry was estimated using 23 ancestry-informative markers. Pearsons correlation test was used to examine the relationship between continuous variables and an independent samples t-test was used to compare the means of continuous traits within categorical variables. Overall ancestry was a combination of European (57.49%), Native American (25.78%) and African (16.73%). Significant correlations were found for European ancestry with body mass index (r = 0.165; p = 0.037) and obesity (mean difference (MD) = 5.3%; p = 0.042). African ancestry showed a significant correlation with LDL (r = 0.159, p = 0.035), VLDL (r = −0.185; p = 0.014), hypertriglyceridemia (MD = 6.4%; p = 0.003) and hyperlipidemia (MD = 4.8%; p = 0.026). Amerindian ancestry showed a significant correlation with triglyceride levels (r = 0.150; p = 0.047) and hypertriglyceridemia (MD = 4.5%; p = 0.039). These findings suggest that genetic admixture may influence the etiology of lipid metabolism-related diseases and obesity in elderly women. PMID:23055794

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

    PubMed

    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.

  10. Genetic Ancestry in Lung-Function Predictions

    PubMed Central

    Kumar, Rajesh; Seibold, Max A.; Aldrich, Melinda C.; Williams, L. Keoki; Reiner, Alex P.; Colangelo, Laura; Galanter, Joshua; Gignoux, Christopher; Hu, Donglei; Sen, Saunak; Choudhry, Shweta; Peterson, Edward L.; Rodriguez-Santana, Jose; Rodriguez-Cintron, William; Nalls, Michael A.; Leak, Tennille S.; O’Meara, Ellen; Meibohm, Bernd; Kritchevsky, Stephen B.; Li, Rongling; Harris, Tamara B.; Nickerson, Deborah A.; Fornage, Myriam; Enright, Paul; Ziv, Elad; Smith, Lewis J.; Liu, Kiang; Burchard, Esteban González

    2010-01-01

    BACKGROUND Self-identified race or ethnic group is used to determine normal reference standards in the prediction of pulmonary function. We conducted a study to determine whether the genetically determined percentage of African ancestry is associated with lung function and whether its use could improve predictions of lung function among persons who identified themselves as African American. METHODS We assessed the ancestry of 777 participants self-identified as African American in the Coronary Artery Risk Development in Young Adults (CARDIA) study and evaluated the relation between pulmonary function and ancestry by means of linear regression. We performed similar analyses of data for two independent cohorts of subjects identifying themselves as African American: 813 participants in the Health, Aging, and Body Composition (HABC) study and 579 participants in the Cardiovascular Health Study (CHS). We compared the fit of two types of models to lung-function measurements: models based on the covariates used in standard prediction equations and models incorporating ancestry. We also evaluated the effect of the ancestry-based models on the classification of disease severity in two asthma-study populations. RESULTS African ancestry was inversely related to forced expiratory volume in 1 second (FEV1) and forced vital capacity in the CARDIA cohort. These relations were also seen in the HABC and CHS cohorts. In predicting lung function, the ancestry-based model fit the data better than standard models. Ancestry-based models resulted in the reclassification of asthma severity (based on the percentage of the predicted FEV1) in 4 to 5% of participants. CONCLUSIONS Current predictive equations, which rely on self-identified race alone, may misestimate lung function among subjects who identify themselves as African American. Incorporating ancestry into normative equations may improve lung-function estimates and more accurately categorize disease severity. (Funded by the National

  11. Pairing correlations in high-spin isomers

    SciTech Connect

    Odahara, A.; Gono, Y.; Fukuchi, T.; Wakabayashi, Y.; Sagawa, H.; Satula, W.; Nazarewicz, W.

    2005-12-15

    High-spin isomers with J{sup {pi}}=49/2{sup +} and 27{sup +} have been systematically observed in a number of N=83 isotones with 60{<=}Z{<=}67 at excitation energies {approx}9 MeV. Based on experimental excitation energies, an odd-even binding energy staggering has been extracted for the first time for these multi-quasiparticle states. Surprisingly, the magnitude of the odd-even effect in high-spin isomers turned out to be very close to that in ground states, thus challenging conventional wisdom that pairing correlations are reduced in highly excited states. Theoretical analysis based on mean-field theory explains the observed proton number dependence of the odd-even effect as a manifestation of strong pairing correlations in the highly excited states. Mean-field effects and the proton-neutron residual interaction on the odd-even staggering are also examined.

  12. Ancestry, admixture and fitness in Colombian genomes.

    PubMed

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

    2015-07-21

    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.

  13. Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

    PubMed Central

    Kessler, Michael D.; Yerges-Armstrong, Laura; Taub, Margaret A.; Shetty, Amol C.; Maloney, Kristin; Jeng, Linda Jo Bone; Ruczinski, Ingo; Levin, Albert M.; Williams, L. Keoki; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Boorgula, Meher Preethi; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Scott, Alan F.; Vergara, Candelaria; Gao, Jingjing; Hu, Yijuan; Johnston, Henry Richard; Qin, Zhaohui S.; Padhukasahasram, Badri; Dunston, Georgia M.; Faruque, Mezbah U.; Kenny, Eimear E.; Gietzen, Kimberly; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-YounA; Kumar, Rajesh; Schleimer, Robert; Bustamante, Carlos; De La Vega, Francisco M.; Gignoux, Chris R.; Shringarpure, Suyash S.; Musharoff, Shaila; Wojcik, Genevieve; Burchard, Esteban G.; Eng, Celeste; Gourraud, Pierre-Antoine; Hernandez, Ryan D.; Lizee, Antoine; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O.; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Abecasis, Goncalo; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Pissamai, Maul R. N.; Trevor, Maul R. N.; Watson, Harold; Araujo, Maria Ilma; Oliveira, Ricardo Riccio; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Herrera-Paz, Edwin Francisco; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Vasquez, Olga Marina; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria; O'Connor, Timothy D.

    2016-01-01

    To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=−0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations. PMID:27725664

  14. A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil.

    PubMed

    Coelho, A V C; Moura, R R; Cavalcanti, C A J; Guimarães, R L; Sandrin-Garcia, P; Crovella, S; Brandão, L A C

    2015-03-31

    Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples' genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries. We tested the feasibility of a subset of the 12 most informative markers from a previously established study to estimate influence from three ancestral populations: European, African and Amerindian. The results showed that in a sample with a diverse ethnicity (N = 822) derived from 1000 Genomes database, the 12 AIMs had the same capacity to estimate ancestries when compared to the original set of 128 AIMs, since estimates from the two panels were closely correlated. Thus, these 12 SNPs were used to estimate ancestry in a new sample (N = 192) from an admixed population in Recife, Northeast Brazil. The ancestry estimates from Recife subjects were in accordance with previous studies, showing that Northeastern Brazilian populations show great influence from European ancestry (59.7%), followed by African (23.0%) and Amerindian (17.3%) ancestries. Ethnicity self-classification according to skin-color was confirmed to be a poor indicator of population substructure in Brazilians, since ancestry estimates overlapped between classifications. Thus, our streamlined panel of 12 markers may substitute panels with more markers, while retaining the capacity to control for population substructure and admixture, thereby reducing sample processing time.

  15. The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected

    PubMed Central

    Pena, Sérgio D. J.; Di Pietro, Giuliano; Fuchshuber-Moraes, Mateus; Genro, Julia Pasqualini; Hutz, Mara H.; Kehdy, Fernanda de Souza Gomes; Kohlrausch, Fabiana; Magno, Luiz Alexandre Viana; Montenegro, Raquel Carvalho; Moraes, Manoel Odorico; de Moraes, Maria Elisabete Amaral; de Moraes, Milene Raiol; Ojopi, Élida B.; Perini, Jamila A.; Racciopi, Clarice; Ribeiro-dos-Santos, Ândrea Kely Campos; Rios-Santos, Fabrício; Romano-Silva, Marco A.; Sortica, Vinicius A.; Suarez-Kurtz, Guilherme

    2011-01-01

    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, should also be

  16. Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition

    PubMed Central

    Mozhui, Khyobeni; Smith, Alicia K.; Tylavsky, Frances A.

    2015-01-01

    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. PMID:25742137

  17. The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans.

    PubMed

    Sankararaman, Sriram; Mallick, Swapan; Patterson, Nick; Reich, David

    2016-05-09

    Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

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

    PubMed Central

    2011-01-01

    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 data. Conclusions For K

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

    PubMed

    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.

  20. Diffraction Correlation to Reconstruct Highly Strained Particles

    NASA Astrophysics Data System (ADS)

    Brown, Douglas; Harder, Ross; Clark, Jesse; Kim, J. W.; Kiefer, Boris; Fullerton, Eric; Shpyrko, Oleg; Fohtung, Edwin

    2015-03-01

    Through the use of coherent x-ray diffraction a three-dimensional diffraction pattern of a highly strained nano-crystal can be recorded in reciprocal space by a detector. Only the intensities are recorded, resulting in a loss of the complex phase. The recorded diffraction pattern therefore requires computational processing to reconstruct the density and complex distribution of the diffracted nano-crystal. For highly strained crystals, standard methods using HIO and ER algorithms are no longer sufficient to reconstruct the diffraction pattern. Our solution is to correlate the symmetry in reciprocal space to generate an a priori shape constraint to guide the computational reconstruction of the diffraction pattern. This approach has improved the ability to accurately reconstruct highly strained nano-crystals.

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

    PubMed Central

    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.

    2011-01-01

    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. PMID:21324875

  2. Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing.

    PubMed

    Phillips, Chris; Fernandez-Formoso, Luis; Gelabert-Besada, Miguel; Garcia-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Carracedo, Angel; Lareu, Maria Victoria

    2013-04-01

    There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population-divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12-STR multiplex composed of ancestry informative marker STRs (AIM-STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM-SNPs: Snipper, to handle multiallele STR data using frequency-based training sets. We assessed the ability of the 12-plex AIM-STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM-SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available.

  3. Disorder and Transport in Highly Correlated Systems

    DTIC Science & Technology

    1992-03-31

    Denr Dow. Vlease find included 1th100 copies of the Annu at [rport for my Grant NOOO 14- 1 j- 14󈧪, entitled " Disorder and Transport in I licility...of N ava1l Research for your support. 1Ian K. Sch~ilter Fnclosures Appr~I ~ir k~ll~ereleae;\\ t)Is~i I gm~U itedl ONR GRANT N00014-91J-1438 " Disorder ...001 i92-11805 ’ Introduction This grant was a new start dedicated to studies of disorder and transport in highly correlated electron systems, mostly

  4. Ancestry, admixture and fitness in Colombian genomes

    PubMed Central

    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

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

    PubMed Central

    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

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

    PubMed

    Gayevskiy, Velimir; Klaere, Steffen; Knight, Sarah; Goddard, Matthew R

    2014-01-01

    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.

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

    PubMed Central

    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

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

    PubMed

    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.

  9. High speed image correlation for vibration analysis

    NASA Astrophysics Data System (ADS)

    Siebert, T.; Wood, R.; Splitthof, K.

    2009-08-01

    Digital speckle correlation techniques have already been successfully proven to be an accurate displacement analysis tool for a wide range of applications. With the use of two cameras, three dimensional measurements of contours and displacements can be carried out. With a simple setup it opens a wide range of applications. Rapid new developments in the field of digital imaging and computer technology opens further applications for these measurement methods to high speed deformation and strain analysis, e.g. in the fields of material testing, fracture mechanics, advanced materials and component testing. The high resolution of the deformation measurements in space and time opens a wide range of applications for vibration analysis of objects. Since the system determines the absolute position and displacements of the object in space, it is capable of measuring high amplitudes and even objects with rigid body movements. The absolute resolution depends on the field of view and is scalable. Calibration of the optical setup is a crucial point which will be discussed in detail. Examples of the analysis of harmonic vibration and transient events from material research and industrial applications are presented. The results show typical features of the system.

  10. Chromosome Connections: Compelling Clues to Common Ancestry

    ERIC Educational Resources Information Center

    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…

  11. Proving universal common ancestry with similar sequences

    PubMed Central

    Martins, Leonardo de Oliveira; Posada, David

    2013-01-01

    Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment. PMID:23814665

  12. Discovering genetic ancestry using spectral graph theory.

    PubMed

    Lee, Ann B; Luca, Diana; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn

    2010-01-01

    As one approach to uncovering the genetic underpinnings of complex disease, individuals are measured at a large number of genetic variants (usually SNPs) across the genome and these SNP genotypes are assessed for association with disease status. We propose a new statistical method called Spectral-GEM for the analysis of genome-wide association studies; the goal of Spectral-GEM is to quantify the ancestry of the sample from such genotypic data. Ignoring structure due to differential ancestry can lead to an excess of spurious findings and reduce power. Ancestry is commonly estimated using the eigenvectors derived from principal component analysis (PCA). To develop an alternative to PCA we draw on connections between multidimensional scaling and spectral graph theory. Our approach, based on a spectral embedding derived from the normalized Laplacian of a graph, can produce more meaningful delineation of ancestry than by using PCA. Often the results from Spectral-GEM are straightforward to interpret and therefore useful in association analysis. We illustrate the new algorithm with an analysis of the POPRES data [Nelson et al., 2008].

  13. Unravelling the distinct strains of Tharu ancestry

    PubMed Central

    Chaubey, Gyaneshwer; Singh, Manvendra; Crivellaro, Federica; Tamang, Rakesh; Nandan, Amrita; Singh, Kamayani; Sharma, Varun Kumar; Pathak, Ajai Kumar; Shah, Anish M; Sharma, Vishwas; Singh, Vipin Kumar; Selvi Rani, Deepa; Rai, Niraj; Kushniarevich, Alena; Ilumäe, Anne-Mai; Karmin, Monika; Phillip, Anand; Verma, Abhilasha; Prank, Erik; Singh, Vijay Kumar; Li, Blaise; Govindaraj, Periyasamy; Chaubey, Akhilesh Kumar; Dubey, Pavan Kumar; Reddy, Alla G; Premkumar, Kumpati; Vishnupriya, Satti; Pande, Veena; Parik, Jüri; Rootsi, Siiri; Endicott, Phillip; Metspalu, Mait; Lahr, Marta Mirazon; van Driem, George; Villems, Richard; Kivisild, Toomas; Singh, Lalji; Thangaraj, Kumarasamy

    2014-01-01

    The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43. PMID:24667789

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

    PubMed Central

    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

  15. The genomic landscape of Neanderthal ancestry in present-day humans.

    PubMed

    Sankararaman, Sriram; Mallick, Swapan; Dannemann, Michael; Prüfer, Kay; Kelso, Janet; Pääbo, Svante; Patterson, Nick; Reich, David

    2014-03-20

    Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

  16. High-Fidelity Coding with Correlated Neurons

    PubMed Central

    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

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

    PubMed Central

    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

  18. Anthropologists' views on race, ancestry, and genetics

    PubMed Central

    Yu, Joon‐Ho; Ifekwunigwe, Jayne O.; Harrell, Tanya M.; Bamshad, Michael J.; Royal, Charmaine D.

    2016-01-01

    Abstract Controversies over race conceptualizations have been ongoing for centuries and have been shaped, in part, by anthropologists. Objective To assess anthropologists' views on race, genetics, and ancestry. Methods In 2012 a broad national survey of anthropologists examined prevailing views on race, ancestry, and genetics. Results Results demonstrate consensus that there are no human biological races and recognition that race exists as lived social experiences that can have important effects on health. Discussion Racial privilege affects anthropologists' views on race, underscoring the importance that anthropologists be vigilant of biases in the profession and practice. Anthropologists must mitigate racial biases in society wherever they might be lurking and quash any sociopolitical attempts to normalize or promote racist rhetoric, sentiment, and behavior. PMID:27874171

  19. The Geography of Recent Genetic Ancestry across Europe

    PubMed Central

    Ralph, Peter; Coop, Graham

    2013-01-01

    The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world. PMID:23667324

  20. The geography of recent genetic ancestry across Europe.

    PubMed

    Ralph, Peter; Coop, Graham

    2013-01-01

    The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2-12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

  1. AncestrySNPminer: A bioinformatics tool to retrieve and develop ancestry informative SNP panels

    PubMed Central

    Amirisetty, Sushil; Khurana Hershey, Gurjit K.; Baye, Tesfaye M.

    2012-01-01

    A wealth of genomic information is available in public and private databases. However, this information is underutilized for uncovering population specific and functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a faster and cost effective approach for investigating the number of SNPs that are informative for ancestry. In this study, we present AncestrySNPminer, the first web-based bioinformatics tool specifically designed to retrieve Ancestry Informative Markers (AIMs) from genomic data sets and link these informative markers to genes and ontological annotation classes. The tool includes an automated and simple “scripting at the click of a button” functionality that enables researchers to perform various population genomics statistical analyses methods with user friendly querying and filtering of data sets across various populations through a single web interface. AncestrySNPminer can be freely accessed at https://research.cchmc.org/mershalab/AncestrySNPminer/login.php. PMID:22584067

  2. Color and genomic ancestry in Brazilians

    PubMed Central

    Parra, Flavia C.; Amado, Roberto C.; Lambertucci, José R.; Rocha, Jorge; Antunes, Carlos M.; Pena, Sérgio D. J.

    2003-01-01

    This work was undertaken to ascertain to what degree the physical appearance of a Brazilian individual was predictive of genomic African ancestry. Using a panel of 10 population-specific alleles, we assigned to each person an African ancestry index (AAI). The procedure was able to tell apart, with no overlaps, 20 males from northern Portugal from 20 males from São Tomé Island on the west coast of Africa. We also tested 10 Brazilian Amerindians and observed that their AAI values fell in the same range as the Europeans. Finally, we studied two different Brazilian population samples. The first consisted of 173 individuals from a rural Southeastern community, clinically classified according to their Color (white, black, or intermediate) with a multivariate evaluation based on skin pigmentation in the medial part of the arm, hair color and texture, and the shape of the nose and lips. In contrast to the clear-cut results with the African and European samples, our results showed large variances and extensive overlaps among the three Color categories. We next embarked on a study of 200 unrelated Brazilian white males who originated from cosmopolitan centers of the four major geographic regions of the country. The results showed AAI values intermediate between Europeans and Africans, even in southern Brazil, a region predominantly peopled by European immigrants. Our data suggest that in Brazil, at an individual level, color, as determined by physical evaluation, is a poor predictor of genomic African ancestry, estimated by molecular markers. PMID:12509516

  3. Interaction between common breast cancer susceptibility variants, genetic ancestry, and non-genetic risk factors in Hispanic women

    PubMed Central

    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.

    2015-01-01

    Background 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 single nucleotide polymorphisms (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. Methods 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. Results 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 odds ratio (OR): 0.94 (95% confidence interval 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, P-interaction 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, and >12 months breastfeeding, respectively, P-interaction 0.014]. Conclusions 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. Impact These results highlight the importance of understanding the interplay between genetic ancestry, genetics, and non-genetic risk factors and their contribution to breast cancer risk. PMID:26364163

  4. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference.

    PubMed

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

    2013-08-08

    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%).

  5. Differentiation of African Components of Ancestry to Stratify Groups in a Case–Control Study of a Brazilian Urban Population

    PubMed Central

    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, Ángel; Salas, Antonio; Freire, Ana; Lareu, Maria Victoria; Phillips, Christopher; Porras-Hurtado, Liliana; Fondevila, Manuel; Hirata, Rosario D.C.

    2012-01-01

    Background: Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies. Methods: 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. Results: 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 <0.25 and >0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study. Conclusions: The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers. PMID:22288895

  6. MESON CORRELATION FUNCTIONS AT HIGH TEMPERATURES.

    SciTech Connect

    WISSEL, S.; DATTA, S.; KARSCH, F.; LAERMANN, E.; SHCHEREDIN, S.

    2005-07-25

    We present preliminary results for the correlation- and spectral functions of different meson channels on the lattice. The main focus lies on gaining control over cut-off as well as on the finite-volume effects. Extrapolations of screening masses above the deconfining temperature are guided by the result of the free (T = {infinity}) case on the lattice and in the continuum. We study the quenched non-perturbatively improved Wilson-clover fermion as well as the hypercube fermion action which might show less cut-off effects.

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

    PubMed

    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

  8. High-order correlation of chaotic bosons and fermions

    NASA Astrophysics Data System (ADS)

    Liu, Hong-Chao

    2016-08-01

    We theoretically study the high-order correlation functions of chaotic bosons and fermions. Based on the different parity of the Stirling number, the products of the first-order correlation functions are well classified and employed to represent the high-order correlation function. The correlation of bosons conduces a bunching effect, which will be enhanced as order N increases. Different from bosons, the anticommutation relation of fermions leads to the parity of the Stirling number, which thereby results in a mixture of bunching and antibunching behaviors in high-order correlation. By further investigating third-order ghost diffraction and ghost imaging, the differences between the high-order correlations of bosons and fermions are discussed in detail. A larger N will dramatically improve the ghost image quality for bosons, but a good strategy should be carefully chosen for the fermionic ghost imaging process due to its complex correlation components.

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

    PubMed

    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) < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the 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.

  10. Highly noise resistant multiqubit quantum correlations

    NASA Astrophysics Data System (ADS)

    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.

  11. Impact of Genetic Ancestry and Socio-Demographic Status on the Clinical Expression of Systemic Lupus Erythematosus in Amerindian-European Populations

    PubMed Central

    Sánchez, Elena; Rasmussen, Astrid; Riba, Laura; Acevedo, Eduardo; Kelly, Jennifer A.; Langefeld, Carl D.; García-De La Torre, Ignacio; Maradiaga-Ceceña, Marco A.; Cardiel, Mario H.; Esquivel-Valerio, Jorge A.; Rodriguez-Amado, Jacqueline; Moctezuma, José Francisco; Miranda, Pedro; Perandones, Carlos; Castel, Cecilia; Laborde, Hugo A.; Alba, Paula; Musuruana, Jorge; Goecke, Annelise; Anaya, Juan-Manuel; Kaufman, Kenneth M.; Adler, Adam; Brown, Elizabeth E.; Alarcón, Graciela S.; Kimberly, Robert P.; Edberg, Jeffrey C.; Criswell, Lindsey A.; Gilkeson, Gary S.; Niewold, Timothy B.; Martin, Javier; Vyse, Timothy J.; Ramsey-Goldman, Rosalind; Petri, Michelle; Merrill, Joan T.; Reveille, John D.; Tsao, Betty P.; Orozco, Lorena; Baca, Vicente; James, Judith A.; Harley, John B.; Tusié-Luna, Teresa; Pons-Estel, Bernardo A.; Jacob, Chaim O.; Alarcón-Riquelme, Marta E.

    2012-01-01

    Objective Amerindian-Europeans, Asians and African-Americans have an excess morbidity from SLE and higher prevalence of lupus nephritis than Caucasians. The aim of this study was to analyze the relationship between genetic ancestry and socio-demographic characteristics and clinical features in a large cohort of Amerindian-European SLE patients. Methods A total of 2116 SLE patients of Amerindian-European origin and 4001 SLE patients of European descent with clinical data were used in the study. Genotyping of 253 continental ancestry informative markers was performed on the Illumina platform. The STRUCTURE and ADMIXTURE software were used to determine genetic ancestry of each individual. Correlation between ancestry and socio-demographic and clinical data were analyzed using logistic regression. Results The average Amerindian genetic ancestry of 2116 SLE patients was 40.7%. There was an increased risk of having renal involvement (P<0.0001, OR= 3.50 95%CI 2.63-4.63) and an early age of onset with the presence of Amerindian genetic ancestry (P<0.0001). Amerindian ancestry protected against photosensitivity (P<0.0001, OR= 0.58 95%CI 0.44-0.76), oral ulcers (P<0.0001, OR= 0.55 95%CI 0.42-0.72), and serositis (P<0.0001, OR= 0.56 95%CI 0.41-0.75) after adjustment by age, gender and age of onset. However, gender and age of onset had stronger effects on malar rash, discoid rash, arthritis and neurological involvement than genetic ancestry. Conclusion In general, genetic Amerindian ancestry correlates with lower socio-demographic status and increases the risk for developing renal involvement and SLE at an earlier age of onset. PMID:22886787

  12. Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes

    PubMed Central

    Florez, J. C.; Price, A. L.; Campbell, D.; Riba, L.; Parra, M. V.; Yu, F.; Duque, C.; Saxena, R.; Gallego, N.; Tello-Ruiz, M.; Franco, L.; Rodríguez-Torres, M.; Villegas, A.; Bedoya, G.; Aguilar-Salinas, C. A.; Tusié-Luna, M. T.; Ruiz-Linares, A.; Reich, D.

    2011-01-01

    Aims/hypothesis Type 2 diabetes is more prevalent in US American minority populations of African or Native American descent than it is in European Americans. However, the proportion of this epidemiological difference that can be ascribed to genetic or environmental factors is unknown. To determine whether genetic ancestry is correlated with diabetes risk in Latinos, we estimated the proportion of European ancestry in case-control samples from Mexico and Colombia in whom socioeconomic status had been carefully ascertained. Methods We genotyped 67 ancestry-informative markers in 499 participants with type 2 diabetes and 197 controls from Medellín (Colombia), as well as in 163 participants with type 2 diabetes and 72 controls from central Mexico. Each participant was assigned a socioeconomic status scale via various measures. Results Although European ancestry was associated with lower diabetes risk in Mexicans (OR [95% CI] 0.06 [0.02–0.21], p=2.0 × 10−5) and Colombians (OR 0.26 [0.08–0.78], p=0.02), adjustment for socioeconomic status eliminated the association in the Colombian sample (OR 0.64 [0.19–2.12], p=0.46) and significantly attenuated it in the Mexican sample (OR 0.17 [0.04–0.71], p=0.02). Adjustment for BMI did not change the results. Conclusions/interpretation The proportion of non-European ancestry is associated with both type 2 diabetes and lower socioeconomic status in admixed Latino populations from North and South America. We conclude that ancestry-directed search for genetic markers associated with type 2 diabetes in Latinos may benefit from information involving social factors, as these factors have a quantitatively important effect on type 2 diabetes risk relative to ancestry effects. PMID:19526211

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

    PubMed Central

    2016-01-01

    Background The influence of genetic ancestry on Trypanosoma cruzi infection and Chagas disease outcomes is unknown. Methodology/Principal Findings 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. Conclusions/Significance 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. PMID:27182885

  14. Genome measures used for quality control are dependent on gene function and ancestry

    PubMed Central

    Wang, Jing; Raskin, Leon; Samuels, David C.; Shyr, Yu; Guo, Yan

    2015-01-01

    Motivation: The transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio have been commonly computed in genetic studies as a quality control (QC) measurement. Additionally, these two ratios are helpful in our understanding of the patterns of DNA sequence evolution. Results: To thoroughly understand these two genomic measures, we performed a study using 1000 Genomes Project (1000G) released genotype data (N = 1092). An additional two datasets (N = 581 and N = 6) were used to validate our findings from the 1000G dataset. We compared the two ratios among continental ancestry, genome regions and gene functionality. We found that the Ti/Tv ratio can be used as a quality indicator for single nucleotide polymorphisms inferred from high-throughput sequencing data. The Ti/Tv ratio varies greatly by genome region and functionality, but not by ancestry. The het/nonref-hom ratio varies greatly by ancestry, but not by genome regions and functionality. Furthermore, extreme guanine + cytosine content (either high or low) is negatively associated with the Ti/Tv ratio magnitude. Thus, when performing QC assessment using these two measures, care must be taken to apply the correct thresholds based on ancestry and genome region. Failure to take these considerations into account at the QC stage will bias any following analysis. Contact: yan.guo@vanderbilt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25297068

  15. Socioeconomic and Nutritional Factors Account for the Association of Gastric Cancer with Amerindian Ancestry in a Latin American Admixed Population

    PubMed Central

    Pereira, Latife; Zamudio, Roxana; Soares-Souza, Giordano; Herrera, Phabiola; Cabrera, Lilia; Hooper, Catherine C.; Cok, Jaime; Combe, Juan M.; Vargas, Gloria; Prado, William A.; Schneider, Silvana; Kehdy, Fernanda; Rodrigues, Maira R.; Chanock, Stephen J.; Berg, Douglas E.; Gilman, Robert H.; Tarazona-Santos, Eduardo

    2012-01-01

    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. PMID:22870209

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

    PubMed

    Pereira, Latife; Zamudio, Roxana; Soares-Souza, Giordano; Herrera, Phabiola; Cabrera, Lilia; Hooper, Catherine C; Cok, Jaime; Combe, Juan M; Vargas, Gloria; Prado, William A; Schneider, Silvana; Kehdy, Fernanda; Rodrigues, Maira R; Chanock, Stephen J; Berg, Douglas E; Gilman, Robert H; Tarazona-Santos, Eduardo

    2012-01-01

    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.

  17. European Ancestry Predominates in Neuromyelitis Optica and Multiple Sclerosis Patients from Brazil

    PubMed Central

    Santos, Antônio Carlos; Lana-Peixoto, Marco Aurélio; Rocha, Cristiane Franklin; Brito, Maria Lucia; de Oliveira, Enedina Maria Lobato; Bichuetti, Denis Bernardi; Gabbai, Alberto Alan; Diniz, Denise Sisterolli; Kaimen-Maciel, Damacio Ramon; Comini-Frota, Elizabeth Regina; Vieira Wiezel, Claudia E.; Muniz, Yara Costa Netto; da Silva Costa, Roberta Martins; Mendes-Junior, Celso Teixeira; Donadi, Eduardo Antônio; Barreira, Amilton Antunes; Simões, Aguinaldo Luiz

    2013-01-01

    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. PMID:23527051

  18. Epidemiology, biology, and treatment of triple-negative breast cancer in women of African ancestry

    PubMed Central

    Brewster, Abenaa M; Chavez-MacGregor, Mariana; Brown, Powel

    2015-01-01

    Breast cancer incidence is increasing worldwide, and breast cancer-related mortality is highest in women of African ancestry, who are more likely to have basal-like or triple-negative breast cancer (TNBC) than are women of European ancestry. Identification of cultural, epidemiological, and genetic risk factors that predispose women of African ancestry to TNBC is an active area of research. Despite the aggressive behaviour of TNBC, achievement of a pathological complete response with chemotherapy is associated with good long-term survival outcomes, and sensitivity to chemotherapy does not seem to differ according to ethnic origin. Discovery of the molecular signalling molecules that define TNBC heterogeneity has led to the development of targeted agents such as inhibitors of poly (ADP-ribose) polymerase-1 and mTOR and immunomodulatory drugs that are in the early stages of clinical testing. First, we summarise the existing published work on the differences reported on the epidemiology, biology, and response to systemic treatment of TNBC between women of African ancestry and white women, and identify some gaps in knowledge. Second, we review the opportunities for development of new therapeutic agents in view of the potential high clinical relevance for patients with TNBC irrespective of race or ethnic origin. PMID:25456381

  19. The Astrobiological Case for Our Cosmic Ancestry

    NASA Astrophysics Data System (ADS)

    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.

  20. The astrobiological case for our cosmic ancestry

    NASA Astrophysics Data System (ADS)

    Wickramasinghe, Chandra

    2010-04-01

    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 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.

  1. Genetics of stroke in a UK African ancestry case-control study

    PubMed Central

    Rutten-Jacobs, Loes; Curtis, Charles; Patel, Hamel; Breen, Gerome; Newhouse, Stephen; Lewis, Cathryn M.; Markus, Hugh S.

    2017-01-01

    Objective: Despite epidemiologic data showing an increased stroke incidence in African ancestry populations, genetic studies in this group have so far been limited, and there has been little characterization of the genetic contribution to stroke liability in this population, particularly for stroke subtypes. Methods: We evaluated the evidence that genetic factors contribute to stroke and stroke subtypes in a population of 917 African and African Caribbean stroke cases and 868 matched controls from London, United Kingdom. We (1) estimated the heritability of stroke in this population using genomic-relatedness matrix-restricted maximum likelihood approaches, (2) assessed loci associated with stroke in Europeans in our population, and (3) evaluated the influence of genetic factors underlying cardiovascular risk factors on stroke using polygenic risk scoring. Results: Our results indicate a substantial genetic contribution to stroke risk in African ancestry populations (h2 = 0.35 [SE = 0.19], p = 0.043). Polygenic risk scores indicate that cardiovascular risk scores contribute to the genetic liability (odds ratio [OR] 1.09 [95% confidence interval (CI) 1.01–1.17], p = 0.029) and point to a strong influence of type 2 diabetes in large vessel stroke (OR 1.62 [95% CI 1.19–2.22], p = 0.0024). Single nucleotide polymorphisms associated with ischemic stroke in Europeans shared direction of effect in SLESS (p = 0.031), suggesting that disease mechanisms are shared across ancestries. Conclusions: Stroke in African ancestry populations is highly heritable and influenced by genetic determinants underlying cardiovascular risk factors. In addition, stroke loci identified in Europeans share direction of effect in African populations. Future genome-wide association studies must focus on incorporating African ancestry individuals. PMID:28349126

  2. Do people from the Jewish community prefer ancestry-based or pan-ethnic expanded carrier screening?

    PubMed Central

    Holtkamp, Kim C A; van Maarle, Merel C; Schouten, Maria J E; Dondorp, Wybo J; Lakeman, Phillis; Henneman, Lidewij

    2016-01-01

    Ancestry-based carrier screening in the Ashkenazi Jewish population entails screening for specific autosomal recessive founder mutations, which are rarer among the general population. As it is now technically feasible to screen for many more diseases, the question arises whether this population prefers a limited ancestry-based offer or a pan-ethnic expanded carrier screening panel that goes beyond the diseases that are frequent in their own population, and is offered regardless of ancestry. An online questionnaire was completed by 145 individuals from the Dutch Jewish community (≥18 years) between April and July 2014. In total, 64.8% were aware of the existence of ancestry-based carrier screening, and respondents were generally positive about screening. About half (53.8%) preferred pan-ethnic expanded carrier screening, whereas 42.8% preferred ancestry-based screening. Reasons for preferring pan-ethnic screening included ‘everyone has a right to be tested', ‘fear of stigmatization when offering ancestry-based panels', and ‘difficulties with identifying risk owing to mixed backgrounds'. ‘Preventing high healthcare costs' was the most important reason against pan-ethnic carrier screening among those in favor of an ancestry-based panel. In conclusion, these findings show that people from the Dutch Jewish community have a positive attitude regarding carrier screening in their community for a wide range of diseases. As costs of expanded carrier screening panels are most likely to drop in the near future, it is expected that these panels will receive more support in the future. PMID:25966636

  3. Do people from the Jewish community prefer ancestry-based or pan-ethnic expanded carrier screening?

    PubMed

    Holtkamp, Kim C A; van Maarle, Merel C; Schouten, Maria J E; Dondorp, Wybo J; Lakeman, Phillis; Henneman, Lidewij

    2016-02-01

    Ancestry-based carrier screening in the Ashkenazi Jewish population entails screening for specific autosomal recessive founder mutations, which are rarer among the general population. As it is now technically feasible to screen for many more diseases, the question arises whether this population prefers a limited ancestry-based offer or a pan-ethnic expanded carrier screening panel that goes beyond the diseases that are frequent in their own population, and is offered regardless of ancestry. An online questionnaire was completed by 145 individuals from the Dutch Jewish community (≥ 18 years) between April and July 2014. In total, 64.8% were aware of the existence of ancestry-based carrier screening, and respondents were generally positive about screening. About half (53.8%) preferred pan-ethnic expanded carrier screening, whereas 42.8% preferred ancestry-based screening. Reasons for preferring pan-ethnic screening included 'everyone has a right to be tested', 'fear of stigmatization when offering ancestry-based panels', and 'difficulties with identifying risk owing to mixed backgrounds'. 'Preventing high healthcare costs' was the most important reason against pan-ethnic carrier screening among those in favor of an ancestry-based panel. In conclusion, these findings show that people from the Dutch Jewish community have a positive attitude regarding carrier screening in their community for a wide range of diseases. As costs of expanded carrier screening panels are most likely to drop in the near future, it is expected that these panels will receive more support in the future.

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

    PubMed Central

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

    2015-01-01

    Background Obesity and breast cancer risk is multifaceted and genes associated with energy homeostasis may modify this relationship. Methods 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. Results 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. Conclusions Energy homeostasis genes were associated with breast cancer risk; menopausal status, body size, and genetic ancestry influenced this relationship. PMID:26395295

  5. Association of Aldosterone Synthase Polymorphism (CYP11B2 -344T>C) and Genetic Ancestry with Atrial Fibrillation and Serum Aldosterone in African Americans with Heart Failure

    PubMed Central

    Bress, Adam; Han, Jin; Patel, Shitalben R.; Desai, Ankit A.; Mansour, Ibrahim; Groo, Vicki; Progar, Kristin; Shah, Ebony; Stamos, Thomas D.; Wing, Coady; Garcia, Joe G. N.; Kittles, Rick; Cavallari, Larisa H.

    2013-01-01

    The objective of this study was to examine the extent to which aldosterone synthase genotype (CYP11B2) and genetic ancestry correlate with atrial fibrillation (AF) and serum aldosterone in African Americans with heart failure. Clinical data, echocardiographic measurements, and a genetic sample for determination of CYP11B2 -344T>C (rs1799998) genotype and genetic ancestry were collected from 194 self-reported African Americans with chronic, ambulatory heart failure. Genetic ancestry was determined using 105 autosomal ancestry informative markers. In a sub-set of patients (n = 126), serum was also collected for determination of circulating aldosterone. The CYP11B2 −344C allele frequency was 18% among the study population, and 19% of patients had AF. Multiple logistic regression revealed that the CYP11B2 −344CC genotype was a significant independent predictor of AF (OR 12.7, 95% CI 1.60–98.4, p = 0.0150, empirical p = 0.011) while holding multiple clinical factors, left atrial size, and percent European ancestry constant. Serum aldosterone was significantly higher among patients with AF (p = 0.036), whereas increased West African ancestry was inversely correlated with serum aldosterone (r = −0.19, p = 0.037). The CYP11B2 −344CC genotype was also overrepresented among patients with extreme aldosterone elevation (≥90th percentile, p = 0.0145). In this cohort of African Americans with chronic ambulatory heart failure, the CYP11B2 −344T>C genotype was a significant independent predictor of AF while holding clinical, echocardiographic predictors, and genetic ancestry constant. In addition, increased West African ancestry was associated with decreased serum aldosterone levels, potentially providing an explanation for the lower risk for AF observed among African Americans. PMID:23936266

  6. Age at onset of multiple sclerosis may be influenced by place of residence during childhood rather than ancestry.

    PubMed

    Kennedy, J; O'Connor, P; Sadovnick, A D; Perara, M; Yee, I; Banwell, B

    2006-01-01

    Multiple sclerosis (MS) most commonly affects individuals of Northern European descent who live in countries at high latitude. The relative contributions of ancestry, country of birth and residence as determinants of MS risk have been studied in adult MS, but have not been explored in the pediatric MS population. In this study, we compare the demographics of pediatric- and adult-onset MS patients cared for in Toronto, Ontario, Canada, a multicultural region. The country of birth, residence during childhood, and ancestry were compared for 44 children and 573 adults. Our results demonstrate that although both the pediatric and adult cohorts were essentially born and raised in the same region of Ontario, Canada, children with MS were more likely to report Caribbean, Asian or Middle Eastern ancestry, and were less likely to have European heritage compared with individuals with adult-onset MS. The difference in ancestry between the pediatric and adult MS cohorts can be explained by two hypotheses: (1) individuals raised in a region of high MS prevalence, but whose ancestors originate from regions in which MS is rare, have an earlier age of MS onset, and (2) the place of residence during childhood, irrespective of ancestry, determines lifetime MS risk -- a fact that will be reflected in a change in the demographics of the adult MS cohort in our region as Canadian-raised children of recent immigrants reach the typical age of adult-onset MS.

  7. A Highly Accurate Face Recognition System Using Filtering Correlation

    NASA Astrophysics Data System (ADS)

    Watanabe, Eriko; Ishikawa, Sayuri; Kodate, Kashiko

    2007-09-01

    The authors previously constructed a highly accurate fast face recognition optical correlator (FARCO) [E. Watanabe and K. Kodate: Opt. Rev. 12 (2005) 460], and subsequently developed an improved, super high-speed FARCO (S-FARCO), which is able to process several hundred thousand frames per second. The principal advantage of our new system is its wide applicability to any correlation scheme. Three different configurations were proposed, each depending on correlation speed. This paper describes and evaluates a software correlation filter. The face recognition function proved highly accurate, seeing that a low-resolution facial image size (64 × 64 pixels) has been successfully implemented. An operation speed of less than 10 ms was achieved using a personal computer with a central processing unit (CPU) of 3 GHz and 2 GB memory. When we applied the software correlation filter to a high-security cellular phone face recognition system, experiments on 30 female students over a period of three months yielded low error rates: 0% false acceptance rate and 2% false rejection rate. Therefore, the filtering correlation works effectively when applied to low resolution images such as web-based images or faces captured by a monitoring camera.

  8. Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry

    PubMed Central

    Ge, Bing; Tayo, Bamidele; Mathias, Rasika A.; Ding, Jingzhong; Nalls, Michael A.; Adeyemo, Adebowale; Adoue, Véronique; Ambrosone, Christine B.; Atwood, Larry; Bandera, Elisa V.; Becker, Lewis C.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Boerwinkle, Eric; Britton, Angela; Casey, Graham; Chanock, Stephen J.; Demerath, Ellen; Deming, Sandra L.; Diver, W. Ryan; Fox, Caroline; Harris, Tamara B.; Hernandez, Dena G.; Hu, Jennifer J.; Ingles, Sue A.; John, Esther M.; Johnson, Craig; Keating, Brendan; Kittles, Rick A.; Kolonel, Laurence N.; Kritchevsky, Stephen B.; Le Marchand, Loic; Lohman, Kurt; Liu, Jiankang; Millikan, Robert C.; Murphy, Adam; Musani, Solomon; Neslund-Dudas, Christine; North, Kari E.; Nyante, Sarah; Ogunniyi, Adesola; Ostrander, Elaine A.; Papanicolaou, George; Patel, Sanjay; Pettaway, Curtis A.; Press, Michael F.; Redline, Susan; Rodriguez-Gil, Jorge L.; Rotimi, Charles; Rybicki, Benjamin A.; Salako, Babatunde; Schreiner, Pamela J.; Signorello, Lisa B.; Singleton, Andrew B.; Stanford, Janet L.; Stram, Alex H.; Stram, Daniel O.; Strom, Sara S.; Suktitipat, Bhoom; Thun, Michael J.; Witte, John S.; Yanek, Lisa R.; Ziegler, Regina G.; Zheng, Wei; Zhu, Xiaofeng; Zmuda, Joseph M.; Zonderman, Alan B.; Evans, Michele K.; Liu, Yongmei; Becker, Diane M.; Cooper, Richard S.; Pastinen, Tomi; Henderson, Brian E.; Hirschhorn, Joel N.; Lettre, Guillaume; Haiman, Christopher A.

    2011-01-01

    Adult height is a classic polygenic trait of high heritability (h 2 ∼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 ∼10% 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. PMID:21998595

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

    PubMed

    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.

  10. Angular correlations in gluon production at high energy

    SciTech Connect

    Kovner, Alex; Lublinsky, Michael

    2011-02-01

    We present a general, model independent argument demonstrating that gluons produced in high energy hadronic collision are necessarily correlated in rapidity and also in the emission angle. The strength of the correlation depends on the process and on the structure/model of the colliding particles. In particular we argue that it is strongly affected (and underestimated) by factorized approximations frequently used to quantify the effect.

  11. Accurate inference of local phased ancestry of modern admixed populations.

    PubMed

    Ma, Yamin; Zhao, Jian; Wong, Jian-Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A; Li, Yun; Song, Qing

    2014-07-23

    Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis.

  12. Ancestry Testing and the Practice of Genetic Counseling.

    PubMed

    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.

  13. PTPN22 Association in Systemic Lupus Erythematosus (SLE) with Respect to Individual Ancestry and Clinical Sub-Phenotypes

    PubMed Central

    Adler, Adam; Chung, Sharon A.; Kaufman, Kenneth M.; Kelly, Jennifer A.; Glenn, Stuart B.; Guthridge, Joel M.; Scofield, Robert H.; Kimberly, Robert P.; Brown, Elizabeth E.; Alarcón, Graciela S.; Edberg, Jeffrey C.; Kim, Jae-Hoon; Choi, Jiyoung; Ramsey-Goldman, Rosalind; Petri, Michelle A.; Reveille, John D.; Vilá, Luis M.; Boackle, Susan A.; Freedman, Barry I.; Tsao, Betty P.; Langefeld, Carl D.; Vyse, Timothy J.; Jacob, Chaim O.; Pons-Estel, Bernardo; Niewold, Timothy B.; Moser Sivils, Kathy L.; Merrill, Joan T.; Anaya, Juan-Manuel; Gilkeson, Gary S.; Gaffney, Patrick M.; Bae, Sang-Cheol; Alarcón-Riquelme, Marta E.; Harley, John B.; Criswell, Lindsey A.; James, Judith A.; Nath, Swapan K.

    2013-01-01

    Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is a negative regulator of T-cell activation associated with several autoimmune diseases, including systemic lupus erythematosus (SLE). Missense rs2476601 is associated with SLE in individuals with European ancestry. Since the rs2476601 risk allele frequency differs dramatically across ethnicities, we assessed robustness of PTPN22 association with SLE and its clinical sub-phenotypes across four ethnically diverse populations. Ten SNPs were genotyped in 8220 SLE cases and 7369 controls from in European-Americans (EA), African-Americans (AA), Asians (AS), and Hispanics (HS). We performed imputation-based association followed by conditional analysis to identify independent associations. Significantly associated SNPs were tested for association with SLE clinical sub-phenotypes, including autoantibody profiles. Multiple testing was accounted for by using false discovery rate. We successfully imputed and tested allelic association for 107 SNPs within the PTPN22 region and detected evidence of ethnic-specific associations from EA and HS. In EA, the strongest association was at rs2476601 (P = 4.7×10−9, OR = 1.40 (95% CI = 1.25–1.56)). Independent association with rs1217414 was also observed in EA, and both SNPs are correlated with increased European ancestry. For HS imputed intronic SNP, rs3765598, predicted to be a cis-eQTL, was associated (P = 0.007, OR = 0.79 and 95% CI = 0.67–0.94). No significant associations were observed in AA or AS. Case-only analysis using lupus-related clinical criteria revealed differences between EA SLE patients positive for moderate to high titers of IgG anti-cardiolipin (aCL IgG >20) versus negative aCL IgG at rs2476601 (P = 0.012, OR = 1.65). Association was reinforced when these cases were compared to controls (P = 2.7×10−5, OR = 2.11). Our results validate that rs2476601 is the most significantly associated SNP in individuals with

  14. PTPN22 association in systemic lupus erythematosus (SLE) with respect to individual ancestry and clinical sub-phenotypes.

    PubMed

    Namjou, Bahram; Kim-Howard, Xana; Sun, Celi; Adler, Adam; Chung, Sharon A; Kaufman, Kenneth M; Kelly, Jennifer A; Glenn, Stuart B; Guthridge, Joel M; Scofield, Robert H; Kimberly, Robert P; Brown, Elizabeth E; Alarcón, Graciela S; Edberg, Jeffrey C; Kim, Jae-Hoon; Choi, Jiyoung; Ramsey-Goldman, Rosalind; Petri, Michelle A; Reveille, John D; Vilá, Luis M; Boackle, Susan A; Freedman, Barry I; Tsao, Betty P; Langefeld, Carl D; Vyse, Timothy J; Jacob, Chaim O; Pons-Estel, Bernardo; Niewold, Timothy B; Moser Sivils, Kathy L; Merrill, Joan T; Anaya, Juan-Manuel; Gilkeson, Gary S; Gaffney, Patrick M; Bae, Sang-Cheol; Alarcón-Riquelme, Marta E; Harley, John B; Criswell, Lindsey A; James, Judith A; Nath, Swapan K

    2013-01-01

    Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is a negative regulator of T-cell activation associated with several autoimmune diseases, including systemic lupus erythematosus (SLE). Missense rs2476601 is associated with SLE in individuals with European ancestry. Since the rs2476601 risk allele frequency differs dramatically across ethnicities, we assessed robustness of PTPN22 association with SLE and its clinical sub-phenotypes across four ethnically diverse populations. Ten SNPs were genotyped in 8220 SLE cases and 7369 controls from in European-Americans (EA), African-Americans (AA), Asians (AS), and Hispanics (HS). We performed imputation-based association followed by conditional analysis to identify independent associations. Significantly associated SNPs were tested for association with SLE clinical sub-phenotypes, including autoantibody profiles. Multiple testing was accounted for by using false discovery rate. We successfully imputed and tested allelic association for 107 SNPs within the PTPN22 region and detected evidence of ethnic-specific associations from EA and HS. In EA, the strongest association was at rs2476601 (P = 4.7 × 10(-9), OR = 1.40 (95% CI = 1.25-1.56)). Independent association with rs1217414 was also observed in EA, and both SNPs are correlated with increased European ancestry. For HS imputed intronic SNP, rs3765598, predicted to be a cis-eQTL, was associated (P = 0.007, OR = 0.79 and 95% CI = 0.67-0.94). No significant associations were observed in AA or AS. Case-only analysis using lupus-related clinical criteria revealed differences between EA SLE patients positive for moderate to high titers of IgG anti-cardiolipin (aCL IgG >20) versus negative aCL IgG at rs2476601 (P = 0.012, OR = 1.65). Association was reinforced when these cases were compared to controls (P = 2.7 × 10(-5), OR = 2.11). Our results validate that rs2476601 is the most significantly associated SNP in individuals with European ancestry. Additionally, rs

  15. Adjusting head circumference for covariates in autism: clinical correlates of a highly heritable continuous trait

    PubMed Central

    Chaste, Pauline; Klei, Lambertus; Sanders, Stephan J.; Murtha, Michael T.; Hus, Vanessa; Lowe, Jennifer K.; Willsey, A. Jeremy; Moreno-De-Luca, Daniel; Yu, Timothy W.; Fombonne, Eric; Geschwind, Daniel; Grice, Dorothy E.; Ledbetter, David H.; Lord, Catherine; Mane, Shrikant M.; Martin, Christa Lese; Martin, Donna M.; Morrow, Eric M.; Walsh, Christopher A.; Sutcliffe, James S.; State, Matthew W.; Devlin, Bernie; Cook, Edwin H.; Kim, Soo-Jeong

    2013-01-01

    BACKGROUND Brain development follows a different trajectory in children with Autism Spectrum Disorders (ASD) than in typically developing children. A proxy for neurodevelopment could be head circumference (HC), but studies assessing HC and its clinical correlates in ASD have been inconsistent. This study investigates HC and clinical correlates in the Simons Simplex Collection cohort. METHODS We used a mixed linear model to estimate effects of covariates and the deviation from the expected HC given parental HC (genetic deviation). After excluding individuals with incomplete data, 7225 individuals in 1891 families remained for analysis. We examined the relationship between HC/genetic deviation of HC and clinical parameters. RESULTS Gender, age, height, weight, genetic ancestry and ASD status were significant predictors of HC (estimate of the ASD effect=0.2cm). HC was approximately normally distributed in probands and unaffected relatives, with only a few outliers. Genetic deviation of HC was also normally distributed, consistent with a random sampling of parental genes. Whereas larger HC than expected was associated with ASD symptom severity and regression, IQ decreased with the absolute value of the genetic deviation of HC. CONCLUSIONS Measured against expected values derived from covariates of ASD subjects, statistical outliers for HC were uncommon. HC is a strongly heritable trait and population norms for HC would be far more accurate if covariates including genetic ancestry, height and age were taken into account. The association of diminishing IQ with absolute deviation from predicted HC values suggests HC could reflect subtle underlying brain development and warrants further investigation. PMID:23746936

  16. Genetic Ancestry, Skin Reflectance and Pigmentation Genotypes in Association with Serum Vitamin D Metabolite Balance

    PubMed Central

    Wilson, Robin Taylor; Roff, Alanna N.; Dai, P. Jenny; Fortugno, Tracey; Douds, Jonathan; Chen, Gang; Grove, Gary L.; Nikiforova, Sheila Ongeri; Barnholtz-Sloan, Jill; Frudakis, Tony; Chinchilli, Vernon M.; Hartman, Terryl J.; Demers, Laurence M.; Shriver, Mark D.; Canfield, Victor A.; Cheng, Keith C.

    2012-01-01

    Background Lower serum vitamin D (25(OH)D) among individuals with African ancestry is attributed primarily to skin pigmentation. However, the influence of genetic polymorphisms controlling for skin melanin content has not been investigated. Therefore, we investigated differences in non-summer serum vitamin D metabolites according to self-reported race, genetic ancestry, skin reflectance and key pigmentation genes (SLC45A2 and SLC24A5). Materials and Methods Healthy individuals reporting at least half African American or half European American heritage were frequency matched to one another on age (+/− 2 years) and sex. 176 autosomal ancestry informative markers were used to estimate genetic ancestry. Melanin index was measured by reflectance spectrometry. Serum vitamin D metabolites (25(OH)D3, 25(OH)D2 and 24,25(OH)2D3) were determined by high performance liquid chromatography (HPLC) tandem mass spectrometry. Percent 24,25(OH)2D3 was calculated as a percent of the parent metabolite (25(OH)D3). Stepwise and backward selection regression models were used to identify leading covariates. Results Fifty African Americans and 50 European Americans participated in the study. Compared with SLC24A5 111Thr homozygotes, individuals with the SLC24A5 111Thr/Ala and 111Ala/Ala genotypes had respectively lower levels of 25(OH)D3 (23.0 and 23.8 nmol/L lower, p-dominant=0.007), and percent 24,25(OH)2D3 (4.1 and 5.2 percent lower, p-dominant=0.003), controlling for tanning bed use, vitamin D/fish oil supplement intake, race/ethnicity, and genetic ancestry. Results were similar with melanin index adjustment, and were not confounded by glucocorticoid, oral contraceptive, or statin use. Conclusions The SLC24A5 111Ala allele was associated with lower serum vitamin 25(OH)D3 and lower percent 24,25(OH)2D3, independently from melanin index and West African genetic ancestry. PMID:23525585

  17. Read-only high accuracy volume holographic optical correlator

    NASA Astrophysics Data System (ADS)

    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.

  18. The Ancestry and Affiliations of Kennewick Man

    PubMed Central

    Rasmussen, Morten; Poznik, G. David; Zollikofer, Christoph P. E.; de León, Marcia Ponce; Allentoft, Morten E.; Moltke, Ida; Jónsson, Hákon; Valdiosera, Cristina; Malhi, Ripan S.; Orlando, Ludovic; Bustamante, Carlos D.; Stafford, Thomas W.; Meltzer, David J.; Nielsen, Rasmus; Willerslev, Eske

    2016-01-01

    Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8340–9200 calibrated years BP1. His population affinities have been the subject of scientific debate and legal controversy. Based on initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the Claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted2. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans2. In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome wide data is available for comparison, several appear to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia. PMID:26087396

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

    SciTech Connect

    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.

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

    ERIC Educational Resources Information Center

    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…

  1. Inference for High-dimensional Differential Correlation Matrices *

    PubMed Central

    Cai, T. Tony; Zhang, Anru

    2015-01-01

    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. PMID:26500380

  2. Inference for High-dimensional Differential Correlation Matrices.

    PubMed

    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.

  3. Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

    PubMed Central

    Monzón, J.; Kays, R.; Dykhuizen, D. E.

    2014-01-01

    The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single nucleotide polymorphisms in 427 canids in order to examine the prevalence, spatial distribution, and ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf-like, suggesting that natural selection for wolf-like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, reveal a pattern of sex-biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry-informative markers. PMID:24148003

  4. Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs.

    PubMed

    Monzón, J; Kays, R; Dykhuizen, D E

    2014-01-01

    The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single-nucleotide polymorphisms in 427 canids to examine the prevalence, spatial distribution and the ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf-like, suggesting that natural selection for wolf-like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, revealed a pattern of sex-biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry-informative markers.

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

    PubMed

    Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E; Metspalu, Mait; Albrechtsen, Anders; Moltke, Ida; Rasmussen, Simon; Stafford, Thomas W; Orlando, Ludovic; Metspalu, Ene; Karmin, Monika; Tambets, Kristiina; Rootsi, Siiri; Mägi, Reedik; Campos, Paula F; Balanovska, Elena; Balanovsky, Oleg; Khusnutdinova, Elza; Litvinov, Sergey; Osipova, Ludmila P; Fedorova, Sardana A; Voevoda, Mikhail I; DeGiorgio, Michael; Sicheritz-Ponten, Thomas; Brunak, Søren; Demeshchenko, Svetlana; Kivisild, Toomas; Villems, Richard; Nielsen, Rasmus; Jakobsson, Mattias; Willerslev, Eske

    2014-01-02

    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 24,000-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 and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting 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

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

    PubMed

    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.

  7. Forensic genetic analysis of bio-geographical ancestry.

    PubMed

    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.

  8. The Role of Adipose Tissue in Insulin Resistance in Women of African Ancestry

    PubMed Central

    Goedecke, Julia H.; Levitt, Naomi S.; Evans, Juliet; Ellman, Nicole; Hume, David John; Kotze, Liske; Tootla, Mehreen; Victor, Hendriena; Keswell, Dheshnie

    2013-01-01

    Women of African ancestry, particularly those living in industrialized countries, experience a disproportionately higher prevalence of type 2 diabetes (T2D) compared to their white counterparts. Similarly, obesity and insulin resistance, which are major risk factors for T2D, are greater in black compared to white women. The exact mechanisms underlying these phenomena are not known. This paper will focus on the role of adipose tissue biology. Firstly, the characteristic body fat distribution of women of African ancestry will be discussed, followed by the depot-specific associations with insulin resistance. Factors involved in adipose tissue biology and their relation to insulin sensitivity will then be explored, including the role of sex hormones, glucocorticoid metabolism, lipolysis and adipogenesis, and their consequent effects on adipose tissue hypoxia, oxidative stress, and inflammation. Finally the role of ectopic fat deposition will be discussed. The paper proposes directions for future research, in particular highlighting the need for longitudinal and/or intervention studies to better understand the mechanisms underlying the high prevalence of insulin resistance and T2D in women of African ancestry. PMID:23401754

  9. Resolving the ancestry of Austronesian-speaking populations.

    PubMed

    Soares, Pedro A; Trejaut, Jean A; Rito, Teresa; Cavadas, Bruno; Hill, Catherine; Eng, Ken Khong; Mormina, Maru; Brandão, Andreia; Fraser, Ross M; Wang, Tse-Yi; Loo, Jun-Hun; Snell, Christopher; Ko, Tsang-Ming; Amorim, António; Pala, Maria; Macaulay, Vincent; Bulbeck, David; Wilson, James F; Gusmão, Leonor; Pereira, Luísa; Oppenheimer, Stephen; Lin, Marie; Richards, Martin B

    2016-03-01

    There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.

  10. Outlining the Ancestry Landscape of Colombian Admixed Populations.

    PubMed

    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.

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

    PubMed Central

    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

    2016-01-01

    Background and objectives 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. Design, setting, participants, & measurements 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). Results 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 (P<0.001 for all). Among African Americans, a higher percentage of African ancestry was associated with lower 24-hour urinary excretion of phosphorus (Ptrend<0.01) in unadjusted analyses. In linear regression models adjusted for socio-demographic characteristics, kidney function, serum phosphorus, and dietary phosphorus intake, higher percentage of African 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, P<0.001) and fractional excretion of phosphorus (each 10% higher African ancestry was associated with an absolute 1.1% lower fractional excretion of phosphorus, P=0.01). Conclusions A higher percentage of African ancestry was independently associated with lower 24-hour urinary phosphorus excretion and lower fractional

  12. Outlining the Ancestry Landscape of Colombian Admixed Populations

    PubMed Central

    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. PMID:27736937

  13. Unravelling the hidden ancestry of American admixed populations

    PubMed Central

    Montinaro, Francesco; Busby, George B.J.; Pascali, Vincenzo L.; Myers, Simon; Hellenthal, Garrett; Capelli, Cristian

    2015-01-01

    The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variety of American, European and African populations to determine the contributions of different ancestral populations to the Americas. Our results provide a fine-scale characterization of the source populations, identify a series of novel, previously unreported contributions from Africa and Europe and highlight geohistorical structure in the ancestry of American admixed populations. PMID:25803618

  14. Unravelling the hidden ancestry of American admixed populations.

    PubMed

    Montinaro, Francesco; Busby, George B J; Pascali, Vincenzo L; Myers, Simon; Hellenthal, Garrett; Capelli, Cristian

    2015-03-24

    The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variety of American, European and African populations to determine the contributions of different ancestral populations to the Americas. Our results provide a fine-scale characterization of the source populations, identify a series of novel, previously unreported contributions from Africa and Europe and highlight geohistorical structure in the ancestry of American admixed populations.

  15. Simultaneous Correlative Scanning Electron and High-NA Fluorescence Microscopy

    PubMed Central

    Liv, Nalan; Zonnevylle, A. Christiaan; Narvaez, Angela C.; Effting, Andries P. J.; Voorneveld, Philip W.; Lucas, Miriam S.; Hardwick, James C.; Wepf, Roger A.; Kruit, Pieter; Hoogenboom, Jacob P.

    2013-01-01

    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. PMID:23409024

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

    SciTech Connect

    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.

  17. The application of high-speed digital image correlation.

    SciTech Connect

    Reu, Phillip L.; Miller, Timothy J.

    2008-02-01

    Digital image correlation (DIC) is a method of using digital images to calculate two-dimensional displacement and deformation or for stereo systems three-dimensional shape, displacement, and deformation. While almost any imaging system can be used with DIC, there are some important challenges when working with the technique in high- and ultra-high-speed applications. This article discusses three of these challenges: camera sensor technology, camera frame rate, and camera motion mitigation. Potential solutions are treated via three demonstration experiments showing the successful application of high-speed DIC for dynamic events. The application and practice of DIC at high speeds, rather than the experimental results themselves, provide the main thrust of the discussion.

  18. Testing for non-random mating: evidence for ancestry-related assortative mating in the Framingham heart study.

    PubMed

    Sebro, Ronnie; Hoffman, Thomas J; Lange, Christoph; Rogus, John J; Risch, Neil J

    2010-11-01

    Population stratification leads to a predictable phenomenon-a reduction in the number of heterozygotes compared to that calculated assuming Hardy-Weinberg Equilibrium (HWE). We show that population stratification results in another phenomenon-an excess in the proportion of spouse-pairs with the same genotypes at all ancestrally informative markers, resulting in ancestrally related positive assortative mating. We use principal components analysis to show that there is evidence of population stratification within the Framingham Heart Study, and show that the first principal component correlates with a North-South European cline. We then show that the first principal component is highly correlated between spouses (r = 0.58, p = 0.0013), demonstrating that there is ancestrally related positive assortative mating among the Framingham Caucasian population. We also show that the single nucleotide polymorphisms loading most heavily on the first principal component show an excess of homozygotes within the spouses, consistent with similar ancestry-related assortative mating in the previous generation. This nonrandom mating likely affects genetic structure seen more generally in the North American population of European descent today, and decreases the rate of decay of linkage disequilibrium for ancestrally informative markers.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Ancient west Eurasian ancestry in southern and eastern Africa

    PubMed Central

    Pickrell, Joseph K.; Patterson, Nick; Loh, Po-Ru; Lipson, Mark; Berger, Bonnie; Stoneking, Mark; Pakendorf, Brigitte; Reich, David

    2014-01-01

    The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa. PMID:24550290

  1. High intensity positron beam and angular correlation experiments at Livermore

    SciTech Connect

    Howell, R.H.; Rosenberg, I.J.; Meyer, P.; Fluss, M.J.

    1985-03-01

    A positron beam apparatus that produces a variable energy positron beam with sufficient intensity to perform new positron experiments in an ultrahigh vacuum environment has been installed at the Lawrence Livermore 100 MeV electron linac. We have installed two large area position sensitive gamma-ray detectors to measure angular correlations in two dimensions and a separate highly collimated detector to measure positronium energy distributions by time-of-flight velocity determination. Data from measurements on single crystals of Cu will be described.

  2. Suicidal ideation in high school students: depression and other correlates.

    PubMed

    De Man, A F; Leduc, C P

    1995-03-01

    English-Canadian high school students (129 boys, 117 girls) participated in a study of the relationship between suicidal ideation and selected personal variables, stress, and social support. Associations were found between suicidal ideation and the variables of gender, self-esteem, locus of control, depression, drug use, stress, perception of health, family status, academic performance, social support, and anomie. Multiple regression analysis identified depression and alcohol use as best individual predictors among these variables. Semi-partial correlation analyses showed that removal of the effect of depression resulted in a loss of initially significant relationships between suicidal ideation and the other variables except for alcohol use, drug use, and health satisfaction.

  3. Differences in vaginal microbiome in African American women versus women of European ancestry.

    PubMed

    Fettweis, Jennifer M; Brooks, J Paul; Serrano, Myrna G; Sheth, Nihar U; Girerd, Philippe H; Edwards, David J; Strauss, Jerome F; Jefferson, Kimberly K; Buck, Gregory A

    2014-10-01

    Women of European ancestry are more likely to harbour a Lactobacillus-dominated microbiome, whereas African American women are more likely to exhibit a diverse microbial profile. African American women are also twice as likely to be diagnosed with bacterial vaginosis and are twice as likely to experience preterm birth. The objective of this study was to further characterize and contrast the vaginal microbial profiles in African American versus European ancestry women. Through the Vaginal Human Microbiome Project at Virginia Commonwealth University, 16S rRNA gene sequence analysis was used to compare the microbiomes of vaginal samples from 1268 African American women and 416 women of European ancestry. The results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences. Major community types were dominated by Gardnerella vaginalis and the uncultivated bacterial vaginosis-associated bacterium-1 (BVAB1) that were common among African Americans. Moreover, the prevalence of multiple bacterial taxa that are associated with microbial invasion of the amniotic cavity and preterm birth, including Mycoplasma, Gardnerella, Prevotella and Sneathia, differed between the two ethnic groups. We investigated the contributions of intrinsic and extrinsic factors, including pregnancy, body mass index, diet, smoking and alcohol use, number of sexual partners, and household income, to vaginal community composition. Ethnicity, pregnancy and alcohol use correlated significantly with the relative abundance of bacterial vaginosis-associated species. Trends between microbial profiles and smoking and number of sexual partners were observed; however, these associations were not statistically significant. These results support and extend previous findings that there are significant differences in the vaginal microbiome related to ethnicity and demonstrate that these differences are pronounced even in healthy women.

  4. High correlations between temperature and nitric oxide in the thermosphere

    NASA Astrophysics Data System (ADS)

    Weimer, D. R.; Mlynczak, M. G.; Hunt, L. A.; Tobiska, W. Kent

    2015-07-01

    Obtaining accurate predictions of the neutral density in the thermosphere has been a long-standing problem. During geomagnetic storms the auroral heating in the polar ionospheres quickly raises the temperature of the thermosphere, resulting in higher neutral densities that exert a greater drag force on objects in low Earth orbit. Rapid increases and decreases in the temperature and density may occur within a couple days. A key parameter in the thermosphere is the total amount of nitric oxide (NO). The production of NO is accelerated by the auroral heating, and since NO is an efficient radiator of thermal energy, higher concentrations of this molecule accelerate the rate at which the thermosphere cools. This paper describes an improved technique that calculates changes in the global temperature of the thermosphere. Starting from an empirical model of the Poynting flux into the ionosphere, a set of differential equations derives the minimum, global value of the exospheric temperature, which can be used in a neutral density model to calculate the global values. The relative variations in NO content are used to obtain more accurate cooling rates. Comparisons with the global rate of NO emissions that are measured with the Sounding of the Atmosphere using Broadband Emission Radiometry instrument show that there is very good agreement with the predicted values. The NO emissions correlate highly with the total auroral heating that has been integrated over time. We also show that the NO emissions are highly correlated with thermospheric temperature, as well as indices of solar extreme ultraviolet radiation.

  5. Spatial Instabilities, Homogeneities and Proximity Effects: Highly Correlated Metals

    SciTech Connect

    Dynes, Robert C.

    2008-10-31

    We have developed a superconducting scanning tunneling microscope (S-STM) which is a direct and local probe of the pair wave function of superconducting materials via the Josephson effect and quasiparticle spectra via scanning tunneling spectroscopy (STS). The novel feature of this device is a superconducting tip (Pb with an Ag capping layer) in close proximity to a superconducting sample to form a superconductor-insulator-superconductor (SIS) tunnel junction. The operation of this S-STM has been verified in the observation of Josephson tunneling between the tip and different sample systems including Pb films and NbSe{sub 2}. This instrument was employed in the study of High T{sub c} superconductors and spatial inhomogeneities. The major accomplishments in the current grant period are observations of c-axis Josephson tunneling between a conventional superconductor (Pb) and variously doped BSSCO samples. These observations are reported: (1) C-axis Josephson couplings between Pb and both OP and OV-BSCCO. This is surprising if BSCCO is strictly a d-wave superconductor; (2) ICRN of the OP sample seemed to be much smaller than those of OV samples; (3) ICRN inhomogeneity is correlated with the gap inhomogeneity on the length scale of ξ in the OV samples; (4) Inverse correlation between ICRN and Δ in OV samples; (5) Degradations of the superconductivity of BSCCO by high current density.

  6. High correlations between temperature and nitric oxide in the thermosphere.

    PubMed

    Weimer, D R; Mlynczak, M G; Hunt, L A; Tobiska, W Kent

    2015-07-01

    Obtaining accurate predictions of the neutral density in the thermosphere has been a long-standing problem. During geomagnetic storms the auroral heating in the polar ionospheres quickly raises the temperature of the thermosphere, resulting in higher neutral densities that exert a greater drag force on objects in low Earth orbit. Rapid increases and decreases in the temperature and density may occur within a couple days. A key parameter in the thermosphere is the total amount of nitric oxide (NO). The production of NO is accelerated by the auroral heating, and since NO is an efficient radiator of thermal energy, higher concentrations of this molecule accelerate the rate at which the thermosphere cools. This paper describes an improved technique that calculates changes in the global temperature of the thermosphere. Starting from an empirical model of the Poynting flux into the ionosphere, a set of differential equations derives the minimum, global value of the exospheric temperature, which can be used in a neutral density model to calculate the global values. The relative variations in NO content are used to obtain more accurate cooling rates. Comparisons with the global rate of NO emissions that are measured with the Sounding of the Atmosphere using Broadband Emission Radiometry instrument show that there is very good agreement with the predicted values. The NO emissions correlate highly with the total auroral heating that has been integrated over time. We also show that the NO emissions are highly correlated with thermospheric temperature, as well as indices of solar extreme ultraviolet radiation.

  7. Exploring the Y Chromosomal Ancestry of Modern Panamanians

    PubMed Central

    Grugni, Viola; Battaglia, Vincenza; Perego, Ugo Alessandro; Raveane, Alessandro; Lancioni, Hovirag; Olivieri, Anna; Ferretti, Luca; Woodward, Scott R.; Pascale, Juan Miguel; Cooke, Richard; Myres, Natalie; Motta, Jorge; Torroni, Antonio; Achilli, Alessandro; Semino, Ornella

    2015-01-01

    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 geographically

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

    PubMed Central

    Soares, Pedro; Garcia, Gissel; Perez, Ana B.; Aguirre, Eglys; Cavadas, Bruno; Regnault, Béatrice; Alvarez, Mayling; Ruiz, Didye; Guzman, Maria G.

    2017-01-01

    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. PMID:28241052

  9. High speed displacement analysis using digital speckle correlation

    NASA Astrophysics Data System (ADS)

    Siebert, T.; Splitthof, K.; Becker, T.; Krupka, R.

    2006-06-01

    Digital speckle correlation techniques have already been successfully proven for accurate displacement analysis. With the use of two cameras, three dimensional measurements of contours and displacements can be carried out. The principle of this technique is pretty easy to understood and realized, opening a nearly unlimited range of applications. Rapid new developments in the field of digital imaging and computer technology, especially for very much dynamic applications, opens further applications for these measurement method up to high speed deformation and strain analysis, e.g. in the fields of, material testing, fracture mechanics, high speed testing, advanced materials and component testing. The dynamic range is combined with the capability to measure very large strains (up to more than 100%). The resolution of the deformation in space and time opens a wide range of applications for vibration analysis of objects. Since the system determines the absolute position and displacements of the object in space it is capable of measuring high amplitudes and even objects with rigid body movements, which is a big advantage against full field ESPI systems. The absolute resolution depends on the field of view and is scalable. Calibration of the optical setup is a crucial point which will be discussed in detail. Examples of the analysis of high speed harmonic vibration and transient events out of material research and industrial applications are presented. Results of measurement performed on a vibrating membrane and a tensile test sample are show typical features of the system.

  10. Examining population stratification via individual ancestry estimates versus self-reported race.

    PubMed

    Barnholtz-Sloan, Jill S; Chakraborty, Ranajit; Sellers, Thomas A; Schwartz, Ann G

    2005-06-01

    Population stratification has the potential to affect the results of genetic marker studies. Estimating individual ancestry provides a continuous measure to assess population structure in case-control studies of complex disease, instead of using self-reported racial groups. We estimate individual ancestry using the Federal Bureau of Investigation CODIS Core short tandem repeat set of 13 loci using two different analysis methods in a case-control study of early-onset lung cancer. Individual ancestry proportions were estimated for "European" and "West African" groups using published allele frequencies. The majority of Caucasian, non-Hispanics had >50% European ancestry, whereas the majority of African Americans had <20% European ancestry, regardless of ancestry estimation method, although significant overlap by self-reported race and ancestry also existed. When we further investigated the effect of ancestry and self-reported race on the frequency of a lung cancer risk genotype, we found that the frequency of the GSTM1 null genotype varies by individual European ancestry and case-control status within self-reported race (particularly for African Americans). Genetic risk models showed that adjusting for individual European ancestry provided a better fit to the data compared with the model with no group adjustment or adjustment for self-reported race. This study suggests that significant population substructure differences exist that self-reported race alone does not capture and that individual ancestry may be confounded with disease status and/or a candidate gene risk genotype.

  11. Estimating ancestry and heterozygosity of hybrids using molecular markers

    PubMed Central

    2012-01-01

    Background Hybridization, genetic mixture of distinct populations, gives rise to myriad recombinant genotypes. Characterizing the genomic composition of hybrids is critical for studies of hybrid zone dynamics, inheritance of traits, and consequences of hybridization for evolution and conservation. Hybrid genomes are often summarized either by an estimate of the proportion of alleles coming from each ancestral population or classification into discrete categories like F1, F2, backcross, or merely “hybrid” vs. “pure”. In most cases, it is not realistic to classify individuals into the restricted set of classes produced in the first two generations of admixture. However, the continuous ancestry index misses an important dimension of the genotype. Joint consideration of ancestry together with interclass heterozygosity (proportion of loci with alleles from both ancestral populations) captures all of the information in the discrete classification without the unrealistic assumption that only two generations of admixture have transpired. Methods I describe a maximum likelihood method for joint estimation of ancestry and interclass heterozygosity. I present two worked examples illustrating the value of the approach for describing variation among hybrid populations and evaluating the validity of the assumption underlying discrete classification. Results Naively classifying natural hybrids into the standard six line cross categories can be misleading, and false classification can be a serious problem for datasets with few molecular markers. My analysis underscores previous work showing that many (50 or more) ancestry informative markers are needed to avoid erroneous classification. Conclusion Although classification of hybrids might often be misleading, valuable inferences can be obtained by focusing directly on distributions of ancestry and heterozygosity. Estimating and visualizing the joint distribution of ancestry and interclass heterozygosity is an effective way

  12. Genomic Variation of Inbreeding and Ancestry in the Remaining Two Isle Royale Wolves.

    PubMed

    Hedrick, Philip W; Kardos, Marty; Peterson, Rolf O; Vucetich, John A

    2016-12-11

    Inbreeding, relatedness, and ancestry have traditionally been estimated with pedigree information, however, molecular genomic data can provide more detailed examination of these properties. For example, pedigree information provides estimation of the expected value of these measures but molecular genomic data can estimate the realized values of these measures in individuals. Here, we generate the theoretical distribution of inbreeding, relatedness, and ancestry for the individuals in the pedigree of the Isle Royale wolves, the first examination of such variation in a wild population with a known pedigree. We use the 38 autosomes of the dog genome and their estimated map lengths in our genomic analysis. Although it is known that the remaining wolves are highly inbred, closely related, and descend from only 3 ancestors, our analyses suggest that there is significant variation in the realized inbreeding and relatedness around pedigree expectations. For example, the expected inbreeding in a hypothetical offspring from the 2 remaining wolves is 0.438 but the realized 95% genomic confidence interval is from 0.311 to 0.565. For individual chromosomes, a substantial proportion of the whole chromosomes are completely identical by descent. This examination provides a background to use when analyzing molecular genomic data for individual levels of inbreeding, relatedness, and ancestry. The level of variation in these measures is a function of the time to the common ancestor(s), the number of chromosomes, and the rate of recombination. In the Isle Royale wolf population, the few generations to a common ancestor results in the high variance in genomic inbreeding.

  13. West African and Amerindian ancestry and risk of myocardial infarction and metabolic syndrome in the Central Valley population of Costa Rica.

    PubMed

    Ruiz-Narváez, Edward A; Bare, Lance; Arellano, Andre; Catanese, Joseph; Campos, Hannia

    2010-06-01

    Genetic ancestry and environmental factors may contribute to the ethnic differences in risk of coronary heart disease (CHD), metabolic syndrome (MS) or its individual components. The population of the Central Valley of Costa Rica offers a unique opportunity to assess the role of genetic ancestry in these chronic diseases because it derived from the admixture of a relatively small number of founders of Southern European, Amerindian, and West African origin. We aimed to determine whether genetic ancestry is associated with risk of myocardial infarction (MI), MS and its individual components in the Central Valley of Costa Rica. We genotyped 39 ancestral informative markers in cases (n = 1,998) with a first non-fatal acute MI and population-based controls (n = 1,998) matched for age, sex, and area of residence, to estimate individual ancestry proportions. Odds ratios (ORs) and 95% confidence intervals (95% CI) were estimated using conditional (MI) and unconditional (MS and its components) logistic regression adjusting for relevant confounders. Mean individual ancestry proportions in cases and controls were 57.5 versus 57.8% for the Southern European, 38.4 versus 38.3% for the Amerindian and 4.1 versus 3.8% for the West African ancestry. Compared with Southern European ancestry, each 10% increase in West African ancestry was associated with a 29% increase in MI, OR (95% CI) = 1.29 (1.07, 1.56), and with a 30% increase on the risk of hypertension, OR (95% CI) = 1.30 (1.00, 1.70). Each 10% increase in Amerindian ancestry was associated with a 14% increase on the risk of MS, OR (95% CI) = 1.14 (1.00, 1.30), and 20% increase on the risk of impaired fasting glucose, OR (95% CI) = 1.20 (1.01, 1.42). These results show that the high variability of admixture proportions in the Central Valley population offers a unique opportunity to uncover the genetic basis of ethnic differences on the risk of disease.

  14. A methodology for high resolution digital image correlation in high temperature experiments

    NASA Astrophysics Data System (ADS)

    Blaber, Justin; Adair, Benjamin S.; Antoniou, Antonia

    2015-03-01

    We propose a methodology for performing high resolution Digital Image Correlation (DIC) analysis during high-temperature mechanical tests. Specifically, we describe a technique for producing a stable, high-quality pattern on metal surfaces along with a simple optical system that uses a visible-range camera and a long-range microscope. The results are analyzed with a high-quality open-source DIC software developed by us. Using the proposed technique, we successfully acquired high-resolution strain maps of the crack tip field in a nickel superalloy sample at 1000 °C.

  15. Absorption and loss of iron in toddlers are highly correlated.

    PubMed

    Fomon, Samuel J; Nelson, Steven E; Serfass, Robert E; Ziegler, Ekhard E

    2005-04-01

    For estimating the requirements for dietary iron, it is important to know the amount of iron that is lost from the body. Inevitable losses of iron have been determined in adult humans but not in infants or children. We administered (58)Fe, the least abundant stable isotope of iron, to free-living infants at 168 d of age (5.6 mo) and followed them to age 26 mo. There was no dietary restriction after isotope administration. Blood was obtained at regular intervals for determination of isotopic enrichment and indices of iron status. We estimated the quantity of circulating iron, noncirculating active iron, and storage iron at each age. The administered isotope equilibrated with total body iron by 13 mo of age. From 13 to 26 mo of age, we estimated inevitable loss and absorption of iron from the change in tracer abundance in circulating iron. The rate of decrease of tracer abundance was proportional to addition of tracee, i.e., absorption of iron. Conversely, the rate of decrease in quantity of tracer was proportional to removal of tracee, i.e., loss of iron. From 13 to 26 mo of age, iron absorption was (mean +/- SD) 0.49 +/- 0.13 mg/d and inevitable iron loss was 0.25 +/- 0.12 mg/d. Intersubject variability of iron loss and iron absorption was high, and iron loss and absorption were highly correlated (r = 0.789, P < 0.001). Iron stores were low throughout the study and decreased significantly from 13 to 26 mo of age, suggesting that iron absorption from the diet was inadequate to maintain or increase iron nutritional status. The data suggest that, in this cohort, which may be representative, the intake of bioavailable iron from 13 to 26 mo of age was insufficient to maintain iron nutritional status.

  16. Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets.

    PubMed

    Vongpaisarnsin, Kornkiat; Listman, Jennifer Beth; Malison, Robert T; Gelernter, Joel

    2015-07-01

    The main purpose of this work was to identify a set of AIMs that stratify the genetic structure and diversity of the Thai population from a high-throughput autosomal genome-wide association study. In this study, more than one million SNPs from the international HapMap database and the Thai depression genome-wide association study have been examined to identify ancestry informative markers (AIMs) that distinguish between Thai populations. An efficient strategy is proposed to identify and characterize such SNPs and to test high-resolution SNP data from international HapMap populations. The best AIMs are identified to stratify the population and to infer genetic ancestry structure. A total of 124 AIMs were clearly clustered geographically across the continent, whereas only 89 AIMs stratified the Thai population from East Asian populations. Finally, a set of 273 AIMs was able to distinguish northern from southern Thai subpopulations. These markers will be of particular value in identifying the ethnic origins in regions where matching by self-reports is unavailable or unreliable, which usually occurs in real forensic cases.

  17. Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs.

    PubMed

    Huson, Heather J; vonHoldt, Bridgett M; Rimbault, Maud; Byers, Alexandra M; Runstadler, Jonathan A; Parker, Heidi G; Ostrander, Elaine A

    2012-02-01

    Alaskan sled dogs are a genetically distinct population shaped by generations of selective interbreeding with purebred dogs to create a group of high-performance athletes. As a result of selective breeding strategies, sled dogs present a unique opportunity to employ admixture-mapping techniques to investigate how breed composition and trait selection impact genomic structure. We used admixture mapping to investigate genetic ancestry across the genomes of two classes of sled dogs, sprint and long-distance racers, and combined that with genome-wide association studies (GWAS) to identify regions that correlate with performance-enhancing traits. The sled dog genome is enhanced by differential contributions from four non-admixed breeds (Alaskan Malamute, Siberian Husky, German Shorthaired Pointer, and Borzoi). A principal components analysis (PCA) of 115,000 genome-wide SNPs clearly resolved the sprint and distance populations as distinct genetic groups, with longer blocks of linkage disequilibrium (LD) observed in the distance versus sprint dogs (7.5-10 and 2.5-3.75 kb, respectively). Furthermore, we identified eight regions with the genomic signal from either a selective sweep or an association analysis, corroborated by an excess of ancestry when comparing sprint and distance dogs. A comparison of elite and poor-performing sled dogs identified a single region significantly associated with heat tolerance. Within the region we identified seven SNPs within the myosin heavy chain 9 gene (MYH9) that were significantly associated with heat tolerance in sprint dogs, two of which correspond to conserved promoter and enhancer regions in the human ortholog.

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

    PubMed

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

    2017-01-30

    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.

  19. [Physical growth in stature of school children of Japanese ancestry in the city of São Paulo, Brazil

    PubMed

    Kac; Santos

    1996-04-01

    This paper reports the results of a cross-sectional survey describing the growth in stature of a sample of school children of Japanese ancestry (three or four grandparents born in Japan) and of high socio-economic status living in São Paulo, Brazil. The sample comprises 124 individuals 7-10 years of age, of both sexes. The results show that the children present mean values of stature below the median values of the NCHS curves ("National Center for Health Statistics", U.S.A.). The values are similar to the medians of a sample of Japanese children and below those of well-to-do Brazilian children of non-Japanese ancestry studied by the PNSN ("Pesquisa Nacional sobre Saúde e Nutrição", Brazil). The findings do not support the hypothesis of uniformity of growth potential in stature, casting doubts on the utilization of a single anthropometric reference in the assessment of nutritional status.

  20. Ancestry Matters: Patrilineage Growth and Extinction

    PubMed Central

    Song, Xi; Campbell, Cameron D.; Lee, James Z.

    2016-01-01

    Patrilineality, the organization of kinship, inheritance, and other key social processes based on patrilineal male descent, has been a salient feature of social organization in China and many other societies for centuries. Because continuity or growth of the patrilineage was the central focus of reproductive strategies in such societies, we introduce the number of patrilineal male descendants generations later as a stratification outcome. By reconstructing and analyzing 20,000 patrilineages in two prospective, multi-generational population databases from 18th and 19th century China, we show that patrilineages founded by high status males had higher growth rates for the next 150 years. The elevated growth rate of these patrilineages was due more to their having a lower probability of extinction at each point in time than to surviving patrilineal male descendants having larger numbers of sons on average. As a result, patrilineal male descendants of high status males account for a disproportionately large share of the male population in later generations. In China and elsewhere, patrilineal kin network characteristics influence individuals’ life chances; thus effects of a male founder’s characteristics on patrilineage size many generations later represent an indirect channel of status transmission that has not been considered previously. PMID:27041745

  1. Developmental validation of mitochondrial DNA genotyping assays for adept matrilineal inference of biogeographic ancestry at a continental level.

    PubMed

    Chaitanya, Lakshmi; van Oven, Mannis; Weiler, Natalie; Harteveld, Joyce; Wirken, Laura; Sijen, Titia; de Knijff, Peter; Kayser, Manfred

    2014-07-01

    Mitochondrial DNA (mtDNA) can be used for matrilineal biogeographic ancestry prediction and can thus provide investigative leads towards identifying unknown suspects, when conventional autosomal short tandem repeat (STR) profiling fails to provide a match. Recently, six multiplex genotyping assays targeting 62 ancestry-informative mitochondrial single nucleotide polymorphisms (mt-SNPs) were developed. This hierarchical system of assays allows detection of the major haplogroups present in Africa, America, Western Eurasia, Eastern Eurasia, Australia and Oceania, thus revealing the broad geographic region of matrilineal origin of a DNA donor. Here, we provide a forensic developmental validation study of five multiplex assays targeting all the 62 ancestry-informative mt-SNPs following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. We demonstrate that the assays are highly sensitive; being able to produce full profiles at input DNA amounts of as little as 1pg. The assays were shown to be highly robust and efficient in providing information from degraded samples and from simulated casework samples of different substrates such as blood, semen, hair, saliva and trace DNA samples. Reproducible results were successfully achieved from concordance testing across three independent laboratories depicting the ease and reliability of these assays. Overall, our results demonstrate the suitability of these five mt-SNP assays for application to forensic casework and other purposes aiming to establish an individual's matrilineal genetic ancestry. With this validated tool, it is now possible to determine the matrilineal biogeographic origin of unknown individuals on the level of continental resolution from forensic DNA samples to provide investigative leads in criminal and missing person cases where autosomal STR profiling is uninformative.

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

    PubMed Central

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

    SciTech Connect

    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.

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

    PubMed

    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.

  5. Admixture dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South American population isolate.

    PubMed

    Bedoya, Gabriel; Montoya, Patricia; García, Jenny; Soto, Ivan; Bourgeois, Stephane; Carvajal, Luis; Labuda, Damian; Alvarez, Victor; Ospina, Jorge; Hedrick, Philip W; Ruiz-Linares, Andrés

    2006-05-09

    Although it is well established that Hispanics generally have a mixed Native American, African, and European ancestry, the dynamics of admixture at the foundation of Hispanic populations is heterogeneous and poorly documented. Genetic analyses are potentially very informative for probing the early demographic history of these populations. Here we evaluate the genetic structure and admixture dynamics of a province in northwest Colombia (Antioquia), which prior analyses indicate was founded mostly by Spanish men and native women. We examined surname, Y chromosome, and mtDNA diversity in a geographically structured sample of the region and obtained admixture estimates with highly informative autosomal and X chromosome markers. We found evidence of reduced surname diversity and support for the introduction of several common surnames by single founders, consistent with the isolation of Antioquia after the colonial period. Y chromosome and mtDNA data indicate little population substructure among founder Antioquian municipalities. Interestingly, despite a nearly complete Native American mtDNA background, Antioquia has a markedly predominant European ancestry at the autosomal and X chromosome level, which suggests that, after foundation, continuing admixture with Spanish men (but not with native women) increased the European nuclear ancestry of Antioquia. This scenario is consistent with historical information and with results from population genetics theory.

  6. Admixture dynamics in Hispanics: A shift in the nuclear genetic ancestry of a South American population isolate

    PubMed Central

    Bedoya, Gabriel; Montoya, Patricia; García, Jenny; Soto, Ivan; Bourgeois, Stephane; Carvajal, Luis; Labuda, Damian; Alvarez, Victor; Ospina, Jorge; Hedrick, Philip W.; Ruiz-Linares, Andrés

    2006-01-01

    Although it is well established that Hispanics generally have a mixed Native American, African, and European ancestry, the dynamics of admixture at the foundation of Hispanic populations is heterogeneous and poorly documented. Genetic analyses are potentially very informative for probing the early demographic history of these populations. Here we evaluate the genetic structure and admixture dynamics of a province in northwest Colombia (Antioquia), which prior analyses indicate was founded mostly by Spanish men and native women. We examined surname, Y chromosome, and mtDNA diversity in a geographically structured sample of the region and obtained admixture estimates with highly informative autosomal and X chromosome markers. We found evidence of reduced surname diversity and support for the introduction of several common surnames by single founders, consistent with the isolation of Antioquia after the colonial period. Y chromosome and mtDNA data indicate little population substructure among founder Antioquian municipalities. Interestingly, despite a nearly complete Native American mtDNA background, Antioquia has a markedly predominant European ancestry at the autosomal and X chromosome level, which suggests that, after foundation, continuing admixture with Spanish men (but not with native women) increased the European nuclear ancestry of Antioquia. This scenario is consistent with historical information and with results from population genetics theory. PMID:16648268

  7. Polymorphisms of Estrogen Metabolism-Related Genes and Prostate Cancer Risk in Two Populations of African Ancestry

    PubMed Central

    Emeville, Elise; Ferdinand, Séverine; Punga, Augustin; Lufuma, Simon; Blanchet, Pascal; Romana, Marc; Multigner, Luc

    2016-01-01

    Background Estrogens are thought to play a critical role in prostate carcinogenesis. It has been suggested that polymorphisms of genes encoding enzymes involved in estrogen metabolism are risk factors for prostate cancer. However, few studies have been performed on populations of African ancestry, which are known to have a high risk of prostate cancer. Objective We investigated whether functional polymorphisms of CYP17, CYP19, CYP1B1, COMT and UGT1A1 affected the risk of prostate cancer in two different populations of African ancestry. Methods In Guadeloupe (French West Indies), we compared 498 prostate cancer patients and 565 control subjects. In Kinshasa (Democratic Republic of Congo), 162 prostate cancer patients were compared with 144 controls. Gene polymorphisms were determined by the SNaPshot technique or short tandem repeat PCR analysis. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Results The AA genotype and the A allele of rs4680 (COMT) appeared to be inversely associated with the risk of prostate cancer in adjusted models for both Afro-Caribbean and native African men. For the A allele, a significant inverse association was observed among cases with low-grade Gleason scores and localized clinical stage, in both populations. Conclusions These preliminary results support the hypothesis that polymorphisms of genes encoding enzymes involved in estrogen metabolism may modulate the risk of prostate cancer in populations of African ancestry. PMID:27074016

  8. IL1B-CGTC haplotype is associated with colorectal cancer in admixed individuals with increased African ancestry

    PubMed Central

    Sanabria-Salas, María Carolina; Hernández-Suárez, Gustavo; Umaña-Pérez, Adriana; Rawlik, Konrad; Tenesa, Albert; Serrano-López, Martha Lucía; Sánchez de Gómez, Myriam; Rojas, Martha Patricia; Bravo, Luis Eduardo; Albis, Rosario; Plata, José Luis; Green, Heather; Borgovan, Theodor; Li, Li; Majumdar, Sumana; Garai, Jone; Lee, Edward; Ashktorab, Hassan; Brim, Hassan; Li, Li; Margolin, David; Fejerman, Laura; Zabaleta, Jovanny

    2017-01-01

    Single-nucleotide polymorphisms (SNPs) in cytokine genes can affect gene expression and thereby modulate inflammation and carcinogenesis. However, the data on the association between SNPs in the interleukin 1 beta gene (IL1B) and colorectal cancer (CRC) are conflicting. We found an association between a 4-SNP haplotype block of the IL1B (-3737C/-1464G/-511T/-31C) and CRC risk, and this association was exclusively observed in individuals with a higher proportion of African ancestry, such as individuals from the Coastal Colombian region (odds ratio, OR 2.06; 95% CI 1.31–3.25; p < 0.01). Moreover, a significant interaction between this CRC risk haplotype and local African ancestry dosage was identified in locus 2q14 (p = 0.03). We conclude that Colombian individuals with high African ancestry proportions at locus 2q14 harbour more IL1B-CGTC copies and are consequently at an increased risk of CRC. This haplotype has been previously found to increase the IL1B promoter activity and is the most frequent haplotype in African Americans. Despite of limitations in the number of samples and the lack of functional analysis to examine the effect of these haplotypes on CRC cell lines, our results suggest that inflammation and ethnicity play a major role in the modulation of CRC risk. PMID:28157220

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

    PubMed

    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.

  10. High-Stakes & Assessment Innovation: A Negative Correlation? Research Report.

    ERIC Educational Resources Information Center

    Ananda, Sri; Rabinowitz, Stanley

    This paper makes the case that, as implemented so far, there has been an inverse correlation between innovation and accountability in statewide assessment systems. The higher the stakes attached to the assessment results, the more conservative the assessment methodology ultimately used. Case studies of two state assessment programs were carried…

  11. HIGH PERPENDICULAR CHARGED PARTICLES AZIMUTHAL CORRELATION IN PHENIX.

    SciTech Connect

    RAK,J. FOR THE PHENIX COLLABORATION

    2002-01-13

    A two-particle azimuthal correlation analysis of the PHENIX data taken at {radical}s{sub NN} = 130 GeV/c is discussed. A comparison of the magnitude of v{sub 2}(p{perpendicular}) extracted from the correlation analysis with those obtained from a reaction plane analysis by the STAR collaboration, indicate surprisingly small non-flow contributions. A similar comparison obtained from the CERES experiment at {radical}s{sub NN} = 17 GeV/c shows stronger non-flow contributions for a similar p{perpendicular}-range which can be attributed to the presence of mini-jets. It is argued that for the p{perpendicular}-range below 2-3 GeV/c the RHIC results may be indicative of a novel particle production mechanism related to low-x gluon saturation.

  12. New World cattle show ancestry from multiple independent domestication events

    PubMed Central

    McTavish, Emily Jane; Decker, Jared E.; Schnabel, Robert D.; Taylor, Jeremy F.; Hillis, David M.

    2013-01-01

    Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment. PMID:23530234

  13. New World cattle show ancestry from multiple independent domestication events.

    PubMed

    McTavish, Emily Jane; Decker, Jared E; Schnabel, Robert D; Taylor, Jeremy F; Hillis, David M

    2013-04-09

    Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment.

  14. Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries.

    PubMed

    Goodman, Morris; Sterner, Kirstin N; Islam, Munirul; Uddin, Monica; Sherwood, Chet C; Hof, Patrick R; Hou, Zhuo-Cheng; Lipovich, Leonard; Jia, Hui; Grossman, Lawrence I; Wildman, Derek E

    2009-12-08

    Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed approximately 6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage.

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

    PubMed Central

    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

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

    PubMed

    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.

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

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    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.

  19. Age at breast cancer diagnosis in populations of african and European ancestry.

    PubMed

    Kadhel, Philippe; Multigner, Luc

    2014-01-01

    Based on US national cancer registry data, age differences at breast cancer diagnosis have been reported between African-American women and European-American women. Such differences between populations of African and European ancestry have not been studied in other countries at a nationwide level. Here, we report and compare descriptive nationwide epidemiological indicators of invasive breast cancer for the populations of European ancestry living in the US and in mainland France and for women of African ancestry living in the US and in the French West Indies (Martinique and Guadeloupe). Based on the available data, we determined age frequency distributions, world age-standardized incidence, and the distribution of expected cases of breast cancer in a standard population of women by age. The age frequency distributions revealed that women of African ancestry were younger at diagnosis than women of European ancestry. By contrast, compared with the US regardless of ancestry and mainland France, the standardized incidences appeared lower, and the largest numbers of expected cases younger, in the French West Indies. The populations with African ancestry were not homogeneous in terms of epidemiologic indicators of age-related breast cancer. These descriptive findings suggest that populations of African ancestry cannot be considered uniform when determining whether it would be appropriate to decrease the age of entry into screening programs for breast cancer.

  20. Race and Ancestry in the Age of Inclusion: Technique and Meaning in Post-Genomic Science

    PubMed Central

    Shim, Janet K.; Ackerman, Sara L.; Darling, Katherine Weatherford; Hiatt, Robert A.; Lee, Sandra Soo-Jin

    2015-01-01

    This paper examines how race and ancestry are taken up in gene-environment interaction (GEI) research on complex diseases such as heart disease, diabetes, and cancer. Using 54 in-depth interviews of 33 scientists and over 200 hours of observation at scientific conferences, we explore how GEI researchers use and interpret race, ethnicity, and ancestry in their work. We find that the use of self-identified race and ethnicity (SIRE) exists alongside ancestry informative markers (AIMs) to ascertain genetic ancestry. Our participants assess the utility of these two techniques in relative terms, downplaying the accuracy and value of SIRE compared to the precision and necessity of AIMs. In doing so, we argue that post-genomic scientists seeking to understand the interactions of genetic and environmental disease determinants actually undermine their ability to do so, by valorizing precise characterizations of individuals’ genetic ancestry over measurement of the social processes and relations that differentiate social groups. PMID:25378251

  1. Ancestry Estimation and Control of Population Stratification for Sequence-based Association Studies

    PubMed Central

    Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y.; Branham, Kari E.; Heckenlively, John; Fulton, Robert; Wilson, Richard K.; Mardis, Elaine R.; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R.

    2014-01-01

    Knowledge of individual ancestry is important for genetic association studies where population structure leads to false positive signals. Estimating individual ancestry with targeted sequence data, which constitutes the bulk of current sequence datasets, is challenging. Here, we propose a new method for accurate estimation of genetic ancestry. Our method skips genotype calling and directly analyzes sequence reads. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry with whole genome shotgun coverage as low as 0.001X. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1X. At an even finer-scale, the method improves discrimination between exome-sequenced participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and reduce the risk of spurious findings due to population structure. PMID:24633160

  2. Characterizing highly correlated video traffic in high-speed asynchronous transfer mode networks

    NASA Astrophysics Data System (ADS)

    Shroff, Ness; Schwartz, Mischa

    1996-04-01

    The enormous bandwidth potential of optical fiber has resulted in a worldwide effort to develop high-speed ATM networks, also called broadband integrated services digital networks (B-ISDN). Many of the applications that ATM networks will support will have a strong video component to them. Hence, it is important to understand the behavior of video traffic as it travels through these networks. To that end, we develop the generalized histogram model (GHM) to characterize 'highly correlated' traffic, such as motion JPEG or 'smoothed' MPEG traffic over ATM networks end-to- end. Using our GHM model we show how to determine the loss rate at any node in an ATM network. We find that, for highly correlated video sources, increasing the buffer size beyond a certain region called the 'cell region' only marginally decreases the probability of loss. This implies that large buffers cannot be used to control the loss for such sources. The analytical model provided in this paper can be used for admission control, and network dimensioning and design in ATM networks. We have validated our results using simulations of real traces of video sources.

  3. Correlation spectrometer having high resolution and multiplexing capability

    NASA Technical Reports Server (NTRS)

    Margolis, J. S.; Martonchik, J. V. (Inventor)

    1984-01-01

    A correlation spectrometer permanently incorporates a reference cell and an electro-optical phase modulator (EOPM) in the light path between a sample cell and a detector. The effect of the EOPM is such that its frequency modulates all of the monochromatic component of the incoherent radiation passing through it. The EOPM is adjusted so that when it is ON all of the energy in the monochromatic components is thrown into sidebands differing from the original frequencies by integral multiples of the modulation frequency with the total amount of energy absorbed from the original radiation remaining constant. When there is no coincidence between the constituents in the two cells, the detector's output is the same when the EOPM is ON and when it is OFF. However, when there is coincidence the detector's output changes when the EOPM is switched between its two states. The change in the detector's output is related to the quantity of the constituents in the sample cell.

  4. Performance correlations for high temperature potassium heat pipes

    SciTech Connect

    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/sup 2/ cross section of the largest sub-scale heat pipe to the 25.5 cm/sup 2/ cross section prototype. Correlation of the model predictions with test data from the prototype is discussed.

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

    PubMed

    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.

  6. Photo-Realistic Statistical Skull Morphotypes: New Exemplars for Ancestry and Sex Estimation in Forensic Anthropology.

    PubMed

    Caple, Jodi; Stephan, Carl N

    2016-12-01

    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.

  7. Vitamin D status of older adults of diverse ancestry living in the greater Toronto area

    PubMed Central

    2013-01-01

    Background Physiological and lifestyle factors put older adults at an increased risk of vitamin D insufficiency and resulting negative health outcomes. Here we explore the vitamin D status in a sample of community dwelling older adults of diverse ancestry living in the Greater Toronto area (GTA). Methods Two hundred and twenty-four (224) adults over 60 years of age were recruited from the Square One Older Adult Centre, in Mississauga, Ontario. Circulating 25-hydroxyvitamin D (25(OH)D) concentrations were measured from dried blood spot cards. Dietary and supplemental intakes of vitamin D were assessed via questionnaires. Skin pigmentation was assessed quantitatively by measuring melanin levels using a reflectometer. Results The mean 25(OH)D concentration in the total sample was 82.4 nmol/L. There were no statistically significant differences in serum 25(OH)D concentrations, supplemental or dietary vitamin D intakes between the three major ancestral groups (East Asians, Europeans and South Asians). Females had significantly higher 25(OH)D concentrations than males (84.5 nmol/L vs. 72.2 nmol/L, p = 0.012). The proportion of participants with 25(OH)D concentrations below 50 nmol/L and 75 nmol/L were 12.1%, and 38.8%, respectively. The mean daily supplemental intake of vitamin D was 917 IU/day. Vitamin D intake from supplements was the major factor determining 25(OH)D concentrations (p < 0.001). Conclusions Mean concentration of 25(OH)D in a sample of older adults of diverse ancestry living in the GTA exceeded 80 nmol/L, and there were no significant differences in 25(OH)D levels between ancestral groups. These results sharply contrast with our recent study focused on young adults of diverse ancestry living in the same geographic area, in which we found substantially lower 25(OH)D concentrations (mean 39.5 nmol/L), low supplemental vitamin D intake (114 IU/day), and significant differences in 25(OH)D levels between ancestral groups. High daily intake

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

    PubMed

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

    2013-01-01

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

  9. The cancer caregiving experience of caregivers of Mexican ancestry.

    PubMed

    Juarez, Gloria; Branin, Joan J; Rosales, Monica

    2014-01-01

    The act of providing care may be the same in all ethnic groups, but the way caregiving is defined by family members is influenced by cultural values and beliefs. This study describes the caregiving experience and challenges of caregivers of Mexican ancestry. Qualitative interviews of 20 family caregivers and thematic analysis of transcribed audiotapes identified four themes that characterized their caregiving experience. These themes include an emphasis on family values, a strong commitment to care, difficulties dealing with everyday life realities, and a reliance on spirituality, all of which added to the meaningfulness and burden of caregiving. Further investigation within a cultural context is warranted in the development of interventions and programs to better assist caregivers in coping with the challenges of providing cancer care.

  10. Spread of pedigree versus genetic ancestry in spatially distributed populations.

    PubMed

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

    2016-04-01

    Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ∼ t rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.

  11. APOL1 and nephropathy progression in populations of African ancestry.

    PubMed

    Freedman, Barry I

    2013-09-01

    Marked familial aggregation of chronic kidney disease suggests that inherited factors play a major role in nephropathy susceptibility. Molecular genetics analyses have identified a number of genes reproducibly associated with a broad range of renal phenotypes. Most associations show polygenic inheritance patterns with limited effect size. In contrast, genetic association between the apolipoprotein L1 (APOL1) gene and several severe nondiabetic forms of kidney disease in African Americans approach Mendelian inheritance patterns and account for a large proportion of glomerulosclerosis in populations of African ancestry. Emerging data support an important role for APOL1 in the progression of diverse etiologies of kidney disease, in concert with requisite environmental (gene*environment) and inherited (gene*gene) interactions. This article reviews the current status of APOL1-associated nephropathy and discusses research questions under active investigation in the search for a cure for these severe and often progressive kidney diseases.

  12. Charge and spin correlations in high temperature superconductors

    NASA Astrophysics Data System (ADS)

    Hayden, Stephen

    2013-03-01

    The cuprate high temperatures superconductors are characterised by numerous competing, and in some cases, co-existing broken symmetries. A important question is to what extent such additional ordered states exist for compositions with high superconducting transition temperatures. I will discuss high-energy X-ray diffraction measurements which show that a charge density wave state (CDW) develops at zero field in the normal state of superconducting YBa2Cu3O6.67 (Tc = 67 K). This material has a hole doping of 0.12 per copper and a well-ordered oxygen chain superstructure. Below Tc, the application of a magnetic field suppresses superconductivity and enhances the CDW. We find that the CDW and superconductivity are competing orders with similar energy scales, and the high-Tc superconductivity forms from a pre-existing CDW environment. Our results provide a mechanism for the formation of small Fermi surface pockets which can explain the negative Hall and Seebeck effects and the Tc plateau in this material. Work performed in collaboration with J. Chang, E. Blackburn, A. T. Holmes, N. B. Christensen, J. Larsen, J. Mesot, Ruixing Liang, D. A. Bonn, W. N. Hardy, A. Watenphul, M. v. Zimmermann and E. M. Forgan.

  13. Some Correlates of High School Foreign Language Achievement.

    ERIC Educational Resources Information Center

    Beanblossom, Gary F.

    This paper investigates the influences of traditional kinds of verbal and quantitative achievement and aptitude variables on high school foreign language achievement, as measured by Modern Language Association and University of Washington tests of language skills administered to entering college students. The report focuses on: (1) the sample and…

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

    PubMed Central

    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

  15. Tracing Cattle Breeds with Principal Components Analysis Ancestry Informative SNPs

    PubMed Central

    Lewis, Jamey; Abas, Zafiris; Dadousis, Christos; Lykidis, Dimitrios; Paschou, Peristera; Drineas, Petros

    2011-01-01

    The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs) for 19 breeds (13 taurine, three zebu, and three hybrid breeds), seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products. PMID:21490966

  16. The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry.

    PubMed

    Waldman, Yedael Y; Biddanda, Arjun; Davidson, Natalie R; Billing-Ross, Paul; Dubrovsky, Maya; Campbell, Christopher L; Oddoux, Carole; Friedman, Eitan; Atzmon, Gil; Halperin, Eran; Ostrer, Harry; Keinan, Alon

    2016-01-01

    The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19-33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.

  17. The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry

    PubMed Central

    Davidson, Natalie R.; Billing-Ross, Paul; Dubrovsky, Maya; Campbell, Christopher L.; Oddoux, Carole; Friedman, Eitan; Atzmon, Gil; Halperin, Eran; Ostrer, Harry; Keinan, Alon

    2016-01-01

    The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so. PMID:27010569

  18. Importance of mitochondrial haplotypes and maternal lineage in sprint performance among individuals of West African ancestry.

    PubMed

    Deason, M; Scott, R; Irwin, L; Macaulay, V; Fuku, N; Tanaka, M; Irving, R; Charlton, V; Morrison, E; Austin, K; Pitsiladis, Y P

    2012-04-01

    Mitochondrial DNA (mtDNA) is inherited solely along the matriline, giving insight into both ancestry and prehistory. Individuals of sub-Saharan ancestry are overrepresented in sprint athletics, suggesting a genetic advantage. The purpose of this study was to compare the mtDNA haplogroup data of elite groups of Jamaican and African-American sprinters against respective controls to assess any differences in maternal lineage. The first hypervariable region of mtDNA was haplogrouped in elite Jamaican athletes (N=107) and Jamaican controls (N=293), and elite African-American athletes (N=119) and African-American controls (N=1148). Exact tests of total population differentiation were performed on total haplogroup frequencies. The frequency of non-sub-Saharan haplogroups in Jamaican athletes and Jamaican controls was similar (1.87% and 1.71%, respectively) and lower than that of African-American athletes and African-American controls (21.01% and 8.19%, respectively). There was no significant difference in total haplogroup frequencies between Jamaican athletes and Jamaican controls (P=0.551 ± 0.005); however, there was a highly significant difference between African-American athletes and African-American controls (P<0.001). The finding of statistically similar mtDNA haplogroup distributions in Jamaican athletes and Jamaican controls suggests that elite Jamaican sprinters are derived from the same source population and there is neither population stratification nor isolation for sprint performance. The significant difference between African-American sprinters and African-American controls suggests that the maternal admixture may play a role in sprint performance.

  19. Higher levels of neanderthal ancestry in East Asians than in Europeans.

    PubMed

    Wall, Jeffrey D; Yang, Melinda A; Jay, Flora; Kim, Sung K; Durand, Eric Y; Stevison, Laurie S; Gignoux, Christopher; Woerner, August; Hammer, Michael F; Slatkin, Montgomery

    2013-05-01

    Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from ∼30,000 to 300,000 years ago (KYA). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 KYA. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

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

    PubMed Central

    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

  1. The genetic ancestry of African Americans, Latinos, and European Americans across the United States.

    PubMed

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

    2015-01-08

    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.

  2. Replication and fine mapping of asthma-associated loci in individuals of African ancestry.

    PubMed

    Kantor, David B; Palmer, Cameron D; Young, Taylor R; Meng, Yan; Gajdos, Zofia K; Lyon, Helen; Price, Alkes L; Pollack, Samuela; London, Stephanie J; Loehr, Laura R; Smith, Lewis J; Kumar, Rajesh; Jacobs, David R; Petrini, Marcy F; O'Connor, George T; White, Wendy B; Papanicolaou, George; Burkart, Kristin M; Heckbert, Susan R; Barr, R Graham; Hirschhorn, Joel N

    2013-09-01

    Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry.

  3. Correlation of theory and experiment for high-pressure hydrogen

    NASA Technical Reports Server (NTRS)

    Hoover, W. G.; Ross, M.; Bender, C. F.; Rogers, F. J.; Olness, R. J.

    1972-01-01

    Recent quantum calculations and high-pressure experiments both agree on the magnitude of the forces with which hydrogen molecules interact. The calculated forces have to be determined in two steps: the repulsion is determined by Hartree-Fock calculations while the attraction is deduced semiempirically. The experimental forces are inferred from recent data on hydrogen shockcompressed to 214 kbar. The agreement indicates the usefulness of a pair-potential description of dense hydrogen and suggests, using potentials consistent with both theory and experiment, that pressures of at least 1.7 Mbar will be required to make metallic hydrogen. The expected lifetime of the metal at atmospheric pressure is very short.

  4. Ancestry and BMI Influences on Facial Soft Tissue Depths for A Cohort of Chinese and Caucasoid Women in Dunedin, New Zealand.

    PubMed

    Baillie, Louisa J; Mirijali, Seyed Ali; Niven, Brian E; Blyth, Phil; Dias, George J

    2015-09-01

    This study measured and assessed facial soft tissue depths (FSTDs) in adult female Chinese and New Zealand (NZ) Europeans (Caucasoids). Ultrasound was used to obtain depths at nine landmarks on 108 healthy subjects (51 Chinese, 57 NZ European), erect positioned, of same age group (18-29 years). Height and weight were also recorded. Statistical analysis focused on comparison of tissue depth between the two ancestry groups and the influence of Body Mass Index (BMI) (kg/m2). Results showed mean depth differences at Supra M2 and Infra M2 landmarks significantly greater for Chinese than Caucasoid women for all three BMI Classes (BMI<20, 20≤BMI<25, 25≤BMI<30), even BMI<20. For both groups BMI positively correlated with FSTD values at all landmarks except Labrale superius. This study enabled ancestry and BMI influence on FSTDs to be observed and compared for two distinct groups. Results add to knowledge about facial tissue depth variation.

  5. European Ancestry as a Risk Factor for Atrial Fibrillation in African Americans

    PubMed Central

    Marcus, Gregory M.; Alonso, Alvaro; Peralta, Carmen A.; Lettre, Guillaume; Vittinghoff, Eric; Lubitz, Steven A.; Fox, Ervin R.; Levitzky, Yamini S.; Mehra, Reena; Kerr, Kathleen F.; Deo, Rajat; Sotoodehnia, Nona; Akylbekova, Meggie; Ellinor, Patrick T.; Paltoo, Dina N.; Soliman, Elsayed Z.; Benjamin, Emelia J.; Heckbert, Susan R.

    2010-01-01

    Background Despite a higher burden of standard atrial fibrillation (AF) risk factors, African Americans have a lower risk of AF than whites. It is unknown if the higher riskis due to genetic or environmental factors. As African Americans have varying degrees of European ancestry, we sought to test the hypothesis that European ancestry is an independent risk factor for AF. Methods and Results We studied whites (n=4,543) and African Americans (n=822) in the Cardiovascular Health Study (CHS) and whites (n=10,902) and Africa Americans (n=3,517) in the Atherosclerosis Risk in Communities (ARIC) Study (n=3,517). Percent European ancestry in African Americans was estimated using 1,747 ancestry informative markers (AIMs) from the Illumina custom ITMAT-Broad-CARe (IBC) array. Among African Americans without baseline AF, 120 of 804 CHS participants and 181 of 3,517 ARIC participants developed incident AF. A meta-analysis from the two studies revealed that every 10% increase in European ancestry increased the risk of AF by 13% (HR 1.13, 95% CI 1.03–1.23, p=0.007). After adjusting for potential confounders, European ancestry remained a predictor of incident AF in each cohort alone, with a combined estimated hazard ratio for each 10% increase in European ancestry of 1.17 (95% CI 1.07–1.29, p=0.001). A second analysis using 3,192 AIMs from a genome wide Affymetrix 6.0 array in ARIC African Americans yielded similar results. Conclusion European ancestry predicted risk of incident AF. Our study suggests that investigating genetic variants contributing to differential AF risk in individuals of African versus European ancestry will be informative. PMID:21098467

  6. Use of animals with partially known ancestries in scientifically managed breeding programs.

    PubMed

    Willis, Kevin; Lacy, Robert C

    2016-07-01

    Animals with only partially known ancestry present a problem for population managers because it can be difficult to determine their relative genetic value to the population. So long as their ancestry is not completely unknown, population management software such as PMx can calculate a mean kinship for these animals, but that mean kinship is calculated such that there is no decrease in relative genetic value or "penalty" for only partially known ancestry. However, there is a longer-term genetic cost to having animals with only partially known ancestry in the population, and thus it is appropriate to "penalize" animals with partially known ancestry to some extent. The challenge is determining the correct "penalty" which will serve to decrease the percent unknown ancestry in subsequent generations while not causing excessive selection against the known ancestry of the animal. A new parameter of relative genetic value is developed which takes into account both an animal's mean kinship as well as its percent known ancestry. The method used in PMx to calculate the mean kinships also in general overestimates the inbreeding coefficients of offspring of animals with partially known ancestry when the known parents share a common ancestor, but can underestimate inbreeding if common ancestors exist within the unknown portion of the pedigree. This may result in population managers selecting less suitable pairs for breeding in an attempt to avoid an apparent higher level of inbreeding. A parameter is developed that adjusts the inbreeding coefficient to more accurately reflect the likely inbreeding coefficient of potential offspring. Zoo Biol. 35:319-325, 2016. © 2016 Wiley Periodicals, Inc.

  7. Future directions for probing two and three nucleon short-range correlations at high energies

    SciTech Connect

    Frankfurt, Leonid; Sargsian, Misak; Strikman, Mark

    2008-10-13

    We summarize recent progress in the studies of the short-rang correlations (SRC) in nuclei in high energy electron and hadron nucleus scattering and suggest directions for the future high energy studies aimed at establishing detailed structure of two-nucleon SRCs, revealing structure of three nucleon SRC correlations and discovering non-nucleonic degrees of freedom in nuclei.

  8. Correlates of gambling on high-school grounds

    PubMed Central

    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 (p<0.0001). In comparison to GS- students, GS+ students were more likely to report poorer academic achievement and more permissive attitudes towards gambling 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

  9. Correlates of hopelessness in the high suicide risk police occupation

    PubMed Central

    Violanti, John M.; Andrew, Michael E.; Mnatsakanova, Anna; Hartley, Tara A.; Fekedulegn, Desta; Burchfiel, Cecil M.

    2015-01-01

    Police officers are chronically exposed to work stress. We examined specific stressors that may be associated with hopelessness, a possible risk factor for suicide in this high suicide risk population. The study included 378 officers (276 men and 102 women) with complete data. Analysis of variance was used to estimate mean levels of hopelessness scores as associated with stress, adjusted for age, gender, and race/ ethnicity. Posttraumatic symptoms were tested as a modifier of the association between stress and hopelessness. Increasing stress of administrative practices and lack of support were significantly associated with increasing hopelessness among officers (p < .006 – hopelessness range: 1.64–2.65; and p < .001 – hopelessness range 1.60–2.80, respectively). Posttraumatic stress disorder (PTSD) symptoms significantly modified the association between lack of organizational support and hopelessness (p < .010) with significant association only among individuals with higher PTSD symptoms (p < .001). Results suggest that hopelessness is associated with specific stressors in police work, and this is modified by posttraumatic symptomatology. PMID:26752981

  10. Global and Local Ancestry in African Americans: Implications for Alzheimer’s Disease Risk

    PubMed Central

    Hohman, Timothy J.; Cooke-Bailey, Jessica N.; Reitz, Christiane; Jun, Gyungah; Naj, Adam; Beecham, Gary W.; Liu, Zhi; Carney, Regina M.; Vance, Jeffrey M.; Cuccaro, Michael L.; Rajbhandary, Ruchita; Vardarajan, Badri Narayan; Wang, Li-San; Valladares, Otto; Lin, Chiao-Feng; Larson, Eric B.; Graff-Radford, Neill R.; Evans, Denis; De Jager, Philip L.; Crane, Paul K.; Buxbaum, Joseph D.; Murrell, Jill R.; Raj, Towfique; Ertekin-Taner, Nilufer; Logue, Mark W.; Baldwin, Clinton T.; Green, Robert C.; Barnes, Lisa L.; Cantwell, Laura B.; Fallin, M. Daniele; Go, Rodney C. P.; Griffith, Patrick; Obisesan, Thomas O.; Manly, Jennifer J.; Lunetta, Kathryn L.; Kamboh, M. Ilyas; Lopez, Oscar L.; Bennett, David A.; Hardy, John; Hendrie, Hugh C.; Hall, Kathleen S.; Goate, Alison M.; Lang, Rosalyn; Byrd, Goldie S.; Kukull, Walter A.; Foroud, Tatiana M.; Farrer, Lindsay A.; Martin, Eden R.; Pericak-Vance, Margaret A.; Schellenberg, Gerard D.; Mayeux, Richard; Haines, Jonathan L.; Thornton-Wells, Tricia A.

    2015-01-01

    African American (AA) individuals have a higher risk for late-onset Alzheimer’s disease (LOAD) than Americans of primarily European ancestry (EA). Recently, the largest genome-wide association study in AAs to date confirmed that six of the AD-related genetic variants originally discovered in EA cohorts are also risk variants in AA; however, the risk attributable to many of the loci (e.g., APOE, ABCA7) differed substantially from previous studies in EA. There likely are risk variants of higher frequency in AAs that have not been discovered. We performed a comprehensive analysis of genetically determined local and global ancestry in AAs with regard to LOAD status. Compared to controls, LOAD cases showed higher levels of African ancestry, both globally and at several LOAD relevant loci, which explained risk for AD beyond global differences. Exploratory post-hoc analyses highlight regions with greatest differences in ancestry as potential candidate regions for future genetic analyses. PMID:26092349

  11. 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

    PubMed Central

    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

    Background 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. Materials/Methods 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. Results 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. Conclusions 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. PMID:26680774

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

    PubMed Central

    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 < 0.05). RESULTS: In the Brazilian sample, NASH was significantly more frequent among the elderly patients with diabetes (NASH 56 ± 1.1 years old vs S. Steatosis 51 ± 1.5 years old, P = 3.7 x 10-9), dyslipidemia (NASH 63% vs S. Steatosis 37%, P = 0.009), higher fasting glucose levels (NASH 124 ± 5.2 vs S. Steatosis 106 ± 5.3, P = 0.001) and Homeostatic Model of Assessment index > 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

  13. European ancestry is positively associated with breast cancer risk in Mexican women

    PubMed Central

    Fejerman, Laura; Romieu, Isabelle; John, Esther M.; Lazcano-Ponce, Eduardo; Huntsman, Scott; Beckman, Kenneth B.; Pérez-Stable, Eliseo J.; Burchard, Esteban Gonzalez; Ziv, Elad; Torres-Mejía, Gabriela

    2010-01-01

    The incidence of breast cancer is 35% lower in Hispanic women living in the San Francisco Bay Area than in non-Hispanic white women. We have previously described a significant association between genetic ancestry and risk of breast cancer in a sample of US Hispanics/Latinas. We re-tested the association in women residing in Mexico because of the possibility that the original finding may be confounded by US specific unmeasured environmental exposures. We genotyped a set of 106 ancestry informative markers (AIMs) in 846 Mexican women with breast cancer and 1,035 unaffected controls and estimated genetic ancestry using a maximum likelihood method. Odds ratios (OR) and 95% confidence intervals (CI) for ancestry modeled as a categorical and continuous variable were estimated using logistic regression and adjusted for reproductive and other known risk factors. Greater European ancestry was associated with increased breast cancer risk in this new and independent sample of Mexican women residing in Mexico. Compared to women with 0-25% European ancestry, the risk was increased for women with 51-75% and 76-100% European ancestry (OR=1.35, 95% CI: 0.96-1.91 and 2.44, 95% CI: 0.94-6.35 respectively, p for trend=0.044). For every 25% increase in European ancestry (modeled as a continuous variable) there was a 20% increase in risk of breast cancer (95% CI: 1.03-1.41, p=0.019). These results suggest that non-genetic factors play a crucial role in explaining the difference in breast cancer incidence between Latinas and non-Latina white women and it also points out to the possibility of a genetic component to this difference. PMID:20332279

  14. Ancestry analysis reveals a predominant Native American component with moderate European admixture in Bolivians.

    PubMed

    Heinz, Tanja; Alvarez-Iglesias, Vanesa; Pardo-Seco, Jacobo; Taboada-Echalar, Patricia; Gómez-Carballa, Alberto; Torres-Balanza, Antonio; Rocabado, Omar; Carracedo, Angel; Vullo, Carlos; Salas, Antonio

    2013-09-01

    We have genotyped 46 Ancestry Informative Markers (AIMs) in two of the most populated areas in Bolivia, namely, La Paz (Andean region; n=105), and Chuquisaca (Sub-Andean region; n=73). Using different analytical tools, we inferred admixture proportions of these two American communities by comparing the genetic profiles with those publicly available from the CEPH (Centre d'Etude du Polymorphisme Humain) panel representing three main continental groups (Africa, Europe, and America). By way of simulations, we first evaluated the minimum sample size needed in order to obtain accurate estimates of ancestry proportions. The results indicated that sample sizes above 30 individuals could be large enough to estimate main continental ancestry proportions using the 46 AIMs panel. With the exception of a few individuals, the results also indicated that Bolivians showed a predominantly Native American ancestry with variable levels of European admixture. The proportions of ancestry were statistically different in La Paz and Chuquisaca: the Native American component was 86% and 77% (Mann-Whitney U-test: un-adjusted P-value=2.1×10(-5)), while the European ancestry was 13% and 21% (Mann-Whitney U-test: un-adjusted P-value=3.6×10(-5)), respectively. The African ancestry in Bolivians captured by the AIMs analyzed in the present study was below 2%. The inferred ancestry of Bolivians fits well with previous studies undertaken on haplotype data, indicating a major proportion of Native American lineages. The genetic differences observed in these two groups suggest that forensic genetic analysis should be better performed based on local databases built in the main Bolivian areas.

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

    ERIC Educational Resources Information Center

    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…

  16. Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

    PubMed Central

    Sun, Kuan; Ye, Yi; Luo, Tao; Hou, Yiping

    2016-01-01

    Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies. PMID:28004788

  17. Regional differences in awareness and attitudes regarding genetic testing for disease risk and ancestry.

    PubMed

    Jonassaint, Charles R; Santos, Eunice R; Glover, Crystal M; Payne, Perry W; Fasaye, Grace-Ann; Oji-Njideka, Nefertiti; Hooker, Stanley; Hernandez, Wenndy; Foster, Morris W; Kittles, Rick A; Royal, Charmaine D

    2010-09-01

    Little is known about the lay public's awareness and attitudes concerning genetic testing and what factors influence their perspectives. The existing literature focuses mainly on ethnic and socioeconomic differences; however, here we focus on how awareness and attitudes regarding genetic testing differ by geographical regions in the US. We compared awareness and attitudes concerning genetic testing for disease risk and ancestry among 452 adults (41% Black and 67% female) in four major US cities, Norman, OK; Cincinnati, OH; Harlem, NY; and Washington, DC; prior to their participation in genetic ancestry testing. The OK participants reported more detail about their personal ancestries (p = 0.02) and valued ancestry testing over disease testing more than all other sites (p < 0.01). The NY participants were more likely than other sites to seek genetic testing for disease (p = 0.01) and to see benefit in finding out more about one's ancestry (p = 0.02), while the DC participants reported reading and hearing more about genetic testing for African ancestry than all other sites (p < 0.01). These site differences were not better accounted for by sex, age, education, self-reported ethnicity, religion, or previous experience with genetic testing/counseling. Regional differences in awareness and attitudes transcend traditional demographic predictors, such as ethnicity, age and education. Local sociocultural factors, more than ethnicity and socioeconomic status, may influence the public's awareness and belief systems, particularly with respect to genetics.

  18. Genetic Ancestry of the Extinct Javan and Bali Tigers

    PubMed Central

    Xue, Hao-Ran; Yamaguchi, Nobuyuki; Driscoll, Carlos A.; Han, Yu; Bar-Gal, Gila Kahila; Zhuang, Yan; Mazak, Ji H.; Macdonald, David W.; O’Brien, Stephen J.

    2015-01-01

    The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1–2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers. PMID:25754539

  19. Race and ancestry in biomedical research: exploring the challenges

    PubMed Central

    2009-01-01

    The use of race in biomedical research has, for decades, been a source of social controversy. However, recent events, such as the adoption of racially targeted pharmaceuticals, have raised the profile of the race issue. In addition, we are entering an era in which genomic research is increasingly focused on the nature and extent of human genetic variation, often examined by population, which leads to heightened potential for misunderstandings or misuse of terms concerning genetic variation and race. Here, we draw together the perspectives of participants in a recent interdisciplinary workshop on ancestry and health in medicine in order to explore the use of race in research issue from the vantage point of a variety of disciplines. We review the nature of the race controversy in the context of biomedical research and highlight several challenges to policy action, including restrictions resulting from commercial or regulatory considerations, the difficulty in presenting precise terminology in the media, and drifting or ambiguous definitions of key terms. PMID:19348695

  20. Biased gene transfer mimics patterns created through shared ancestry

    PubMed Central

    Andam, Cheryl P.; Williams, David; Gogarten, J. Peter

    2010-01-01

    In phylogenetic reconstruction, two types of bacterial tyrosyl-tRNA synthetases (TyrRS) form distinct clades with many bacterial phyla represented in both clades. Very few taxa possess both forms, and maximum likelihood analysis of the distribution of TyrRS types suggests horizontal gene transfer (HGT), rather than an ancient duplication followed by differential gene loss, as the contributor to the evolutionary history of TyrRS in bacteria. However, for each TyrRS type, phylogenetic reconstruction yields phylogenies similar to the ribosomal phylogeny, revealing that frequent gene transfer has not destroyed the expected phylogeny; rather, the expected phylogenetic signal was reinforced or even created by HGT. We show that biased HGT can mimic patterns created through shared ancestry by in silico simulation. Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative gene positions, both tyrRS types occupy equivalent positions in closely related genomes, rejecting the loss hypothesis. Although the two types of bacterial TyrRS are only distantly related and only rarely coexist in a single genome, they have many features in common with alleles that are swapped between related lineages. We propose to label these functionally similar homologs as homeoalleles. We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer. PMID:20495090

  1. Biased gene transfer mimics patterns created through shared ancestry.

    PubMed

    Andam, Cheryl P; Williams, David; Gogarten, J Peter

    2010-06-08

    In phylogenetic reconstruction, two types of bacterial tyrosyl-tRNA synthetases (TyrRS) form distinct clades with many bacterial phyla represented in both clades. Very few taxa possess both forms, and maximum likelihood analysis of the distribution of TyrRS types suggests horizontal gene transfer (HGT), rather than an ancient duplication followed by differential gene loss, as the contributor to the evolutionary history of TyrRS in bacteria. However, for each TyrRS type, phylogenetic reconstruction yields phylogenies similar to the ribosomal phylogeny, revealing that frequent gene transfer has not destroyed the expected phylogeny; rather, the expected phylogenetic signal was reinforced or even created by HGT. We show that biased HGT can mimic patterns created through shared ancestry by in silico simulation. Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative gene positions, both tyrRS types occupy equivalent positions in closely related genomes, rejecting the loss hypothesis. Although the two types of bacterial TyrRS are only distantly related and only rarely coexist in a single genome, they have many features in common with alleles that are swapped between related lineages. We propose to label these functionally similar homologs as homeoalleles. We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.

  2. Genetic ancestry of the extinct Javan and Bali tigers.

    PubMed

    Xue, Hao-Ran; Yamaguchi, Nobuyuki; Driscoll, Carlos A; Han, Yu; Bar-Gal, Gila Kahila; Zhuang, Yan; Mazak, Ji H; Macdonald, David W; O'Brien, Stephen J; Luo, Shu-Jin

    2015-01-01

    The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.

  3. Clines of nuclear DNA markers suggest a largely neolithic ancestry of the European gene pool.

    PubMed

    Chikhi, L; Destro-Bisol, G; Bertorelle, G; Pascali, V; Barbujani, G

    1998-07-21

    Comparisons between archaeological findings and allele frequencies at protein loci suggest that most genes of current Europeans descend from populations that have been expanding in Europe in the last 10, 000 years, in the Neolithic period. Recent mitochondrial data have been interpreted as indicating a much older, Paleolithic ancestry. In a spatial autocorrelation study at seven hypervariable loci in Europe (four microsatellites, two larger, tandem-repeat loci, and a sequence polymorphism) broad clinal patterns of DNA variation were recognized. The observed clines closely match those described at the protein level, in agreement with a possible Near Eastern origin for the ancestral population. Separation times between populations were estimated on the basis of a stepwise mutation model. Even assuming low mutation rates and long generation times, we found no evidence for population splits older than 10,000 years, with the predictable exception of Saami (Lapps). The simplest interpretation of these results is that the current nuclear gene pool largely reflects the westward and northward expansion of a Neolithic group. This conclusion is now supported by purely genetic evidence on the levels and patterns of microsatellite diversity, rather than by correlations of biological and nonbiological data. We argue that many mitochondrial lineages whose origin has been traced back to the Paleolithic period probably reached Europe at a later time.

  4. Fabrication and Electrical Characterization of Correlated Oxide Field Effect Switching Devices for High Speed Electronics

    DTIC Science & Technology

    2015-11-19

    AFRL-AFOSR-VA-TR-2015-0381 Fabrication and Electrical Characterization of Correlated Oxide Field Effect Switching Devices for High Speed Electronics ...high speed electronics 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-12-1-0189 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Shriram Ramanathan 5d... electronic properties of thin film correlated oxides was investigated via electrical transport measurements and electronic structure studies

  5. New Perspectives on the Correlation of SAT Scores, High School Grades, and Socioeconomic Factors

    ERIC Educational Resources Information Center

    Zwick, Rebecca; Greif Green, Jennifer

    2007-01-01

    In studies of the SAT, correlations of SAT scores, high school grades, and socioeconomic factors (SES) are usually obtained using a university as the unit of analysis. This approach obscures an important structural aspect of the data: The high school grades received by a given institution come from a large number of high schools, all of which have…

  6. Afro-derived Amazonian populations: inferring continental ancestry and population substructure.

    PubMed

    Lopes Maciel, Luana Gomes; Ribeiro Rodrigues, Elzemar Martins; Carneiro Dos Santos, Ney Pereira; Ribeiro Dos Santos, Ândrea; Guerreiro, João Farias; Santos, Sidney

    2011-10-01

    A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations.

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

    PubMed

    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.

  8. Calibration of ultra high speed laser engraving processes by correlating influencing variables including correlative evaluation with SEM and CLSM

    NASA Astrophysics Data System (ADS)

    Bohrer, Markus; Vaupel, Matthias; Nirnberger, Robert; Weinberger, Bernhard

    2016-03-01

    Laser engraving is used for decades as a well-established process e. g. for the production of print and embossing forms for many goods in daily life, e. g. decorated cans and printed bank notes. Up to now it is more or less a so-called fire-and-forget process. From the original artist's plan to the digitization, then from the laser source itself (with electronic signals, RF and plasma discharge regarding CO2 lasers) to the behavior of the optical beam delivery — especially if an AOM is used — to the interaction of the laser beam with the material itself is a long process chain. The most recent results using CO2 lasers with AOMs and the research done with scanning electron microscope (SEM) and confocal laser scanning microscope (CLSM) — as a set for correlative microscopy to evaluate the high speed engraving characteristics — are presented in this paper.

  9. The feasibility and application of gray scale adjustment method in high temperature digital image correlation

    NASA Astrophysics Data System (ADS)

    Wang, Shen; Yao, Xue Feng; Su, Yun Quan; Liu, Wei

    2017-02-01

    In this paper, the basic principle and application of linear gray scale adjustment method are investigated in high temperature digital image correlation (DIC) technology. First, the simple linear gray scale adjustment method is proposed, which can adjust the gray scale value of the saturated pixels and diminish the correlation error caused by the saturated pixels. Then, both the simulated high temperature images and DIC correlation results before and after the gray scale adjustment are provided and analyzed to verify its effectiveness, in which the displacement error decreased from 0.1 pixels to 0.04 pixels after the linear gray scale adjustment for high temperature images. Finally, the linear gray scale adjustment method is used to extract the displacement with high accuracy in high temperature experiment of SiC specimen, and the displacement error decreased from 0.5 pixels to 0.1 pixels after the linear gray scale adjustment.

  10. Dental morphology and ancestry in Albuquerque, New Mexico Hispanics.

    PubMed

    Willermet, C M; Edgar, H J H

    2009-01-01

    The term "Hispanic" groups people from Central and South America and the Caribbean, combining disparate cultures, languages, and ancestry, and masking biological differences. Historical and current admixture patterns within these populations and with indigenous and European-, African-, and/or Asian- derived populations complicate the biological picture. Although "Hispanic" has little biological meaning, it is used widely in epidemiology, disease management, and forensics as a biologically significant group. An interdisciplinary approach combining historical, cultural, and biological data can characterize regional and temporal differences between Hispanic populations. We examined biological distances with a population of central New Mexico Hispanics, as a case study of the local specificity of population history. We collected dental morphological trait frequencies from samples of recent Albuquerque-area Hispanic Americans and several ancestral and contemporary groups. To explore regional admixture patterns we calculated biological distances using the modified Mahalanobis D(2) statistic. Our results indicate that Albuquerque Hispanics are more similar to their European and African ancestral groups than to Native Americans in New Mexico. Additionally, their affinity to Native Americans is greater with prehistoric rather than contemporary samples. We argue that these results reflect a local rather than pan-Hispanic admixture pattern; they underscore that populations are better understood at the local and regional levels. It is undesirable to make sweeping biological generalizations for groups known to be geographically and genetically disparate. This research is part of a growing trend in biological research concerning Hispanics and other groups-an emphasis on local samples, informed by historical, cultural, and biological factors.

  11. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Nora, Sofia; Aparicio, Abelardo; Albaladejo, Rafael G.

    2016-01-01

    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. PMID:27835658

  13. Genomic Insights into the Ancestry and Demographic History of South America.

    PubMed

    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

  14. Genomic Insights into the Ancestry and Demographic History of South America

    PubMed Central

    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

  15. Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries.

    PubMed

    Phillips, C; Freire Aradas, A; Kriegel, A K; Fondevila, M; Bulbul, O; Santos, C; Serrulla Rech, F; Perez Carceles, M D; Carracedo, Á; Schneider, P M; Lareu, M V

    2013-05-01

    We have selected a set of single nucleotide polymorphisms (SNPs) with the specific aim of differentiating European and South Asian ancestries. The SNPs were combined into a 23-plex SNaPshot primer extension assay: Eurasiaplex, designed to complement an existing 34-plex forensic ancestry test with both marker sets occupying well-spaced genomic positions, enabling their combination as single profile submissions to the Bayesian Snipper forensic ancestry inference system. We analyzed the ability of Eurasiaplex plus 34plex SNPs to assign ancestry to a total 1648 profiles from 16 European, 7 Middle East, 13 Central-South Asian and 21 East Asian populations. Ancestry assignment likelihoods were estimated from Snipper using training sets of five-group data (three Eurasian groups, East Asian and African genotypes) and four-group data (Middle East genotypes removed). Five-group differentiations gave assignment success of 91% for NW European populations, 72% for Middle East populations and 39% for Central-South Asian populations, indicating Middle East individuals are not reliably differentiated from either Europeans or Central-South Asians. Four-group differentiations provided markedly improved assignment success rates of 97% for most continental Europeans tested (excluding Turkish and Adygei at the far eastern edge of Europe) and 95% for Central-South Asians, despite applying a probability threshold for the highest likelihood ratio above '100 times more likely'. As part of the assessment of the sensitivity of Eurasiaplex to analyze challenging forensic material we detail Eurasiaplex and 34-plex SNP typing to infer ancestry of a cranium recovered from the sea, achieving 82% SNP genotype completeness. Therefore, Eurasiaplex provides an informative and forensically robust approach to the differentiation of European and South Asian ancestries amongst Eurasian populations.

  16. Associations among ancestry, geography and breast cancer incidence, mortality, and survival in Trinidad and Tobago

    PubMed Central

    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

    2015-01-01

    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 (Incidence: 66.96; Mortality: 30.82 per 100,000) compared to women of East Indian (Incidence: 41.04, Mortality: 14.19 per 100,000) or mixed ancestry (Incidence: 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. PMID:26338451

  17. Race, genetic ancestry and response to antidepressant treatment for major depression.

    PubMed

    Murphy, Eleanor; Hou, Liping; Maher, Brion S; Woldehawariat, Girma; Kassem, Layla; Akula, Nirmala; Laje, Gonzalo; McMahon, Francis J

    2013-12-01

    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.

  18. Evaluation of 19 susceptibility loci of breast cancer in women of African ancestry.

    PubMed

    Huo, Dezheng; Zheng, Yonglan; Ogundiran, Temidayo O; Adebamowo, Clement; Nathanson, Katherine L; Domchek, Susan M; Rebbeck, Timothy R; Simon, Michael S; John, Esther M; Hennis, Anselm; Nemesure, Barbara; Wu, Suh-Yuh; Leske, M Cristina; Ambs, Stefan; Niu, Qun; Zhang, Jing; Cox, Nancy J; Olopade, Olufunmilayo I

    2012-04-01

    Multiple breast cancer susceptibility loci have been identified in genome-wide association studies (GWAS) in populations of European and Asian ancestry using array chips optimized for populations of European ancestry. It is important to examine whether these loci are associated with breast cancer risk in women of African ancestry. We evaluated 25 single nucleotide polymorphisms (SNPs) at 19 loci in a pooled case-control study of breast cancer, which included 1509 cases and 1383 controls. Cases and controls were enrolled in Nigeria, Barbados and the USA; all women were of African ancestry. We found significant associations for three SNPs, which were in the same direction and of similar magnitude as those reported in previous fine-mapping studies in women of African ancestry. The allelic odds ratios were 1.24 [95% confidence interval (CI): 1.04-1.47; P = 0.018] for the rs2981578-G allele (10q26/FGFR2), 1.34 (95% CI: 1.10-1.63; P = 0.0035) for the rs9397435-G allele (6q25) and 1.12 (95% CI: 1.00-1.25; P = 0.04) for the rs3104793-C allele (16q12). Although a significant association was observed for an additional index SNP (rs3817198), it was in the opposite direction to prior GWAS studies. In conclusion, this study highlights the complexity of applying current GWAS findings across racial/ethnic groups, as none of GWAS-identified index SNPs could be replicated in women of African ancestry. Further fine-mapping studies in women of African ancestry will be needed to reveal additional and causal variants for breast cancer.

  19. Evaluation of 19 susceptibility loci of breast cancer in women of African ancestry

    PubMed Central

    Huo, Dezheng; Zheng, Yonglan; Ogundiran, Temidayo O.; Adebamowo, Clement; Nathanson, Katherine L.; Domchek, Susan M.; Rebbeck, Timothy R.; Simon, Michael S.; John, Esther M.; Hennis, Anselm; Nemesure, Barbara; Wu, Suh-Yuh; Leske, M.Cristina; Ambs, Stefan; Niu, Qun; Zhang, Jing; Cox, Nancy J.; Olopade, Olufunmilayo I.

    2012-01-01

    Multiple breast cancer susceptibility loci have been identified in genome-wide association studies (GWAS) in populations of European and Asian ancestry using array chips optimized for populations of European ancestry. It is important to examine whether these loci are associated with breast cancer risk in women of African ancestry. We evaluated 25 single nucleotide polymorphisms (SNPs) at 19 loci in a pooled case–control study of breast cancer, which included 1509 cases and 1383 controls. Cases and controls were enrolled in Nigeria, Barbados and the USA; all women were of African ancestry. We found significant associations for three SNPs, which were in the same direction and of similar magnitude as those reported in previous fine-mapping studies in women of African ancestry. The allelic odds ratios were 1.24 [95% confidence interval (CI): 1.04–1.47; P = 0.018] for the rs2981578-G allele (10q26/FGFR2), 1.34 (95% CI: 1.10–1.63; P = 0.0035) for the rs9397435-G allele (6q25) and 1.12 (95% CI: 1.00–1.25; P = 0.04) for the rs3104793-C allele (16q12). Although a significant association was observed for an additional index SNP (rs3817198), it was in the opposite direction to prior GWAS studies. In conclusion, this study highlights the complexity of applying current GWAS findings across racial/ethnic groups, as none of GWAS-identified index SNPs could be replicated in women of African ancestry. Further fine-mapping studies in women of African ancestry will be needed to reveal additional and causal variants for breast cancer. PMID:22357627

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

    ERIC Educational Resources Information Center

    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…

  1. Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition

    ERIC Educational Resources Information Center

    Vul, Edward; Harris, Christine; Winkielman, Piotr; Pashler, Harold

    2009-01-01

    Functional Magnetic Resonance Imaging (fMRI) studies of emotion, personality, and social cognition have drawn much attention in recent years, with high-profile studies frequently reporting extremely high (e.g., > 8) correlations between behavioral and self-report measures of personality or emotion and measures of brain activation. We show…

  2. Angular and Long Range Rapidity Correlations in Particle Production at High Energy

    NASA Astrophysics Data System (ADS)

    Kovner, Alex; Lublinsky, Michael

    2013-01-01

    We discuss the general mechanism leading to long-range rapidity and angular correlations produced in high energy collisions (the "ridge"). This effect naturally appears in the high energy QCD and is strongly sensitive to physics of the gluon saturation. We comment on various recent practical realizations of the main idea, paying special attention to Nc counting and stress the relevance of Pomeron loops.

  3. Digital cross-correlation at 250 MHz using high-performance FPGAs

    NASA Astrophysics Data System (ADS)

    von Herzen, Brian

    1998-07-01

    This paper describes a 250 MHz cross-correlator for radio astronomy built using field-programmable gate arrays (FPGA's). Experimental results indicate that CMOS FPGA's can operate reliably at 250 MHz. Long-term integration tests of up to 10(superscript 12) samples have been taken, demonstrating the correlator accuracy down to the limits of the testing apparatus. Recent estimates indicate that higher-performance FPGA's available early in 1998 can attain speeds of over 300 MHz using 20% fewer logic elements than previous designs. The FPGA correlator can be reconfigured for 2, 3, 4, or even 9 levels of sensitivity, permitting a tradeoff of the number of lags with the sensitivity desired. Although FPGA's have historically been more expensive than custom chips, starting this year FPGA correlators are actually less expensive than custom correlator chips. This cost reduction is due to the fact that FPGA's are standard components in the electronics industry and are produced in much higher volumes than custom correlators. As an example, a 1024-lag 4-level cross- correlator can be produced for an FPG chip cost of less than $80 in 1998. FPGA's continue to drop in price faster than custom devices because volumes continue to increase and FPGA architectures continue to improve. The demonstrated high performance of FPGA's coupled with their extreme flexibility, reconfigurability and lower cost make FPGA's ideally suited for the next generation of large correlator arrays.

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

    NASA Technical Reports Server (NTRS)

    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.

  5. Quantification of Maxillary Dental Arcade Curvature and the Estimation of Biological Ancestry in Forensic Anthropology.

    PubMed

    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.

  6. Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set.

    PubMed

    Phillips, C; Parson, W; Lundsberg, B; Santos, C; Freire-Aradas, A; Torres, M; Eduardoff, M; Børsting, C; Johansen, P; Fondevila, M; Morling, N; Schneider, P; Carracedo, A; Lareu, M V

    2014-07-01

    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 identify the most divergent markers for a five population group differentiation of Africans, Europeans, East Asians, Native Americans and Oceanians by using our own online genome variation browsers. We prioritized careful balancing of population differentiation across the five group comparisons in order to minimize bias when estimating co-ancestry proportions in individuals with admixed ancestries. The differentiation of European from Middle East or South Asian ancestries was not chosen as a characteristic in order to concentrate on introducing Oceanian differentiation for the first time in a forensic AIM set. We describe a complete set of 128 AIM-SNPs that have near identical population-specific divergence across five continentally defined population groups. The full set can be systematically reduced in size, while preserving the most informative markers and the balance of population-specific divergence in at least four groups. We describe subsets of 88, 55, 28, 20 and 12 AIMs, enabling both new and existing SNP genotyping technologies to exploit the best markers identified for forensic ancestry analysis.

  7. Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors.

    PubMed

    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.

  8. Socioeconomic Position, But Not African Genomic Ancestry, Is Associated With Blood Pressure in the Bambui-Epigen (Brazil) Cohort Study of Aging.

    PubMed

    Lima-Costa, M Fernanda; Mambrini, Juliana Vaz de Mello; Leite, Maria Lea Corrêa; Peixoto, Sérgio Viana; Firmo, Josélia Oliveira Araújo; Loyola Filho, Antônio Ignácio de; Gouveia, Mateus H; Leal, Thiago P; Pereira, Alexandre Costa; Macinko, James; Tarazona-Santos, Eduardo

    2016-02-01

    The study objective is to examine the role of African genome origin on baseline and 11-year blood pressure trajectories in community-based ethnoracially admixed older adults in Brazil. Data come from 1272 participants (aged ≥60 years) of the Bambui cohort study of aging during 11 years of follow-up. Outcome measures were systolic blood pressure, diastolic blood pressure, and hypertension control. Potential confounding variables were demographic characteristics, socioeconomic position (schooling and household income), and health indicators (smoking, sedentary lifestyle, high-density lipoprotein cholesterol, waist circumference, diabetes mellitus, and cardiovascular diseases), including antihypertensive drug use. We used 370 539 single-nucleotide polymorphisms to estimate each individual's African, European, and Native American trihybrid ancestry proportions. Median African, European, and Native American ancestry were 9.6%, 84.0%, and 5.3%, respectively. Among those with African ancestry, 59.4% came from East and 40.6% from West Africa. Baseline systolic and diastolic blood pressure, controlled hypertension, and their respective trajectories, were not significantly (P>0.05) associated with level (in quintiles) of African genomic ancestry. Similar results were found for West and East African subcontinental origins. Lower schooling level (<4 years versus higher) showed a significant and positive association with systolic blood pressure (Adjusted β=2.92; 95% confidence interval, 0.85-4.99). Lower monthly household income per capita (

  9. First all-in-one diagnostic tool for DNA intelligence: genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip.

    PubMed

    Keating, Brendan; Bansal, Aruna T; Walsh, Susan; Millman, Jonathan; Newman, Jonathan; Kidd, Kenneth; Budowle, Bruce; Eisenberg, Arthur; Donfack, Joseph; Gasparini, Paolo; Budimlija, Zoran; Henders, Anjali K; Chandrupatla, Hareesh; Duffy, David L; Gordon, Scott D; Hysi, Pirro; Liu, Fan; Medland, Sarah E; Rubin, Laurence; Martin, Nicholas G; Spector, Timothy D; Kayser, Manfred

    2013-05-01

    When a forensic DNA sample cannot be associated directly with a previously genotyped reference sample by standard short tandem repeat profiling, the investigation required for identifying perpetrators, victims, or missing persons can be both costly and time consuming. Here, we describe the outcome of a collaborative study using the Identitas Version 1 (v1) Forensic Chip, the first commercially available all-in-one tool dedicated to the concept of developing intelligence leads based on DNA. The chip allows parallel interrogation of 201,173 genome-wide autosomal, X-chromosomal, Y-chromosomal, and mitochondrial single nucleotide polymorphisms for inference of biogeographic ancestry, appearance, relatedness, and sex. The first assessment of the chip's performance was carried out on 3,196 blinded DNA samples of varying quantities and qualities, covering a wide range of biogeographic origin and eye/hair coloration as well as variation in relatedness and sex. Overall, 95 % of the samples (N = 3,034) passed quality checks with an overall genotype call rate >90 % on variable numbers of available recorded trait information. Predictions of sex, direct match, and first to third degree relatedness were highly accurate. Chip-based predictions of biparental continental ancestry were on average ~94 % correct (further support provided by separately inferred patrilineal and matrilineal ancestry). Predictions of eye color were 85 % correct for brown and 70 % correct for blue eyes, and predictions of hair color were 72 % for brown, 63 % for blond, 58 % for black, and 48 % for red hair. From the 5 % of samples (N = 162) with <90 % call rate, 56 % yielded correct continental ancestry predictions while 7 % yielded sufficient genotypes to allow hair and eye color prediction. Our results demonstrate that the Identitas v1 Forensic Chip holds great promise for a wide range of applications including criminal investigations, missing person investigations, and for national security

  10. Bio science: genetic genealogy testing and the pursuit of African ancestry.

    PubMed

    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.

  11. Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation

    PubMed Central

    Dash, Debasis; Mukerji, Mitali

    2014-01-01

    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. PMID:25398783

  12. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites

    PubMed Central

    Djuika, Carine F.; Huerta-Cepas, Jaime; Przyborski, Jude M.; Deil, Sophia; Sanchez, Cecilia P.; Doerks, Tobias; Bork, Peer; Lanzer, Michael; Deponte, Marcel

    2015-01-01

    Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones. PMID:28357258

  13. A SNP test to identify Africanized honeybees via proportion of 'African' ancestry.

    PubMed

    Chapman, Nadine C; Harpur, Brock A; Lim, Julianne; Rinderer, Thomas E; Allsopp, Michael H; Zayed, Amro; Oldroyd, Benjamin P

    2015-11-01

    The honeybee, Apis mellifera, is the world's most important pollinator and is ubiquitous in most agricultural ecosystems. Four major evolutionary lineages and at least 24 subspecies are recognized. Commercial populations are mainly derived from subspecies originating in Europe (75-95%). The Africanized honeybee is a New World hybrid of A. m. scutellata from Africa and European subspecies, with the African component making up 50-90% of the genome. Africanized honeybees are considered undesirable for bee-keeping in most countries, due to their extreme defensiveness and poor honey production. The international trade in honeybees is restricted, due in part to bans on the importation of queens (and semen) from countries where Africanized honeybees are extant. Some desirable strains from the United States of America that have been bred for traits such as resistance to the mite Varroa destructor are unfortunately excluded from export to countries such as Australia due to the presence of Africanized honeybees in the USA. This study shows that a panel of 95 single nucleotide polymorphisms, chosen to differentiate between the African, Eastern European and Western European lineages, can detect Africanized honeybees with a high degree of confidence via ancestry assignment. Our panel therefore offers a valuable tool to mitigate the risks of spreading Africanized honeybees across the globe and may enable the resumption of queen and bee semen imports from the Americas.

  14. Vestibular Performance During High-Acceleration Stimuli Correlates with Clinical Decline in SCA6.

    PubMed

    Huh, Young Eun; Kim, Ji-Soo; Kim, Hyo-Jung; Park, Seong-Ho; Jeon, Beom Seok; Kim, Jong-Min; Cho, Jin Whan; Zee, David S

    2015-06-01

    In spinocerebellar ataxia type 6 (SCA6), the vestibular dysfunction and its correlation with other clinical parameters require further exploration. We determined vestibular responses over a broad range of stimulus acceleration in 11 patients with SCA6 (six men, age range=33-72 years, mean age±SD=59±12 years) using bithermal caloric irrigations, rotary chair, and head impulse tests. Correlations were also pursued among disability scores, as measured using the International Cooperative Ataxia Rating Scale, disease duration, age at onset, cytosine-adenine-guanine (CAG) repeat length, and the gain of the vestibulo-ocular reflex (VOR). In response to relatively low-acceleration, low-frequency rotational and bithermal caloric stimuli, the VOR gains were normal or increased regardless of the severity of disease. On the other hand, with relatively high-acceleration, high-frequency head impulses, there was a relative increase in gain in the mildly affected patients and a decrease in gain in the more severely affected patients and gains were negatively correlated with the severity of disease (Spearman correlation, R=-0.927, p<0.001). Selective decrease of the vestibular responses during high-acceleration, high-frequency stimuli may be ascribed to degeneration of either the flocculus or vestibular nuclei. The performance of the VOR during high-acceleration, high-frequency head impulses may be a quantitative indicator of clinical decline in SCA6.

  15. Detection of Unexpected High Correlations between Balance Calibration Loads and Load Residuals

    NASA Technical Reports Server (NTRS)

    Ulbrich, N.; Volden, T.

    2014-01-01

    An algorithm was developed for the assessment of strain-gage balance calibration data that makes it possible to systematically investigate potential sources of unexpected high correlations between calibration load residuals and applied calibration loads. The algorithm investigates correlations on a load series by load series basis. The linear correlation coefficient is used to quantify the correlations. It is computed for all possible pairs of calibration load residuals and applied calibration loads that can be constructed for the given balance calibration data set. An unexpected high correlation between a load residual and a load is detected if three conditions are met: (i) the absolute value of the correlation coefficient of a residual/load pair exceeds 0.95; (ii) the maximum of the absolute values of the residuals of a load series exceeds 0.25 % of the load capacity; (iii) the load component of the load series is intentionally applied. Data from a baseline calibration of a six-component force balance is used to illustrate the application of the detection algorithm to a real-world data set. This analysis also showed that the detection algorithm can identify load alignment errors as long as repeat load series are contained in the balance calibration data set that do not suffer from load alignment problems.

  16. Multielectron Correlation in High-Harmonic Generation: A 2D Model Analysis

    SciTech Connect

    Sukiasyan, Suren; McDonald, Chris; Destefani, Carlos; Brabec, Thomas; Ivanov, Misha Yu.

    2009-06-05

    We analyze the role of multielectron dynamics in high-harmonic generation spectroscopy, using an example of a two-electron system. We identify and systematically quantify the importance of correlation and exchange effects. One of the main sources for correlation is identified to be the polarization of the ion by the recombining continuum electron. This effect, which plays an important qualitative and quantitative role, seriously undermines the validity of the standard approaches to high-harmonic generation, which ignore the contribution of excited ionic states to the radiative recombination of the continuum electron.

  17. Identification of Noise Sources in High Speed Jets via Correlation Measurements: A Review

    NASA Technical Reports Server (NTRS)

    Bridges, James (Technical Monitor); Panda, Jayanta

    2005-01-01

    Significant advancement has been made in the last few years to identify noise sources in high speed jets via direct correlation measurements. In this technique turbulent fluctuations in the flow are correlated with far field acoustics signatures. In the 1970 s there was a surge of work using mostly intrusive probes, and a few using Laser Doppler Velocimetry, to measure turbulent fluctuations. The later experiments established "shear noise" as the primary source for the shallow angle noise. Various interpretations and criticisms from this time are described in the review. Recent progress in the molecular Rayleigh scattering based technique has provided a completely non-intrusive means of measuring density and velocity fluctuations. This has brought a renewed interest on correlation measurements. We have performed five different sets of experiments in single stream jets of different Mach number, temperature ratio and nozzle configurations. The present paper tries to summarize the correlation data from these works.

  18. Ancestry Estimation in Forensic Anthropology: Geometric Morphometric versus Standard and Nonstandard Interlandmark Distances.

    PubMed

    Katherine Spradley, M; Jantz, Richard L

    2016-07-01

    Standard cranial measurements are commonly used for ancestry estimation; however, 3D digitizers have made cranial landmark data collection and geometric morphometric (GM) analyses more popular within forensic anthropology. Yet there has been little focus on which data type works best. The goal of the present research is to test the discrimination ability of standard and nonstandard craniometric measurements and data derived from GM analysis. A total of 31 cranial landmarks were used to generate 465 interlandmark distances, including a subset of 20 commonly used measurements, and to generate principal component scores from procrustes coordinates. All were subjected to discriminant function analysis to ascertain which type of data performed best for ancestry estimation of American Black and White and Hispanic males and females. The nonstandard interlandmark distances generated the highest classification rates for females (90.5%) and males (88.2%). Using nonstandard interlandmark distances over more commonly used measurements leads to better ancestry estimates for our current population structure.

  19. Translating Population Difference: The Use and Re-Use of Genetic Ancestry in Brazilian Cancer Genetics

    PubMed Central

    Gibbon, Sahra

    2016-01-01

    ABSTRACT In the past ten years, there has been an expansion of scientific interest in population genetics linked to both understanding histories of human migration and the way that population difference and diversity may account for and/or be implicated in health and disease. In this article, I examine how particular aspects of a globalizing research agenda related to population differences and genetic ancestry are taken up in locally variant ways in the nascent field of Brazilian cancer genetics. Drawing on a broad range of ethnographic data from clinical and nonclinical contexts in the south of Brazil, I examine the ambiguities that attention to genetic ancestry generates, so revealing the disjunctured and diverse ways a global research agenda increasingly orientated to questions of population difference and genetic ancestry is being used and reused. PMID:26452039

  20. Forensic Applicability of Femur Subtrochanteric Shape to Ancestry Assessment in Thai and White American Males.

    PubMed

    Tallman, Sean D; Winburn, Allysha P

    2015-09-01

    Ancestry assessment from the postcranial skeleton presents a significant challenge to forensic anthropologists. However, metric dimensions of the femur subtrochanteric region are believed to distinguish between individuals of Asian and non-Asian descent. This study tests the discriminatory power of subtrochanteric shape using modern samples of 128 Thai and 77 White American males. Results indicate that the samples' platymeric index distributions are significantly different (p≤0.001), with the Thai platymeric index range generally lower and the White American range generally higher. While the application of ancestry assessment methods developed from Native American subtrochanteric data results in low correct classification rates for the Thai sample (50.8-57.8%), adapting these methods to the current samples leads to better classification. The Thai data may be more useful in forensic analysis than previously published subtrochanteric data derived from Native American samples. Adapting methods to include appropriate geographic and contemporaneous populations increases the accuracy of femur subtrochanteric ancestry methods.

  1. Translating Population Difference: The Use and Re-Use of Genetic Ancestry in Brazilian Cancer Genetics.

    PubMed

    Gibbon, Sahra

    2016-01-01

    In the past ten years, there has been an expansion of scientific interest in population genetics linked to both understanding histories of human migration and the way that population difference and diversity may account for and/or be implicated in health and disease. In this article, I examine how particular aspects of a globalizing research agenda related to population differences and genetic ancestry are taken up in locally variant ways in the nascent field of Brazilian cancer genetics. Drawing on a broad range of ethnographic data from clinical and nonclinical contexts in the south of Brazil, I examine the ambiguities that attention to genetic ancestry generates, so revealing the disjunctured and diverse ways a global research agenda increasingly orientated to questions of population difference and genetic ancestry is being used and reused.

  2. Spatial correlation of the high intensity zone in deep-water acoustic field

    NASA Astrophysics Data System (ADS)

    Li, Jun; Li, Zheng-Lin; Ren, Yun

    2016-12-01

    The spatial correlations of acoustic field have important implications for underwater target detection and other applications in deep water. In this paper, the spatial correlations of the high intensity zone in the deep-water acoustic field are investigated by using the experimental data obtained in the South China Sea. The experimental results show that the structures of the spatial correlation coefficient at different ranges and depths are similar to the transmission loss structure in deep water. The main reason for this phenomenon is analyzed by combining the normal mode theory with the ray theory. It is shown that the received signals in the high intensity zone mainly include one or two main pulses which are contributed by the interference of a group of waterborne modes with similar phases. The horizontal-longitudinal correlations at the same receiver depth but in different high intensity zones are analyzed. At some positions, more pulses are received in the arrival structure of the signal due to bottom reflection and the horizontal-longitudinal correlation coefficient decreases accordingly. The multi-path arrival structure of receiving signal becomes more complex with increasing receiver depth. Project supported by the National Natural Science Foundation of China (Grant Nos. 11434012 and 41561144006).

  3. Speckle-correlation imaging through highly scattering turbid media with LED illumination

    NASA Astrophysics Data System (ADS)

    Shao, Xiaopeng; Dai, Weijia; Wu, Tengfei; Li, Huijuan; Wang, Lin

    2015-05-01

    We address an optical imaging method that allows imaging, which owing to the "memory-effect" for speckle correlations, through highly scattering turbid media with "Error Reduction - Hybid Input Ouput (ER-HIO)" algorithm. When light propagates through the opaque materials, such as white paint, paper or biological tissues, it will be scattered away due to the inhomogeneity of the refractive index. Multiple scattering of light in highly scattering media forms speckle field, which will greatly reduce the imaging depth and degrade the imaging quality. Some methods have been developed to solve this problem in recent years, including wavefront modulation method (WMM), transmission matrix method (TMM) and speckle correlations method (SCM). A novel approach is proposed to image through a highly scattering turbid medium, which combines speckle correlations method (SCM) with phase retrieval algorithm (PRA). Here, we show that, owing to the "optical memory effect" for speckle correlations, a single frame image of the speckle field, captured with a high performance detector, encodes sufficient information to image through highly scattering turbid media. Theoretical and experimental results show that, neither the light source, nor wave-front shaping is required in this method, and that the imaging can be easily realized here using just a simple optical system with the help of optical memory effect. Our method does not require coherent light source, which can be achieved with LED illumination, unlike previous approaches, and therefore is potentially suitable for more and more areas. Consequently, it will be beneficial to achieve imaging in currently inaccessible scenarios.

  4. High-resolution correlation of Gulf of Mexico Pliocene-Pleistocene sands

    SciTech Connect

    Ragan, G.M.; Abbott, W.H.

    1989-03-01

    Correlating individual sands is critical to field development and reservoir management. High-resolution biostratigraphy can provide this correlation. Bioevents identified in the hemipelagic muds, provide an additional framework for calibrating seismic record sections. Applying this high-resolution data set can reduce the risk in development drilling. Regional extinction data, typically separated by hundreds or even thousands of feet, permit calibration of regional mapping horizons between which reservoir objectives most often occur. New studies in the Gulf of Mexico Pliocene-Pleistocene reveal local and semiregional signals between regional extinctions. These signals, or events, are caused by physical and/or chemical fluctuations in oceanic water masses through time. Planktonic assemblages reflect and imprint this signal on the accumulating sediments. Identifying and documenting these events is the principal behind high-resolution biostratigraphy. Plotted on electric logs and seismic sections, such signals allow for refined correlation and subdivision of sediment packages. From conventional well cuttings, the authors present high-resolution biostratigraphic analyses from two fields in the High Island and Green Canyon areas. Biostratigraphic events have been identified and local zonations established through the sand-rich productive intervals of both fields. Individual sands and sandy intervals are correlated using this technique.

  5. Genetic ancestry is associated with colorectal adenomas and adenocarcinomas in Latino populations.

    PubMed

    Hernandez-Suarez, Gustavo; Sanabria, Maria Carolina; Serrano, Marta; Herran, Oscar F; Perez, Jesus; Plata, Jose L; Zabaleta, Jovanny; Tenesa, Albert

    2014-10-01

    Colorectal cancer rates in Latin American countries are less than half of those observed in the United States. Latin Americans are the resultant of generations of an admixture of Native American, European, and African individuals. The potential role of genetic admixture in colorectal carcinogenesis has not been examined. We evaluate the association of genetic ancestry with colorectal neoplasms in 190 adenocarcinomas, 113 sporadic adenomas and 243 age- and sex-matched controls enrolled in a multicentric case-control study in Colombia. Individual ancestral genetic fractions were estimated using the STRUCTURE software, based on allele frequencies and assuming three distinct population origins. We used the Illumina Cancer Panel to genotype 1,421 sparse single-nucleotide polymorphisms (SNPs), and Northern and Western European ancestry, LWJ and Han Chinese in Beijing, China populations from the HapMap project as references. A total of 678 autosomal SNPs overlapped with the HapMap data set SNPs and were used for ancestry estimations. African mean ancestry fraction was higher in adenomas (0.13, 95% confidence interval (95% CI)=0.11-0.15) and cancer cases (0.14, 95% CI=0.12-0.16) compared with controls (0.11, 95% CI=0.10-0.12). Conditional logistic regression analysis, controlling for known risk factors, showed a positive association of African ancestry per 10% increase with both colorectal adenoma (odds ratio (OR)=1.12, 95% CI=0.97-1.30) and adenocarcinoma (OR=1.19, 95% CI=1.05-1.35). In conclusion, increased African ancestry (or variants linked to it) contributes to the increased susceptibility of colorectal cancer in admixed Latin American population.

  6. Genomic ancestry of North Africans supports back-to-Africa migrations.

    PubMed

    Henn, Brenna M; Botigué, Laura R; 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.

  7. Possible multiparticle ridge-like correlations in very high multiplicity proton–proton collisions

    SciTech Connect

    Bjorken, James D.; Brodsky, Stanley J.; Scharff Goldhaber, Alfred

    2013-10-01

    The CMS Collaboration at the LHC has reported a remarkable and unexpected phenomenon in very high-multiplicity high energy proton–proton collisions: a positive correlation between two particles produced at similar azimuthal angles, spanning a large range in rapidity. We suggest that this “ridge”-like correlation may be a reflection of the rare events generated by the collision of aligned flux tubes connecting the valence quarks in the wave functions of the colliding protons. The “spray” of particles resulting from the approximate line source produced in such inelastic collisions then gives rise to events with a strong correlation between particles produced over a large range of both positive and negative rapidity. We suggest an additional variable that is sensitive to such a line source which is related to a commonly used measure, ellipticity.

  8. Distinct Transcript Isoforms of the Atypical Chemokine Receptor 1 (ACKR1) / Duffy Antigen Receptor for Chemokines (DARC) Gene Are Expressed in Lymphoblasts and Altered Isoform Levels Are Associated with Genetic Ancestry and the Duffy-Null Allele

    PubMed Central

    Davis, Melissa B.; Walens, Andrea; Hire, Rupali; Mumin, Kauthar; Brown, Andrea M.; Ford, DeJuana; Howerth, Elizabeth W.; Monteil, Michele

    2015-01-01

    The Atypical ChemoKine Receptor 1 (ACKR1) gene, better known as Duffy Antigen Receptor for Chemokines (DARC or Duffy), is responsible for the Duffy Blood Group and plays a major role in regulating the circulating homeostatic levels of pro-inflammatory chemokines. Previous studies have shown that one common variant, the Duffy Null (Fy-) allele that is specific to African Ancestry groups, completely removes expression of the gene on erythrocytes; however, these individuals retain endothelial expression. Additional alleles are associated with a myriad of clinical outcomes related to immune responses and inflammation. In addition to allele variants, there are two distinct transcript isoforms of DARC which are expressed from separate promoters, and very little is known about the distinct transcriptional regulation or the distinct functionality of these protein isoforms. Our objective was to determine if the African specific Fy- allele alters the expression pattern of DARC isoforms and therefore could potentially result in a unique signature of the gene products, commonly referred to as antigens. Our work is the first to establish that there is expression of DARC on lymphoblasts. Our data indicates that people of African ancestry have distinct relative levels of DARC isoforms expressed in these cells. We conclude that the expression of both isoforms in combination with alternate alleles yields multiple Duffy antigens in ancestry groups, depending upon the haplotypes across the gene. Importantly, we hypothesize that DARC isoform expression patterns will translate into ancestry-specific inflammatory responses that are correlated with the axis of pro-inflammatory chemokine levels and distinct isoform-specific interactions with these chemokines. Ultimately, this work will increase knowledge of biological mechanisms underlying disparate clinical outcomes of inflammatory-related diseases among ethnic and geographic ancestry groups. PMID:26473357

  9. Evaluation of fall Sun Exposure Score in predicting vitamin D status in young Canadian adults, and the influence of ancestry.

    PubMed

    Sham, Lauren; Yeh, E Ann; Magalhaes, Sandra; Parra, Esteban J; Gozdzik, Agnes; Banwell, Brenda; Hanwell, Heather E

    2015-04-01

    Query of sun-related habits or ancestry could help screen for risk of vitamin D insufficiency (serum 25-hydroxyvitamin D<75nmol/L). We evaluated the association between Sun Exposure Score (calculated from recall of Time Exposed to Sun and Skin Exposed to Sun in the previous week), demographics and anthropometrics (including self-reported ancestry and skin melanin reflectometry), and serum 25(OH)D levels in healthy young Canadian adults in the Greater Toronto Area (GTA; 43°N) during fall. 310 adults (67% female) of European, East Asian, and South Asian ancestries were evaluated. The median (interquartile range) 25(OH)D level was 49.7nmol/L (36.7-70.3) and 80% of participants were vitamin D insufficient. The vast majority of those of East and South Asian ancestry were vitamin D insufficient (91% and 97%, respectively), as were 55% of those of European ancestry. Sun Exposure Score and 25(OH)D concentrations were not associated after accounting for confounders. A multivariable model showed ancestry, recent summer sun exposure, sex, melanin, vitamin D intake, age and year of study significantly predicted 25(OH)D concentration; ancestry was the strongest independent predictor (adjusted R(2)=43%). Although Sun Exposure Score was not a significant predictor of serum 25(OH)D levels, inquiry of ancestry has potential use in screening for vitamin D insufficiency.

  10. Suppression of back-to-back particle-antiparticle correlations in high-energy nuclear collisions

    SciTech Connect

    Knoll, Joern

    2011-04-15

    Analytical formulas are presented which provide quantitative estimates for the suppression of the anticipated back-to-back particle-antiparticle correlations in high-energy nuclear collisions, due to both the finite duration of the transition dynamics and the continuous freeze-out. They show that the effect is unlikely to be observed.

  11. Long range correlations in high multiplicity hadron collisions: Building bridges with ridges

    SciTech Connect

    Venugopalan, Raju

    2015-01-15

    We discuss the physics of the ridge–azimuthally collimated long range rapidity correlations–in high multiplicity proton–proton and proton–nucleus collisions. We outline some of the theoretical discussions in the literature that address the systematics of these ridge correlations.

  12. The costs of ignoring high-order correlations in populations of model neurons.

    PubMed

    Michel, Melchi M; Jacobs, Robert A

    2006-03-01

    Investigators debate the extent to which neural populations use pair-wise and higher-order statistical dependencies among neural responses to represent information about a visual stimulus. To study this issue, three statistical decoders were used to extract the information in the responses of model neurons about the binocular disparities present in simulated pairs of left-eye and right-eye images: (1) the full joint probability decoder considered all possible statistical relations among neural responses as potentially important; (2) the dependence tree decoder also considered all possible relations as potentially important, but it approximated high-order statistical correlations using a computationally tractable procedure; and (3) the independent response decoder, which assumed that neural responses are statistically independent, meaning that all correlations should be zero and thus can be ignored. Simulation results indicate that high-order correlations among model neuron responses contain significant information about binocular disparities and that the amount of this high-order information increases rapidly as a function of neural population size. Furthermore, the results highlight the potential importance of the dependence tree decoder to neuroscientists as a powerful but still practical way of approximating high-order correlations among neural responses.

  13. Beyond Correlations: Usefulness of High School GPA and Test Scores in Making College Admissions Decisions

    ERIC Educational Resources Information Center

    Sawyer, Richard

    2013-01-01

    Correlational evidence suggests that high school GPA is better than admission test scores in predicting first-year college GPA, although test scores have incremental predictive validity. The usefulness of a selection variable in making admission decisions depends in part on its predictive validity, but also on institutions' selectivity and…

  14. A Person-Centered Investigation of Academic Motivation and Its Correlates in High School

    ERIC Educational Resources Information Center

    Wormington, Stephanie V.; Corpus, Jennifer Henderlong; Anderson, Kristen G.

    2012-01-01

    This study used a person-centered approach to identify naturally occurring combinations of intrinsic motivation and controlled forms of extrinsic motivation (i.e., introjected and external regulation) and their correlates in an academic context. 1061 high school students completed measures of academic motivation, performance, and school-related…

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

    PubMed Central

    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. PMID:24262358

  16. Multilabel image classification via high-order label correlation driven active learning.

    PubMed

    Zhang, Bang; Wang, Yang; Chen, Fang

    2014-03-01

    Supervised machine learning techniques have been applied to multilabel image classification problems with tremendous success. Despite disparate learning mechanisms, their performances heavily rely on the quality of training images. However, the acquisition of training images requires significant efforts from human annotators. This hinders the applications of supervised learning techniques to large scale problems. In this paper, we propose a high-order label correlation driven active learning (HoAL) approach that allows the iterative learning algorithm itself to select the informative example-label pairs from which it learns so as to learn an accurate classifier with less annotation efforts. Four crucial issues are considered by the proposed HoAL: 1) unlike binary cases, the selection granularity for multilabel active learning need to be fined from example to example-label pair; 2) different labels are seldom independent, and label correlations provide critical information for efficient learning; 3) in addition to pair-wise label correlations, high-order label correlations are also informative for multilabel active learning; and 4) since the number of label combinations increases exponentially with respect to the number of labels, an efficient mining method is required to discover informative label correlations. The proposed approach is tested on public data sets, and the empirical results demonstrate its effectiveness.

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

    PubMed

    Hu, Sheng Li; Xiong, Wei; Dai, Zhi Qiang; Zhao, Heng Li; Feng, Hua

    2016-01-01

    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.

  18. 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.

    PubMed

    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.

  19. Genetic ancestry modifies the association between genetic risk variants and breast cancer risk among Hispanic and non-Hispanic white women

    PubMed Central

    Fejerman, Laura

    2013-01-01

    Hispanic women in the USA have lower breast cancer incidence than non-Hispanic white (NHW) women. Genetic factors may contribute to this difference. Breast cancer genome-wide association studies (GWAS) conducted in women of European or Asian descent have identified multiple risk variants. We tested the association between 10 previously reported single nucleotide polymorphisms (SNPs) and risk of breast cancer in a sample of 4697 Hispanic and 3077 NHW women recruited as part of three population-based case–control studies of breast cancer. We used stratified logistic regression analyses to compare the associations with different genetic variants in NHWs and Hispanics classified by their proportion of Indigenous American (IA) ancestry. Five of 10 SNPs were statistically significantly associated with breast cancer risk. Three of the five significant variants (rs17157903-RELN, rs7696175-TLR1 and rs13387042-2q35) were associated with risk among Hispanics but not in NHWs. The odds ratio (OR) for the heterozygous at 2q35 was 0.75 [95% confidence interval (CI) = 0.50–1.15] for low IA ancestry and 1.38 (95% CI = 1.04–1.82) for high IA ancestry (P interaction 0.02). The ORs for association at RELN were 0.87 (95% CI = 0.59–1.29) and 1.69 (95% CI = 1.04–2.73), respectively (P interaction 0.03). At the TLR1 locus, the ORs for women homozygous for the rare allele were 0.74 (95% CI = 0.42–1.31) and 1.73 (95% CI = 1.19–2.52) (P interaction 0.03). Our results suggest that the proportion of IA ancestry modifies the magnitude and direction of the association of 3 of the 10 previously reported variants. Genetic ancestry should be considered when assessing risk in women of mixed descent and in studies designed to discover causal mutations. PMID:23563089

  20. Domain Specific Changes in Cognition at High Altitude and Its Correlation with Hyperhomocysteinemia

    PubMed Central

    Sharma, Vijay K.; Das, Saroj K.; Dhar, Priyanka; Hota, Kalpana B.; Mahapatra, Bidhu B.; Vashishtha, Vivek; Kumar, Ashish; Hota, Sunil K.; Norboo, Tsering; Srivastava, Ravi B.

    2014-01-01

    Though acute exposure to hypobaric hypoxia is reported to impair cognitive performance, the effects of prolonged exposure on different cognitive domains have been less studied. The present study aimed at investigating the time dependent changes in cognitive performance on prolonged stay at high altitude and its correlation with electroencephalogram (EEG) and plasma homocysteine. The study was conducted on 761 male volunteers of 25–35 years age who had never been to high altitude and baseline data pertaining to domain specific cognitive performance, EEG and homocysteine was acquired at altitude ≤240 m mean sea level (MSL). The volunteers were inducted to an altitude of 4200–4600 m MSL and longitudinal follow-ups were conducted at durations of 03, 12 and 18 months. Neuropsychological assessment was performed for mild cognitive impairment (MCI), attention, information processing rate, visuo-spatial cognition and executive functioning. Total homocysteine (tHcy), vitamin B12 and folic acid were estimated. Mini Mental State Examination (MMSE) showed temporal increase in the percentage prevalence of MCI from 8.17% on 03 months of stay at high altitude to 18.54% on 18 months of stay. Impairment in visuo-spatial executive, attention, delayed recall and procedural memory related cognitive domains were detected following prolonged stay in high altitude. Increase in alpha wave amplitude in the T3, T4 and C3 regions was observed during the follow-ups which was inversely correlated (r = −0.68) to MMSE scores. The tHcy increased proportionately with duration of stay at high altitude and was correlated with MCI. No change in vitamin B12 and folic acid was observed. Our findings suggest that cognitive impairment is progressively associated with duration of stay at high altitude and is correlated with elevated tHcy in the plasma. Moreover, progressive MCI at high altitude occurs despite acclimatization and is independent of vitamin B12 and folic acid. PMID:24988417

  1. Domain specific changes in cognition at high altitude and its correlation with hyperhomocysteinemia.

    PubMed

    Sharma, Vijay K; Das, Saroj K; Dhar, Priyanka; Hota, Kalpana B; Mahapatra, Bidhu B; Vashishtha, Vivek; Kumar, Ashish; Hota, Sunil K; Norboo, Tsering; Srivastava, Ravi B

    2014-01-01

    Though acute exposure to hypobaric hypoxia is reported to impair cognitive performance, the effects of prolonged exposure on different cognitive domains have been less studied. The present study aimed at investigating the time dependent changes in cognitive performance on prolonged stay at high altitude and its correlation with electroencephalogram (EEG) and plasma homocysteine. The study was conducted on 761 male volunteers of 25-35 years age who had never been to high altitude and baseline data pertaining to domain specific cognitive performance, EEG and homocysteine was acquired at altitude ≤240 m mean sea level (MSL). The volunteers were inducted to an altitude of 4200-4600 m MSL and longitudinal follow-ups were conducted at durations of 03, 12 and 18 months. Neuropsychological assessment was performed for mild cognitive impairment (MCI), attention, information processing rate, visuo-spatial cognition and executive functioning. Total homocysteine (tHcy), vitamin B12 and folic acid were estimated. Mini Mental State Examination (MMSE) showed temporal increase in the percentage prevalence of MCI from 8.17% on 03 months of stay at high altitude to 18.54% on 18 months of stay. Impairment in visuo-spatial executive, attention, delayed recall and procedural memory related cognitive domains were detected following prolonged stay in high altitude. Increase in alpha wave amplitude in the T3, T4 and C3 regions was observed during the follow-ups which was inversely correlated (r = -0.68) to MMSE scores. The tHcy increased proportionately with duration of stay at high altitude and was correlated with MCI. No change in vitamin B12 and folic acid was observed. Our findings suggest that cognitive impairment is progressively associated with duration of stay at high altitude and is correlated with elevated tHcy in the plasma. Moreover, progressive MCI at high altitude occurs despite acclimatization and is independent of vitamin B12 and folic acid.

  2. Correlated sputtering from a hydrogen-terminated Si surface by individual highly charged ion impacts

    NASA Astrophysics Data System (ADS)

    Tona, Masahide; Sakurai, Makoto; Yamada, Chikashi; Ohtani, Shunsuke

    2010-09-01

    The interaction of slow iodine highly charged ions (HCIs), Iq+, with a hydrogen-terminated Si(1 1 1)-(1 × 1) surface was investigated for a wide range of q from 17 to 53 (fully stripped ion). The coincidence measurement for secondary ion emission reveals that correlated sputtering is enhanced toward higher q, that is, while Si+ sputtering is anti-correlated with H+, multiple H+ are simultaneously emitted. The direct observation of the HCI-bombarded surface with a scanning tunneling microscope supports the result of the multiple hydrogen emission. These results are discussed in consideration of the strong Coulomb interaction of incident HCIs with the surface and subsurface atoms.

  3. High-pT azimuthal correlations of neutral strange baryons and mesons in STAR at RHIC

    SciTech Connect

    Bielcikova, Jana

    2006-07-11

    We present results on two-particle azimuthal correlations of high-pT neutral strange baryons ({lambda},{lambda}-bar) and mesons (K{sub S}{sup 0}) associated with non-identified charged particles in d+Au and Au+Au collisions at {radical}(s{sub NN}) = 200 GeV. In particular, we discuss properties of the near-side yield of associated charged particles as a function of centrality, transverse momentum and zT, as well as possible baryon/meson and particle/antiparticle differences. The results are compared to the proton and pion triggered correlations and to fragmentation and recombination models.

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

    SciTech Connect

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

    2010-09-15

    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 {phi}{phi} pairs at the Relativistic Heavy Ion Collider (RHIC) energies.

  5. High Interleukin 17 Expression Is Correlated With Better Cardiac Function in Human Chagas Disease

    PubMed Central

    Magalhães, Luisa M. D.; Villani, Fernanda N. A.; Nunes, Maria do Carmo P.; Gollob, Kenneth J.; Rocha, Manoel O. C.; Dutra, Walderez O.

    2013-01-01

    This study was designed to investigate whether the expression of interleukin 17 (IL-17) is associated with the indeterminate or cardiac clinical forms of Chagas disease and whether IL-17 expression can be correlated with patients' cardiac function. Our results demonstrated that cardiac Chagas patients have a lower intensity of expression of IL-17 by total lymphocytes and lower frequency of circulating T helper 17 cells. Correlative analysis showed that high IL-17 expression was associated with better cardiac function, as determined by left ventricular ejection fraction and left ventricular diastolic diameter values. Therefore, IL-17 expression can be a protective factor to prevent myocardial damage in human Chagas disease. PMID:23204182

  6. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora.

    PubMed

    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.

  7. Low Speed and High Speed Correlation of SMART Active Flap Rotor Loads

    NASA Technical Reports Server (NTRS)

    Kottapalli, Sesi B. R.

    2010-01-01

    Measured, open loop and closed loop data from the SMART rotor test in the NASA Ames 40- by 80- Foot Wind Tunnel are compared with CAMRAD II calculations. One open loop high-speed case and four closed loop cases are considered. The closed loop cases include three high-speed cases and one low-speed case. Two of these high-speed cases include a 2 deg flap deflection at 5P case and a test maximum-airspeed case. This study follows a recent, open loop correlation effort that used a simple correction factor for the airfoil pitching moment Mach number. Compared to the earlier effort, the current open loop study considers more fundamental corrections based on advancing blade aerodynamic conditions. The airfoil tables themselves have been studied. Selected modifications to the HH-06 section flap airfoil pitching moment table are implemented. For the closed loop condition, the effect of the flap actuator is modeled by increased flap hinge stiffness. Overall, the open loop correlation is reasonable, thus confirming the basic correctness of the current semi-empirical modifications; the closed loop correlation is also reasonable considering that the current flap model is a first generation model. Detailed correlation results are given in the paper.

  8. High capsid-genome correlation facilitates creation of AAV libraries for directed evolution.

    PubMed

    Nonnenmacher, Mathieu; van Bakel, Harm; Hajjar, Roger J; Weber, Thomas

    2015-04-01

    Directed evolution of adeno-associated virus (AAV) through successive rounds of phenotypic selection is a powerful method to isolate variants with improved properties from large libraries of capsid mutants. Importantly, AAV libraries used for directed evolution are based on the "natural" AAV genome organization where the capsid proteins are encoded in cis from replicating genomes. This is necessary to allow the recovery of the capsid DNA after each step of phenotypic selection. For directed evolution to be used successfully, it is essential to minimize the random mixing of capsomers and the encapsidation of nonmatching viral genomes during the production of the viral libraries. Here, we demonstrate that multiple AAV capsid variants expressed from Rep/Cap containing viral genomes result in near-homogeneous capsids that display an unexpectedly high capsid-DNA correlation. Next-generation sequencing of AAV progeny generated by bulk transfection of a semi-random peptide library showed a strong counter-selection of capsid variants encoding premature stop codons, which further supports a strong capsid-genome identity correlation. Overall, our observations demonstrate that production of "natural" AAVs results in low capsid mosaicism and high capsid-genome correlation. These unique properties allow the production of highly diverse AAV libraries in a one-step procedure with a minimal loss in phenotype-genotype correlation.

  9. High Capsid–Genome Correlation Facilitates Creation of AAV Libraries for Directed Evolution

    PubMed Central

    Nonnenmacher, Mathieu; van Bakel, Harm; Hajjar, Roger J; Weber, Thomas

    2015-01-01

    Directed evolution of adeno-associated virus (AAV) through successive rounds of phenotypic selection is a powerful method to isolate variants with improved properties from large libraries of capsid mutants. Importantly, AAV libraries used for directed evolution are based on the “natural” AAV genome organization where the capsid proteins are encoded in cis from replicating genomes. This is necessary to allow the recovery of the capsid DNA after each step of phenotypic selection. For directed evolution to be used successfully, it is essential to minimize the random mixing of capsomers and the encapsidation of nonmatching viral genomes during the production of the viral libraries. Here, we demonstrate that multiple AAV capsid variants expressed from Rep/Cap containing viral genomes result in near-homogeneous capsids that display an unexpectedly high capsid–DNA correlation. Next-generation sequencing of AAV progeny generated by bulk transfection of a semi-random peptide library showed a strong counter-selection of capsid variants encoding premature stop codons, which further supports a strong capsid–genome identity correlation. Overall, our observations demonstrate that production of “natural” AAVs results in low capsid mosaicism and high capsid–genome correlation. These unique properties allow the production of highly diverse AAV libraries in a one-step procedure with a minimal loss in phenotype–genotype correlation. PMID:25586687

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

    PubMed Central

    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.

    2013-01-01

    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. PMID:23579869

  11. Correlating the ancient Maya and modern European calendars with high-precision AMS 14C dating.

    PubMed

    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

    2013-01-01

    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 (14)C 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.

  12. Teaching through the Prism of Difference: A Dialogue among Four Bilingual, African-Ancestry Teachers.

    ERIC Educational Resources Information Center

    Casimir, Myriam; Mattox, Norman; Hays, John; Vasquez, Carla Llewelyn

    2000-01-01

    Four bilingual educators of African ancestry discuss issues that affect them as teachers and that affect their students as ethnolinguistic minorities. The paper discusses views of culture and language; teachers' identity construction; students' identity construction; and a twofold educational response to students' academic and social needs as…

  13. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

    PubMed

    Nédélec, Yohann; Sanz, Joaquín; Baharian, Golshid; Szpiech, Zachary A; Pacis, Alain; Dumaine, Anne; Grenier, Jean-Christophe; Freiman, Andrew; Sams, Aaron J; Hebert, Steven; Pagé Sabourin, Ariane; Luca, Francesca; Blekhman, Ran; Hernandez, Ryan D; Pique-Regi, Roger; Tung, Jenny; Yotova, Vania; Barreiro, Luis B

    2016-10-20

    Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.

  14. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.

    PubMed

    Kosoy, Roman; Nassir, Rami; Tian, Chao; White, Phoebe A; Butler, Lesley M; Silva, Gabriel; Kittles, Rick; Alarcon-Riquelme, Marta E; Gregersen, Peter K; Belmont, John W; De La Vega, Francisco M; Seldin, Michael F

    2009-01-01

    To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations.

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

    NASA Astrophysics Data System (ADS)

    Moharana, Reetanjali; Razzaque, Soebur

    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 gtrsim 20 TeV is considered. However when we consider the HESE sample with deposited energy gtrsim 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.

  16. High correlation of Middle East respiratory syndrome spread with Google search and Twitter trends in Korea

    PubMed Central

    Shin, Soo-Yong; Seo, Dong-Woo; An, Jisun; Kwak, Haewoon; Kim, Sung-Han; Gwack, Jin; Jo, Min-Woo

    2016-01-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV) was exported to Korea in 2015, resulting in a threat to neighboring nations. We evaluated the possibility of using a digital surveillance system based on web searches and social media data to monitor this MERS outbreak. We collected the number of daily laboratory-confirmed MERS cases and quarantined cases from May 11, 2015 to June 26, 2015 using the Korean government MERS portal. The daily trends observed via Google search and Twitter during the same time period were also ascertained using Google Trends and Topsy. Correlations among the data were then examined using Spearman correlation analysis. We found high correlations (>0.7) between Google search and Twitter results and the number of confirmed MERS cases for the previous three days using only four simple keywords: “MERS”, “” (“MERS (in Korean)”), “” (“MERS symptoms (in Korean)”), and “” (“MERS hospital (in Korean)”). Additionally, we found high correlations between the Google search and Twitter results and the number of quarantined cases using the above keywords. This study demonstrates the possibility of using a digital surveillance system to monitor the outbreak of MERS. PMID:27595921

  17. High correlation of Middle East respiratory syndrome spread with Google search and Twitter trends in Korea.

    PubMed

    Shin, Soo-Yong; Seo, Dong-Woo; An, Jisun; Kwak, Haewoon; Kim, Sung-Han; Gwack, Jin; Jo, Min-Woo

    2016-09-06

    The Middle East respiratory syndrome coronavirus (MERS-CoV) was exported to Korea in 2015, resulting in a threat to neighboring nations. We evaluated the possibility of using a digital surveillance system based on web searches and social media data to monitor this MERS outbreak. We collected the number of daily laboratory-confirmed MERS cases and quarantined cases from May 11, 2015 to June 26, 2015 using the Korean government MERS portal. The daily trends observed via Google search and Twitter during the same time period were also ascertained using Google Trends and Topsy. Correlations among the data were then examined using Spearman correlation analysis. We found high correlations (>0.7) between Google search and Twitter results and the number of confirmed MERS cases for the previous three days using only four simple keywords: "MERS", " ("MERS (in Korean)"), " ("MERS symptoms (in Korean)"), and " ("MERS hospital (in Korean)"). Additionally, we found high correlations between the Google search and Twitter results and the number of quarantined cases using the above keywords. This study demonstrates the possibility of using a digital surveillance system to monitor the outbreak of MERS.

  18. Azimuthal anisotropy harmonics from long-range correlations in high multiplicity pp collisions at CMS

    NASA Astrophysics Data System (ADS)

    Chen, Zhenyu

    2016-12-01

    Measurements of two-particle angular correlations in pp collisions at √{ s} = 7 TeV are presented as a function of charged-particle multiplicities. The data, corresponding to an integrated luminosity of about 6.2 pb-1, were collected during the 2010 LHC pp run using the CMS detector. In high-multiplicity events, a long-range (| Δη | > 2), near-side (Δϕ ≈ 0) structure is found in the two-particle Δη - Δϕ correlation functions. The second-order (v2) and third-order (v3) azimuthal anisotropy harmonics of charged particles, KS0 and Λ / Λ ‾ particles are extracted from long-range two-particle correlations as a function of particle multiplicity and transverse momentum, after correcting for the contribution of back-to-back jet correlations. A v2 and v3 value of about 4% and 1%, averaging over 0.3 high-multiplicity region, and are found to be smaller than values obtained in pPb and PbPb collisions at similar multiplicities.

  19. African Genetic Ancestry is Associated with Sleep Depth in Older African Americans

    PubMed Central

    Halder, Indrani; Matthews, Karen A.; Buysse, Daniel J.; Strollo, Patrick J.; Causer, Victoria; Reis, Steven E.; Hall, Martica H.

    2015-01-01

    Study Objectives: The mechanisms that underlie differences in sleep characteristics between European Americans (EA) and African Americans (AA) are not fully known. Although social and psychological processes that differ by race are possible mediators, the substantial heritability of sleep characteristics also suggests genetic underpinnings of race differences. We hypothesized that racial differences in sleep phenotypes would show an association with objectively measured individual genetic ancestry in AAs. Design: Cross sectional. Setting: Community-based study. Participants: Seventy AA adults (mean age 59.5 ± 6.7 y; 62% female) and 101 EAs (mean age 60.5 ± 7 y, 39% female). Measurements and Results: Multivariate tests were used to compare the Pittsburgh Sleep Quality Index (PSQI) and in-home polysomnographic measures of sleep duration, sleep efficiency, apnea-hypopnea index (AHI), and indices of sleep depth including percent visually scored slow wave sleep (SWS) and delta EEG power of EAs and AAs. Sleep duration, efficiency, and sleep depth differed significantly by race. Individual % African ancestry (%AF) was measured in AA subjects using a panel of 1698 ancestry informative genetic markers and ranged from 10% to 88% (mean 67%). Hierarchical linear regression showed that higher %AF was associated with lower percent SWS in AAs (β (standard error) = −4.6 (1.5); P = 0.002), and explained 11% of the variation in SWS after covariate adjustment. A similar association was observed for delta power. No association was observed for sleep duration and efficiency. Conclusion: African genetic ancestry is associated with indices of sleep depth in African Americans. Such an association suggests that part of the racial differences in slow-wave sleep may have genetic underpinnings. Citation: Halder I, Matthews KA, Buysse DJ, Strollo PJ, Causer V, Reis SE, Hall MH. African genetic ancestry is associated with sleep depth in older African Americans. SLEEP 2015;38(8):1185–1193

  20. African genetic ancestry is associated with a protective effect on Dengue severity in colombian populations.

    PubMed

    Chacón-Duque, Juan Camilo; Adhikari, Kaustubh; Avendaño, Efren; Campo, Omer; Ramirez, Ruth; Rojas, Winston; Ruiz-Linares, Andrés; Restrepo, Berta Nelly; Bedoya, Gabriel

    2014-10-01

    The wide variation in severity displayed during Dengue Virus (DENV) infection may be influenced by host susceptibility. In several epidemiological approaches, differences in disease outcomes have been found between some ethnic groups, suggesting that human genetic background has an important role in disease severity. In the Caribbean, It has been reported that populations of African descent present considerable less frequency of severe forms compared with Mestizo and White self-reported groups. Admixed populations offer advantages for genetic epidemiology studies due to variation and distribution of alleles, such as those involved in disease susceptibility, as well to provide explanations of individual variability in clinical outcomes. The current study analysed three Colombian populations, which like most of Latin American populations, are made up of the product of complex admixture processes between European, Native American and African ancestors; having as a main goal to assess the effect of genetic ancestry, estimated with 30 Ancestry Informative Markers (AIMs), on DENV infection severity. We found that African ancestry has a protective effect against severe outcomes under several systems of clinical classification: Severe Dengue (OR: 0.963 for every 1% increase in African ancestry, 95% confidence interval (0.934-0.993), p-value: 0.016), Dengue Haemorrhagic Fever (OR: 0.969, 95% CI (0.947-0.991), p-value: 0.006), and occurrence of haemorrhages (OR: 0.971, 95% CI (0.952-0.989), p-value: 0.002). Conversely, decrease from 100% to 0% African ancestry significantly increases the chance of severe outcomes: OR is 44-fold for Severe Dengue, 24-fold for Dengue Haemorrhagic Fever, and 20-fold for occurrence of haemorrhages. Furthermore, several warning signs also showed statistically significant association given more evidences in specific stages of DENV infection. These results provide consistent evidence in order to infer statistical models providing a framework for

  1. Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

    PubMed

    Tofanelli, Sergio; Taglioli, Luca; Bertoncini, Stefania; Francalacci, Paolo; Klyosov, Anatole; Pagani, Luca

    2014-01-01

    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.

  2. Neonatal variables, altitude of residence and Aymara ancestry in northern Chile.

    PubMed

    Rothhammer, Francisco; Fuentes-Guajardo, Macarena; Chakraborty, Ranajit; Lorenzo Bermejo, Justo; Dittmar, Manuela

    2015-01-01

    Studies performed in the Andean plateau, one of the highest inhabited areas in the world, have reported that reduced availability of oxygen is associated to fetal growth retardation and lower birth weight, which are established predictors of morbidity and mortality during the first year of life. To test this hypothesis, perinatal variables of neonates born at the Juan Noé Hospital of Arica, Chile, were analyzed in relation to altitude of residence and Aymara ancestry of their mothers. The study population comprised the offspring of 5,295 mothers born between February 2004 and August 2010. Information included birth weight, height, head circumference, gestational age, altitude of residence and socioeconomic status, and was obtained from medical records. Mother´s ancestry was assessed based on surnames which were linked to percentages of Aymara admixture estimates relying on 40 selected ancestry informative markers. After correcting for the effect of multicollinearity among predictor variables, neonates born to mothers with an increased component of Aymara ancestry showed significantly higher birth weight and height at sea level, a marginally significant (p-value 0.06) decrease of birth weight and a significant decrease of height with altitude in comparison with the offspring of mothers with low Aymara ancestry. Since observed tendencies are suggestive of a possible genetic adaptation to hypoxia of the Chilean Aymara, we discuss briefly preliminary evidence related to fetal oxygen transport, particularly polymorphisms in the promoters of the HBG1 and HBG2 genes that are modulators of HbF synthesis, obtained in this ethnic group.

  3. Neonatal Variables, Altitude of Residence and Aymara Ancestry in Northern Chile

    PubMed Central

    Rothhammer, Francisco; Fuentes-Guajardo, Macarena; Chakraborty, Ranajit; Lorenzo Bermejo, Justo; Dittmar, Manuela

    2015-01-01

    Studies performed in the Andean plateau, one of the highest inhabited areas in the world, have reported that reduced availability of oxygen is associated to fetal growth retardation and lower birth weight, which are established predictors of morbidity and mortality during the first year of life. To test this hypothesis, perinatal variables of neonates born at the Juan Noé Hospital of Arica, Chile, were analyzed in relation to altitude of residence and Aymara ancestry of their mothers. The study population comprised the offspring of 5,295 mothers born between February 2004 and August 2010. Information included birth weight, height, head circumference, gestational age, altitude of residence and socioeconomic status, and was obtained from medical records. Mother´s ancestry was assessed based on surnames which were linked to percentages of Aymara admixture estimates relying on 40 selected ancestry informative markers. After correcting for the effect of multicollinearity among predictor variables, neonates born to mothers with an increased component of Aymara ancestry showed significantly higher birth weight and height at sea level, a marginally significant (p-value 0.06) decrease of birth weight and a significant decrease of height with altitude in comparison with the offspring of mothers with low Aymara ancestry. Since observed tendencies are suggestive of a possible genetic adaptation to hypoxia of the Chilean Aymara, we discuss briefly preliminary evidence related to fetal oxygen transport, particularly polymorphisms in the promoters of the HBG1 and HBG2 genes that are modulators of HbF synthesis, obtained in this ethnic group. PMID:25885573

  4. Completion of a worldwide reference panel of samples for an ancestry informative Indel assay.

    PubMed

    Santos, Carla; Phillips, Christopher; Oldoni, Fabio; Amigo, Jorge; Fondevila, Manuel; Pereira, Rui; Carracedo, Ángel; Lareu, Maria Victoria

    2015-07-01

    The use of ancestry informative markers (AIMs) in forensic analysis is of considerable utility since ancestry inference can progress an investigation when no identification has been made of DNA from the crime-scene. Short-amplicon markers, including insertion deletion polymorphisms, are particularly useful in forensic analysis due to their mutational stability, capacity to amplify degraded samples and straightforward amplification technique. In this study we report the completion of H952 HGDP-CEPH panel genotyping with a set of 46 AIM-Indels. The study adds Central South Asian and Middle Eastern population data, allowing a comparison of patterns of variation in Eurasia for these markers, in order to enhance their use in forensic analyses, particularly when combined with sets of ancestry informative SNPs. Ancestry analysis using principal component analysis and Bayesian methods indicates that a proportion of classification error occurs with European-Middle East population comparisons, but the 46 AIM-Indels have the capability to differentiate six major population groups when European-Central South Asian comparisons are made. These findings have relevance for forensic ancestry analyses in countries where South Asians form much of the demographic profile, including the UK, USA and South Africa. A novel third allele detected in MID-548 was characterized - despite a low frequency in the HGDP-CEPH panel samples, it appears confined to Central South Asian populations, increasing the ability to differentiate this population group. The H952 data set was implemented in a new open access SPSmart frequency browser - forInDel: Forensic Indel browser.

  5. Brain correlates of non-symbolic numerosity estimation in low and high mathematical ability children.

    PubMed

    Kovas, Yulia; Giampietro, Vincent; Viding, Essi; Ng, Virginia; Brammer, Michael; Barker, Gareth J; Happé, Francesca G E; Plomin, Robert

    2009-01-01

    Previous studies have implicated several brain areas as subserving numerical approximation. Most studies have examined brain correlates of adult numerical approximation and have not considered individual differences in mathematical ability. The present study examined non-symbolic numerical approximation in two groups of 10-year-olds: Children with low and high mathematical ability. The aims of this study were to investigate the brain mechanisms associated with approximate numerosity in children and to assess whether individual differences in mathematical ability are associated with differential brain correlates during the approximation task. The results suggest that, similarly to adults, multiple and distributed brain areas are involved in approximation in children. Despite equal behavioral performance, there were differences in the brain activation patterns between low and high mathematical ability groups during the approximation task. This suggests that individual differences in mathematical ability are reflected in differential brain response during approximation.

  6. High-dynamic-range cross-correlator for shot-to-shot measurement of temporal contrast

    NASA Astrophysics Data System (ADS)

    Kon, Akira; Nishiuchi, Mamiko; Kiriyama, Hiromitsu; Ogura, Koichi; Mori, Michiaki; Sakaki, Hironao; Kando, Masaki; Kondo, Kiminori

    2017-01-01

    The temporal contrast of an ultrahigh-intensity laser is a crucial parameter for laser plasma experiments. We have developed a multichannel cross-correlator (MCCC) for single-shot measurements of the temporal contrast in a high-power laser system. The MCCC is based on third-order cross-correlation, and has four channels and independent optical delay lines. We have experimentally demonstrated that the MCCC system achieves a high dynamic range of ˜1012 and a large temporal window of ˜1 ns. Moreover, we were able to measure the shot-to-shot fluctuations of a short-prepulse intensity at -26 ps and long-pulse (amplified spontaneous emission, ASE) intensities at -30, -450, and -950 ps before the arrival of the main pulse at the interaction point.

  7. Correlates of Sexually Transmitted Infections among Adolescents Attending Public High Schools, Panama, 2015

    PubMed Central

    Gabster, Amanda; Mohammed, Debbie Y.; Arteaga, Griselda B.; Castillero, Omar; Mojica, Nataly; Dyamond, José; Varela, Maria; Pascale, Juan Miguel

    2016-01-01

    Background Sexually transmitted infections (STIs) are common in adolescents worldwide. Vulnerability to STIs increases with risky sexual practices. This study described the sexual practices, estimated the prevalence of STIs, and identified correlates associated with STIs among participants, enrolled in public high schools, in the District of Panama, Panama. Methods A cross sectional study, using multistage cluster sampling, was conducted among participants, aged 14–18 years, enrolled in public high schools, in the District of Panama, Panama City, Panama, from August to November, 2015. Participants completed a self-administered questionnaire and provided biological samples. The samples of those reporting sexual activity (oral, vaginal, and/or anal intercourse) were tested for STIs. Odds ratios were used to identify correlates of STIs in this population. Results A total of 592 participants were included, of whom, 60.8% reported a history of sexual activity, and 24.4% tested positive for least one STI. STIs were more common in female participants, (33.5%). Compared to those without STIs, higher proportions of those with at least one STI reported ≥3 sexual partners in their lifetime (60.0%) and current sexual activity (76.3%). In the multivariable model, correlates of STI included female participants (Adjusted Odds Ratio (AOR) = 5.8, 95% Confidence Interval (CI) 2.3–14.6) and those who engaged in sexual intercourse with casual partners (AOR = 3.0, 95% CI: 1.2–7.5). Conclusions We report a high STI prevalence among adolescents attending public high schools, in the District of Panama. Reported risky sexual practices were common and correlated with STIs. Female participants and those reporting sexual intercourse with casual partners were more likely test positive for at least one STI. Our study identified a need for effective interventions to curb future infections in this population. PMID:27657700

  8. [Correlations of lipoprotein metabolism indicators in persons with low and high cholesterol ester transport activity].

    PubMed

    Tvorogova, M G; Rozhkova, T A; Kukharchuk, V V; Titov, V N

    1999-01-01

    For clarifying the role of plasma cholesterol ester transfer activity (CETA) in forming hyperlipoproteinemia (HLP) and determination of high density lipoproteins cholesterol (Ch HDL) level, lipoprotein metabolism indicators were compared for individuals with high and low CETA. 257 subjects were investigated: 195 patients with different forms of hereditary HLP and individuals without HLP: 34 healthy and 28 with coronary heart disease (CHD). Lipids were determined enzymatically, apoproteins content by immunoturbodimetric and immunodiffusion methods. CETA and cholesterol esterification rate (CER) were measured through autological methods. Selected groups of patients with high and low CETA were significantly distinguished only by plasma Ch level (average Ch > 6.2 mmol/l in both groups), free Ch HDL and CER. The groups were not significantly different by men-women ratio (chi 2 = 0.016, p = 0.9) and CHD patients share (chi 2 = 0.126, p = 0.723). The correlation between CETA and Ch levels was significant for healthy individuals only. The data does not correspond to assumption of exclusively atherogenic influence of high CETA: 1) no correlation between CETA and atherogenic parameters of LP metabolism among different HLP forms was found; 2) Ch HDL levels were not distinguished at high and low CETA; 3) no domination of CHD patients among the subjects with high CETA was found.

  9. High rates of sexual behavior in the general population: correlates and predictors.

    PubMed

    Långström, Niklas; Hanson, R Karl

    2006-02-01

    We studied 2450, 18-60-year-old men and women from a 1996 national survey of sexuality and health in Sweden to identify risk factors and correlates of elevated rates of sexual behavior (hypersexuality) in a representative, non-clinical population. Interviews and questionnaires measured various sexual behaviors, developmental risk factors, behavioral problems, and health indicators. The results suggested that correlates of high rates of intercourse were mostly positive, whereas the correlates of high rates of masturbation and impersonal sex were typically undesirable. For both men and women, high rates of impersonal sex were related to separation from parents during childhood, relationship instability, sexually transmitted disease, tobacco smoking, substance abuse, and dissatisfaction with life in general. The association between hypersexuality and paraphilic sexual interests (exhibitionism, voyeurism, masochism/sadism) was particularly and equally strong for both genders (odds ratios of 4.6-25.6). The results held, with a few exceptions, when controlling for age, being in a stable relationship, living in a major city, and same-sex sexual orientation. We conclude that elevated rates of impersonal sex are associated with a range of negative health indicators in the general population.

  10. Galactic Synchrotron Emission and the Far-infrared-Radio Correlation at High Redshift

    NASA Astrophysics Data System (ADS)

    Schober, J.; Schleicher, D. R. G.; Klessen, R. S.

    2016-08-01

    Theoretical scenarios, including the turbulent small-scale dynamo, predict that strong magnetic fields already exist in young galaxies. Based on the assumption of energy equipartition between magnetic fields and turbulence, we determine the galactic synchrotron flux as a function of redshift z. Galaxies in the early universe are different from local galaxies, in particular, the former have more intense star formation. To cover a large range of conditions, we consider two different systems: one model galaxy comparable to the Milky Way and one typical high-z starburst galaxy. We include a model of the steady-state cosmic ray spectrum and find that synchrotron emission can be detected up to cosmological redshifts with current and future radio telescopes. The turbulent dynamo theory is in agreement with the origin of the observed correlation between the far-infrared (FIR) luminosity L FIR and the radio luminosity L radio. Our model reproduces this correlation well at z = 0. We extrapolate the FIR-radio correlation to higher redshifts and predict a time evolution with a significant deviation from its present-day appearance already at z≈ 2 for a gas density that increases strongly with z. In particular, we predict a decrease of the radio luminosity with redshift which is caused by the increase of cosmic ray energy losses at high z. The result is an increase of the ratio between L FIR and L radio. Simultaneously, we predict that the slope of the FIR-radio correlation becomes shallower with redshift. This behavior of the correlation could be observed in the near future with ultra-deep radio surveys.

  11. Determining the Effects and Challenges of Incorporating Genetic Testing into Primary Care Management of Hypertensive Patients with African Ancestry

    PubMed Central

    Abul-Husn, NS; Ellis, S; Ramos, MA; Negron, R; Suprun, M; Zinberg, RE; Sabin, T; Hauser, D; Calman, N; Bagiella, E; Bottinger, EP

    2016-01-01

    People of African ancestry (Blacks) have increased risk of kidney failure due to numerous socioeconomic, environmental, and clinical factors. Two variants in the APOL1 gene are now thought to account for much of the racial disparity associated with hypertensive kidney failure in Blacks. However, this knowledge has not been translated into clinical care to help improve patient outcomes and address disparities. GUARDD is a randomized trial to evaluate the effects and challenges of incorporating genetic risk information into primary care. Hypertensive, non-diabetic, adults with self-reported African ancestry, without kidney dysfunction, are recruited from diverse clinical settings and randomized to undergo APOL1 genetic testing at baseline (intervention) or at one year (waitlist control). Providers are educated about genomics and APOL1. Guided by a genetic counselor, trained staff return APOL1 results to patients and provide low-literacy educational materials. Real-time clinical decision support tools alert clinicians of their patients’ APOL1 results and associated risk status at the point of care. Our academic-community-clinical partnership designed a study to generate information about the impact of genetic risk information on patient care (blood pressure and renal surveillance) and on patient and provider knowledge, attitudes, beliefs, and behaviors. GUARDD will help establish the effective implementation of APOL1 risk-informed management of hypertensive patients at high risk of CKD, and will provide a robust framework for future endeavors to implement genomic medicine in diverse clinical practices. It will also add to the important dialogue about factors that contribute to and may help eliminate racial disparities in kidney disease. PMID:26747051

  12. Identification of a New Susceptibility Locus for Systemic Lupus Erythematosus on Chromosome 12 in Individuals of European Ancestry

    PubMed Central

    Demirci, F. Yesim; Wang, Xingbin; Kelly, Jennifer A.; Morris, David L.; Barmada, M. Michael; Feingold, Eleanor; Kao, Amy H.; Sivils, Kathy L.; Bernatsky, Sasha; Pineau, Christian; Clarke, Ann; Ramsey-Goldman, Rosalind; Vyse, Timothy J.; Gaffney, Patrick M.; Manzi, Susan; Kamboh, M. Ilyas

    2016-01-01

    Objective Genome-wide association studies (GWASs) in individuals of European ancestry identified a number of systemic lupus erythematosus (SLE) susceptibility loci using earlier versions of high-density genotyping platforms. Follow-up studies on suggestive GWAS regions using larger samples and more markers identified additional SLE loci in European-descent subjects. Here we report the results of a multi-stage study that we performed to identify novel SLE loci. Methods In Stage 1, we conducted a new GWAS of SLE in a North American case-control sample of European ancestry (n=1,166) genotyped on Affymetrix Genome-Wide Human SNP Array 6.0. In Stage 2, we further investigated top new suggestive GWAS hits by in silico evaluation and meta-analysis using an additional dataset of European-descent subjects (>2,500 individuals), followed by replication of top meta-analysis findings in another dataset of European-descent subjects (>10,000 individuals) in Stage 3. Results As expected, our GWAS revealed most significant associations at the major histocompatibility complex locus (6p21), which easily surpassed genome-wide significance threshold (P<5×10−8). Several other SLE signals/loci previously implicated in Caucasians and/or Asians were also supported in Stage 1 discovery sample and strongest signals were observed at 2q32/STAT4 (P=3.6×10−7) and at 8p23/BLK (P=8.1×10−6). Stage 2 meta-analyses identified a new genome-wide significant SLE locus at 12q12 (meta P=3.1×10−8), which was replicated in Stage 3. Conclusion Our multi-stage study identified and replicated a new SLE locus that warrants further follow-up in additional studies. Publicly available databases suggest that this new SLE signal falls within a functionally relevant genomic region and near biologically important genes. PMID:26316170

  13. Mosaic maternal ancestry in the Great Lakes region of East Africa.

    PubMed

    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.

  14. Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists.

    PubMed

    Breton, Gwenna; Schlebusch, Carina M; Lombard, Marlize; Sjödin, Per; Soodyall, Himla; Jakobsson, Mattias

    2014-04-14

    The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles. Specific LP polymorphisms are associated with particular geographic regions and populations; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.

  15. Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

    PubMed Central

    Fornarino, Simona; Nesheva, Desislava; Al-Zahery, Nadia; Battaglia, Vincenza; Carossa, Valeria; Yordanov, Yordan; Torroni, Antonio; Galabov, Angel S.; Toncheva, Draga; Semino, Ornella

    2013-01-01

    To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ∼ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible. PMID:23483890

  16. Spectrum of mutations in the CFTR gene in cystic fibrosis patients of Spanish ancestry.

    PubMed

    Alonso, M J; Heine-Suñer, D; Calvo, M; Rosell, J; Giménez, J; Ramos, M D; Telleria, J J; Palacio, A; Estivill, X; Casals, T

    2007-03-01

    We analyzed 1,954 Spanish cystic fibrosis (CF) alleles in order to define the molecular spectrum of mutations in the CFTR gene in Spanish CF patients. Commercial panels showed a limited detection power, leading to the identification of only 76% of alleles. Two scanning techniques, denaturing gradient gel electrophoresis (DGGE) and single strand conformation polymorphism/hetroduplex (SSCP/HD), were carried out to detect CFTR sequence changes. In addition, intragenic markers IVS8CA, IVS8-6(T)n and IVS17bTA were also analyzed. Twelve mutations showed frequencies above 1%, p.F508del being the most frequent mutation (51%). We found that eighteen mutations need to be studied to achieve a detection level of 80%. Fifty-one mutations (42%) were observed once. In total, 121 disease-causing mutations were identified, accounting for 96% (1,877 out of 1,954) of CF alleles. Specific geographic distributions for the most common mutations, p.F508del, p.G542X, c.1811 + 1.6kbA > G and c.1609delCA, were confirmed. Furthermore, two other relatively common mutations (p.V232D and c.2789 + 5G > A) showed uneven geographic distributions. This updated information on the spectrum of CF mutations in Spain will be useful for improving genetic testing, as well as to facilitate counselling in people of Spanish ancestry. In addition, this study contributes to defining the molecular spectrum of CF in Europe, and corroborates the high molecular mutation heterogeneity of Mediterranean populations.

  17. Kinematical Correlations for Higgs Boson Plus High P_{T} Jet Production at Hadron Colliders.

    PubMed

    Sun, Peng; Yuan, C-P; Yuan, Feng

    2015-05-22

    We investigate the effect of QCD resummation to kinematical correlations in the Higgs boson plus high transverse momentum (P(T)) jet events produced at hadron colliders. We show that at the complete one-loop order, the Collins-Soper-Sterman resummation formalism can be applied to derive the Sudakov form factor. We compare the singular behavior of resummation calculation to fixed order prediction in the case that a Higgs boson and high P(T) jet are produced nearly back to back in their transverse momenta, and find perfect agreement. The phenomenological importance of the resummation effect at the LHC is also demonstrated.

  18. On The Origin Of High Energy Correlations in Gamma-ray Bursts

    SciTech Connect

    Kocevski, Daniel

    2012-04-03

    I investigate the origin of the observed correlation between a gamma-ray burst's {nu}F{sub {nu}} spectral peak E{sub pk} and its isotropic equivalent energy E{sub iso} through the use of a population synthesis code to model the prompt gamma-ray emission from GRBs. By using prescriptions for the distribution of prompt spectral parameters as well as the population's luminosity function and co-moving rate density, I generate a simulated population of GRBs and examine how bursts of varying spectral properties and redshift would appear to a gamma-ray detector here on Earth. I find that a strong observed correlation can be produced between the source frame Epk and Eiso for the detected population despite the existence of only a weak and broad correlation in the original simulated population. The energy dependance of a gamma-ray detector's flux-limited detection threshold acts to produce a correlation between the source frame E{sub pk} and E{sub iso} for low luminosity GRBs, producing the left boundary of the observed correlation. Conversely, very luminous GRBs are found at higher redshifts than their low luminosity counterparts due to the standard Malquest bias, causing bursts in the low E{sub pk}, high E{sub iso} regime to go undetected because their E{sub pk} values would be redshifted to energies at which most gamma-ray detectors become less sensitive. I argue that it is this previously unexamined effect which produces the right boundary of the observed correlation. Therefore, the origin of the observed correlation is a complex combination of the instrument's detection threshold, the intrinsic cutoff in the GRB luminosity function, and the broad range of redshifts over which GRBs are detected. Although the GRB model presented here is a very simplified representation of the complex nature of GRBs, these simulations serve to demonstrate how selection effects caused by a combination of instrumental sensitivity and the cosmological nature of an astrophysical population

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

    NASA Astrophysics Data System (ADS)

    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 <5 electrons. By means of ab initio 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.

  20. Depth imaging in highly scattering underwater environments using time-correlated single-photon counting

    NASA Astrophysics Data System (ADS)

    Maccarone, Aurora; McCarthy, Aongus; Halimi, Abderrahim; Tobin, Rachael; Wallace, Andy M.; Petillot, Yvan; McLaughlin, Steve; Buller, Gerald S.

    2016-10-01

    This paper presents an optical depth imaging system optimized for highly scattering environments such as underwater. The system is based on the time-correlated single-photon counting (TCSPC) technique and the time-of-flight approach. Laboratory-based measurements demonstrate the potential of underwater depth imaging, with specific attention given to environments with a high level of scattering. The optical system comprised a monostatic transceiver unit, a fiber-coupled supercontinuum laser source with a wavelength tunable acousto-optic filter (AOTF), and a fiber-coupled single-element silicon single-photon avalanche diode (SPAD) detector. In the optical system, the transmit and receive channels in the transceiver unit were overlapped in a coaxial optical configuration. The targets were placed in a 1.75 meter long tank, and raster scanned using two galvo-mirrors. Laboratory-based experiments demonstrate depth profiling performed with up to nine attenuation lengths between the transceiver and target. All of the measurements were taken with an average laser power of less than 1mW. Initially, the data was processed using a straightforward pixel-wise cross-correlation of the return timing signal with the system instrumental timing response. More advanced algorithms were then used to process these cross-correlation results. These results illustrate the potential for the reconstruction of images in highly scattering environments, and to permit the investigation of much shorter acquisition time scans. These algorithms take advantage of the data sparseness under the Discrete Cosine Transform (DCT) and the correlation between adjacent pixels, to restore the depth and reflectivity images.

  1. Nine-locus Y-STR profiles of Afrikaner Caucasian and mixed ancestry populations from Cape Town, South Africa.

    PubMed

    Ehrenreich, Liezle; Benjeddou, Mongi; Davison, Sean; D'Amato, Maria; Leat, Neil

    2008-07-01

    Samples were collected from 108 Afrikaner males and 114 males of mixed ancestry. The term mixed ancestry is being used to denote a complex community which was established with contributions from Asians, Caucasians and Indigenous populations and constitutes a significant proportion of the Cape Town metropolitan population. Allele and haplotype frequencies were determined for nine Y-STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and the duplicated locus DYS385). Unique haplotypes were obtained for 64 Afrikaner males and 90 males of mixed ancestry. Both population groups shared the same most common haplotype.

  2. Inverse correlation between quasiparticle mass and Tc in a cuprate high-Tc superconductor

    PubMed Central

    Putzke, Carsten; Malone, Liam; Badoux, Sven; Vignolle, Baptiste; Vignolles, David; Tabis, Wojciech; Walmsley, Philip; Bird, Matthew; Hussey, Nigel E.; Proust, Cyril; Carrington, Antony

    2016-01-01

    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 Tc 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-Tc superconductivity. We have tested the robustness of this correlation between m* and Tc 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 Tc increases under pressure. This inverse correlation between m* and Tc suggests that quantum fluctuations of the charge order enhance m* but do not enhance Tc. PMID:27034989

  3. Inverse correlation between quasiparticle mass and T c in a cuprate high-T c superconductor.

    PubMed

    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.

  4. Statistical and spatiotemporal correlation based low-complexity video coding for high-efficiency video coding

    NASA Astrophysics Data System (ADS)

    Shang, Xiwu; Wang, Guozhong; Fan, Tao; Li, Yan

    2015-03-01

    High-efficiency video coding (HEVC) is a new coding standard that adopts the quadtree splitting structure based on coding tree units instead of macroblocks, and can support more coding modes and more partitions. Although it can improve compression efficiency, the flexible quadtree block partition and mode selection result in high computational complexity in real-time applications. We propose a low-complexity video coding algorithm for HEVC by utilizing statistical correlation and spatiotemporal correlation, which consists of an early determination of SKIP mode (EDSM) method and an early termination of reference frame selection (ETRFS) method. Since there is a strong correlation for the rate distortion (RD) cost for the SKIP mode between adjacent frames, EDSM detects the SKIP mode according to the threshold derived from the former training frame. Meanwhile, ETRFS terminates the process of reference frame selection using the motion vector and reference frame information from neighboring blocks to skip unnecessary candidate frames. Experimental results demonstrate that the proposed method can achieve about 45.01% complexity reduction on average with a 1.11% BD-rate increase and 0.04 BD-PSNR decrease for random access. The complexity reduction, BD-rate increase, and BD-PSNR decrease for low delay are 46.16%, 0.99%, and 0.03, respectively.

  5. Smoking, drinking, and drug use among American high school students: correlates and trends, 1975-1979.

    PubMed Central

    Bachman, J G; Johnston, L D; O'Malley, P M

    1981-01-01

    This paper uses findings from five nationally representative surveys of high school seniors from 1975 through 1979 to examine the correlates of licit and illicit drug use, and to consider whether recent changes in youthful drug use are linked to any changes in the correlates. Males still exceed females in use of alcohol and marijuana, but no longer in cigarette smoking. Black seniors now report less drug use than Whites. Other dimensions of family background, region, and urbanicity show only modest associations with drug use. Above average drug use occurs among those less successful in adaptation to the educational environment, as indicated by truancy and low grades; those who spend many evenings out for recreation; and those with heavy time commitments to a job and/or relatively high incomes. Drug use is below average among seniors with strong religious commitments and conservative political views. From 1975 through 1979, among seniors cigarette use peaked and subsequently declined, marijuana use rose and then leveled off, and the (still infrequent) use of cocaine rose rapidly. However, these shifts in drug use were not accompanied by substantial shifts in the above correlates of use. The findings thus suggest that the kinds of young people most at risk remain much the same, while the types and amounts of substances they use shift somewhat from year to year. PMID:6973285

  6. Phase behaviour and correlations of parallel hard squares: from highly confined to bulk systems.

    PubMed

    González-Pinto, Miguel; Martínez-Ratón, Yuri; Varga, Szabolcs; Gurin, Peter; Velasco, Enrique

    2016-06-22

    We study a fluid of two-dimensional parallel hard squares in bulk and under confinement in channels, with the aim of evaluating the performance of fundamental-measure theory (FMT). To this purpose, we first analyse the phase behaviour of the bulk system using FMT and Percus-Yevick (PY) theory, and compare the results with molecular dynamics and Monte Carlo simulations. In a second step, we study the confined system and check the results against those obtained from the transfer matrix method and from our own Monte Carlo simulations. Squares are confined to channels with parallel walls at angles of 0° or 45° relative to the diagonals of the parallel hard squares, respectively, which allows for an assessment of the effect of the external-potential symmetry on the fluid structural properties. In general FMT overestimates bulk correlations, predicting the existence of a columnar phase (absent in simulations) prior to crystallization. The equation of state predicted by FMT compares well with simulations, although the PY approach with the virial route is better in some range of packing fractions. The FMT is highly accurate for the structure and correlations of the confined fluid due to the dimensional crossover property fulfilled by the theory. Both density profiles and equations of state of the confined system are accurately predicted by the theory. The highly non-uniform pair correlations inside the channel are also very well described by FMT.

  7. Yes, pair correlations alone do determine sedimentation profiles of highly charged colloids.

    PubMed

    Belloni, Luc

    2005-11-22

    Recent analyses of sedimentation profiles in charged colloidal suspensions are examined in view of general, somewhat underestimated, concepts. It is recalled that the standard equation for osmotic pressure equilibrium, which involves pair correlations between colloids only, remains valid in the presence of long-range Coulombic interactions. The entropy of the counterions and the electric field generated by the spatial inhomogeneity are implicitly taken into account in the colloid structure factor through the compressibility equation and local electroneutrality conditions. Limiting the macroscopic analysis to the pure electric-field contribution or, equivalently, to the ideal ionic pressure, corresponds to the incorrect, bare Debye-Huckel approximation for the colloid-colloid correlations. A one-component description with reasonable Derjaguin-Landau-Verwey-Overbeek-type ion-averaged effective pair potential between colloids is sufficient to derive the sedimentation profile of highly charged, weakly screened colloidal suspensions. The macroscopic electric field is directly related to the microscopic electrostatic potential around the colloids.

  8. Correlation between nonexponential relaxation and non-Arrhenius behavior under conditions of high compression.

    PubMed

    Gapiński, Jacek; Paluch, Marian; Patkowski, Adam

    2002-07-01

    Photon correlation spectroscopy was used to investigate the behavior of the dynamical properties of 1,1'-di(4-methoxy-5-methyl-phenyl)cyclohexane (BMMPC) at elevated pressures. The fragility of BMMPC measured by the steepness index m(T) is decreasing and the nonexponentiality parameter beta(KWW) is increasing with increasing pressure. This result strongly suggests that the phenomenological correlation between the steepness index and nonexponentionality is also preserved under high compression. The pressure dependence of the structural relaxation times is well characterized by a simple activation volume form. The activation volume continuously increases with decreasing temperature, which is probably due to the increase of cooperativity of the structural relaxation process. Moreover, we found that the glass-transition temperature exhibits a significant dependence on pressure.

  9. High chondroitin sulfate proteoglycan 4 expression correlates with poor outcome in patients with breast cancer.

    PubMed

    Hsu, Nicholas C; Nien, Pei-Yung; Yokoyama, Kazunari K; Chu, Pei-Yi; Hou, Ming-Feng

    2013-11-15

    Chondroitin sulfate proteoglycan 4 (CSPG4), a transmembrane proteoglycan originally identified in melanoma cells, has been reported to be expressed in breast cancer cells. This study was performed to examine the expression and significance of CSPG4 in a cohort of breast cancer patients. Immunohistochemical analysis of CSPG4 was performed on tissue microarrays constructed from tissue specimens from 240 breast cancer patients. CSPG4 staining was correlated with clinical and pathological characteristics, overall survival (OS), and disease recurrence. Contradicting to a previous report, our results showed that high CSPG4 expression was not related to triple-negative status of breast cancer patients. The Kaplan-Meier method showed that high CSPG4 expression was significantly associated with shorter time to recurrence (TTR). Patients with high CSPG4 expression had poorer OS and shorter TTR in a multivariate survival analysis after adjustment for stage, tumor grade, expression of estrogen receptor and progesterone receptor, and HER2 overexpression. This study showed that high CSPG4 expression correlates with disease recurrence and OS in breast cancers.

  10. Identification of Transcription Factor Genes and Their Correlation with the High Diversity of Stramenopiles

    PubMed Central

    Buitrago-Flórez, Francisco Javier; Restrepo, Silvia; Riaño-Pachón, Diego Mauricio

    2014-01-01

    The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles. PMID:25375671

  11. Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.

    PubMed

    Buitrago-Flórez, Francisco Javier; Restrepo, Silvia; Riaño-Pachón, Diego Mauricio

    2014-01-01

    The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.

  12. Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

    PubMed Central

    Wall, Jeffrey D; Schlebusch, Stephen A; Alberts, Susan C; Cox, Laura A; Snyder-Mackler, Noah; Nevonen, Kimberly; Carbone, Lucia; Tung, Jenny

    2017-01-01

    Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low coverage genome-wide resequencing data from yellow baboons, anubis baboons, and known hybrids (n=44). Using a novel composite likelihood method for estimating local ancestry from low coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history, and morphology-based estimates (r2=0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared versus fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, are inconsistent with simple isolation-migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioral barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage. PMID:27145036

  13. Associations between CYP19A1 polymorphisms, Native American ancestry, and breast cancer risk and mortality: the Breast Cancer Health Disparities Study

    PubMed Central

    Baumgartner, Kathy B.; Baumgartner, Richard N.; Connor, Avonne E.; Pinkston, Christina M.; Rai, Shesh N.; Riley, Elizabeth C.; Hines, Lisa M.; Giuliano, Anna R.; John, Esther M.; Stern, Mariana C.; Torres-Mejía, Gabriela; Wolff, Roger K.; Slattery, Martha L.

    2015-01-01

    The cytochrome p450 family 19 gene (CYP19A1) encodes for aromatase, which catalyzes the final step in estrogen biosynthesis and conversion of androgens to estrogens. Genetic variation in CYP19A1 is linked to higher circulating estrogen levels and increased aromatase expression. Using data from the Breast Cancer Health Disparities Study, a consortium of three population-based case–control studies in the United States (n = 3,030 non-Hispanic Whites; n = 2,893 Hispanic/Native Americans (H/NA) and Mexico (n = 1,810), we examined influence of 25 CYP19A1 tagging single-nucleotide polymorphisms (SNPs) on breast cancer risk and mortality, considering NA ancestry. Odds ratios (ORs) and 95 % confidence intervals (CIs) and hazard ratios estimated breast cancer risk and mortality. After multiple comparison adjustment, none of the SNPs were significantly associated with breast cancer risk or mortality. Two SNPs remained significantly associated with increased breast cancer risk in women of moderate to high NA ancestry (≥29 %): rs700518, ORGG 1.36, 95 % CI 1.11–1.67 and rs11856927, ORGG 1.35, 95 % CI 1.05–1.72. A significant interaction was observed for rs2470144 and menopausal status (padj = 0.03); risk was increased in postmenopausal (ORAA 1.22, 95 % CI 1.05–1.14), but not premenopausal (ORAA 0.78, 95 % CI 0.64–0.95) women. The absence of an overall association with CYP19A1 and breast cancer risk is similar to previous literature. However, this analysis provides support that variation in CYP19A1 may influence breast cancer risk differently in women with moderate to high NA ancestry. Additional research is warranted to investigate the how variation in an estrogen-regulating gene contributes to racial/ethnic disparities in breast cancer. PMID:25088806

  14. Antiparkinson therapeutic potencies correlate with their affinities at dopamine D2(High) receptors.

    PubMed

    Seeman, Philip

    2007-12-01

    To determine whether antiparkinson dopamine agonists preferentially act on the high-affinity or the low-affinity states of dopamine D1 and D2 receptors, the agonist potencies were obtained by competition against [(3)H]SCH23390 for D1(High) and D1(Low), and against [(3)H]domperidone for D2(High) and D2(Low). N-propylnorapomorphine and cabergoline were the most potent at D2(High), with dissociation constants of 0.18 and 0.36 nM, respectively. Other agonists had D2(High)K(i) values of 0.52 nM for quinagolide, 0.6 nM for (+)PHNO, 0.9 for bromocriptine, 1.8 nM for apomorphine, 2.4 nM for pergolide, 3 nM for quinpirole, and 6.2 nM for lergotrile. There was a clear correlation between the K(i) values at D2(High) and their therapeutic concentrations in the plasma water, as derived from the known concentrations after correction for the fraction bound to the human plasma proteins. The data suggest that D2(High) is the primary and common target for the antiparkinson action of dopamine agonists. Bromocriptine, cabergoline, lergotrile, pergolide, and pramipexole had no affinity for D1(High), consistent with the clinical observations that the D2-selective bromocriptine and pramipexole elicit low levels of dyskinesia.

  15. Effect of Strong Correlations on the High Energy Anomaly in Hole- and Electron-Doped High-Tc Superconductors

    SciTech Connect

    Moritz, B.; Schmitt, F.; Meevasana, W.; Johnston, S.; Motoyama, E.M.; Greven, M.; Lu, D.H.; Kim, C.; Scalettar, R.T.; Shen, Z.-X.; Devereaux, T.P.; /SLAC, SIMES

    2010-02-15

    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 byproduct 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.

  16. Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

    PubMed Central

    Alsmadi, Osama; Hebbar, Prashantha; Antony, Dinu; Behbehani, Kazem; Thanaraj, Thangavel Alphonse

    2014-01-01

    Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are ‘novel’. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10−16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3′ UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian

  17. On transpolar arc formation correlated with solar wind entry at high latitude magnetosphere

    NASA Astrophysics Data System (ADS)

    Mailyan, B. G.; Shi, Q.; Maggiolo, R.; Zong, Q.; Fu, S.; Zhang, Y.; Yao, Z.; Sun, W.

    2014-12-01

    Recently, Cluster observations revealed the existence of new regions of solar wind plasma entry at the high latitudes of the Earth's magnetosphere, at the lobes tailward of the cusp region, mostly during periods of northward IMF. Such periods of northward IMF are associated with the presence of transpolar arcs. Observations from Global Ultraviolet Imager (GUVI) instrument onboard TIMED spacecraft are used to investigate a possible link between solar wind entry in the high latitude magnetosphere and the formation of transpolar arcs. Data from IMAGE and DMSP spacecraft are also used to investigate the time evolution and particle characteristics of the transpolar arc.We present a case study of a theta aurora correlated with the solar wind entry. The observations show a simultaneous occurrence of aurora activity at the magnetotail and high latitudes, suggesting two-part structure of the apparent continuous band of the transpolar arc.

  18. Herschel-ATLAS: The Angular Correlation Function of Submillimetre Galaxies at High and Low Redshift

    NASA Technical Reports Server (NTRS)

    Maddox, S. J.; Dunne, L.; Rigby, E.; Eales, S.; Cooray, A.; Scott, D.; Peacock, J. A.; Negrello, M.; Smith, D. J. B.; Benford, D.; Amblard, A.; Auld, R.; Baes, M.; Bonfield, D.; Burgarella, D.; Buttiglione, S.; Cava, A.; Clements, D.; Dariush, A.; deZotti, G.; Dye, S.; Frayer, D.; Fritz, J.; Gonzalez-Nuevo, J.; Herranz, D.

    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 < or equal to 1. For our 350 micrometer and 500 micrometer-selected samples we detect relatively strong clustering with correlation amplitudes A of 0.2 and 1.2 at 1', but with relatively large uncertainties. For samples which preferentially select 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.

  19. Application of High Speed Digital Image Correlation in Rocket Engine Hot Fire Testing

    NASA Technical Reports Server (NTRS)

    Gradl, Paul R.; Schmidt, Tim

    2016-01-01

    Hot fire testing of rocket engine components and rocket engine systems is a critical aspect of the development process to understand performance, reliability and system interactions. Ground testing provides the opportunity for highly instrumented development testing to validate analytical model predictions and determine necessary design changes and process improvements. To properly obtain discrete measurements for model validation, instrumentation must survive in the highly dynamic and extreme temperature application of hot fire testing. Digital Image Correlation has been investigated and being evaluated as a technique to augment traditional instrumentation during component and engine testing providing further data for additional performance improvements and cost savings. The feasibility of digital image correlation techniques were demonstrated in subscale and full scale hotfire testing. This incorporated a pair of high speed cameras to measure three-dimensional, real-time displacements and strains installed and operated under the extreme environments present on the test stand. The development process, setup and calibrations, data collection, hotfire test data collection and post-test analysis and results are presented in this paper.

  20. Advances in Neutron Spectroscopy and High Magnetic Field Instrumentation for studies of Correlated Electron Systems

    SciTech Connect

    Granroth, Garrett E

    2011-01-01

    Neutron Spectroscopy has provided critical information on the magnetism in correlated electron systems. Specifically quantum magnets, superconductors, and multi-ferroics are areas of productive research. A discussion of recent measurements on the SEQUOIA spectrometer will provide examples of how novel instrumentation concepts are used on the latest generation of spectrometers to extend our knowledge in such systems. The now ubiquitous function of sample rotation allows for full mapping of volumes of $Q$ and $\\omega$ space. An instrument focused on low angles could extend these maps to cover more of the first Brillioun zone. Innovative chopper cascades allow two unique modes of operation. Multiplexed measurements allow the simultaneous measurement of high and low energy features in an excitation spectrum. Alternatively by limiting the neutron bandwidth incident on the Fermi Chopper, background from subsequent time frames is removed, enabling the observation of weak, large energy transfer features. Finally the implementation of event-based detection for neutron experiments is time correlated experiments. Diffraction studies of the high field spin states in MnWO$_4$ using magnetic fields up to 30 T, provided by a pulsed magnet, illustrate this method. Expanding the high field studies to spectroscopy will require a novel instrument, focused around a world class DC magnet, like Zeemans proposed for the SNS.

  1. Reconstruction of noise-driven nonlinear networks from node outputs by using high-order correlations

    PubMed Central

    Chen, Yang; Zhang, Zhaoyang; Chen, Tianyu; Wang, Shihong; Hu, Gang

    2017-01-01

    Many practical systems can be described by dynamic networks, for which modern technique can measure their outputs, and accumulate extremely rich data. Nevertheless, the network structures producing these data are often deeply hidden in the data. The problem of inferring network structures by analyzing the available data, turns to be of great significance. On one hand, networks are often driven by various unknown facts, such as noises. On the other hand, network structures of practical systems are commonly nonlinear, and different nonlinearities can provide rich dynamic features and meaningful functions of realistic networks. Although many works have considered each fact in studying network reconstructions, much less papers have been found to systematically treat both difficulties together. Here we propose to use high-order correlation computations (HOCC) to treat nonlinear dynamics; use two-time correlations to decorrelate effects of network dynamics and noise driving; and use suitable basis and correlator vectors to unifiedly infer all dynamic nonlinearities, topological interaction links and noise statistical structures. All the above theoretical frameworks are constructed in a closed form and numerical simulations fully verify the validity of theoretical predictions. PMID:28322230

  2. Long range rapidity correlations and jet production in high energy nuclear collisions

    SciTech Connect

    STAR Collaboration; Abelev, Betty

    2010-07-05

    The STAR Collaboration at RHIC presents a systematic study of high transverse momentum charged di-hadron correlations at small azimuthal pair separation {Delta}{phi}, in d+Au and central Au+Au collisions at {radical}s{sub NN} = 200 GeV. Significant correlated yield for pairs with large longitudinal separation {Delta}{eta} is observed in central Au+Au, in contrast to d+Au collisions. The associated yield distribution in {Delta}{eta} x {delta}{phi} can be decomposed into a narrow jet-like peak at small angular separation which has a similar shape to that found in d+Au collisions, and a component which is narrow in {Delta}{phi} and depends only weakly on {Delta}{eta}, the 'ridge'. Using two systematically independent analyses, finite ridge yield is found to persist for trigger p{sub t} > 6 GeV/c, indicating that it is correlated with jet production. The transverse momentum spectrum of hadrons comprising the ridge is found to be similar to that of bulk particle production in the measured range (2 < p{sub t} < 4 GeV/c).

  3. Squeezed K{sup +}K{sup -} correlations in high energy heavy ion collisions

    SciTech Connect

    Dudek, Danuce M.; Padula, Sandra S.

    2010-09-15

    The hot and dense medium formed in high energy heavy ion collisions may modify some hadronic properties. In particular, if hadron masses are shifted in-medium, it was demonstrated that this could lead to back-to-back squeezed correlations (BBC) of particle-antiparticle pairs. Although well-established theoretically, the squeezed correlations have not yet been discovered experimentally. A method has been suggested for the empirical search of this effect, which was previously illustrated for {phi}{phi} pairs. We apply here the formalism and the suggested method to the case of K{sup +}K{sup -} pairs, since they may be easier to identify experimentally. The time distribution of the emission process plays a crucial role in the survival of the BBC's. We analyze the cases where the emission is supposed to occur suddenly or via a Lorentzian distribution, and compare with the case of a Levy distribution in time. Effects of squeezing on the correlation function of identical particles are also analyzed.

  4. Reconstruction of noise-driven nonlinear networks from node outputs by using high-order correlations

    NASA Astrophysics Data System (ADS)

    Chen, Yang; Zhang, Zhaoyang; Chen, Tianyu; Wang, Shihong; Hu, Gang

    2017-03-01

    Many practical systems can be described by dynamic networks, for which modern technique can measure their outputs, and accumulate extremely rich data. Nevertheless, the network structures producing these data are often deeply hidden in the data. The problem of inferring network structures by analyzing the available data, turns to be of great significance. On one hand, networks are often driven by various unknown facts, such as noises. On the other hand, network structures of practical systems are commonly nonlinear, and different nonlinearities can provide rich dynamic features and meaningful functions of realistic networks. Although many works have considered each fact in studying network reconstructions, much less papers have been found to systematically treat both difficulties together. Here we propose to use high-order correlation computations (HOCC) to treat nonlinear dynamics; use two-time correlations to decorrelate effects of network dynamics and noise driving; and use suitable basis and correlator vectors to unifiedly infer all dynamic nonlinearities, topological interaction links and noise statistical structures. All the above theoretical frameworks are constructed in a closed form and numerical simulations fully verify the validity of theoretical predictions.

  5. High Frequency Sampling of TTL Pulses on a Raspberry Pi for Diffuse Correlation Spectroscopy Applications

    PubMed Central

    Tivnan, Matthew; Gurjar, Rajan; Wolf, David E.; Vishwanath, Karthik

    2015-01-01

    Diffuse Correlation Spectroscopy (DCS) is a well-established optical technique that has been used for non-invasive measurement of blood flow in tissues. Instrumentation for DCS includes a correlation device that computes the temporal intensity autocorrelation of a coherent laser source after it has undergone diffuse scattering through a turbid medium. Typically, the signal acquisition and its autocorrelation are performed by a correlation board. These boards have dedicated hardware to acquire and compute intensity autocorrelations of rapidly varying input signal and usually are quite expensive. Here we show that a Raspberry Pi minicomputer can acquire and store a rapidly varying time-signal with high fidelity. We show that this signal collected by a Raspberry Pi device can be processed numerically to yield intensity autocorrelations well suited for DCS applications. DCS measurements made using the Raspberry Pi device were compared to those acquired using a commercial hardware autocorrelation board to investigate the stability, performance, and accuracy of the data acquired in controlled experiments. This paper represents a first step toward lowering the instrumentation cost of a DCS system and may offer the potential to make DCS become more widely used in biomedical applications. PMID:26274961

  6. High Frequency Sampling of TTL Pulses on a Raspberry Pi for Diffuse Correlation Spectroscopy Applications.

    PubMed

    Tivnan, Matthew; Gurjar, Rajan; Wolf, David E; Vishwanath, Karthik

    2015-08-12

    Diffuse Correlation Spectroscopy (DCS) is a well-established optical technique that has been used for non-invasive measurement of blood flow in tissues. Instrumentation for DCS includes a correlation device that computes the temporal intensity autocorrelation of a coherent laser source after it has undergone diffuse scattering through a turbid medium. Typically, the signal acquisition and its autocorrelation are performed by a correlation board. These boards have dedicated hardware to acquire and compute intensity autocorrelations of rapidly varying input signal and usually are quite expensive. Here we show that a Raspberry Pi minicomputer can acquire and store a rapidly varying time-signal with high fidelity. We show that this signal collected by a Raspberry Pi device can be processed numerically to yield intensity autocorrelations well suited for DCS applications. DCS measurements made using the Raspberry Pi device were compared to those acquired using a commercial hardware autocorrelation board to investigate the stability, performance, and accuracy of the data acquired in controlled experiments. This paper represents a first step toward lowering the instrumentation cost of a DCS system and may offer the potential to make DCS become more widely used in biomedical applications.

  7. Study of Isospin Correlation in High Energy Heavy Ion Interactions with the RHIC PHENIX. Final Report

    SciTech Connect

    Takahashi, Y.

    2003-06-08

    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.

  8. Damage correlations in semiconductor devices exposed to gamma and high energy swift heavy ions

    NASA Astrophysics Data System (ADS)

    Pushpa, N.; Prakash, A. P. Gnana

    2015-05-01

    NPN rf power transistors and N-channel depletion MOSFETs are irradiated by different high energy swift heavy ions and 60Co gamma radiation in the dose range of 100 krad to 100 Mrad. The damage created by different heavy ions and 60Co gamma radiation in NPN rf power transistors and N-channel depletion MOSFETs have been correlated and studied in the same dose range. The recoveries in the electrical characteristics of different swift heavy ions and 60Co gamma irradiated devices have been studied after annihilation.

  9. Damage correlations in semiconductor devices exposed to gamma and high energy swift heavy ions

    SciTech Connect

    Pushpa, N.; Prakash, A. P. Gnana

    2015-05-15

    NPN rf power transistors and N-channel depletion MOSFETs are irradiated by different high energy swift heavy ions and {sup 60}Co gamma radiation in the dose range of 100 krad to 100 Mrad. The damage created by different heavy ions and {sup 60}Co gamma radiation in NPN rf power transistors and N-channel depletion MOSFETs have been correlated and studied in the same dose range. The recoveries in the electrical characteristics of different swift heavy ions and {sup 60}Co gamma irradiated devices have been studied after annihilation.

  10. Pulse-to-pulse jitter measurement by photon correlation in high-β lasers

    SciTech Connect

    Lebreton, Armand; Abram, Izo; Belabas, Nadia; Sagnes, Isabelle; Robert-Philip, Isabelle Beveratos, Alexios; Braive, Rémy; Marsili, Francesco; Verma, Varun B.; Nam, Sae Woo; Gerrits, Thomas; Stevens, Martin J.

    2015-01-19

    The turn-on delay jitter in pulsed lasers in which a large fraction (β) of spontaneous emission is channeled into the lasing mode is measured by use of a photon correlation technique. This jitter is found to significantly increase with β, reaching values of the order of the pulse width at threshold. This is due to the increase in the relative value of the discretization noise when the number of photons at threshold becomes small, as is the case in high-β lasers.

  11. Genetic ancestry of a Moroccan population as inferred from autosomal STRs

    PubMed Central

    Bentayebi, K.; Abada, F.; Ihzmad, H.; Amzazi, S.

    2014-01-01

    Detecting population substructure and ancestry is a critical issue for both association studies of health behaviors and forensic genetics. Determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Within this context, fifteen autosomal short tandem repeat (STR), were used to examine population genetic structure and hypotheses of the origin of the modern Moroccan population from individuals belonging to three different ethnical groups from Morocco (Arab, Berber and Sahrawi), by comparing their autosomal STR variation with that of neighboring and non-neighboring populations in North Africa, Europe and Middle East as well as proposed ancestral populations in Morocco (Berber). We report on the results that the gradient of North African ancestry accounts for previous observations of low levels of sharing with Near East and a substantially increased gene flow especially from Morocco and Spain. PMID:25606427

  12. ICE-Based Custom Full-Mesh Network for the CHIME High Bandwidth Radio Astronomy Correlator

    NASA Astrophysics Data System (ADS)

    Bandura, K.; Cliche, J. F.; Dobbs, M. A.; Gilbert, A. J.; Ittah, D.; Mena Parra, J.; Smecher, G.

    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. An Examination of Sociodemographic Correlates of Ecstasy Use Among High School Seniors in the United States

    PubMed Central

    Palamar, Joseph J.; Kamboukos, Dimitra

    2016-01-01

    Background 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. Methods 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. Results 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. Conclusion 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. PMID:24955818

  14. The Impact of the Correlation between the No Child Left Behind Act's High Stakes Testing and the High Drop-Out Rates of Minority Students

    ERIC Educational Resources Information Center

    Walden, Lavada M.; Kritsonis, William Allan

    2008-01-01

    The author looks at critical dialogue surrounding the causes for the alarming high numbers of high school dropouts in states that use high stakes standardized testing mandated by the No Child Left Behind Act, and investigates the perceived correlations between high stakes testing and high numbers of high school dropouts of minority students.

  15. Cytokine and cytokine receptor genes of the adaptive immune response are differentially associated with breast cancer risk in American women of African and European ancestry.

    PubMed

    Quan, Lei; Gong, Zhihong; Yao, Song; Bandera, Elisa V; Zirpoli, Gary; Hwang, Helena; Roberts, Michelle; Ciupak, Gregory; Davis, Warren; Sucheston, Lara; Pawlish, Karen; Bovbjerg, Dana H; Jandorf, Lina; Cabasag, Citadel; Coignet, Jean-Gabriel; Ambrosone, Christine B; Hong, Chi-Chen

    2014-03-15

    Disparities in breast cancer biology are evident between American women of African ancestry (AA) and European ancestry (EA) and may be due, in part, to differences in immune function. To assess the potential role of constitutional host immunity on breast carcinogenesis, we tested associations between breast cancer risk and 47 single nucleotide polymorphisms (SNPs) in 26 cytokine-related genes of the adaptive immune system using 650 EA (n = 335 cases) and 864 AA (n = 458 cases) women from the Women's Circle of Health Study (WCHS). With additional participant accrual to the WCHS, promising SNPs from the initial analysis were evaluated in a larger sample size (1,307 EAs and 1,365 AAs). Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (IFNGR2 rs1059293, IL15RA rs2296135, LTA rs1041981), Th2 immunity (IL4R rs1801275), and T regulatory cell-mediated immunosuppression (TGFB1 rs1800469) associated with breast cancer risk, mainly among AAs. The combined effect of these five SNPs was highly significant among AAs (P-trend = 0.0005). When stratified by estrogen receptor (ER) status, LTA rs1041981 was associated with ER-positive breast cancers among EAs and marginally among AAs. Only among AA women, IL15 rs10833 and IL15RA rs2296135 were associated with ER-positive tumors, and IL12RB1 rs375947, IL15 rs10833 and TGFB1 rs1800469 were associated with ER-negative tumors. Our study systematically identified genetic variants in the adaptive immune response pathway associated with breast cancer risk, which appears to differ by ancestry groups, menopausal status and ER status.

  16. Higher endothelin concentrations in the fetoplacental unit of pregnant women of African ancestry.

    PubMed

    Carbonne, B; Mignot, T M; Papiernik, E; Ferré, F

    1998-03-01

    Immunoreactive endothelin was assayed in maternal and fetal biologic fluids of women of African and European ancestry with normal singleton pregnancies undergoing cesarean section at term for obstetric reasons. Endothelin concentration was found to be higher in the umbilical vein and artery blood of women of African origin. Higher production of endothelins in the fetoplacental unit may place these women at a greater risk of preeclampsia.

  17. Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry.

    PubMed

    Wang, Zhaoming; Parikh, Hemang; Jia, Jinping; Myers, Timothy; Yeager, Meredith; Jacobs, Kevin B; Hutchinson, Amy; Burdett, Laurie; Ghosh, Arpita; Thun, Michael J; Gapstur, Susan M; Ryan Diver, W; Virtamo, Jarmo; Albanes, Demetrius; Cancel-Tassin, Geraldine; Valeri, Antoine; Cussenot, Olivier; Offit, Kenneth; Giovannucci, Ed; Ma, Jing; Stampfer, Meir J; Michael Gaziano, J; Hunter, David J; Dutra-Clarke, Ana; Kirchhoff, Tomas; Alavanja, Michael; Freeman, Laura B; Koutros, Stella; Hoover, Robert; Berndt, Sonja I; Hayes, Richard B; Agalliu, Ilir; Burk, Robert D; Wacholder, Sholom; Thomas, Gilles; Amundadottir, Laufey

    2012-07-01

    Genetic variation on the Y chromosome has not been convincingly implicated in prostate cancer risk. To comprehensively analyze the role of inherited Y chromosome variation in prostate cancer risk in individuals of European ancestry, we genotyped 34 binary Y chromosome markers in 3,995 prostate cancer cases and 3,815 control subjects drawn from four studies. In this set, we identified nominally significant association between a rare haplogroup, E1b1b1c, and prostate cancer in stage I (P = 0.012, OR = 0.51; 95% confidence interval 0.30-0.87). Population substructure of E1b1b1c carriers suggested Ashkenazi Jewish ancestry, prompting a replication phase in individuals of both European and Ashkenazi Jewish ancestry. The association was not significant for prostate cancer overall in studies of either Ashkenazi Jewish (1,686 cases and 1,597 control subjects) or European (686 cases and 734 control subjects) ancestry (P(meta) = 0.078), but a meta-analysis of stage I and II studies revealed a nominally significant association with prostate cancer risk (P(meta) = 0.010, OR = 0.77; 95% confidence interval 0.62-0.94). Comparing haplogroup frequencies between studies, we noted strong similarities between those conducted in the US and France, in which the majority of men carried R1 haplogroups, resembling Northwestern European populations. On the other hand, Finns had a remarkably different haplogroup distribution with a preponderance of N1c and I1 haplogroups. In summary, our results suggest that inherited Y chromosome variation plays a limited role in prostate cancer etiology in European populations but warrant follow-up in additional large and well characterized studies of multiple ethnic backgrounds.

  18. Disparities in Birth Weight and Gestational Age by Ethnic Ancestry in South American countries

    PubMed Central

    Wehby, George L.; Gili, Juan A.; Pawluk, Mariela; Castilla, Eduardo E.; López-Camelo, Jorge S.

    2015-01-01

    Objective We examine disparities in birth weight and gestational age by ethnic ancestry in 2000–2011 in eight South American countries. Methods The sample included 60480 singleton live-births. Regression models were estimated to evaluate differences in birth outcomes by ethnic ancestry controlling for time trends. Results Significant disparities were found in seven countries. In four countries – Brazil, Ecuador, Uruguay, and Venezuela – we found significant disparities in both low birth weight and preterm birth. Disparities in preterm birth alone were observed in Argentina, Bolivia, and Colombia. Several differences in continuous birth weight, gestational age, and fetal growth rate were also observed. There were no systematic patterns of disparities between the evaluated ethnic ancestry groups across the study countries, in that no racial/ethnic group consistently had the best or worst outcomes in all countries. Conclusions Racial/ethnic disparities in infant health are common in several South American countries. Differences across countries suggest that racial/ethnic disparities are driven by social and economic mechanisms. Researchers and policymakers should acknowledge these disparities and develop research and policy programs to effectively target them. PMID:25542227

  19. A genome-wide association study of breast cancer in women of African ancestry

    PubMed Central

    Chen, Fang; Chen, Gary K.; Stram, Daniel O.; Millikan, Robert C.; Ambrosone, Christine B.; John, Esther M.; Bernstein, Leslie; Zheng, Wei; Palmer, Julie R.; Hu, Jennifer J.; Rebbeck, Tim R.; Ziegler, Regina G.; Nyante, Sarah; Bandera, Elisa V.; Ingles, Sue A.; Press, Michael F.; Ruiz-Narvaez, Edward A.; Deming, Sandra L.; Rodriguez-Gil, Jorge L.; DeMichele, Angela; Chanock, Stephen J.; Blot, William; Signorello, Lisa; Cai, Qiuyin; Li, Guoliang; Long, Jirong; Huo, Dezheng; Zheng, Yonglan; Cox, Nancy J.; Olopade, Olufunmilayo I.; Ogundiran, Temidayo O.; Adebamowo, Clement; Nathanson, Katherine L.; Domchek, Susan M.; Simon, Michael S.; Hennis, Anselm; Nemesure, Barbara; Wu, Suh-Yuh; Leske, M. Cristina; Ambs, Stefan; Hutter, Carolyn M.; Young, Alicia; Kooperberg, Charles; Peters, Ulrike; Rhie, Suhn K.; Wan, Peggy; Sheng, Xin; Pooler, Loreall C.; Van Den Berg, David J.; Le Marchand, Loic; Kolonel, Laurence N.; Henderson, Brian E.; Haiman, Christopher A.

    2013-01-01

    Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of > 1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10−6 and 10−5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3×10−6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5×10−5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample. PMID:22923054

  20. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    PubMed

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns.

  1. A genome-wide association study of breast cancer in women of African ancestry.

    PubMed

    Chen, Fang; Chen, Gary K; Stram, Daniel O; Millikan, Robert C; Ambrosone, Christine B; John, Esther M; Bernstein, Leslie; Zheng, Wei; Palmer, Julie R; Hu, Jennifer J; Rebbeck, Tim R; Ziegler, Regina G; Nyante, Sarah; Bandera, Elisa V; Ingles, Sue A; Press, Michael F; Ruiz-Narvaez, Edward A; Deming, Sandra L; Rodriguez-Gil, Jorge L; Demichele, Angela; Chanock, Stephen J; Blot, William; Signorello, Lisa; Cai, Qiuyin; Li, Guoliang; Long, Jirong; Huo, Dezheng; Zheng, Yonglan; Cox, Nancy J; Olopade, Olufunmilayo I; Ogundiran, Temidayo O; Adebamowo, Clement; Nathanson, Katherine L; Domchek, Susan M; Simon, Michael S; Hennis, Anselm; Nemesure, Barbara; Wu, Suh-Yuh; Leske, M Cristina; Ambs, Stefan; Hutter, Carolyn M; Young, Alicia; Kooperberg, Charles; Peters, Ulrike; Rhie, Suhn K; Wan, Peggy; Sheng, Xin; Pooler, Loreall C; Van Den Berg, David J; Le Marchand, Loic; Kolonel, Laurence N; Henderson, Brian E; Haiman, Christopher A

    2013-01-01

    Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10(-6) and 10(-5) in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10(-6); rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10(-5)). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.

  2. Cascade Error Projection with Low Bit Weight Quantization for High Order Correlation Data

    NASA Technical Reports Server (NTRS)

    Duong, Tuan A.; Daud, Taher

    1998-01-01

    In this paper, we reinvestigate the solution for chaotic time series prediction problem using neural network approach. The nature of this problem is such that the data sequences are never repeated, but they are rather in chaotic region. However, these data sequences are correlated between past, present, and future data in high order. We use Cascade Error Projection (CEP) learning algorithm to capture the high order correlation between past and present data to predict a future data using limited weight quantization constraints. This will help to predict a future information that will provide us better estimation in time for intelligent control system. In our earlier work, it has been shown that CEP can sufficiently learn 5-8 bit parity problem with 4- or more bits, and color segmentation problem with 7- or more bits of weight quantization. In this paper, we demonstrate that chaotic time series can be learned and generalized well with as low as 4-bit weight quantization using round-off and truncation techniques. The results show that generalization feature will suffer less as more bit weight quantization is available and error surfaces with the round-off technique are more symmetric around zero than error surfaces with the truncation technique. This study suggests that CEP is an implementable learning technique for hardware consideration.

  3. Elongation factor 1 alpha concentration is highly correlated with the lysine content of maize endosperm.

    PubMed Central

    Habben, J E; Moro, G L; Hunter, B G; Hamaker, B R; Larkins, B A

    1995-01-01

    Lysine is the most limiting essential amino acid in cereals, and for many years plant breeders have attempted to increase its concentration to improve the nutritional quality of these grains. The opaque2 mutation in maize doubles the lysine content in the endosperm, but the mechanism by which this occurs is unknown. We show that elongation factor 1 alpha (EF-1 alpha) is overexpressed in opaque2 endosperm compared with its normal counterpart and that there is a highly significant correlation between EF-1 alpha concentration and the total lysine content of the endosperm. This relationship is also true for two other cereals, sorghum and barley. It appears that genetic selection for genotypes with a high concentration of EF-1 alpha can significantly improve the nutritional quality of maize and other cereals. Images Fig. 1 Fig. 2 PMID:7567989

  4. Nanoscale deformation analysis with high-resolution transmission electron microscopy and digital image correlation

    DOE PAGES

    Wang, Xueju; Pan, Zhipeng; Fan, Feifei; ...

    2015-09-10

    We present an application of the digital image correlation (DIC) method to high-resolution transmission electron microscopy (HRTEM) images for nanoscale deformation analysis. The combination of DIC and HRTEM offers both the ultrahigh spatial resolution and high displacement detection sensitivity that are not possible with other microscope-based DIC techniques. We demonstrate the accuracy and utility of the HRTEM-DIC technique through displacement and strain analysis on amorphous silicon. Two types of error sources resulting from the transmission electron microscopy (TEM) image noise and electromagnetic-lens distortions are quantitatively investigated via rigid-body translation experiments. The local and global DIC approaches are applied for themore » analysis of diffusion- and reaction-induced deformation fields in electrochemically lithiated amorphous silicon. As a result, the DIC technique coupled with HRTEM provides a new avenue for the deformation analysis of materials at the nanometer length scales.« less

  5. Transplantation tolerance correlates with high levels of T- and B-lymphocyte activity.

    PubMed Central

    Bandeira, A; Coutinho, A; Carnaud, C; Jacquemart, F; Forni, L

    1989-01-01

    Mice tolerized (treated to make them tolerant) at birth to transplantation antigens by injection of semiallogeneic cells contain very high numbers of activated T and B lymphocytes in their spleen. Lymphoid hyperactivity correlates with the tolerant state: it is present only in animals accepting skin allografts. Tolerized mice that reject the allogeneic skin graft have approximately the same numbers of total and activated lymphocytes as normal mice. The high level of lymphocyte activation in tolerant mice persists for up to 1 year of age, although it declines with age, and is markedly increased by a secondary allograft. The magnitudes of both primary and secondary tolerant responses are significantly higher than the immunological response of a normal mouse rejecting the same type of allograft. These observations contradict concepts of clonal deletion or anergy as the basis of neonatally induced transplantation tolerance and may contribute additional approaches to experimentation and control of transplantation reactions. PMID:2783487

  6. Nanoscale deformation analysis with high-resolution transmission electron microscopy and digital image correlation

    SciTech Connect

    Wang, Xueju; Pan, Zhipeng; Fan, Feifei; Wang, Jiangwei; Liu, Yang; Mao, Scott X.; Zhu, Ting; Xia, Shuman

    2015-09-10

    We present an application of the digital image correlation (DIC) method to high-resolution transmission electron microscopy (HRTEM) images for nanoscale deformation analysis. The combination of DIC and HRTEM offers both the ultrahigh spatial resolution and high displacement detection sensitivity that are not possible with other microscope-based DIC techniques. We demonstrate the accuracy and utility of the HRTEM-DIC technique through displacement and strain analysis on amorphous silicon. Two types of error sources resulting from the transmission electron microscopy (TEM) image noise and electromagnetic-lens distortions are quantitatively investigated via rigid-body translation experiments. The local and global DIC approaches are applied for the analysis of diffusion- and reaction-induced deformation fields in electrochemically lithiated amorphous silicon. As a result, the DIC technique coupled with HRTEM provides a new avenue for the deformation analysis of materials at the nanometer length scales.

  7. Frequency of TNFA, INFG, and IL10 Gene Polymorphisms and Their Association with Malaria Vivax and Genomic Ancestry

    PubMed Central

    dos Santos, Sidney Emanuel Batista

    2016-01-01

    Polymorphisms in cytokine genes can alter the production of these proteins and consequently affect the immune response. The trihybrid heterogeneity of the Brazilian population is characterized as a condition for the use of ancestry informative markers. The objective of this study was to evaluate the frequency of -1031T>C, -308G>A and -238G>A TNFA, +874 A>T IFNG and -819C>T, and -592C>A IL10 gene polymorphisms and their association with malaria vivax and genomic ancestry. Samples from 90 vivax malaria-infected individuals and 51 noninfected individuals from northern Brazil were evaluated. Genotyping was carried out by using ASO-PCR or PCR/RFLP. The genomic ancestry of the individuals was classified using 48 insertion/deletion polymorphism biallelic markers. There were no differences in the proportions of African, European, and Native American ancestry between men and women. No significant association was observed for the allele and genotype frequencies of the 6 SNPs between malaria-infected and noninfected individuals. However, there was a trend toward decreasing the frequency of individuals carrying the TNF-308A allele with the increasing proportion of European ancestry. No ethnic-specific SNPs were identified, and there was no allelic or genotype association with susceptibility or resistance to vivax malaria. Understanding the genomic mechanisms by which ancestry influences this association is critical and requires further study. PMID:27999453

  8. Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA.

    PubMed

    Lao, Oscar; Vallone, Peter M; Coble, Michael D; Diegoli, Toni M; van Oven, Mannis; van der Gaag, Kristiaan J; Pijpe, Jeroen; de Knijff, Peter; Kayser, Manfred

    2010-12-01

    The 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 DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification.

  9. Evaluating Self-declared Ancestry of U.S. Americans with Autosomal, Y-chromosomal and Mitochondrial DNA

    PubMed Central

    Lao, Oscar; Vallone, Peter M; Coble, Michael D; Diegoli, Toni M; van Oven, Mannis; van der Gaag, Kristiaan J; Pijpe, Jeroen; de Knijff, Peter; Kayser, Manfred

    2010-01-01

    The 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 DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification. © 2010 Wiley-Liss, Inc. PMID:20886636

  10. Differences in early cognitive and receptive-expressive neurodevelopment by ancestry and underlying pathways in Brazil and Argentina.

    PubMed

    Wehby, George L; Trujillo, Antonio J

    2017-02-01

    We examine disparities in early child cognitive and receptive-expressive skills by ethnic ancestry among infants aged 3-24 months from Brazil and Argentina. We employ unique data on the neurodevelopment of children who were seeking routine well-child care at a set of pediatric clinics in these countries. The sample included children who had normal birth outcomes and no major health complications, allowing us to focus on variation in neurodevelopment among children without major physical health limitations. The physicians attending the pediatric clinics were trained in administering the Bayley Infant Neurodevelopmental Screener, a standardized instrument used to screen an infant's risk of neurodevelopmental problems on various domains of abilities. We evaluate disparities in overall neurodevelopmental scores and risk for neurodevelopmental problems as well as in cognitive functioning and receptive-expressive neurodevelopment. We also examine the extent to which household demographic and socioeconomic characteristics and geographic location explain these disparities. We find large gaps in both cognitive and receptive-expressive neurodevelopment by ancestry. In Brazil, children of African ancestry have lower scores on both cognitive and receptive-expressive domains and on overall neurodevelopment than children of European ancestry. In Argentina, children of Native ancestry have lower scores on these outcomes than children of European ancestry. These gaps however are largely explained by differences in geographic location and household characteristics, highlighting the importance of policies that reduce socioeconomic and geographic disparities in social capital and economic development for eliminating ethnic disparities in infant neurodevelopment.

  11. Doping dependence of spin excitations and its correlations with high-temperature superconductivity in iron pnictides.

    PubMed

    Wang, Meng; Zhang, Chenglin; Lu, Xingye; Tan, Guotai; Luo, Huiqian; Song, Yu; Wang, Miaoyin; Zhang, Xiaotian; Goremychkin, E A; Perring, T G; Maier, T A; Yin, Zhiping; Haule, Kristjan; Kotliar, Gabriel; Dai, Pengcheng

    2013-01-01

    High-temperature superconductivity in iron pnictides occurs when electrons and holes are doped into their antiferromagnetic parent compounds. Since spin excitations may be responsible for electron pairing and superconductivity, it is important to determine their electron/hole-doping evolution and connection with superconductivity. Here we use inelastic neutron scattering to show that while electron doping to the antiferromagnetic BaFe₂As₂ parent compound modifies the low-energy spin excitations and their correlation with superconductivity (<50 meV) without affecting the high-energy spin excitations (>100 meV), hole-doping suppresses the high-energy spin excitations and shifts the magnetic spectral weight to low-energies. In addition, our absolute spin susceptibility measurements for the optimally hole-doped iron pnictide reveal that the change in magnetic exchange energy below and above T(c) can account for the superconducting condensation energy. These results suggest that high-T(c) superconductivity in iron pnictides is associated with both the presence of high-energy spin excitations and a coupling between low-energy spin excitations and itinerant electrons.

  12. Doping dependence of spin excitations and its correlations with high-temperature superconductivity in iron pnictides

    PubMed Central

    Wang, Meng; Zhang, Chenglin; Lu, Xingye; Tan, Guotai; Luo, Huiqian; Song, Yu; Wang, Miaoyin; Zhang, Xiaotian; Goremychkin, E.A.; Perring, T.G.; Maier, T.A.; Yin, Zhiping; Haule, Kristjan; Kotliar, Gabriel; Dai, Pengcheng

    2013-01-01

    High-temperature superconductivity in iron pnictides occurs when electrons and holes are doped into their antiferromagnetic parent compounds. Since spin excitations may be responsible for electron pairing and superconductivity, it is important to determine their electron/hole-doping evolution and connection with superconductivity. Here we use inelastic neutron scattering to show that while electron doping to the antiferromagnetic BaFe2As2 parent compound modifies the low-energy spin excitations and their correlation with superconductivity (<50 meV) without affecting the high-energy spin excitations (>100 meV), hole-doping suppresses the high-energy spin excitations and shifts the magnetic spectral weight to low-energies. In addition, our absolute spin susceptibility measurements for the optimally hole-doped iron pnictide reveal that the change in magnetic exchange energy below and above Tc can account for the superconducting condensation energy. These results suggest that high-Tc superconductivity in iron pnictides is associated with both the presence of high-energy spin excitations and a coupling between low-energy spin excitations and itinerant electrons. PMID:24301219

  13. High Mobility Group Box Protein-1 correlates with renal function in chronic kidney disease (CKD).

    PubMed

    Bruchfeld, Annette; Qureshi, Abdul Rashid; Lindholm, Bengt; Barany, Peter; Yang, Lihong; Stenvinkel, Peter; Tracey, Kevin J

    2008-01-01

    Chronic kidney disease (CKD) is associated with inflammation and malnutrition and carries a markedly increased risk of cardiovascular disease (CVD). High Mobility Group Box Protein-1 (HMGB-1) is a 30-kDa nuclear and cytosolic protein known as a transcription and growth factor, recently identified as a proinflammatory mediator of tissue injury. Recent data implicates HMGB-1 in endotoxin lethality, rheumatoid arthritis, and atherosclerosis. The aim of this post-hoc, cross-sectional study was to determine whether HMGB-1 serum levels are elevated in CKD patients. The study groups were categorized as follows: 110 patients starting dialysis defined as CKD 5; 67 patients with moderately to severely reduced renal function or CKD 3-4; and 48 healthy controls. High-sensitivity C-reactive-protein (hs-CRP), interleukin-6 (IL-6), tumor necrosis factor (TNF), serum-albumin (S-albumin), hemoglobin A(1c) (HbA(1c)), hemoglobin, subjective global nutritional assessment (SGA), and glomerular filtration rate (GFR) were analyzed. Kruskal-Wallis test was used to compare groups and Spearman's rank correlation test was used for continuous variables. HMGB-1, measured by Western blot, was significantly (P < 0.001) elevated in CKD 5 (146.7 +/- 58.6 ng/mL) and CKD 3-4 (85.6 +/- 31.8) compared with controls (10.9 +/- 10.5). HMGB-1 levels were correlated positively with TNF (Rho = 0.52; P < 0.001), hs-CRP (Rho = 0.38; P < 0.001), IL-6 (Rho = 0.30; P < 0.001), HbA(1c) (Rho = 0.14; P = 0.02) and SGA (Rho = 0.21; P = 0.002) and negatively correlated with GFR (Rho = -0.69; P = 0.0001), Hb (Rho = -0.60; P < 0.001), S-albumin (Rho = -0.31; P < 0.001). The current study has revealed that HMGB-1 is elevated significantly in CKD patients and correlates with GFR as well as markers of inflammation and malnutrition. Future studies may delineate whether HMGB-1 is also a marker of disease activity and severity as well as a predictor of outcome in CKD.

  14. High Ki-67 Immunohistochemical Reactivity Correlates With Poor Prognosis in Bladder Carcinoma

    PubMed Central

    Luo, Yihuan; Zhang, Xin; Mo, Meile; Tan, Zhong; Huang, Lanshan; Zhou, Hong; Wang, Chunqin; Wei, Fanglin; Qiu, Xiaohui; He, Rongquan; Chen, Gang

    2016-01-01

    correlated with all 5 clinical outcome in Asian and European-American patients (P < 0.05). For multivariate analysis, however, the pooled results were only significant for DFS, OS, and RFS in Asian patients, for CSS, DFS, PFS, and RFS in European-American patients (P < 0.05). In the subgroup with low cut-off value (<20%), our meta-analysis indicated that high Ki-67 reactivity was significantly correlated with worsened CSS, DFS, OS, PFS, and RFS on univariate analysis (P < 0.05). For multivariate analysis, the meta-analysis of literature with low cut-off value (<20%) demonstrated that high Ki-67 reactivity predicted shorter DFS, PFS, and RFS in BC patients (P < 0.05). In the subgroup analysis of high cut-off value (≥20%), our meta-analysis indicated that high Ki-67 reactivity, in either univariate or multivariate analysis, significantly correlated with all five clinical outcomes in BC patients (P < 0.05). The meta-analysis indicates that high Ki-67 reactivity significantly correlates with deteriorated clinical outcomes in BC patients and that Ki-67 can be considered as an independent indicator for the prognosis by the meta-analyses of multivariate analysis. PMID:27082587

  15. Viscosity and structure correlations in NaCl and KCl melts at high pressures

    NASA Astrophysics Data System (ADS)

    Kono, Y.; Kenney-Benson, C.; Park, C.; Shen, G.; Wang, Y.

    2012-12-01

    Knowledge of the structure and physical property change of melts and fluids at high pressures is important for understanding the nature of the Earth's interior. Recently, we have developed synchrotron techniques that are capable of conducting structure measurement of liquid at high-pressure and high-temperature conditions in a Paris-Edinburgh cell by using multi-angle energy-dispersive x-ray diffraction at the 16-BM-B, HPCAT at the Advanced Photon Source (APS), in collaboration with GSECARS. In addition to the structure measurement, we newly developed falling sphere viscosity measurement using x-ray radiography with high-speed camera (> 1000 frame/second), which enables us to investigate viscosity of not only high viscos melts such as silicate or oxide melts but also low viscos liquids and fluids such as H2O and CO2 (around 1 mPa s or less at ambient pressure). Here we report a study of viscosity and structure change in NaCl and KCl melts at high pressures to 7.3 GPa. Viscosity of the NaCl melt continuously increased with increasing pressure to 7.3 GPa. In contrast, viscosity of the KCl melt first increased up to 2.2 GPa, and then remained at a certain level at higher pressures in 2.2-5.9 GPa. Structure measurement of NaCl and KCl melts revealed that the nearest (r1) and the second nearest (r2) neighbor distance gradually shortened with increasing pressure, while the ratio (r2/r1) changes as a function of pressure resembled the behavior of viscosity of both melts. These observations suggest that viscosities of NaCl and KCl melts at high pressures strongly correlate with the changes of the r2/r1 ratio rather than the distance variation only.

  16. A high performance cost-effective digital complex correlator for an X-band polarimetry survey.

    PubMed

    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

  17. Correlates of sexual experience among a nationally representative sample of alternative high school students.

    PubMed

    Shrier, Lydia A; Crosby, Richard

    2003-05-01

    Little is known about risk and protective factors associated with sexual experience among alternative school students that might prove useful in targeting and guiding early interventions to prevent onset of sexual risk behavior. Researchers analyzed data from the national Alternative High School Youth Risk Behavior Survey. Principal components analysis identified six risk and protective factors: weapon carrying; tobacco use; cocaine, inhalant, and needle use; alcohol and marijuana use; participation in sports; and fighting. Composite variables with significant bivariate relationships to sexual experience, as well as demographic variables, were entered into a logistic regression analysis to determine independent effects of these correlates on students' sexual experience (N = 6.037). Nearly 90% of students reported having sexual intercourse. In multivariate analysis, significant demographic correlates of sexual experience included female gender (58% more likely than males to report ever having sex), African American race (2.83 times more likely than non-Hispanic Whites), and age (28% more likely with each advancing year). Attending school in a rural or suburban region corresponded to a 31% decrease and 46% decrease, respectively, in the odds of ever having sex. Weapon carrying, and cocaine, inhalant, and needle use, were associated with a 35% and 46% increase, respectively, in the odds of ever having sex. Students reporting they had ever used alcohol or marijuana, and those reporting recent fighting behavior, were 2.7 and 1.6 times more likely, respectively, to report sexual experience. Most alternative school students have had sexual intercourse, with those students engaging in substance use, weapon carrying, and fighting behaviors being at greater risk for sexual experience. Prevention programs for high-risk youth attending alternative high schools need to consider how to promote continued abstinence among the small but important minority of alternative school

  18. Correlation of microstructure, tensile properties and hole expansion ratio in cold rolled advanced high strength steels

    NASA Astrophysics Data System (ADS)

    Terrazas, Oscar R.

    The demand for advanced high strength steels (AHSS) with higher strengths is increasing in the automotive industry. While there have been major improvements recently in the trade-off between ductility and strength, sheared-edge formability of AHSS remains a critical issue. AHSS sheets exhibit cracking during stamping and forming operations below the predictions of forming limits. It has become important to understand the correlation between microstructure and sheared edge formability. The present work investigates the effects of shearing conditions, microstructure, and tensile properties on sheared edge formability. Seven commercially produced steels with tensile strengths of 1000 +/- 100 MPa were evaluated: five dual-phase (DP) steels with different compositions and varying microstructural features, one trip aided bainitic ferrite (TBF) steel, and one press-hardened steel tempered to a tensile strength within the desired range. It was found that sheared edge formability is influenced by the martensite in DP steels. Quantitative stereology measurements provided results that showed martensite size and distribution affect hole expansion ratio (HER). The overall trend is that HER increases with more evenly dispersed martensite throughout the microstructure. This microstructure involves a combination of martensite size, contiguity, mean free distance, and number of colonies per unit area. Additionally, shear face characterization showed that the fracture and burr region affect HER. The HER decreases with increasing size of fracture and burr region. With a larger fracture and burr region more defects and/or micro-cracks will be present on the shear surface. This larger fracture region on the shear face facilitates cracking in sheared edge formability. Finally, the sheared edge formability is directly correlated to true fracture strain (TFS). The true fracture strain from tensile samples correlates to the HER values. HER increases with increasing true fracture strain.

  19. High blood Pressure in children and its correlation with three definitions of obesity in childhood

    PubMed Central

    de Moraes, Leonardo Iezzi; Nicola, Thaís Coutinho; de Jesus, Julyanna Silva Araújo; Alves, Eduardo Roberty Badiani; Giovaninni, Nayara Paula Bernurdes; Marcato, Daniele Gasparini; Sampaio, Jéssica Dutra; Fuly, Jeanne Teixeira Bessa; Costalonga, Everlayny Fiorot

    2014-01-01

    Background 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. Objectives 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. Methods 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). Results 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. Conclusions 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. PMID:24676372

  20. Effect of Intercritical Temperature on the Structure Property Correlation of Multiphase High-C Spheroidized Steel

    NASA Astrophysics Data System (ADS)

    Monia, S.; Varshney, A.; Gouthama; Sangal, S.; Kundu, S.; Samanta, S.; Mondal, K.

    2016-02-01

    The present investigation deals with the development of multiphase steels combining spheroidal carbides and bainite in a ductile ferrite matrix. An attempt is made to get a promising combination of high strength and ductility through changes of microstructure by heat treatment. A high-carbon (0.61 wt.%) and high-silicon (1.71 wt.%) spring steel (EN45) was annealed to obtain an initial ferrite pearlite microstructure. The samples were given 10% cold working followed by holding at a temperature just below Ac1 for 180 min. Then the samples were held at intercritical temperatures of 770 and 800 °C for different durations varying from 10 to 30 min for partial re-austenitization followed by quenching in a salt bath kept at 350 °C and holding there for 10 min for bainite transformation. The samples were finally water quenched. The heat-treated samples were characterized by optical microscopy, x-ray diffraction, and scanning electron microscopy. The effects of intercritical temperature and holding time on the microstructure and mechanical properties were studied. With more bainitic transformation, the strength values went up considerably with a compromised elongation. The best combination of tensile strength (~805 MPa) with high elongation (~28%) was obtained. Finally, structure property correlation was established.

  1. Electrophysiological changes correlated with temperature increases induced by high-intensity focused ultrasound ablation.

    PubMed

    Wu, Ziqi; Kumon, Ronald E; Laughner, Jacob I; Efimov, Igor R; Deng, Cheri X

    2015-02-01

    To gain better understanding of the detailed mechanisms of high-intensity focused ultrasound (HIFU) ablation for cardiac arrhythmias, we investigated how the cellular electrophysiological (EP) changes were correlated with temperature increases and thermal dose (cumulative equivalent minutes [CEM43]) during HIFU application using Langendorff-perfused rabbit hearts. Employing voltage-sensitive dye di-4-ANEPPS, we measured the EP and temperature during HIFU using simultaneous optical mapping and infrared imaging. Both action potential amplitude (APA) and action potential duration at 50% repolarization (APD50) decreased with temperature increases, and APD50 was more thermally sensitive than APA. EP and tissue changes were irreversible when HIFU-induced temperature increased above 52.3 ± 1.4°C and log10(CEM43) above 2.16 ± 0.51 (n = 5), but were reversible when temperature was below 50.1 ± 0.8°C and log10(CEM43) below -0.9 ± 0.3 (n = 9). EP and temperature/thermal dose changes were spatially correlated with HIFU-induced tissue necrosis surrounded by a transition zone.

  2. Monte Carlo approach for hadron azimuthal correlations in high energy proton and nuclear collisions

    NASA Astrophysics Data System (ADS)

    Ayala, Alejandro; Dominguez, Isabel; Jalilian-Marian, Jamal; Magnin, J.; Tejeda-Yeomans, Maria Elena

    2012-09-01

    We use a Monte Carlo approach to study hadron azimuthal angular correlations in high-energy proton-proton and central nucleus-nucleus collisions at the BNL Relativistic Heavy Ion Collider energies at midrapidity. We build a hadron event generator that incorporates the production of 2→2 and 2→3 parton processes and their evolution into hadron states. For nucleus-nucleus collisions we include the effect of parton energy loss in the quark-gluon plasma using a modified fragmentation function approach. In the presence of the medium, for the case when three partons are produced in the hard scattering, we analyze the Monte Carlo sample in parton and hadron momentum bins to reconstruct the angular correlations. We characterize this sample by the number of partons that are able to hadronize by fragmentation within the selected bins. In the nuclear environment the model allows hadronization by fragmentation only for partons with momentum above a threshold pTthresh=2.4 GeV. We argue that one should treat properly the effect of those partons with momentum below the threshold, because their interaction with the medium may lead to showers of low-momentum hadrons along the direction of motion of the original partons as the medium becomes diluted.

  3. Electrophysiological Changes Correlated with Temperature Increases Induced by High-Intensity Focused Ultrasound Ablation

    PubMed Central

    Wu, Z.; Kumon, R. E.; Laughner, J. I.; Efimov, I. R.; Deng, C. X.

    2014-01-01

    To gain better understanding of the detailed mechanisms of high-intensity focused ultrasound (HIFU) ablation for cardiac arrhythmias, we investigated how the cellular electrophysiological (EP) changes were correlated with temperature increases and thermal dose (cumulative equivalent minutes [CEM43]) during HIFU application using Langendorff-perfused rabbit hearts. Employing voltage-sensitive dye di-4-ANEPPS, we measured the EP and temperature during HIFU using simultaneous optical mapping and infrared imaging. Both action potential amplitude (APA) and AP duration at 50% repolarization (APD50) decreased with temperature increases, and APD50 was more thermally sensitive than APA. EP and tissue changes were irreversible when HIFU-induced temperature increased above 52.3 ± 1.4 °C and log10(CEM43) above 2.16 ± 0.51 (n = 5), but were reversible when temperature was below 50.1 ± 0.8 °C and log10(CEM43) below −0.9 ± 0.3 (n = 9). EP and temperature/thermal dose changes were spatially correlated with HIFU induced tissue necrosis surrounded by a transition zone. PMID:25516446

  4. Thalamo-Sensorimotor Functional Connectivity Correlates with World Ranking of Olympic, Elite, and High Performance Athletes.

    PubMed

    Huang, Zirui; Davis Iv, Henry Hap; Wolff, Annemarie; Northoff, Georg

    2017-01-01

    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.

  5. Thalamo-Sensorimotor Functional Connectivity Correlates with World Ranking of Olympic, Elite, and High Performance Athletes

    PubMed Central

    Wolff, Annemarie

    2017-01-01

    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. PMID:28261504

  6. Spider dragline silk: correlated and mosaic evolution in high-performance biological materials.

    PubMed

    Swanson, Brook O; Blackledge, Todd A; Summers, Adam P; Hayashi, Cheryl Y

    2006-12-01

    The evolution of biological materials is a critical, yet poorly understood, component in the generation of biodiversity. For example, the diversification of spiders is correlated with evolutionary changes in the way they use silk, and the material properties of these fibers, such as strength, toughness, extensibility, and stiffness, have profound effects on ecological function. Here, we examine the evolution of the material properties of dragline silk across a phylogenetically diverse sample of species in the Araneomorphae (true spiders). The silks we studied are generally stronger than other biological materials and tougher than most biological or man-made fibers, but their material properties are highly variable; for example, strength and toughness vary more than fourfold among the 21 species we investigated. Furthermore, associations between different properties are complex. Some traits, such as strength and extensibility, seem to evolve independently and show no evidence of correlation or trade-off across species, even though trade-offs between these properties are observed within species. Material properties retain different levels of phylogenetic signal, suggesting that traits such as extensibility and toughness may be subject to different types or intensities of selection in several spider lineages. The picture that emerges is complex, with a mosaic pattern of trait evolution producing a diverse set of materials across spider species. These results show that the properties of biological materials are the target of selection, and that these changes can produce evolutionarily and ecologically important diversity.

  7. Correlation of Thermally Induced Pores with Microstructural Features Using High Energy X-rays

    NASA Astrophysics Data System (ADS)

    Menasche, David B.; Shade, Paul A.; Lind, Jonathan; Li, Shiu Fai; Bernier, Joel V.; Kenesei, Peter; Schuren, Jay C.; Suter, Robert M.

    2016-11-01

    Combined application of a near-field High Energy Diffraction Microscopy measurement of crystal lattice orientation fields and a tomographic measurement of pore distributions in a sintered nickel-based superalloy sample allows pore locations to be correlated with microstructural features. Measurements were carried out at the Advanced Photon Source beamline 1-ID using an X-ray energy of 65 keV for each of the measurement modes. The nickel superalloy sample was prepared in such a way as to generate significant thermally induced porosity. A three-dimensionally resolved orientation map is directly overlaid with the tomographically determined pore map through a careful registration procedure. The data are shown to reliably reproduce the expected correlations between specific microstructural features (triple lines and quadruple nodes) and pore positions. With the statistics afforded by the 3D data set, we conclude that within statistical limits, pore formation does not depend on the relative orientations of the grains. The experimental procedures and analysis tools illustrated are being applied to a variety of materials problems in which local heterogeneities can affect materials properties.

  8. Resummation of threshold, low- and high-energy expansions for heavy-quark correlators

    SciTech Connect

    Greynat, David; Peris, Santiago

    2010-08-01

    With the help of the Mellin-Barnes transform, we show how to simultaneously resum the expansion of a heavy-quark correlator around q{sup 2}=0 (low-energy), q{sup 2}=4m{sup 2} (threshold, where m is the quark mass), and q{sup 2}{yields}-{infinity} (high-energy) in a systematic way. We exemplify the method for the perturbative vector correlator at O({alpha}{sub s}{sup 2}) and O({alpha}{sub s}{sup 3}). We show that the coefficients, {Omega}(n), of the Taylor expansion of the vacuum polarization function in terms of the conformal variable {omega} admit, for large n, an expansion in powers of 1/n (up to logarithms of n) that we can calculate exactly. This large-n expansion has a sign-alternating component given by the logarithms of the operator-product expansion, and a fixed-sign component given by the logarithms of the threshold expansion in the external momentum q{sup 2}.

  9. Improvements in High Speed, High Resolution Dynamic Digital Image Correlation for Experimental Evaluation of Composite Drive System Components

    NASA Technical Reports Server (NTRS)

    Kohlman, Lee W.; Ruggeri, Charles R.; Roberts, Gary D.; Handschuh, Robert Frederick

    2013-01-01

    Composite materials have the potential to reduce the weight of rotating drive system components. However, these components are more complex to design and evaluate than static structural components in part because of limited ability to acquire deformation and failure initiation data during dynamic tests. Digital image correlation (DIC) methods have been developed to provide precise measurements of deformation and failure initiation for material test coupons and for structures under quasi-static loading. Attempts to use the same methods for rotating components (presented at the AHS International 68th Annual Forum in 2012) are limited by high speed camera resolution, image blur, and heating of the structure by high intensity lighting. Several improvements have been made to the system resulting in higher spatial resolution, decreased image noise, and elimination of heating effects. These improvements include the use of a high intensity synchronous microsecond pulsed LED lighting system, different lenses, and changes in camera configuration. With these improvements, deformation measurements can be made during rotating component tests with resolution comparable to that which can be achieved in static tests

  10. Improvements in High Speed, High Resolution Dynamic Digital Image Correlation for Experimental Evaluation of Composite Drive System Components

    NASA Technical Reports Server (NTRS)

    Kohlman, Lee; Ruggeri, Charles; Roberts, Gary; Handshuh, Robert

    2013-01-01

    Composite materials have the potential to reduce the weight of rotating drive system components. However, these components are more complex to design and evaluate than static structural components in part because of limited ability to acquire deformation and failure initiation data during dynamic tests. Digital image correlation (DIC) methods have been developed to provide precise measurements of deformation and failure initiation for material test coupons and for structures under quasi-static loading. Attempts to use the same methods for rotating components (presented at the AHS International 68th Annual Forum in 2012) are limited by high speed camera resolution, image blur, and heating of the structure by high intensity lighting. Several improvements have been made to the system resulting in higher spatial resolution, decreased image noise, and elimination of heating effects. These improvements include the use of a high intensity synchronous microsecond pulsed LED lighting system, different lenses, and changes in camera configuration. With these improvements, deformation measurements can be made during rotating component tests with resolution comparable to that which can be achieved in static tests.

  11. Empirical Correlates of the Overcontrolled-Hostility Scale and the MMPI 4-3 High-Point Pair.

    ERIC Educational Resources Information Center

    Walters, Glenn D.; And Others

    1982-01-01

    Compared the behavioral correlates of the Minnesota Multiphasic Personality Inventory 4-3 high-point pair and the Overcontrolled-Hostility scale in a sample of university psychology clinic outpatients (N=97). Behavioral correlates of two groups of outpatients were more similar to each other than they were to the group of outpatient controls.…

  12. Correlates of violent and nonviolent victimization in a sample of public high school students.

    PubMed

    Van Dorn, Richard A

    2004-06-01

    This study investigates the extent to which student reports of violent and nonviolent victimization in public high schools is associated the presence of hate-related words or symbols, the availability of hard and soft drugs, and the presence of gangs. Data from the 1999 School Crime Supplement of the National Crime Victimization Survey were used for this analysis. In the final multinomial logistic regression model, the presence of hate-related words, the availability of hard drugs, and a gang presence were significantly associated with reports of violent victimization. The availability of soft drugs was significantly associated with nonviolent victimization. Findings held across gender, race/ethnicity, and urbanicity of the school's location with younger students more likely to be both violently and nonviolently victimized than older students. Implications for primary and secondary interventions aimed at school climate and the reduction of correlates of victimization are discussed.

  13. High correlation of double Debye model parameters in skin cancer detection.

    PubMed

    Truong, Bao C Q; Tuan, H D; Fitzgerald, Anthony J; Wallace, Vincent P; Nguyen, H T

    2014-01-01

    The double Debye model can be used to capture the dielectric response of human skin in terahertz regime due to high water content in the tissue. The increased water proportion is widely considered as a biomarker of carcinogenesis, which gives rise of using this model in skin cancer detection. Therefore, the goal of this paper is to provide a specific analysis of the double Debye parameters in terms of non-melanoma skin cancer classification. Pearson correlation is applied to investigate the sensitivity of these parameters and their combinations to the variation in tumor percentage of skin samples. The most sensitive parameters are then assessed by using the receiver operating characteristic (ROC) plot to confirm their potential of classifying tumor from normal skin. Our positive outcomes support further steps to clinical application of terahertz imaging in skin cancer delineation.

  14. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi

    PubMed Central

    Telleria, Jenny; Biron, David G.; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J.; Tibayrenc, Michel

    2010-01-01

    We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi–subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10−4) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

  15. High resolution MRI of the normal finger at 0.1 T: anatomic correlations.

    PubMed

    Drapé, J L; Constantinesco, A; Arbogast, S; Sick, H; Wolfram-Gabel, R; Brunot, B

    1992-01-01

    MR images of the fingers are obtained in a 128 x 128 or 256 x 256 matrix format using a prototype of a mini imager dedicated to the hand. The vertical field of 0.1 T is provided by an electro-magnet with an air gap of 15 cm equipped with a single solenoidal coil. No Faraday cage is used. The maximum in plane pixel resolution of 100 mu is obtained for a field of view of 2.5 cm with a slice thickness of 2 mm. The identification of fine structures of the finger is demonstrated by the anatomical and histological correlations. This type of imager which is adapted to very limited field of views demonstrate that high resolution MRI of limb extremities can be achieved at 0.1 T.

  16. Two-photon fluorescence correlation spectroscopy with high count rates and low background using dielectric microspheres

    PubMed Central

    Aouani, Heykel; Schön, Peter; Brasselet, Sophie; Rigneault, Hervé; Wenger, Jérôme

    2010-01-01

    Two-photon excitation fluorescence is a powerful technique commonly used for biological imaging. However, the low absorption cross section of this non-linear process is a critical issue for performing biomolecular spectroscopy at the single molecule level. Enhancing the two-photon fluorescence signal would greatly improve the effectiveness of this technique, yet current methods struggle with medium enhancement factors and/or high background noise. Here, we show that the two-photon fluorescence signal from single Alexa Fluor 488 molecules can be enhanced up to 10 times by using a 3 µm diameter latex sphere while adding almost no photoluminescence background. We report a full characterization of the two-photon fluorescence enhancement by a single microsphere using fluorescence correlation spectroscopy. This opens new routes to enhance non-linear optical signals and extend biophotonic applications. PMID:21258531

  17. Brief report: biochemical correlates of clinical impairment in high functioning autism and Asperger's disorder.

    PubMed

    Kleinhans, Natalia M; Richards, Todd; Weaver, Kurt E; Liang, Olivia; Dawson, Geraldine; Aylward, Elizabeth

    2009-07-01

    Amygdala dysfunction has been proposed as a critical contributor to social impairment in autism spectrum disorders (ASD). The current study investigated biochemical abnormalities in the amygdala in 20 high functioning adults with autistic disorder or Asperger's disorder and 19 typically developing adults matched on age and IQ. Magnetic resonance spectroscopy was used to measure N-acetyl aspartate (NAA), creatine/phosphocreatine (Cre), choline/choline containing compounds (Cho), and Myoinositol (mI) in the right and left amygdala. There were no significant between-group differences in any of the metabolites. However, NAA and Cre levels were significantly correlated to clinical ratings on the Autism Diagnostic Interview-Revised. This suggests that altered metabolite levels in the amygdala may be associated with a more severe early developmental course in ASD.

  18. The impact of highly correlated potential energy surfaces on the anharmonically corrected IR spectrum of acetonitrile

    NASA Astrophysics Data System (ADS)

    Lutz, Oliver M. D.; Rode, Bernd M.; Bonn, Günther K.; Huck, Christian W.

    2014-10-01

    This paper discusses the quality and feasibility of highly correlated ab initio techniques in a vibrational self-consistent field (VSCF) approach using acetonitrile as a model system. The topical renormalized coupled-cluster technique exploiting the similarity-transformed Hamiltonian's left eigenstates (i.e. CR-CC(2,3)) is investigated alongside the well-known Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. The inclusion of mode triple interactions is discussed and it is found that the use of an effective core potential (ECP) serves as a viable compromise during the highly demanding task of computing such contributions, thus enabling a grid-based evaluation of three mode interaction terms with coupled cluster techniques also for larger molecules. In this context, a previously proposed reduced coupling scheme [1] is investigated, confirming the applicability of this technique to a system exhibiting a rather complex electronic structure. A combination of Ahlrichs' triple-ζ valence polarized (TZVP) basis set with Dunning's set of core-valence correlation functions is found to deliver results in good agreement with experiment while being computationally very feasible. Since CH3CN exhibits four degenerate vibrational degrees of freedom, it serves as an ideal model system for critically assessing the qualities of the degenerate second-order perturbation theory corrected (DPT2) VSCF technique. Besides fundamental vibrations, a thorough investigation of overtone transitions and combination bands is conducted by means of comparing the results to both available and newly recorded experimental data.

  19. A Correlation Study of Student Attitudes Toward Science in a Southern State High School

    NASA Astrophysics Data System (ADS)

    Barco-Southall, Crystal

    The purpose of this correlational research study was to examine the attitudes toward science of students in Grades 11 and 12 and to investigate if there were differences resulting from gender, grade level, ethnicity, and the level of the curriculum received in average or advanced placement (AP) honors science. The participants of this study consisted of 50 randomly selected male and female high school students who were enrolled in AP and average science classes in an urban Southern state high school. The study used the Test of Science Related Attitudes (TOSRA) instrument to measure students' attitudes toward science in seven categories including (a) Social Implications of Science, (b) Normality of Scientists, (c) Attitude Toward Scientific Inquiry, (d) Adoption of Scientific Attitudes, (e) Enjoyment of Science Lessons, (f) Leisure Interest in Science, and (g) Career Interest in Science. The quantitative component of the study allowed the researcher to determine whether there were gender differences in attitudes toward science based on the seven subscales and measuring different aspects of science attitudes. Statistical treatment of the TOSRA survey involved the use of descriptive statistics, Pearson correlation, and multiple and linear regression. Findings did not reveal significant gender differences on the total attitude scores although there were differences on several of the subscales. In addition, there were no significant differences in the mean attitude scores for grade level. However, the study did reveal differences in ethnicity and attitudes toward science. With regard to ethnicity, scores for Native Americans and Whites were higher than scores for Asians, African Americans, and Hispanics indicating that Native Americans and White students showed a more positive attitude toward science. Regarding the level of curriculum received by students who were exposed to advanced level science courses showed more positive attitudes toward science than those students

  20. High level methicillin resistance correlates with reduced Staphylococcus aureus endothelial cell damage.

    PubMed

    Seidl, Kati; Leemann, Michèle; Palheiros Marques, Miguel; Rachmühl, Carole; Leimer, Nadja; Andreoni, Federica; Achermann, Yvonne; Zinkernagel, Annelies S

    2017-01-01

    There has been controversy about the intrinsic virulence of methicillin-resistant Staphylococcus aureus (MRSA) as compared to methicillin-susceptible S. aureus (MSSA). To address this discrepancy, the intrinsic virulence of 42 MRSA and 40 MSSA clinical isolates was assessed by testing endothelial cell (EC) damage, a surrogate marker for virulence in blood stream infections. Since these clinical isolates represent a heterogeneous group, well characterized S. aureus laboratory strains with SCCmec loss- and gain-of-function mutations were used in addition. The clinical MRSA isolates carrying typical hospital acquired SCCmec types (I, II or III) induced significantly less damage (47.8%) as compared to isolates with other SCCmec types (62.3%, p=0.03) and MSSA isolates (64.2%, p<0.01). There was a strong inverse correlation between high-level oxacillin resistance and low EC damage induction (R(2)=0.4464, p<0.001). High-level oxacillin resistant strains (MIC >32μ/ml) grew significantly slower as compared to isolates with low-level resistance (p=0.047). The level of EC damage positively correlated with α- and δ-toxin production (p<0.0001 and p<0.05, respectively) but not with β-toxin production. Invasive MRSA isolates (n=21, 56.3%) were significantly less cytotoxic as compared to invasive MSSA isolates (n=20, 68.0%, p<0.05). There was no difference between EC damage induced by superficial versus invasive isolates in either MRSA or MSSA strains. Our data suggest that the intrinsic virulence of MRSA is similar or even reduced as compared to MSSA strains but is linked to the level of methicillin resistance.

  1. Ultrasonic attenuation measurements at very high SNR: Correlation, information theory and performance

    NASA Astrophysics Data System (ADS)

    Challis, Richard; Ivchenko, Vladimir; Al-Lashi, Raied

    2013-08-01

    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.

  2. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset.

    PubMed

    Shi, Ming-Guang; Xia, Jun-Feng; Li, Xue-Ling; Huang, De-Shuang

    2010-03-01

    Identifying protein-protein interactions (PPIs) is critical for understanding the cellular function of the proteins and the machinery of a proteome. Data of PPIs derived from high-throughput technologies are often incomplete and noisy. Therefore, it is important to develop computational methods and high-quality interaction dataset for predicting PPIs. A sequence-based method is proposed by combining correlation coefficient (CC) transformation and support vector machine (SVM). CC transformation not only adequately considers the neighboring effect of protein sequence but describes the level of CC between two protein sequences. A gold standard positives (interacting) dataset MIPS Core and a gold standard negatives (non-interacting) dataset GO-NEG of yeast Saccharomyces cerevisiae were mined to objectively evaluate the above method and attenuate the bias. The SVM model combined with CC transformation yielded the best performance with a high accuracy of 87.94% using gold standard positives and gold standard negatives datasets. The source code of MATLAB and the datasets are available on request under smgsmg@mail.ustc.edu.cn.

  3. Associations between Common Variants in Iron-Related Genes with Haematological Traits in Populations of African Ancestry

    PubMed Central

    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

    Background 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. Methods 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. Results 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 = <0.0001) in the meta analysis including the African cohorts only. Conclusions In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European 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. PMID:27332551

  4. The Effects of Socioeconomic Status, Clinical Factors, and Genetic Ancestry on Pulmonary Tuberculosis Disease in Northeastern Mexico

    PubMed Central

    Young, Bonnie N.; Rendón, Adrian; Rosas-Taraco, Adrian; Baker, Jack; Healy, Meghan; Gross, Jessica M.; Long, Jeffrey; Burgos, Marcos; Hunley, Keith L.

    2014-01-01

    Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB

  5. The effects of socioeconomic status, clinical factors, and genetic ancestry on pulmonary tuberculosis disease in northeastern Mexico.

    PubMed

    Young, Bonnie N; Rendón, Adrian; Rosas-Taraco, Adrian; Baker, Jack; Healy, Meghan; Gross, Jessica M; Long, Jeffrey; Burgos, Marcos; Hunley, Keith L

    2014-01-01

    Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB

  6. Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers.

    PubMed

    Zheng, Yonglan; Ogundiran, Temidayo O; Falusi, Adeyinka G; Nathanson, Katherine L; John, Esther M; Hennis, Anselm J M; Ambs, Stefan; Domchek, Susan M; Rebbeck, Timothy R; Simon, Michael S; Nemesure, Barbara; Wu, Suh-Yuh; Leske, Maria Cristina; Odetunde, Abayomi; Niu, Qun; Zhang, Jing; Afolabi, Chibuzor; Gamazon, Eric R; Cox, Nancy J; Olopade, Christopher O; Olopade, Olufunmilayo I; Huo, Dezheng

    2013-07-01

    Numerous single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified by genome-wide association studies (GWAS). However, these SNPs were primarily discovered and validated in women of European and Asian ancestry. Because linkage disequilibrium is ancestry-dependent and heterogeneous among racial/ethnic populations, we evaluated common genetic variants at 22 GWAS-identified breast cancer susceptibility loci in a pooled sample of 1502 breast cancer cases and 1378 controls of African ancestry. None of the 22 GWAS index SNPs could be validated, challenging the direct generalizability of breast cancer risk variants identified in Caucasians or Asians to other populations. Novel breast cancer risk variants for women of African ancestry were identified in regions including 5p12 (odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.11-1.76; P = 0.004), 5q11.2 (OR = 1.22, 95% CI = 1.09-1.36; P = 0.00053) and 10p15.1 (OR = 1.22, 95% CI = 1.08-1.38; P = 0.0015). We also found positive association signals in three regions (6q25.1, 10q26.13 and 16q12.1-q12.2) previously confirmed by fine mapping in women of African ancestry. In addition, polygenic model indicated that eight best markers in this study, compared with 22 GWAS-identified SNPs, could better predict breast cancer risk in women of African ancestry (per-allele OR = 1.21, 95% CI = 1.16-1.27; P = 9.7 × 10(-16)). Our results demonstrate that fine mapping is a powerful approach to better characterize the breast cancer risk alleles in diverse populations. Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora.

  7. Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases*

    PubMed Central

    Lai, Shenshen; Safaei, Javad

    2016-01-01

    The reversible phosphorylation of proteins catalyzed by protein kinases in eukaryotes supports an important role for eukaryotic protein kinases (ePKs) in the emergence of nucleated cells in the third superkingdom of life. Choline kinases (ChKs) could also be critical in the early evolution of eukaryotes, because of their function in the biosynthesis of phosphatidylcholine, which is unique to eukaryotic membranes. However, the genomic origins of ePKs and ChKs are unclear. The high degeneracy of protein sequences and broad expansion of ePK families have made this fundamental question difficult to answer. In this study, we identified two class-I aminoacyl-tRNA synthetases with high similarities to consensus amino acid sequences of human protein-serine/threonine kinases. Comparisons of primary and tertiary structures supported that ePKs and ChKs evolved from a common ancestor related to glutaminyl aminoacyl-tRNA synthetases, which may have been one of the key factors in the successful of emergence of ancient eukaryotic cells from bacterial colonies. PMID:26742849

  8. One in Four Individuals of African-American Ancestry Harbors a 5.5kb Deletion at chromosome 11q13.1

    PubMed Central

    Zainabadi, Kayvan; Jain, Anuja V.; Donovan, Frank X.; Elashoff, David; Rao, Nagesh P.; Murty, Vundavalli V.; Chandrasekharappa, Settara C.; Srivatsan, Eri S.

    2014-01-01

    Cloning and sequencing of 5.5kb deletion at chromosome 11q13.1 from the HeLa cells, tumorigenic hybrids and two fibroblast cell lines has revealed homologous recombination between AluSx and AluY resulting in the deletion of intervening sequences. Long-range PCR of the 5.5kb sequence in 494 normal lymphocyte samples showed heterozygous deletion in 28.3% of African- American ancestry samples but only in 4.8% of Caucasian samples (p<0.0001). This observation is strengthened by the copy number variation (CNV) data of the HapMap samples which showed that this deletion occurs in 27% of YRI (Yoruba – West African) population but none in non-African populations. The HapMap analysis further identified strong linkage disequilibrium between 5 single nucleotide polymorphisms and the 5.5kb deletion in the people of African ancestry. Computational analysis of 175kb sequence surrounding the deletion site revealed enhanced flexibility, low thermodynamic stability, high repetitiveness, and stable stem-loop/hairpin secondary structures that are hallmarks of common fragile sites. PMID:24412158

  9. Genetic evidence for the Mongolian ancestry of Kalmyks.

    PubMed

    Nasidze, Ivan; Quinque, Dominique; Dupanloup, Isabelle; Cordaux, Richard; Kokshunova, Lyudmila; Stoneking, Mark

    2005-12-01

    The Kalmyks are an ethnic group along the lower Volga River in Russia who are thought to have migrated there from Mongolia about 300 years ago. To investigate their origins, we studied mtDNA and Y-chromosome variation in 99 Kalmyks. Both mtDNA HV1 sequences and Y-chromosome SNP haplogroups indicate a close relationship of Kalmyks with Mongolians. In addition, genetic diversity for both mtDNA and the Y chromosome are comparable in Kalmyks, Mongolians, and other Central Asian groups, indicating that the Kalmyk migration was not associated with a substantial bottleneck. The so-called "Genghis Khan" Y-chromosome short tandem repeat (STR) haplotype was found in high frequency (31.3%) among Kalmyks, further supporting a strong genetic connection between Kalmyks and Mongolians. Genetic analyses of even recent, relatively well-documented migrations such as of the Kalmyks can therefore lead to new insights concerning such migrations.

  10. Ancestry of modern Europeans: contributions of ancient DNA.

    PubMed

    Lacan, Marie; Keyser, Christine; Crubézy, Eric; Ludes, Bertrand

    2013-07-01

    Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.

  11. Prevalence and correlates of excessive daytime sleepiness in high school students in Korea.

    PubMed

    Joo, Soonjae; Shin, Chol; Kim, Jinkwan; Yi, Hyeryeon; Ahn, Yongkyu; Park, Minkyu; Kim, Jehyeong; Lee, SangDuck

    2005-08-01

    The purpose of the present study was to determine the prevalence of excessive daytime sleepiness (EDS) and its associations with sleep habits, sleep problems, and school performance in high school students in South Korea. A total of 3871 students (2703 boys and 1168 girls with a mean age of 16.8 years and 16.9 years, respectively) aged 15-18 years in the 11th grade of high school completed a questionnaire that contained items about individual sociodemographic characteristics, sleep habits, and sleep-related problems. The overall prevalence of EDS was 15.9% (14.9% for boys and 18.2% for girls). Mean reported total sleep time was similar in EDS and non-EDS (6.4 +/- 1.6 and 6.4 +/- 1.3 h/day, respectively). The increased risk of EDS was related to perceived sleep insufficiency (P < 0.001), teeth grinding > or = 4 days/week (P < 0.001), witnessed apnea > or = 1-3 days/week (P < 0.01), nightmares > or = 4 days/week (P < 0.05), low school performance (P < 0.01), and two or more insomnia symptoms (P < 0.05). Students with low school performance had a 60% excess in the odds of EDS compared to those whose school performance was high. These findings suggest that EDS is associated with multiple sleep-related factors in adolescents. Whether interventions to modify associated correlates can alter EDS warrants consideration, especially because it may also improve academic performance in high school students.

  12. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry.

    PubMed

    Flegontov, Pavel; Changmai, Piya; Zidkova, Anastassiya; Logacheva, Maria D; Altınışık, N Ezgi; Flegontova, Olga; Gelfand, Mikhail S; Gerasimov, Evgeny S; Khrameeva, Ekaterina E; Konovalova, Olga P; Neretina, Tatiana; Nikolsky, Yuri V; Starostin, George; Stepanova, Vita V; Travinsky, Igor V; Tříska, Martin; Tříska, Petr; Tatarinova, Tatiana V

    2016-02-11

    The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

  13. Morpho morphometrics: Shared ancestry and selection drive the evolution of wing size and shape in Morpho butterflies.

    PubMed

    Chazot, Nicolas; Panara, Stephen; Zilbermann, Nicolas; Blandin, Patrick; Le Poul, Yann; Cornette, Raphaël; Elias, Marianne; Debat, Vincent

    2016-01-01

    Butterfly wings harbor highly diverse phenotypes and are involved in many functions. Wing size and shape result from interactions between adaptive processes, phylogenetic history, and developmental constraints, which are complex to disentangle. Here, we focus on the genus Morpho (Nymphalidae: Satyrinae, 30 species), which presents a high diversity of sizes, shapes, and color patterns. First, we generate a comprehensive molecular phylogeny of these 30 species. Next, using 911 collection specimens, we quantify the variation of wing size and shape across species, to assess the importance of shared ancestry, microhabitat use, and sexual selection in the evolution of the wings. While accounting for phylogenetic and allometric effects, we detect a significant difference in wing shape but not size among microhabitats. Fore and hindwings covary at the individual and species levels, and the covariation differs among microhabitats. However, the microhabitat structure in covariation disappears when phylogenetic relationships are taken into account. Our results demonstrate that microhabitat has driven wing shape evolution, although it has not strongly affected forewing and hindwing integration. We also found that sexual dimorphism of forewing shape and color pattern are coupled, suggesting a common selective force.

  14. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

    PubMed Central

    Flegontov, Pavel; Changmai, Piya; Zidkova, Anastassiya; Logacheva, Maria D.; Altınışık, N. Ezgi; Flegontova, Olga; Gelfand, Mikhail S.; Gerasimov, Evgeny S.; Khrameeva, Ekaterina E.; Konovalova, Olga P.; Neretina, Tatiana; Nikolsky, Yuri V.; Starostin, George; Stepanova, Vita V.; Travinsky, Igor V.; Tříska, Martin; Tříska, Petr; Tatarinova, Tatiana V.

    2016-01-01

    The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal’ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal’ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed. PMID:26865217

  15. Differential effects of stress and African ancestry on preterm birth and related traits among US born and immigrant Black mothers

    PubMed Central

    Tsai, Hui-Ju; Surkan, Pamela J.; Yu, Stella M.; Caruso, Deanna; Hong, Xiumei; Bartell, Tami R.; Wahl, Anastacia D.; Sampankanpanich, Claire; Reily, Anne; Zuckerman, Barry S.; Wang, Xiaobin

    2017-01-01

    Abstract Preterm birth (PTB, <37 weeks of gestation) is influenced by a wide range of environmental, genetic and psychosocial factors, and their interactions. However, the individual and joint effects of genetic factors and psychosocial stress on PTB have remained largely unexplored among U.S. born versus immigrant mothers. We studied 1121 African American women from the Boston Birth Cohort enrolled from 1998 to 2008. Regression-based analyses were performed to examine the individual and joint effects of genetic ancestry and stress (including lifetime stress [LS] and stress during pregnancy [PS]) on PTB and related traits among U.S. born and immigrant mothers. Significant associations between LS and PTB and related traits were found in the total study population and in immigrant mothers, including gestational age, birthweight, PTB, and spontaneous PTB; but no association was found in U.S. born mothers. Furthermore, significant joint associations of LS (or PS) and African ancestral proportion (AAP) on PTB were found in immigrant mothers, but not in U.S. born mothers. Although, overall, immigrant women had lower rates of PTB compared to U.S. born women, our study is one of the first to identify a subset of immigrant women could be at significantly increased risk of PTB and related outcomes if they have high AAP and are under high LS or PS. In light of the growing number of immigrant mothers in the U.S., our findings may have important clinical and public health implications. PMID:28151865

  16. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    PubMed

    Adissu, Hibret A; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M; Clarke, Kay; Karp, Natasha A; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K; McKerlie, Colin

    2014-05-01

    The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  17. Reverse correlating love: highly passionate women idealize their partner's facial appearance.

    PubMed

    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.

  18. Chloroplast movement behavior varies widely among species and does not correlate with high light stress tolerance.

    PubMed

    Königer, Martina; Bollinger, Nicole

    2012-08-01

    It is well known that chloroplasts move in response to changes in blue light intensity in order to optimize light interception, however, little is known about interspecific variation and the relative importance of this mechanism for the high light stress tolerance of plants. We characterized chloroplast movement behavior as changes in light transmission through a leaf in a variety of species ranging from ferns to monocots and eudicots and found a wide spectrum of responses. Most species exhibited a distinct accumulation response compared to the dark positioning, and all species showed a distinct avoidance response. The speed with which transmission values changed during the avoidance response was consistently faster than that during the accumulation response and speeds varied greatly between species. Plants thriving in higher growth light intensities showed greater degrees of accumulation responses and faster changes in transmission than those that prefer lower light intensities. In some species, the chloroplasts on both the adaxial and abaxial leaf surfaces changed their positioning in response to light, while in other species only the chloroplasts on one leaf side responded. No correlation was found between high light stress tolerance and the speed or degree of transmission changes, indicating that plants can compensate for slow and limited transmission changes using other photoprotective mechanisms.

  19. Correlation of microstructure and fracture toughness in high-chromium white iron hardfacing alloys

    SciTech Connect

    Lee, S.; Choo, S.H.; Kim, N.J.; Baek, E.R.; Ahn, S.

    1996-12-01

    A correlation is made of microstructure and fracture toughness in hypereutectic high-chromium white iron hardfacing alloys. In order to investigate the matrix effect of these alloys, in particular, four different matrices such as pearlite, austenite, and a mixture of pearlite and austenite were employed by changing the ratio of Mn/Si, while the total volume fraction of carbides was fixed. The hardfacing alloys were deposited twice on a mild steel plate by the self-shielding flux-cored arc-welding method. Fracture toughness was increased by increasing the volume fraction of austenite in the matrix, whereas hardness and abrasion resistance were nearly constant. In situ observation of the fracture process showed that cracks initiated at large primary carbides tended to be blocked at the austenitic matrix. This suggested that fracture toughness was controlled mainly by the amount of austenite in the matrix, thereby yielding the better toughness in the hardfacing alloy having the austenitic matrix. Considering both abrasion resistance and fracture toughness, therefore, the austenitic matrix was preferred for the high-chromium white iron hardfacing alloys.

  20. Correlates of bullying in Quebec high school students: the vulnerability of sexual-minority youth

    PubMed Central

    Cénat, Jude Mary; Blais, Martin; Hébert, Martine; Lavoie, Francine; Guerrier, Mireille

    2015-01-01

    Purpose 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). Method A representative sample of 8,194 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. Results 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 experienced cyberbullying and other form 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. Conclusions The results underscore the relevance of taking into account gender and sexual orientation variations in efforts to prevent bullying experience and its consequences. PMID:26047959

  1. High-speed 3D digital image correlation vibration measurement: Recent advancements and noted limitations

    NASA Astrophysics Data System (ADS)

    Beberniss, Timothy J.; Ehrhardt, David A.

    2017-03-01

    A review of the extensive studies on the feasibility and practicality of utilizing high-speed 3 dimensional digital image correlation (3D-DIC) for various random vibration measurement applications is presented. Demonstrated capabilities include finite element model updating utilizing full-field 3D-DIC static displacements, modal survey natural frequencies, damping, and mode shape results from 3D-DIC are baselined against laser Doppler vibrometry (LDV), a comparison between foil strain gage and 3D-DIC strain, and finally the unique application to a high-speed wind tunnel fluid-structure interaction study. Results show good agreement between 3D-DIC and more traditional vibration measurement techniques. Unfortunately, 3D-DIC vibration measurement is not without its limitations, which are also identified and explored in this study. The out-of-plane sensitivity required for vibration measurement for 3D-DIC is orders of magnitude less than LDV making higher frequency displacements difficult to sense. Furthermore, the digital cameras used to capture the DIC images have no filter to eliminate temporal aliasing of the digitized signal. Ultimately DIC is demonstrated as a valid alternative means to measure structural vibrations while one unique application achieves success where more traditional methods would fail.

  2. High expression of CRAM correlates with poor prognosis in patients with cervical carcinoma

    PubMed Central

    Hou, Teng; Liang, Dongxia; Yang, Dong; He, Jiehua; Huang, Yongwen; Zhang, Yanna

    2014-01-01

    Aims: Atypical chemokine receptors (ACRs) have been reported to scavenge or alter the localization of their chemokine ligands. However, CRAM, a newly identified ACR member, is lack of ligand scavenging properties. The present study was to investigate the clinical significance of CRAM in cervical carcinoma. Methods: The expression of CRAM in primary cervical cancer and paired normal tissues from adjacent regions was examined using Real time PCR. Moreover, CRAM protein expression was analyzed in 272 cervical specimens including 50 normal cervical tissues, 40 cases of carcinoma in situ of cervix (CIS), and 182 cases of cervical cancer by immunohistochemistry. Results: Real time PCR showed that the expression level of CRAM was markedly higher in cervical cancer than that in normal cervical tissues. The expression rate of CRAM in normal cervical tissues, CIS, and cervical cancer increased gradually (p < 0.01). In addition, the expression level of CCL19 was positively associated with that of CRAM (p < 0.05). Moreover, high expression level of CRAM was correlated with lymph node metastasis and histological subtype. In multivariate Cox regression analysis, high expression level of CRAM was a negative indicator for both overall (p = 0.028) and recurrence-free survival (p = 0.010). Conclusion: The present study suggested that CRAM could be a clinical prognostic marker for patients with cervical cancer and might be a potential therapeutic target for cervical cancer. Our data extended previous research on the predictive value of ACRs. PMID:24695578

  3. Magnetic resonance imaging assessed cortical porosity is highly correlated with μCT porosity.

    PubMed

    Bae, Won C; Patil, Shantanu; Biswas, Reni; Li, Shihong; Chang, Eric Y; Statum, Sheronda; D'Lima, Darryl D; Chung, Christine B; Du, Jiang

    2014-09-01

    Cortical bone is typically regarded as "MR invisible" with conventional clinical magnetic resonance imaging (MRI) pulse sequences. However, recent studies have demonstrated that free water in the microscopic pores of cortical bone has a short T2* but a relatively long T2, and may be detectable with conventional clinical spin echo (SE) or fast spin echo (FSE) sequences. In this study we describe the use of a conventional two-dimensional (2D) FSE sequence to assess cortical bone microstructure and measure cortical porosity using a clinical 3T scanner. Twelve cadaveric human cortical bone samples were studied with MRI and microcomputed tomography (μCT) (downsampled to the same spatial resolution). Preliminary results show that FSE-determined porosity is highly correlated (R(2)=0.83; P<0.0001) with μCT porosity. Bland-Altman analysis suggested a good agreement between FSE and μCT with tight limit of agreement at around 3%. There is also a small bias of -2% for the FSE data, which suggested that the FSE approach slightly underestimated μCT porosity. The results demonstrate that cortical porosity can be directly assessed using conventional clinical FSE sequences. The clinical feasibility of this approach was also demonstrated on six healthy volunteers using 2D FSE sequences as well as 2D ultrashort echo time (UTE) sequences with a minimal echo time (TE) of 8μs, which provide high contrast imaging of cortical bone in vivo.

  4. Nonvolcanic Tremor Activity is Highly Correlated With Slow Slip Events, Mexico

    NASA Astrophysics Data System (ADS)

    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

  5. High Statistics Analysis using Anisotropic Clover Lattices: (I) Single Hadron Correlation Functions

    SciTech Connect

    Will Detmold,Konstantinos Orginos,Silas R. Beane,Will Detmold,William Detmold,Thomas C. Luu,Konstantinos Orginos,Assumpta Parreno,Martin J. Savage,Aaron Torok,Andre Walker-Loud

    2009-06-01

    We present the results of high-statistics calculations of correlation functions generated with single-baryon interpolating operators on an ensemble of dynamical anisotropic gauge-field configurations generated by the Hadron Spectrum Collaboration using a tadpole-improved clover fermion action and Symanzik-improved gauge action. A total of 292,500 sets of measurements are made using 1194 gauge configurations of size 20^3 x 128 with an anisotropy parameter \\xi= b_s/b_t = 3.5, a spatial lattice spacing of b_s=0.1227\\pm 0.0008 fm, and pion mass of m_\\pi ~ 390 MeV. Ground state baryon masses are extracted with fully quantified uncertainties that are at or below the ~0.2%-level in lattice units. The lowest-lying negative-parity states are also extracted albeit with a somewhat lower level of precision. In the case of the nucleon, this negative-parity state is above the N\\pi threshold and, therefore, the isospin-1/2 \\pi N s-wave scattering phase-shift can be extracted using Luescher's method. The disconnected contributions to this process are included indirectly in the gauge-field configurations and do not require additional calculations. The signal-to-noise ratio in the various correlation functions is explored and is found to degrade exponentially faster than naive expectations on many time-slices. This is due to backward propagating states arising from the anti-periodic boundary conditions imposed on the quark-propagators in the time-direction. We explore how best to distribute computational resources between configuration generation and propagator measurements in order to optimize the extraction of single baryon observables.

  6. Depolarized Photon Correlation Spectroscopic Study of the Glass-Forming Liquid Cumene at Very High Pressures

    NASA Astrophysics Data System (ADS)

    Lyon, Kevin; Ransom, Tim; Oliver, William

    2014-03-01

    In recent years full-spectrum analysis of light-scattering data has been utilized to explore the liquid-glass transition at variable temperatures and ambient pressure. We have developed methods for doing depolarized photon correlation spectroscopy (PCS) in the diamond anvil cell in order to probe directly the structural relaxation time of glass-forming liquids at very high pressures. Here we present results for liquid cumene at 25 C between 1 bar and pressures approaching the room-temperature glass transition at 2.1 GPa. Data along higher-temperature isotherms will also be presented. Methods for minimizing any undesired heterodyne component in the collected light as well as the use of the longitudinal modes of the Brillouin spectrum to aid in the acquisition and spatial filtering of the scattered light will be discussed. Intensity-intensity correlation data were found to be well represented by the KWW equation with a nearly constant stretching parameter of g = 0.66 for 25 C. Furthermore, the relaxation time as a function of pressure is described will using a modified VTF expression: (P)=0exp{DP/(P0-P)}, with values of 0 = 11.9 ps, D = 18.6, and P0 = 3.4 GPa at T = 25 °C. Thus, (P) has been obtained at 25 °C for Cumene over seven decades from about a microsecond to several seconds and is found to be in excellent agreement with previously determined values for the alpha relaxation at lower pressures obtained from Brillouin data [G. Li, et al., Phys. Rev. Lett. 74, 2280 (1995)]. Partially supported by NSF Grant Number: DMR 0552944.

  7. Ontogenetic evidence for the Paleozoic ancestry of salamanders.

    PubMed

    Schoch, Rainer R; Carroll, Robert L

    2003-01-01

    The phylogenetic positions of frogs, salamanders, and caecilians have been difficult to establish. Data matrices based primarily on Paleozoic taxa support a monophyletic origin of all Lissamphibia but have resulted in widely divergent hypotheses of the nature of their common ancestor. Analysis that concentrates on the character states of the stem taxa of the extant orders, in contrast, suggests a polyphyletic origin from divergent Paleozoic clades. Comparison of patterns of larval development in Paleozoic and modern amphibians provides a means to test previous phylogenies based primarily on adult characteristics. This proves to be highly informative in the case of the origin of salamanders. Putative ancestors of salamanders are recognized from the Permo-Carboniferous boundary of Germany on the basis of ontogenetic changes observed in fossil remains of larval growth series. The entire developmental sequence from hatching to metamorphosis is revealed in an assemblage of over 600 specimens from a single locality, all belonging to the genus Apateon. Apateon forms the most speciose genus of the neotenic temnospondyl family Branchiosauridae. The sequence of ossification of individual bones and the changing configuration of the skull closely parallel those observed in the development of primitive living salamanders. These fossils provide a model of how derived features of the salamander skull may have evolved in the context of feeding specializations that appeared in early larval stages of members of the Branchiosauridae. Larvae of Apateon share many unique derived characters with salamanders of the families Hynobiidae, Salamandridae, and Ambystomatidae, which have not been recognized in any other group of Paleozoic amphibians.

  8. Emergent high-Tc ferroelectric ordering of strongly correlated and frustrated protons in a heteroepitaxial ice film

    NASA Astrophysics Data System (ADS)

    Sugimoto, Toshiki; Aiga, Norihiro; Otsuki, Yuji; Watanabe, Kazuya; Matsumoto, Yoshiyasu

    2016-11-01

    Materials containing strong correlation and frustration have the potential to respond to external perturbations in an unusual way. In the case of common water ice, protons in the hydrogen-bond network are strongly correlated and highly frustrated under Pauling's ice rules. At low temperature, the strongly correlated protons lose ergodicity, and little is understood about the cooperative thermodynamic and electric response to external stimuli. Here, using a model platinum substrate, we demonstrate emergent high-Tc ferroelectric proton ordering in a heteroepitaxial ice film. Such proton ordering is thermodynamically stable and has an extremely high critical temperature of ~175 K. We found that anisotropy and protolysis driven by the electrostatistics at the heterointerface are key factors in stimulating this novel exotic ordering in the many-body correlated proton system. The significant increase in Tc due to the heterointerface suggests the ubiquity of ferroelectric ice in nature--specifically, in space and the polar stratosphere.

  9. African Ancestry Gradient Is Associated with Lower Systemic F2-Isoprostane Levels

    PubMed Central

    Annor, Francis; Okosun, Ike; Gower, Barbara A.

    2017-01-01

    Context. Low levels of systemic F2-isoprostanes (F2-IsoP) increase the risk of diabetes and weight gain and were found in African Americans. Low F2-IsoPs could reflect an unfavorable metabolic characteristic, namely, slow mitochondrial metabolism in individuals with African ancestry. Objective. To examine differences in plasma F2-IsoPs in three groups with a priori different proportion of African ancestry: non-Hispanic Whites (NHWs), US-born African Americans (AAs), and West African immigrants (WAI). Design. Cross-sectional study. Setting. Georgia residents recruited from church communities. Participants. 218 males and females 25–74 years of age, who are self-identified as NHW (n = 83), AA (n = 56), or WAI (n = 79). Main Outcome Measure(s). Plasma F2-IsoPs quantified by gas chromatography-mass spectrometry. Results. After adjustment for age, gender, obesity, and other comorbidities, WAI had lower levels of plasma F2-IsoP than AA (beta-coefficient = −9.8, p < 0.001) and AA had lower levels than NHW (beta-coefficient = −30.3, p < 0.001). Similarly, among healthy nonobese participants, F2-IsoP levels were lowest among WAI, followed by AA, and the highest levels were among NHW. Conclusion. Plasma F2-IsoPs are inversely associated with African ancestry gradient. Additional studies are required to test whether optimization of systemic F2-IsoP levels can serve as means to improve race-specific lifestyle and pharmacological intervention targeted to obesity prevention and treatment. PMID:28250893

  10. The missing link of Jewish European ancestry: contrasting the Rhineland and the Khazarian hypotheses.

    PubMed

    Elhaik, Eran

    2013-01-01

    The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The "Rhineland hypothesis" depicts Eastern European Jews as a "population isolate" that emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the "Khazarian hypothesis" suggests that Eastern European Jews descended from the Khazars, an amalgam of Turkic clans that settled the Caucasus in the early centuries CE and converted to Judaism in the 8th century. Mesopotamian and Greco-Roman Jews continuously reinforced the Judaized empire until the 13th century. Following the collapse of their empire, the Judeo-Khazars fled to Eastern Europe. The rise of European Jewry is therefore explained by the contribution of the Judeo-Khazars. Thus far, however, the Khazars' contribution has been estimated only empirically, as the absence of genome-wide data from Caucasus populations precluded testing the Khazarian hypothesis. Recent sequencing of modern Caucasus populations prompted us to revisit the Khazarian hypothesis and compare it with the Rhineland hypothesis. We applied a wide range of population genetic analyses to compare these two hypotheses. Our findings support the Khazarian hypothesis and portray the European Jewish genome as a mosaic of Near Eastern-Caucasus, European, and Semitic ancestries, thereby consolidating previous contradictory reports of Jewish ancestry. We further describe a major difference among Caucasus populations explained by the early presence of Judeans in the Southern and Central Caucasus. Our results have important implications for the demographic forces that shaped the genetic diversity in the Caucasus and for medical studies.

  11. The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses

    PubMed Central

    Elhaik, Eran

    2013-01-01

    The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The “Rhineland hypothesis” depicts Eastern European Jews as a “population isolate” that emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the “Khazarian hypothesis” suggests that Eastern European Jews descended from the Khazars, an amalgam of Turkic clans that settled the Caucasus in the early centuries CE and converted to Judaism in the 8th century. Mesopotamian and Greco–Roman Jews continuously reinforced the Judaized empire until the 13th century. Following the collapse of their empire, the Judeo–Khazars fled to Eastern Europe. The rise of European Jewry is therefore explained by the contribution of the Judeo–Khazars. Thus far, however, the Khazars’ contribution has been estimated only empirically, as the absence of genome-wide data from Caucasus populations precluded testing the Khazarian hypothesis. Recent sequencing of modern Caucasus populations prompted us to revisit the Khazarian hypothesis and compare it with the Rhineland hypothesis. We applied a wide range of population genetic analyses to compare these two hypotheses. Our findings support the Khazarian hypothesis and portray the European Jewish genome as a mosaic of Near Eastern-Caucasus, European, and Semitic ancestries, thereby consolidating previous contradictory reports of Jewish ancestry. We further describe a major difference among Caucasus populations explained by the early presence of Judeans in the Southern and Central Caucasus. Our results have important implications for the demographic forces that shaped the genetic diversity in the Caucasus and for medical studies. PMID:23241444

  12. Prostate Cancer Susceptibility in Men of African Ancestry at 8q24.

    PubMed

    Han, Ying; Rand, Kristin A; Hazelett, Dennis J; Ingles, Sue A; Kittles, Rick A; Strom, Sara S; Rybicki, Benjamin A; Nemesure, Barbara; Isaacs, William B; Stanford, Janet L; Zheng, Wei; Schumacher, Fredrick R; Berndt, Sonja I; Wang, Zhaoming; Xu, Jianfeng; Rohland, Nadin; Reich, David; Tandon, Arti; Pasaniuc, Bogdan; Allen, Alex; Quinque, Dominique; Mallick, Swapan; Notani, Dimple; Rosenfeld, Michael G; Jayani, Ranveer Singh; Kolb, Suzanne; Gapstur, Susan M; Stevens, Victoria L; Pettaway, Curtis A; Yeboah, Edward D; Tettey, Yao; Biritwum, Richard B; Adjei, Andrew A; Tay, Evelyn; Truelove, Ann; Niwa, Shelley; Chokkalingam, Anand P; John, Esther M; Murphy, Adam B; Signorello, Lisa B; Carpten, John; Leske, M Cristina; Wu, Suh-Yuh; Hennis, Anslem J M; Neslund-Dudas, Christine; Hsing, Ann W; Chu, Lisa; Goodman, Phyllis J; Klein, Eric A; Zheng, S Lilly; Witte, John S; Casey, Graham; Lubwama, Alex; Pooler, Loreall C; Sheng, Xin; Coetzee, Gerhard A; Cook, Michael B; Chanock, Stephen J; Stram, Daniel O; Watya, Stephen; Blot, William J; Conti, David V; Henderson, Brian E; Haiman, Christopher A

    2016-07-01

    The 8q24 region harbors multiple risk variants for distinct cancers, including >8 for prostate cancer. In this study, we conducted fine mapping of the 8q24 risk region (127.8-128.8Mb) in search of novel associations with common and rare variation in 4853 prostate cancer case patients and 4678 control subjects of African ancestry. All statistical tests were two-sided. We identified three independent associations at P values of less than 5.00×10(-8), all of which were replicated in studies from Ghana and Uganda (combined sample = 5869 case patients, 5615 control subjects; rs114798100: risk allele frequency [RAF] = 0.04, per-allele odds ratio [OR] = 2.31, 95% confidence interval [CI] = 2.04 to 2.61, P = 2.38×10(-40); rs72725879: RAF = 0.33, OR = 1.37, 95% CI = 1.30 to 1.45, P = 3.04×10(-27); and rs111906932: RAF = 0.03, OR = 1.79, 95% CI = 1.53 to 2.08, P = 1.39×10(-13)). Risk variants rs114798100 and rs111906923 are only found in men of African ancestry, with rs111906923 representing a novel association signal. The three variants are located within or near a number of prostate cancer-associated long noncoding RNAs (lncRNAs), including PRNCR1, PCAT1, and PCAT2. These findings highlight ancestry-specific risk variation and implicate prostate-specific lncRNAs at the 8q24 prostate cancer susceptibility region.

  13. Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico

    PubMed Central

    Gravlee, Clarence C.; Non, Amy L.; Mulligan, Connie J.

    2009-01-01

    Background The role of race in human genetics and biomedical research is among the most contested issues in science. Much debate centers on the relative importance of genetic versus sociocultural factors in explaining racial inequalities in health. However, few studies integrate genetic and sociocultural data to test competing explanations directly. Methodology/Principal Findings We draw on ethnographic, epidemiologic, and genetic data collected in southeastern Puerto Rico to isolate two distinct variables for which race is often used as a proxy: genetic ancestry versus social classification. We show that color, an aspect of social classification based on the culturally defined meaning of race in Puerto Rico, better predicts blood pressure than does a genetic-based estimate of continental ancestry. We also find that incorporating sociocultural variables reveals a new and significant association between a candidate gene polymorphism for hypertension (α2C adrenergic receptor deletion) and blood pressure. Conclusions/Significance This study addresses the recognized need to measure both genetic and sociocultural factors in research on racial inequalities in health. Our preliminary results provide the most direct evidence to date that previously reported associations between genetic ancestry and health may be attributable to sociocultural factors related to race and racism, rather than to functional genetic differences between racially defined groups. Our results also imply that including sociocultural variables in future research may improve our ability to detect significant allele-phenotype associations. Thus, measuring sociocultural factors related to race may both empower future genetic association studies and help to clarify the biological consequences of social inequalities. PMID:19742303

  14. Associations of adiponectin with individual European ancestry in African Americans: the Jackson Heart Study

    PubMed Central

    Bidulescu, Aurelian; Choudhry, Shweta; Musani, Solomon K.; Buxbaum, Sarah G.; Liu, Jiankang; Rotimi, Charles N.; Wilson, James G.; Taylor, Herman A.; Gibbons, Gary H.

    2014-01-01

    Background: Compared with European Americans, African Americans (AAs) exhibit lower levels of the cardio-metabolically protective adiponectin even after accounting for adiposity measures. Because few studies have examined in AA the association between adiponectin and genetic admixture, a dense panel of ancestry informative markers (AIMs) was used to estimate the individual proportions of European ancestry (PEA) for the AAs enrolled in a large community-based cohort, the Jackson Heart Study (JHS). We tested the hypothesis that plasma adiponectin and PEA are directly associated and assessed the interaction with a series of cardio-metabolic risk factors. Methods: Plasma specimens from 1439 JHS participants were analyzed by ELISA for adiponectin levels. Using pseudo-ancestral population genotype data from the HapMap Consortium, PEA was estimated with a panel of up to 1447 genome-wide preselected AIMs by a maximum likelihood approach. Interaction assessment, stepwise linear and cubic multivariable-adjusted regression models were used to analyze the cross-sectional association between adiponectin and PEA. Results: Among the study participants (62% women; mean age 48 ± 12 years), the median (interquartile range) of PEA was 15.8 (9.3)%. Body mass index (BMI) (p = 0.04) and insulin resistance (p = 0.0001) modified the association between adiponectin and PEA. Adiponectin was directly and linearly associated with PEA (β = 0.62 ± 0.28, p = 0.03) among non-obese (n = 673) and insulin sensitive participants (n = 1141; β = 0.74 ± 0.23, p = 0.001), but not among those obese or with insulin resistance. No threshold point effect was detected for non-obese participants. Conclusions: In a large AA population, the individual proportion of European ancestry was linearly and directly associated with plasma adiponectin among non-obese and non insulin-resistant participants, pointing to the interaction of genetic and metabolic factors influencing adiponectin levels. PMID:24575123

  15. Correlation between high perfusion syndrome and stent restenosis after stent implantation

    PubMed Central

    Li, Yingyi; Tang, Lingtao; Qi, Dong; Wang, Chunlei; Zhang, Suxia; Hu, Pengfei; Wang, Yun; Zhang, Bogang; Zhang, Kunxi

    2016-01-01

    The present study was conducted to determine the correlation between high perfusion syndrome and stent restenosis after cerebral vascular stent implantation. A total of 146 patients diagnosed with cerebral vascular stenosis and stent implantation were selected. A total of 55 cases (37.67%) of cerebral hyperperfusion syndrome patients were diagnosed by xenon-enhanced computer tomography (Xe-CT) examination and clinical symptoms within 3 days after surgery and were chosen as the observation group. A total of 91 cases were selected as the control group. After treatment, blood flow of the anterior cerebral artery, middle cerebral artery, posterior cerebral artery, anterior border zone, posterior border zone and the inner border zone of the two groups increased, with values in the observation group increasing more significantly, and the differences were statistically significant (P<0.05). The rate of restenosis and target lesion diameter one month and one year after operation in the observation group were significantly higher than those in the control group (P<0.05). Multivariate logistic regression analysis showed that the mean systolic blood pressure (mSBP), mean diastolic blood pressure (mDBP), stenosis rate of cerebral vascular diameter and high perfusion syndrome were independent risk factors for restenosis (P<0.05). The application of Xe-CT examination is important for early diagnosis of hyperperfusion syndrome. Hyperperfusion syndrome and the occurrence of stent restenosis are closely related. mSBP, mDBP, cerebral blood vessel diameter stenosis rate and high perfusion comprehensive syndrome are the independent risk factors of restenosis. PMID:28101162

  16. Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry

    PubMed Central

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

    2014-01-01

    We investigated ancestry of 3,528 modern humans from 163 samples. We identified 19 ancestral components, with 94.4% of individuals showing mixed ancestry. After using whole genome sequences to correct for ascertainment biases in genome-wide genotype data, we dated the oldest divergence event to 140,000 years ago. We detected an Out-of-Africa migration 100,000–87,000 years ago, leading to peoples of the Americas, east and north Asia, and Oceania, followed by another migration 61,000–44,000 years ago, leading to peoples of the Caucasus, Europe, the Middle East, and south Asia. We dated eight divergence events to 33,000–20,000 years ago, coincident with the Last Glacial Maximum. We refined understanding of the ancestry of several ethno-linguistic groups, including African Americans, Ethiopians, the Kalash, Latin Americans, Mozabites, Pygmies, and Uygurs, as well as the CEU sample. Ubiquity of mixed ancestry emphasizes the importance of accounting for ancestry in history, forensics, and health. PMID:25116736

  17. Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages

    PubMed Central

    Palopoli, Michael F.; Fergus, Daniel J.; Minot, Samuel; Pei, Dorothy T.; Simison, W. Brian; Fernandez-Silva, Iria; Thoemmes, Megan S.; Dunn, Robert R.; Trautwein, Michelle

    2015-01-01

    Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries and analyzed 241 sequences from the mitochondrial genome of the species Demodex folliculorum. Phylogenetic analyses recovered multiple deep lineages including a globally distributed lineage common among hosts of European ancestry and three lineages that primarily include hosts of Asian, African, and Latin American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years and that some Asian and African American hosts maintain specific mite lineages over the course of years or generations outside their geographic region of birth or ancestry. D. folliculorum haplotypes were much more likely to be shared within families and between spouses than between unrelated individuals, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model system for further understanding the history of human movement. PMID:26668374

  18. Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages.

    PubMed

    Palopoli, Michael F; Fergus, Daniel J; Minot, Samuel; Pei, Dorothy T; Simison, W Brian; Fernandez-Silva, Iria; Thoemmes, Megan S; Dunn, Robert R; Trautwein, Michelle

    2015-12-29

    Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries and analyzed 241 sequences from the mitochondrial genome of the species Demodex folliculorum. Phylogenetic analyses recovered multiple deep lineages including a globally distributed lineage common among hosts of European ancestry and three lineages that primarily include hosts of Asian, African, and Latin American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years and that some Asian and African American hosts maintain specific mite lineages over the course of years or generations outside their geographic region of birth or ancestry. D. folliculorum haplotypes were much more likely to be shared within families and between spouses than between unrelated individuals, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model system for further understanding the history of human movement.

  19. Asians demonstrate reduced sensitivity to unpredictable threat: a preliminary startle investigation using genetic ancestry in a multiethnic sample.

    PubMed

    Nelson, Brady D; Bishop, Jeffrey R; Sarapas, Casey; Kittles, Rick A; Shankman, Stewart A

    2014-06-01

    Research has indicated that individuals of Asian descent, relative to other racial groups, demonstrate reduced emotional responding and lower prevalence rates of several anxiety disorders. It is unclear though whether these group differences extend to biomarkers of anxiety disorders and whether genetic differences play a role. This study compared self-identified Caucasian, Latino, and Asian persons (total N = 174) on startle response during a baseline period and while anticipating unpredictable threat-a putative biomarker for certain anxiety disorders--as well as predictable threat. In addition, the association between genetic ancestry and startle response was examined within each racial group to determine potential genetic influences on responding. For the baseline period, Asian participants exhibited a smaller startle response relative to Caucasian and Latino participants, who did not differ. Within each racial group, genetic ancestry was associated with baseline startle. Furthermore, genetic ancestry mediated racial group differences in baseline startle. For the threat conditions, a Race × Condition interaction indicated that Asian participants exhibited reduced startle potentiation to unpredictable, but not predicable, threat relative to Caucasian and Latino participants, who did not differ. However, genetic ancestry was not associated with threat-potentiated startle in any racial group. This study adds to the growing literature on racial differences in emotional responding and provides preliminary evidence suggesting that genetic ancestry may play an important role. Moreover, reduced sensitivity to unpredictable threat may reflect a mechanism for why individuals of Asian descent are at less risk for particular anxiety disorders relative to other racial groups.

  20. Using ancestry matching to combine family-based and unrelated samples for genome-wide association studies.

    PubMed

    Crossett, Andrew; Kent, Brian P; Klei, Lambertus; Ringquist, Steven; Trucco, Massimo; Roeder, Kathryn; Devlin, Bernie

    2010-12-10

    We propose a method to analyze family-based samples together with unrelated cases and controls. The method builds on the idea of matched case-control analysis using conditional logistic regression (CLR). For each trio within the family, a case (the proband) and matched pseudo-controls are constructed, based upon the transmitted and untransmitted alleles. Unrelated controls, matched by genetic ancestry, supplement the sample of pseudo-controls; likewise unrelated cases are also paired with genetically matched controls. Within each matched stratum, the case genotype is contrasted with control/pseudo-control genotypes via CLR, using a method we call matched-CLR (mCLR). Eigenanalysis of numerous SNP genotypes provides a tool for mapping genetic ancestry. The result of such an analysis can be thought of as a multidimensional map, or eigenmap, in which the relative genetic similarities and differences amongst individuals is encoded in the map. Once constructed, new individuals can be projected onto the ancestry map based on their genotypes. Successful differentiation of individuals of distinct ancestry depends on having a diverse, yet representative sample from which to construct the ancestry map. Once samples are well-matched, mCLR yields comparable power to competing methods while ensuring excellent control over Type I error.