WorldWideScience

Sample records for wide age-ranged population

  1. Micro-planning in a wide age range measles rubella (MR) campaign using mobile phone app, a case of Kenya, 2016.

    Science.gov (United States)

    Ismail, Amina; Tabu, Collins; Onuekwusi, Iheoma; Otieno, Samuel Kevin; Ademba, Peter; Kamau, Peter; Koki, Beatrice; Ngatia, Anthony; Wainaina, Anthony; Davis, Robert

    2017-01-01

    A Measles rubella campaign that targeted 9 months to 14 year old children was conducted in all the 47 counties in Kenya between 16th and 24th of May 2016. Micro-planning using an android phone-based app was undertaken to map out the target population and logistics in all the counties 4 weeks to the campaign implementation instead of 6 months as per the WHO recommendation. The outcomes of the micro-planning exercise were a detailed micro-plan that served as a guide in ensuring that every eligible individual in the population was vaccinated with potent vaccine. A national Trainer of Trainers training was done to equip key officers with new knowledge and skills in developing micro-plans at all levels. The micro planning was done using a mobile phone app, the doforms that enabled data to be transmitted real time to the national level. The objective of the study was to establish whether use of mobile phone app would contribute to quality of sub national micro plans that can be used for national level planning and implementation of the campaign. There were 9 data collection forms but only forms 1-7 were to be uploaded onto the app. Forms 8A and 9A were to be filled but were to remain at the implementation level for use intra campaign. The forms were coded; Form 1A&B, 2A, 3A, 4A, 5A, 6A, 7A, 8A and 9A The Village form (form 1A&B) captured information by household which included village names, name of head of household, cell phone contact of head of household, number of children aged 9 months to 14years in the household, possible barriers to reaching the children, appropriate vaccination strategy based on barriers identified and estimated or proposed number of teams and type. This was the main form and from this every other form picked the population figures to estimate other supplies and logistics. On advocacy, communication and social mobilization the information collected included mobile network coverage, public amenities such as churches, mosques and key partners at

  2. Population Pharmacokinetic Analysis of Bortezomib in Pediatric Leukemia Patients: Model-Based Support for Body Surface Area-Based Dosing Over the 2- to 16-Year Age Range.

    Science.gov (United States)

    Hanley, Michael J; Mould, Diane R; Taylor, Timothy J; Gupta, Neeraj; Suryanarayan, Kaveri; Neuwirth, Rachel; Esseltine, Dixie-Lee; Horton, Terzah M; Aplenc, Richard; Alonzo, Todd A; Lu, Xiaomin; Milton, Ashley; Venkatakrishnan, Karthik

    2017-09-01

    This population analysis described the pharmacokinetics of bortezomib after twice-weekly, repeat-dose, intravenous administration in pediatric patients participating in 2 clinical trials: the phase 2 AALL07P1 (NCT00873093) trial in relapsed acute lymphoblastic leukemia and the phase 3 AAML1031 (NCT01371981) trial in de novo acute myelogenous leukemia. The sources of variability in the pharmacokinetic parameters were characterized and quantified to support dosing recommendations. Patients received intravenous bortezomib 1.3 mg/m(2) twice-weekly, on days 1, 4, and 8 during specific blocks or cycles of both trials and on day 11 of block 1 of study AALL07P1, in combination with multiagent chemotherapy. Blood samples were obtained and the plasma was harvested on day 8 over 0-72 hours postdose to measure bortezomib concentrations by liquid chromatography-tandem mass spectrometry. Concentration-time data were analyzed by nonlinear mixed-effects modeling. Covariates were examined using forward addition (P < .01)/backward elimination (P < .001). Data were included from 104 patients (49%/51% acute lymphoblastic leukemia/acute myelogenous leukemia; 60%/40% aged 2-11 years/12-16 years). Bortezomib pharmacokinetics were described by a 3-compartment model with linear elimination. Body surface area adequately accounted for variability in clearance (exponent 0.97), supporting body surface area-based dosing. Stratified visual predictive check simulations verified that neither age group nor patient population represented sources of meaningful pharmacokinetic heterogeneity not accounted for by the final population pharmacokinetic model. Following administration of 1.3 mg/m(2) intravenous bortezomib doses, body surface area-normalized clearance in pediatric patients was similar to that observed in adult patients, thereby indicating that this dose achieves similar systemic exposures in pediatric patients. © 2017, The Authors. The Journal of Clinical Pharmacology published by Wiley

  3. Formation of the wide asynchronous binary asteroid population

    Energy Technology Data Exchange (ETDEWEB)

    Jacobson, Seth A. [Department of Astrophysical and Planetary Science, UCB 391, University of Colorado, Boulder, CO 80309 (United States); Scheeres, Daniel J.; McMahon, Jay [Department of Aerospace Engineering Sciences, UCB 429, University of Colorado, Boulder, CO 80309 (United States)

    2014-01-01

    We propose and analyze a new mechanism for the formation of the wide asynchronous binary population. These binary asteroids have wide semimajor axes relative to most near-Earth and main belt asteroid systems. Confirmed members have rapidly rotating primaries and satellites that are not tidally locked. Previously suggested formation mechanisms from impact ejecta, from planetary flybys, and directly from rotational fission events cannot satisfy all of the observations. The newly hypothesized mechanism works as follows: (1) these systems are formed from rotational fission, (2) their satellites are tidally locked, (3) their orbits are expanded by the binary Yarkovsky-O'Keefe-Radzievskii-Paddack (BYORP) effect, (4) their satellites desynchronize as a result of the adiabatic invariance between the libration of the secondary and the mutual orbit, and (5) the secondary avoids resynchronization because of the YORP effect. This seemingly complex chain of events is a natural pathway for binaries with satellites that have particular shapes, which define the BYORP effect torque that acts on the system. After detailing the theory, we analyze each of the wide asynchronous binary members and candidates to assess their most likely formation mechanism. Finally, we suggest possible future observations to check and constrain our hypothesis.

  4. Population-wide emergence of antiviral resistance during pandemic influenza.

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    Seyed M Moghadas

    Full Text Available BACKGROUND: The emergence of neuraminidase inhibitor resistance has raised concerns about the prudent use of antiviral drugs in response to the next influenza pandemic. While resistant strains may initially emerge with compromised viral fitness, mutations that largely compensate for this impaired fitness can arise. Understanding the extent to which these mutations affect the spread of disease in the population can have important implications for developing pandemic plans. METHODOLOGY/PRINCIPAL FINDINGS: By employing a deterministic mathematical model, we investigate possible scenarios for the emergence of population-wide resistance in the presence of antiviral drugs. The results show that if the treatment level (the fraction of clinical infections which receives treatment is maintained constant during the course of the outbreak, there is an optimal level that minimizes the final size of the pandemic. However, aggressive treatment above the optimal level can substantially promote the spread of highly transmissible resistant mutants and increase the total number of infections. We demonstrate that resistant outbreaks can occur more readily when the spread of disease is further delayed by applying other curtailing measures, even if treatment levels are kept modest. However, by changing treatment levels over the course of the pandemic, it is possible to reduce the final size of the pandemic below the minimum achieved at the optimal constant level. This reduction can occur with low treatment levels during the early stages of the pandemic, followed by a sharp increase in drug-use before the virus becomes widely spread. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that an adaptive antiviral strategy with conservative initial treatment levels, followed by a timely increase in the scale of drug-use, can minimize the final size of a pandemic while preventing large outbreaks of resistant infections.

  5. Genome-wide association study of schizophrenia in Japanese population.

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    Kazuo Yamada

    Full Text Available Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits. Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS is a potentially powerful tool for identifying the risk variants that underlie the disease. Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach. Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs in 120 patient-parents trio samples from Japanese schizophrenia pedigrees. In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p<0.01 and 473 SNPs of p<0.05 that located in previously reported linkage regions. The second sample consisted of 1,012 case-control samples of Japanese origin. The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila-like 2] gene located on 9p21.3 (p = 0.00087. In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026. The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology.

  6. Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.

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    Silvia Teresa Rodríguez-Ramilo

    Full Text Available Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry or runs of homozygosity (inbreeding. The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

  7. Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.

    Science.gov (United States)

    Rodríguez-Ramilo, Silvia Teresa; Fernández, Jesús; Toro, Miguel Angel; Hernández, Delfino; Villanueva, Beatriz

    2015-01-01

    Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

  8. World-wide parliamentarians join forces to resolve population problems.

    Science.gov (United States)

    1979-01-01

    Subjects selected for discussion at the International Conference on Population and Development held from August 28 to September 1, 1979 included world population trends and prospects; government laws and policies; the status of women in family law, literacy and health; employment policies, rural to urban migration and appropriate technology; economic growth with equity and a new economic order; environmental impact and world resources; community participation in motivation and service delivery programs; international coordination of donor policies; research priorities; and governmental responsibilities. The following were among the specific objectives and goals identified: 1) formulate population policies as an integral part of socioeconomic development plans; 2) examine the impact of domestic population trends on health, education, employment, agricultural and industrial development, housing and environmental conditions; 3) strengthen the integration of population programs in all development activities; 4) ensure the basic right of people to decide the number and spacing of their children and ensure that they have the information and means to do so; and 5) promote the role and status of women in the family and society and enhance their access to education, employment, health services and financial credit. A strong commitment was made for implementation of population policies as an integral part of socioeconomic development plans.

  9. Implementation of a Population-wide Program to Reduce Salt and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Implementation of a Population-wide Program to Reduce Salt and Sodium Consumption in Costa Rica. Population-wide salt reduction initiatives which target sodium levels in foods and consumer education have the potential to reduce salt intake across all population sectors and improve cardiovascular health outcomes.

  10. Genome-Wide Population-Based Association Study of Extremely Overweight Young Adults - The GOYA Study

    DEFF Research Database (Denmark)

    Paternoster, L.; Evans, D. M.; Nohr, E. A.

    2011-01-01

    Background: Thirty-two common variants associated with body mass index (BMI) have been identified in genome-wide association studies, explaining,similar to 1.45% of BMI variation in general population cohorts. We performed a genome-wide association study in a sample of young adults enriched...

  11. Genome-wide linkage disequilibrium in nine-spined stickleback populations.

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    Yang, Ji; Shikano, Takahito; Li, Meng-Hua; Merilä, Juha

    2014-08-12

    Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them. Copyright © 2014 Yang et al.

  12. Genome-Wide Linkage Disequilibrium in Nine-Spined Stickleback Populations

    Science.gov (United States)

    Yang, Ji; Shikano, Takahito; Li, Meng-Hua; Merilä, Juha

    2014-01-01

    Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D’ > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them. PMID:25122668

  13. A genome wide association study identifies common variants associated with lipid levels in the Chinese population.

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    Li Zhou

    Full Text Available Plasma lipid levels are important risk factors for cardiovascular disease and are influenced by genetic and environmental factors. Recent genome wide association studies (GWAS have identified several lipid-associated loci, but these loci have been identified primarily in European populations. In order to identify genetic markers for lipid levels in a Chinese population and analyze the heterogeneity between Europeans and Asians, especially Chinese, we performed a meta-analysis of two genome wide association studies on four common lipid traits including total cholesterol (TC, triglycerides (TG, low-density lipoprotein cholesterol (LDL and high-density lipoprotein cholesterol (HDL in a Han Chinese population totaling 3,451 healthy subjects. Replication was performed in an additional 8,830 subjects of Han Chinese ethnicity. We replicated eight loci associated with lipid levels previously reported in a European population. The loci genome wide significantly associated with TC were near DOCK7, HMGCR and ABO; those genome wide significantly associated with TG were near APOA1/C3/A4/A5 and LPL; those genome wide significantly associated with LDL were near HMGCR, ABO and TOMM40; and those genome wide significantly associated with HDL were near LPL, LIPC and CETP. In addition, an additive genotype score of eight SNPs representing the eight loci that were found to be associated with lipid levels was associated with higher TC, TG and LDL levels (P = 5.52 × 10(-16, 1.38 × 10(-6 and 5.59 × 10(-9, respectively. These findings suggest the cumulative effects of multiple genetic loci on plasma lipid levels. Comparisons with previous GWAS of lipids highlight heterogeneity in allele frequency and in effect size for some loci between Chinese and European populations. The results from our GWAS provided comprehensive and convincing evidence of the genetic determinants of plasma lipid levels in a Chinese population.

  14. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  15. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

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

    DEFF Research Database (Denmark)

    Byrne, Stephen; Czaban, Adrian; Studer, Bruno

    2013-01-01

    is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how...

  17. Genome-wide patterns of identity-by-descent sharing in the French Canadian founder population.

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    Gauvin, Héloïse; Moreau, Claudia; Lefebvre, Jean-François; Laprise, Catherine; Vézina, Hélène; Labuda, Damian; Roy-Gagnon, Marie-Hélène

    2014-06-01

    In genetics the ability to accurately describe the familial relationships among a group of individuals can be very useful. Recent statistical tools succeeded in assessing the degree of relatedness up to 6-7 generations with good power using dense genome-wide single-nucleotide polymorphism data to estimate the extent of identity-by-descent (IBD) sharing. It is therefore important to describe genome-wide patterns of IBD sharing for more remote and complex relatedness between individuals, such as that observed in a founder population like Quebec, Canada. Taking advantage of the extended genealogical records of the French Canadian founder population, we first compared different tools to identify regions of IBD in order to best describe genome-wide IBD sharing and its correlation with genealogical characteristics. Results showed that the extent of IBD sharing identified with FastIBD correlates best with relatedness measured using genealogical data. Total length of IBD sharing explained 85% of the genealogical kinship's variance. In addition, we observed significantly higher sharing in pairs of individuals with at least one inbred ancestor compared with those without any. Furthermore, patterns of IBD sharing and average sharing were different across regional populations, consistent with the settlement history of Quebec. Our results suggest that, as expected, the complex relatedness present in founder populations is reflected in patterns of IBD sharing. Using these patterns, it is thus possible to gain insight on the types of distant relationships in a sample from a founder population like Quebec.

  18. A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population.

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    Downie, Jonathan M; Tashi, Tsewang; Lorenzo, Felipe Ramos; Feusier, Julie Ellen; Mir, Hyder; Prchal, Josef T; Jorde, Lynn B; Koul, Parvaiz A

    2016-01-01

    The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.

  19. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves.

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    Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

    2014-04-01

    Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.

  20. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep.

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    Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric

    2015-11-24

    Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.

  1. Revisiting rose: comparing the benefits and costs of population-wide and targeted interventions.

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    Ahern, Jennifer; Jones, Matthew R; Bakshis, Erin; Galea, Sandro

    2008-12-01

    Geoffrey Rose's two principal approaches to public health intervention are (1) targeted strategies focusing on individuals at a personal increased risk of disease and (2) population-wide approaches focusing on the whole population. Beyond his discussion of the strengths and weaknesses of these approaches, there is no empiric work examining the conditions under which one of these approaches may be better than the other. This article uses mathematical simulations to model the benefits and costs of the two approaches, varying the cut points for treatment, effect magnitudes, and costs of the interventions. These techniques then were applied to the specific example of an intervention on blood pressure to reduce cardiovascular disease. In the general simulation (using an inverse logit risk curve), lower costs of intervention, treating people with risk factor values at or above where the slope on the risk curve is at its steepest (for targeted interventions), and interventions with larger effects on reducing the risk factor (for population-wide interventions) provided benefit/cost advantages. In the specific blood pressure intervention example, lower-cost population-wide interventions had better benefit/cost ratios, but some targeted treatments with lower cutoffs prevented more absolute cases of disease. These simulations empirically evaluate some of Rose's original arguments. They can be replicated for particular interventions being considered and may be useful in helping public health decision makers assess potential intervention strategies.

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

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    Joseph K Pickrell

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

  3. Characterisation of genome-wide association epistasis signals for serum uric acid in human population isolates.

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    Wenhua Wei

    Full Text Available Genome-wide association (GWA studies have identified a number of loci underlying variation in human serum uric acid (SUA levels with the SLC2A9 gene having the largest effect identified so far. Gene-gene interactions (epistasis are largely unexplored in these GWA studies. We performed a full pair-wise genome scan in the Italian MICROS population (n = 1201 to characterise epistasis signals in SUA levels. In the resultant epistasis profile, no SNP pairs reached the Bonferroni adjusted threshold for the pair-wise genome-wide significance. However, SLC2A9 was found interacting with multiple loci across the genome, with NFIA-SLC2A9 and SLC2A9-ESRRAP2 being significant based on a threshold derived for interactions between GWA significant SNPs and the genome and jointly explaining 8.0% of the phenotypic variance in SUA levels (3.4% by interaction components. Epistasis signal replication in a CROATIAN population (n = 1772 was limited at the SNP level but improved dramatically at the gene ontology level. In addition, gene ontology terms enriched by the epistasis signals in each population support links between SUA levels and neurological disorders. We conclude that GWA epistasis analysis is useful despite relatively low power in small isolated populations.

  4. netview p: a network visualization tool to unravel complex population structure using genome-wide SNPs.

    Science.gov (United States)

    Steinig, Eike J; Neuditschko, Markus; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2016-01-01

    Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in wild and captive populations. netview p combines data quality control with the construction of population networks through mutual k-nearest neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs. The pipeline was used for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive silver-lipped pearl oysters (n = 415, SNPs = 1107), wild populations of the European hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and grey wolves from North America (n = 239, SNPs = 78 255). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. netview p comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in python. © 2015 John Wiley & Sons Ltd.

  5. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.

    Directory of Open Access Journals (Sweden)

    Jennifer K Lowe

    2009-02-01

    Full Text Available It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining >/=5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment.

  6. Population stratification in the context of diverse epidemiologic surveys sans genome-wide data

    Directory of Open Access Journals (Sweden)

    Matthew T. Oetjens

    2016-05-01

    Full Text Available Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES, population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n=14,998 were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2 and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n=6,634, non-Hispanic blacks (n=3,458, and Mexican Americans (n=3,950. We as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology (PAGE I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants

  7. A multi-scenario genome-wide medical population genetics simulation framework.

    Science.gov (United States)

    Mugo, Jacquiline W; Geza, Ephifania; Defo, Joel; Elsheikh, Samar S M; Mazandu, Gaston K; Mulder, Nicola J; Chimusa, Emile R

    2017-10-01

    Recent technological advances in high-throughput sequencing and genotyping have facilitated an improved understanding of genomic structure and disease-associated genetic factors. In this context, simulation models can play a critical role in revealing various evolutionary and demographic effects on genomic variation, enabling researchers to assess existing and design novel analytical approaches. Although various simulation frameworks have been suggested, they do not account for natural selection in admixture processes. Most are tailored to a single chromosome or a genomic region, very few capture large-scale genomic data, and most are not accessible for genomic communities. Here we develop a multi-scenario genome-wide medical population genetics simulation framework called 'FractalSIM'. FractalSIM has the capability to accurately mimic and generate genome-wide data under various genetic models on genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations. Moreover, the framework accounts for natural selection in both homogeneous and admixture processes. The outputs of FractalSIM have been assessed using popular tools, and the results demonstrated its capability to accurately mimic real scenarios. They can be used to evaluate the performance of a range of genomic tools from ancestry inference to genome-wide association studies. The FractalSIM package is available at http://www.cbio.uct.ac.za/FractalSIM. emile.chimusa@uct.ac.za. Supplementary data are available at Bioinformatics online.

  8. A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia.

    Science.gov (United States)

    Fu, Ruiqing; Mokhtar, Siti Shuhada; Phipps, Maude Elvira; Hoh, Boon-Peng; Xu, Shuhua

    2018-02-23

    Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.

  9. Swedish population substructure revealed by genome-wide single nucleotide polymorphism data.

    Directory of Open Access Journals (Sweden)

    Elina Salmela

    Full Text Available The use of genome-wide single nucleotide polymorphism (SNP data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes--especially southern Swedes--were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F(ST = 0.0005 between provinces was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.

  10. A genome-wide association study of periodontitis in a Japanese population.

    Science.gov (United States)

    Shimizu, S; Momozawa, Y; Takahashi, A; Nagasawa, T; Ashikawa, K; Terada, Y; Izumi, Y; Kobayashi, H; Tsuji, M; Kubo, M; Furuichi, Y

    2015-04-01

    Periodontitis is a multifactorial disease in which bacterial, lifestyle, and genetic factors are involved. Although previous genetic association studies identified several susceptibility genes for periodontitis in European populations, there is little information for Asian populations. Here, we conducted a genome-wide association study and a replication study consisting of 2,760 Japanese periodontitis patients and 15,158 Japanese controls. Although single-nucleotide polymorphisms that surpassed a stringent genome-wide significance threshold (P periodontitis: KCNQ5 on chromosome 6q13 (rs9446777, P = 4.83 × 10(-6), odds ratio = 0.82) and GPR141-NME8 at chromosome 7p14.1 (rs2392510, P = 4.17 × 10(-6), odds ratio = 0.87). A stratified analysis indicated that the GPR141-NME8 locus had a strong genetic effect on the susceptibility to generalized periodontitis in Japanese individuals with a history of smoking. In conclusion, this study identified 2 suggestive loci for periodontitis in a Japanese population. This study should contribute to a further understanding of genetic factors for enhanced susceptibility to periodontitis. © International & American Associations for Dental Research 2015.

  11. Understanding sub-stellar populations using wide-field infrared surveys

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    Hewett P.C.

    2011-07-01

    Full Text Available This paper discusses benchmark brown dwarfs in various environments, and focuses on those in wide binary systems. We present a summary of the recently discovered T dwarf population from the UKIDSS Large Area Survey, and describe the constraints that it places on our knowledge of the sub-stellar initial mass function. We also present some exciting results from our ongoing search for wide companions to this sample, that has so far revealed an M4-T8.5 binary system at ∼12 parsecs and also the first ever Tdwarf-white dwarf binary system. The T dwarfs in these binaries have their properties constrained by the primary object and are thus benchmark objects that are already testing the predictions of theoretical model atmospheres.

  12. Loneliness in relation to suicide ideation and parasuicide: a population-wide study.

    Science.gov (United States)

    Stravynski, A; Boyer, R

    2001-01-01

    Some links between loneliness and different manifestations of suicidal conduct have been reported in variety of subgroups (e.g., college students, the elderly, psychiatric patients). We tested this hypothesis by using the results of a population-wide survey. Strong associations among suicide ideation, parasuicide and different ways of being lonely and alone, defined either subjectively (i.e., the feeling), or objectively (i.e., living alone or being without friends), were observed. Moreover, prevalence of suicide ideation and parasuicide increased with the degree of loneliness. Only minimal differences between men and women were found.

  13. Genome-wide analysis of genetic susceptibility to language impairment in an isolated Chilean population

    Science.gov (United States)

    Villanueva, Pia; Newbury, Dianne F; Jara, Lilian; De Barbieri, Zulema; Mirza, Ghazala; Palomino, Hernán M; Fernández, María Angélica; Cazier, Jean-Baptiste; Monaco, Anthony P; Palomino, Hernán

    2011-01-01

    Specific language impairment (SLI) is an unexpected deficit in the acquisition of language skills and affects between 5 and 8% of pre-school children. Despite its prevalence and high heritability, our understanding of the aetiology of this disorder is only emerging. In this paper, we apply genome-wide techniques to investigate an isolated Chilean population who exhibit an increased frequency of SLI. Loss of heterozygosity (LOH) mapping and parametric and non-parametric linkage analyses indicate that complex genetic factors are likely to underlie susceptibility to SLI in this population. Across all analyses performed, the most consistently implicated locus was on chromosome 7q. This locus achieved highly significant linkage under all three non-parametric models (max NPL=6.73, P=4.0 × 10−11). In addition, it yielded a HLOD of 1.24 in the recessive parametric linkage analyses and contained a segment that was homozygous in two affected individuals. Further, investigation of this region identified a two-SNP haplotype that occurs at an increased frequency in language-impaired individuals (P=0.008). We hypothesise that the linkage regions identified here, in particular that on chromosome 7, may contain variants that underlie the high prevalence of SLI observed in this isolated population and may be of relevance to other populations affected by language impairments. PMID:21248734

  14. Genome-wide analysis of genetic susceptibility to language impairment in an isolated Chilean population.

    Science.gov (United States)

    Villanueva, Pia; Newbury, Dianne F; Jara, Lilian; De Barbieri, Zulema; Mirza, Ghazala; Palomino, Hernán M; Fernández, María Angélica; Cazier, Jean-Baptiste; Monaco, Anthony P; Palomino, Hernán

    2011-06-01

    Specific language impairment (SLI) is an unexpected deficit in the acquisition of language skills and affects between 5 and 8% of pre-school children. Despite its prevalence and high heritability, our understanding of the aetiology of this disorder is only emerging. In this paper, we apply genome-wide techniques to investigate an isolated Chilean population who exhibit an increased frequency of SLI. Loss of heterozygosity (LOH) mapping and parametric and non-parametric linkage analyses indicate that complex genetic factors are likely to underlie susceptibility to SLI in this population. Across all analyses performed, the most consistently implicated locus was on chromosome 7q. This locus achieved highly significant linkage under all three non-parametric models (max NPL = 6.73, P = 4.0 × 10(-11)). In addition, it yielded a HLOD of 1.24 in the recessive parametric linkage analyses and contained a segment that was homozygous in two affected individuals. Further, investigation of this region identified a two-SNP haplotype that occurs at an increased frequency in language-impaired individuals (P = 0.008). We hypothesise that the linkage regions identified here, in particular that on chromosome 7, may contain variants that underlie the high prevalence of SLI observed in this isolated population and may be of relevance to other populations affected by language impairments.

  15. Genome-wide patterns of population structure and admixture in West Africans and African Americans.

    Science.gov (United States)

    Bryc, Katarzyna; Auton, Adam; Nelson, Matthew R; Oksenberg, Jorge R; Hauser, Stephen L; Williams, Scott; Froment, Alain; Bodo, Jean-Marie; Wambebe, Charles; Tishkoff, Sarah A; Bustamante, Carlos D

    2010-01-12

    Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

  16. A new mechanised cultural practice to reduce Ceratitis capitata Wied. populations in area-wide IPM

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    P. Chueca

    2013-11-01

    Full Text Available The Mediterranean fruit fly (or medfly, Ceratitis capitata (Wiedemann (Diptera: Tephritidae, affects most of the fruit species grown in temperate and tropical climate regions, causing significant economic damage. One of the classical cultural strategies against this pest is to gather and bury the remaining fruit after harvest, but this is economically unfeasible today. Wood shredders already available in current Spanish groves can be used to grind or crush fruits laying on the soil as an alternative to this practice and to the use of pesticides in area-wide integrated pest management (IPM. With the purpose of evaluating this alternative, the initial step of this study was to perform laboratory tests to assess the efficacy of crushing and grinding as a method for controlling medflies. The results showed that grinding was 78% effective against larval stages, while crushing resulted in a 17% efficacy, leading us to choose the first alternative. As a second step, the operational parameters (type of cutting tool, shaft rotation speed and tractor speed of the wood shredders were adjusted to efficiently carry out this practice under field conditions. Finally, the effect of the mechanised grinding of fallen fruit on C. capitata populations was evaluated for two consecutive years in commercial citrus orchards. The results showed a significant 27-46% reduction in C. capitata populations the following spring, thus demonstrating that the newly proposed mechanised alternative can be included in the current area-wide IPM of the pest in Spain.

  17. Analysis of family- and population-based samples in cohort genome-wide association studies.

    Science.gov (United States)

    Manichaikul, Ani; Chen, Wei-Min; Williams, Kayleen; Wong, Quenna; Sale, Michèle M; Pankow, James S; Tsai, Michael Y; Rotter, Jerome I; Rich, Stephen S; Mychaleckyj, Josyf C

    2012-02-01

    Cohort studies typically sample unrelated individuals from a population, although family members of index cases may also be recruited to investigate shared familial risk factors. Recruitment of family members may be incomplete or ancillary to the main cohort, resulting in a mixed sample of independent family units, including unrelated singletons and multiplex families. Multiple methods are available to perform genome-wide association (GWA) analysis of binary or continuous traits in families, but it is unclear whether methods known to perform well on ascertained pedigrees, sibships, or trios are appropriate in analysis of a mixed unrelated cohort and family sample. We present simulation studies based on Multi-Ethnic Study of Atherosclerosis (MESA) pedigree structures to compare the performance of several popular methods of GWA analysis for both quantitative and dichotomous traits in cohort studies. We evaluate approaches suitable for analysis of families, and combined the best performing methods with population-based samples either by meta-analysis, or by pooled analysis of family- and population-based samples (mega-analysis), comparing type 1 error and power. We further assess practical considerations, such as availability of software and ability to incorporate covariates in statistical modeling, and demonstrate our recommended approaches through quantitative and binary trait analysis of HDL cholesterol (HDL-C) in 2,553 MESA family- and population-based African-American samples. Our results suggest linear modeling approaches that accommodate family-induced phenotypic correlation (e.g., variance-component model for quantitative traits or generalized estimating equations for dichotomous traits) perform best in the context of combined family- and population-based cohort GWAS.

  18. Population-Wide Failure to Breed in the Clark's Nutcracker (Nucifraga columbiana.

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    Taza D Schaming

    Full Text Available In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark's nutcrackers (Nucifraga Columbiana in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark's nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years. The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1, a nonbreeding year, as compared to 2012 (6.2 ± 2.0, a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark's nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark's nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.

  19. Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

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    Susanna Lemmelä

    Full Text Available Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6 were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981 at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08 and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively. The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04. Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7% than in other European populations (1-2%. Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109 were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB, which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.

  20. Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

    Science.gov (United States)

    Lemmelä, Susanna; Solovieva, Svetlana; Shiri, Rahman; Benner, Christian; Heliövaara, Markku; Kettunen, Johannes; Anttila, Verneri; Ripatti, Samuli; Perola, Markus; Seppälä, Ilkka; Juonala, Markus; Kähönen, Mika; Salomaa, Veikko; Viikari, Jorma; Raitakari, Olli T; Lehtimäki, Terho; Palotie, Aarno; Viikari-Juntura, Eira; Husgafvel-Pursiainen, Kirsti

    2016-01-01

    Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (psciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7%) than in other European populations (1-2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.

  1. No large population of unbound or wide-orbit Jupiter-mass planets.

    Science.gov (United States)

    Mróz, Przemek; Udalski, Andrzej; Skowron, Jan; Poleski, Radosław; Kozłowski, Szymon; Szymański, Michał K; Soszyński, Igor; Wyrzykowski, Łukasz; Pietrukowicz, Paweł; Ulaczyk, Krzysztof; Skowron, Dorota; Pawlak, Michał

    2017-08-10

    Planet formation theories predict that some planets may be ejected from their parent systems as result of dynamical interactions and other processes. Unbound planets can also be formed through gravitational collapse, in a way similar to that in which stars form. A handful of free-floating planetary-mass objects have been discovered by infrared surveys of young stellar clusters and star-forming regions as well as wide-field surveys, but these studies are incomplete for objects below five Jupiter masses. Gravitational microlensing is the only method capable of exploring the entire population of free-floating planets down to Mars-mass objects, because the microlensing signal does not depend on the brightness of the lensing object. A characteristic timescale of microlensing events depends on the mass of the lens: the less massive the lens, the shorter the microlensing event. A previous analysis of 474 microlensing events found an excess of ten very short events (1-2 days)-more than known stellar populations would suggest-indicating the existence of a large population of unbound or wide-orbit Jupiter-mass planets (reported to be almost twice as common as main-sequence stars). These results, however, do not match predictions of planet-formation theories and surveys of young clusters. Here we analyse a sample of microlensing events six times larger than that of ref. 11 discovered during the years 2010-15. Although our survey has very high sensitivity (detection efficiency) to short-timescale (1-2 days) microlensing events, we found no excess of events with timescales in this range, with a 95 per cent upper limit on the frequency of Jupiter-mass free-floating or wide-orbit planets of 0.25 planets per main-sequence star. We detected a few possible ultrashort-timescale events (with timescales of less than half a day), which may indicate the existence of Earth-mass and super-Earth-mass free-floating planets, as predicted by planet-formation theories.

  2. Genome-wide association of body fat distribution in African ancestry populations suggests new loci.

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    Ching-Ti Liu

    Full Text Available Central obesity, measured by waist circumference (WC or waist-hip ratio (WHR, is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS of fat distribution among those of predominantly African ancestry (AA. We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1. Overall, 25 SNPs with single genomic control (GC-corrected p-values<5.0 × 10(-6 were followed-up (stage 2 in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8 for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8 for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8; RREB1: p = 5.7 × 10(-8. Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN. Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02. In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept

  3. Exome-wide association study of endometrial cancer in a multiethnic population.

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    Maxine M Chen

    Full Text Available Endometrial cancer (EC contributes substantially to total burden of cancer morbidity and mortality in the United States. Family history is a known risk factor for EC, thus genetic factors may play a role in EC pathogenesis. Three previous genome-wide association studies (GWAS have found only one locus associated with EC, suggesting that common variants with large effects may not contribute greatly to EC risk. Alternatively, we hypothesize that rare variants may contribute to EC risk. We conducted an exome-wide association study (EXWAS of EC using the Infinium HumanExome BeadChip in order to identify rare variants associated with EC risk. We successfully genotyped 177,139 variants in a multiethnic population of 1,055 cases and 1,778 controls from four studies that were part of the Epidemiology of Endometrial Cancer Consortium (E2C2. No variants reached global significance in the study, suggesting that more power is needed to detect modest associations between rare genetic variants and risk of EC.

  4. Genome-wide genetic homogeneity between sexes and populations for human height and body mass index.

    Science.gov (United States)

    Yang, Jian; Bakshi, Andrew; Zhu, Zhihong; Hemani, Gibran; Vinkhuyzen, Anna A E; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hamsten, Anders; Magnusson, Patrik K E; Pedersen, Nancy L; Ingelsson, Erik; Visscher, Peter M

    2015-12-20

    Sex-specific genetic effects have been proposed to be an important source of variation for human complex traits. Here we use two distinct genome-wide methods to estimate the autosomal genetic correlation (rg) between men and women for human height and body mass index (BMI), using individual-level (n = ∼44 000) and summary-level (n = ∼133 000) data from genome-wide association studies. Results are consistent and show that the between-sex genetic correlation is not significantly different from unity for both traits. In contrast, we find evidence of genetic heterogeneity between sexes for waist-hip ratio (rg = ∼0.7) and between populations for BMI (rg = ∼0.9 between Europe and the USA) but not for height. The lack of evidence for substantial genetic heterogeneity for body size is consistent with empirical findings across traits and species. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Epidemiological and Genome-Wide Association Study of Gastritis or Gastric Ulcer in Korean Populations

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    Sumin Oh

    2014-09-01

    Full Text Available Gastritis is a major disease that has the potential to grow as gastric cancer. Gastric cancer is a very common cancer, and it is related to a very high mortality rate in Korea. This disease is known to have various reasons, including infection with Helicobacter pylori, dietary habits, tobacco, and alcohol. The incidence rate of gastritis has reported to differ between age, population, and gender. However, unlike other factors, there has been no analysis based on gender. So, we examined the high risk factors of gastritis in each gender in the Korean population by focusing on sex. We performed an analysis of 120 clinical characteristics and genome-wide association studies (GWAS using 349,184 single-nucleotide polymorphisms from the results of Anseong and Ansan cohort study in the Korea Association Resource (KARE project. As the result, we could not prove a strong relation with these factors and gastritis or gastric ulcer in the GWAS. However, we confirmed several already-known risk factors and also found some differences of clinical characteristics in each gender using logistic regression. As a result of the logistic regression, a relation with hyperlipidemia, coronary artery disease, myocardial infarction, hyperlipidemia therapy, hypotensive or antihypotensive drug, diastolic blood pressure, and gastritis was seen in males; the results of this study suggest that vascular disease has a potential association with gastritis in males.

  6. A genome-wide association study of neuroticism in a population-based sample.

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    Federico C F Calboli

    Full Text Available Neuroticism is a moderately heritable personality trait considered to be a risk factor for developing major depression, anxiety disorders and dementia. We performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism, making this the largest association study for neuroticism to date. Neuroticism was measured by the Eysenck Personality Questionnaire. After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. We found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect (p < 10(-6 and GPC6 showed suggestive evidence for interaction with age (p approximately = 10(-7. We found support for one previously-reported association (PDE4D, but failed to replicate other recent reports. These results suggest common SNP variation does not strongly influence neuroticism. Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism.

  7. Population genetic analysis and genome-wide association study of patellar luxation in a Thai population of Pomeranian dogs.

    Science.gov (United States)

    Wangdee, C; Leegwater, P A J; Heuven, H C M; van Steenbeek, F G; Techakumphu, M; Hazewinkel, H A W

    2017-04-01

    The genetics of patellar luxation (PL) were investigated in Pomeranian dogs presented at the Small Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University. A cohort of 339 Pomeranian dogs, part of a four-generation pedigree of 842 Pomeranians, was screened for PL from 2006 to 2013. PL was present in 77% of the screened dogs, with 84% having bilateral and 16% unilateral luxation. Medial PL was more common (95%) than lateral PL (2%) or bidirectional PL (3%). The risk of PL was similar in male and female dogs (female:male relative risk 1.11, 95% CI 0.98-1.25). The heritability of PL in the screened population was 0.44±0.04 using a threshold model. A genome-wide association study of PL (48 cases and 48 controls) using a high-density SNP array indicated the possible involvement of 15 chromosomal regions, of which CFA05 and CFA32 remained associated in a larger study involving an additional 128 cases and 7 controls. Candidate genes in these regions may be involved in the pathogenesis of PL in Pomeranian dogs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Estimates of the world-wide prevalence of cancer for 25 sites in the adult population.

    Science.gov (United States)

    Pisani, Paola; Bray, Freddie; Parkin, D Maxwell

    2002-01-01

    In health services planning, in addition to the basic measures of disease occurrence incidence and mortality, other indexes expressing the demand of care are also required to develop strategies for service provision. One of these is prevalence of the disease, which measures the absolute number, and relative proportion in the population, of individuals affected by the disease and that require some form of medical attention. For most cancer sites, cases surviving 5 years from diagnosis experience thereafter the same survival as the general population, so most of the workload is therefore due to medical acts within these first 5 years. This article reports world-wide estimates of 1-, 2-3- and 4-5-year point prevalence in 1990 in the population aged 15 years or over, and hence describes the number of cancer cases diagnosed between 1986 and 1990 who were still alive at the end of 1990. These estimates of prevalence at 1, 2-3 and 4-5 years are applicable to the evaluation of initial treatment, clinical follow-up and point of cure, respectively, for the majority of cancers. We describe the computational procedure and data sources utilised to obtain these figures and compare them with data published by 2 cancer registries. The highest prevalence of cancer is in North America with 1.5% of the population affected and diagnosed in the previous 5 years (about 0.5% of the population in years 4-5 and 2-3 of follow-up and 0.4% within the first year of diagnosis). This corresponds to over 3.2 million individuals. Western Europe and Australia and New Zealand show very similar percentages with 1.2% and 1.1% of the population affected (about 3.9 and 0.2 million cases respectively). Japan and Eastern Europe form the next batch with 1.0% and 0.7%, followed by Latin America and the Caribbean (overall prevalence of 0.4%), and all remaining regions are around 0.2%. Cancer prevalence in developed countries is very similar in men and women, 1.1% of the sex-specific population, while in

  9. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands.

    Science.gov (United States)

    Schurink, Anouk; Wolc, Anna; Ducro, Bart J; Frankena, Klaas; Garrick, Dorian J; Dekkers, Jack C M; van Arendonk, Johan A M

    2012-10-30

    Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Data on 200 Shetland pony mares and 146 Icelandic horses were collected according to a matched case-control design. Cases and controls were matched on various factors (e.g. region, sire) to minimize effects of population stratification. Breed-specific genome-wide association studies were performed using 70 k single nucleotide polymorphisms genotypes. Bayesian variable selection method Bayes-C with a threshold model implemented in GenSel software was applied. A 1 Mb non-overlapping window approach that accumulated contributions of adjacent single nucleotide polymorphisms was used to identify associated genomic regions. The percentage of variance explained by all single nucleotide polymorphisms was 13% in Shetland pony mares and 28% in Icelandic horses. The 20 non-overlapping windows explaining the largest percentages of genetic variance were found on nine chromosomes in Shetland pony mares and on 14 chromosomes in Icelandic horses. Overlap in identified associated genomic regions between breeds would suggest interesting candidate regions to follow-up on. Such regions common to both breeds (within 15 Mb) were found on chromosomes 3, 7, 11, 20 and 23. Positional candidate genes within 2 Mb from the associated windows were identified on chromosome 20 in both breeds. Candidate genes are within the equine lymphocyte antigen class II region, which evokes an immune response by recognizing many foreign molecules. The genome-wide association study identified several genomic regions associated with insect bite

  10. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands

    Directory of Open Access Journals (Sweden)

    Schurink Anouk

    2012-10-01

    Full Text Available Abstract Background Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Methods Data on 200 Shetland pony mares and 146 Icelandic horses were collected according to a matched case–control design. Cases and controls were matched on various factors (e.g. region, sire to minimize effects of population stratification. Breed-specific genome-wide association studies were performed using 70 k single nucleotide polymorphisms genotypes. Bayesian variable selection method Bayes-C with a threshold model implemented in GenSel software was applied. A 1 Mb non-overlapping window approach that accumulated contributions of adjacent single nucleotide polymorphisms was used to identify associated genomic regions. Results The percentage of variance explained by all single nucleotide polymorphisms was 13% in Shetland pony mares and 28% in Icelandic horses. The 20 non-overlapping windows explaining the largest percentages of genetic variance were found on nine chromosomes in Shetland pony mares and on 14 chromosomes in Icelandic horses. Overlap in identified associated genomic regions between breeds would suggest interesting candidate regions to follow-up on. Such regions common to both breeds (within 15 Mb were found on chromosomes 3, 7, 11, 20 and 23. Positional candidate genes within 2 Mb from the associated windows were identified on chromosome 20 in both breeds. Candidate genes are within the equine lymphocyte antigen class II region, which evokes an immune response by recognizing many foreign molecules. Conclusions The genome-wide association

  11. Assessment Of Noise-induced Sleep Fragility In Two Age Ranges By Means Of Polysomnographic Microstructure

    Science.gov (United States)

    Terzano, M. G.; Parrino, L.; Spaggiari, M. C.; Buccino, G. P.; Fioriti, G.; Depoortere, H.

    1993-04-01

    The microstructure of sleep, which translates the short-lived fluctuations of the arousal level, is a commonly neglected feature in polysomnographic studies. Specifically arranged microstructural EEG events may provide important information on the dynamic characteristics of the sleep process. CAP (cyclic alternating pattern) and non-CAP are complementary modalities in which arousal-related "phasic" EEG phenomena are organized in non-REM sleep, and they correspond to opposite conditions of unstable and stable sleep depth, respectively. Thus, arousal instability can be measured by the CAP rate, the percentage ratio of total CAP time to total non-REM sleep time. The CAP rate, an age-related physiological variable that increases in several pathological conditions, is highly sensitive to acoustic perturbation. In the present study, two groups of healthy subjects without complaints about sleep, belonging to different age ranges (six young adults, three males and three females, between 20 and 30 years, and six middle-aged individuals, three males and three females, between 40 and 55 years) slept, after adaptation to the sleep laboratory, in a random sequence for two non-consecutive nights either under silent baseline (27·3 dB(A) Lcq) or noise-disturbed (continuous 55 dB(A) white noise) conditions. Age-related and noise-related effects on traditional sleep parameters and on the CAP rate were statistically evaluated by a split-plot test. Compared to young adults, the middle-aged individuals showed a significant reduction of total sleep time, stage 2 and REM sleep and significantly higher values of nocturnal awakenings and the CAP rate. The noisy nights were characterized by similar alterations. The disruptive effects of acoustic perturbation were greater on the more fragile sleep architecture of the older group. The increased fragility of sleep associated with aging probably reflects the decreased capacity of the sleeping brain to maintain steady states of vigilance. Total

  12. Evaluation of mental foramen location in the 10–70 years age range ...

    African Journals Online (AJOL)

    Evaluation of mental foramen location in the 10–70 years age range using ... limit from the lower edge of the mandible, and vertical size of the MF were measured. ... Conclusions: Knowing both the position and the distance of the MF from the ...

  13. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays.

    Science.gov (United States)

    Gross, Arnd; Tönjes, Anke; Kovacs, Peter; Veeramah, Krishna R; Ahnert, Peter; Roshyara, Nab R; Gieger, Christian; Rueckert, Ina-Maria; Loeffler, Markus; Stoneking, Mark; Wichmann, Heinz-Erich; Novembre, John; Stumvoll, Michael; Scholz, Markus

    2011-07-28

    The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD

  14. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays

    Directory of Open Access Journals (Sweden)

    Gieger Christian

    2011-07-01

    Full Text Available Abstract Background The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644 and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. Results The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Conclusions Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the

  15. Genome-wide association study of pancreatic cancer in Japanese population.

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    Siew-Kee Low

    Full Text Available Pancreatic cancer shows very poor prognosis and is the fifth leading cause of cancer death in Japan. Previous studies indicated some genetic factors contributing to the development and progression of pancreatic cancer; however, there are limited reports for common genetic variants to be associated with this disease, especially in the Asian population. We have conducted a genome-wide association study (GWAS using 991 invasive pancreatic ductal adenocarcinoma cases and 5,209 controls, and identified three loci showing significant association (P-value<5x10(-7 with susceptibility to pancreatic cancer. The SNPs that showed significant association carried estimated odds ratios of 1.29, 1.32, and 3.73 with 95% confidence intervals of 1.17-1.43, 1.19-1.47, and 2.24-6.21; P-value of 3.30x10(-7, 3.30x10(-7, and 4.41x10(-7; located on chromosomes 6p25.3, 12p11.21 and 7q36.2, respectively. These associated SNPs are located within linkage disequilibrium blocks containing genes that have been implicated some roles in the oncogenesis of pancreatic cancer.

  16. A genome-wide association study for reading and language abilities in two population cohorts.

    Science.gov (United States)

    Luciano, M; Evans, D M; Hansell, N K; Medland, S E; Montgomery, G W; Martin, N G; Wright, M J; Bates, T C

    2013-08-01

    Candidate genes have been identified for both reading and language, but most of the heritable variance in these traits remains unexplained. Here, we report a genome-wide association meta-analysis of two large cohorts: population samples of Australian twins and siblings aged 12-25 years (n = 1177 from 538 families), and a younger cohort of children of the UK Avon Longitudinal Study of Parents and their Children (aged 8 and 9 years; maximum n = 5472). Suggestive association was indicated for reading measures and non-word repetition (NWR), with the greatest support found for single nucleotide polymorphisms (SNPs) in the pseudogene, ABCC13 (P = 7.34 × 10(-8)), and the gene, DAZAP1 (P = 1.32 × 10(-6)). Gene-based analyses showed significant association (P reading and spelling with genes CD2L1, CDC2L2 and RCAN3 in two loci on chromosome 1. Some support was found for the same SNPs having effects on both reading skill and NWR, which is compatible with behavior genetic evidence for influences of reading acquisition on phonological-task performance. The results implicate novel candidates for study in additional cohorts for reading and language abilities. © 2013 The Authors. Genes, Brain and Behavior published by John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  17. Genome wide association study of age at menarche in the Japanese population.

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    Chizu Tanikawa

    Full Text Available Age at menarche (AAM is a complex trait involving both genetic and environmental factors. To identify the genetic factors associated with AAM, we conducted a large-scale meta-analysis of genome-wide association studies using more than 15,000 Japanese female samples. Here, we identified an association between SNP (single nucleotide polymorphism rs364663 at the LIN28B locus and AAM, with a P-value of 5.49×10(-7 and an effect size of 0.089 (year. We also evaluated 33 SNPs that were previously reported to be associated with AAM in women of European ancestry. Among them, two SNPs rs4452860 and rs7028916 in TMEM38B indicated significant association with AAM in the same directions as reported in previous studies (P = 0.0013 with an effect size of 0.051 even after Bonferroni correction for the 33 SNPs. In addition, six loci in or near CCDC85A, LOC100421670, CA10, ZNF483, ARNTL, and RXRG exhibited suggestive association with AAM (P<0.05. Our findings elucidated the impact of genetic variations on AAM in the Japanese population.

  18. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations.

    Science.gov (United States)

    Munshi-South, Jason; Zolnik, Christine P; Harris, Stephen E

    2016-04-01

    Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

  19. Primary prevention of cardiovascular disease through population-wide motivational strategies: insights from using smartphones in stroke prevention.

    Science.gov (United States)

    Feigin, Valery L; Norrving, Bo; Mensah, George A

    2016-01-01

    The fast increasing stroke burden across all countries of the world suggests that currently used primary stroke and cardiovascular disease (CVD) prevention strategies are not sufficiently effective. In this article, we overview the gaps in, and pros and cons of, population-wide and high-risk prevention strategies. We suggest that motivating and empowering people to reduce their risk of having a stroke/CVD by using increasingly used smartphone technologies would bridge the gap in the population-wide and high-risk prevention strategies and reduce stroke/CVD burden worldwide. We emphasise that for primary stroke prevention to be effective, the focus should be shifted from high-risk prevention to prevention at any level of CVD risk, with the focus on behavioural risk factors. Such a motivational population-wide strategy could open a new page in primary prevention of not only stroke/CVD but also other non-communicable disorders worldwide.

  20. Pathogen exposure varies widely among sympatric populations of wild and domestic felids across the United States.

    Science.gov (United States)

    Carver, Scott; Bevins, Sarah N; Lappin, Michael R; Boydston, Erin E; Lyren, Lisa M; Alldredge, Mathew; Logan, Kenneth A; Sweanor, Linda L; Riley, Seth P D; Serieys, Laurel E K; Fisher, Robert N; Vickers, T Winston; Boyce, Walter; Mcbride, Roy; Cunningham, Mark C; Jennings, Megan; Lewis, Jesse; Lunn, Tamika; Crooks, Kevin R; Vandewoude, Sue

    2016-03-01

    Understanding how landscape, host, and pathogen traits contribute to disease exposure requires systematic evaluations of pathogens within and among host species and geographic regions. The relative importance of these attributes is critical for management of wildlife and mitigating domestic animal and human disease, particularly given rapid ecological changes, such as urbanization. We screened > 1000 samples from sympatric populations of puma (Puma concolor), bobcat (Lynx rufus), and domestic cat (Felis catus) across urban gradients in six sites, representing three regions, in North America for exposure to a representative suite of bacterial, protozoal, and viral pathogens (Bartonella sp., Toxoplasma gondii, feline herpesvirus-1, feline panleukopenea virus, feline calicivirus, and feline immunodeficiency virus). We evaluated prevalence within each species, and examined host trait and land cover determinants of exposure; providing an unprecedented analysis of factors relating to potential for infections in domesticated and wild felids. Prevalence differed among host species (highest for puma and lowest for domestic cat) and was greater for indirectly transmitted pathogens. Sex was inconsistently predictive of exposure to directly transmitted pathogens only, and age infrequently predictive of both direct and indirectly transmitted pathogens. Determinants of pathogen exposure were widely divergent between the wild felid species. For puma, suburban land use predicted increased exposure to Bartonella sp. in southern California, and FHV-1 exposure increased near urban edges in Florida. This may suggest interspecific transmission with domestic cats via flea vectors (California) and direct contact (Florida) around urban boundaries. Bobcats captured near urban areas had increased exposure to T. gondii in Florida, suggesting an urban source of prey Bobcats captured near urban areas in Colorado and Florida had higher FIV exposure, possibly suggesting increased intraspecific

  1. Pathogen exposure varies widely among sympatric populations of wild and domestic felids across the United States

    Science.gov (United States)

    Carver, Scott; Bevins, Sarah N.; Lappin, Michael R.; Boydston, Erin E.; Lyren, Lisa M.; Alldredge, Mathew W.; Logan, Kenneth A.; Sweanor, Linda L.; Riley, Seth P.D.; Serieys, Laurel E.K.; Fisher, Robert N.; Vickers, T. Winston; Boyce, Walter M.; McBride, Roy; Cunnigham, Mark C.; Jennings, Megan; Lewis, Jesse S.; Lunn, Tamika; Crooks, Kevin R.; VandeWoude, Sue

    2016-01-01

    Understanding how landscape, host, and pathogen traits contribute to disease exposure requires systematic evaluations of pathogens within and among host species and geographic regions. The relative importance of these attributes is critical for management of wildlife and mitigating domestic animal and human disease, particularly given rapid ecological changes, such as urbanization. We screened >1,000 samples from sympatric populations of puma (Puma concolor), bobcat (Lynx rufus) and domestic cat (Felis catus) across urban gradients in six sites, representing three regions, in North America for exposure to a representative suite of bacterial, protozoal and viral pathogens (Bartonella sp., Toxoplasma gondii, feline herpesvirus-1, feline panleukopenea virus, feline calicivirus, feline immunodeficiency virus). We evaluated prevalence within each species, and examined host trait and land cover determinants of exposure-providing an unprecedented analysis of factors relating to potential for infections in domesticated and wild felids. Prevalence differed among host species (highest for puma and lowest for domestic cat) and was greater for indirectly transmitted pathogens. Sex was inconsistently predictive of exposure to directly transmitted pathogens only, and age infrequently predictive of both direct and indirectly transmitted pathogens. Determinants of pathogen exposure were widely divergent between the wild felid species. For puma, suburban landuse predicted increased exposure to Bartonella sp. in southern California, and FHV-1 exposure increased near urban edges in Florida. This may suggest inter-specific transmission with domestic cats via flea vectors (California) and direct contact (Florida) around urban boundaries. Bobcats captured near urban areas had increased exposure to T. gondii in Florida, suggesting an urban source of prey. Bobcats captured near urban areas in Colorado and Florida had higher FIV exposure, possibly suggesting increased intra

  2. Range-wide population genetics and variation in morph ratio in style-dimorphic Narcissus papyraceus.

    Science.gov (United States)

    Simón-Porcar, Violeta I; Picó, F Xavier; Arroyo, Juan

    2015-03-01

    • Theoretical models state that natural selection and mating patterns account for floral morph ratio in style-polymorphic plants. However, the demographic history of populations can also influence variation in morph ratios. If so, we hypothesize an association between the morph ratios and the genetic structure across populations.• We used nuclear microsatellites to assess genetic variation and structure in populations of Narcissus papyraceus, a style-dimorphic plant whose floral morph ratios (L-morph to S-morph) gradually vary throughout its distribution range in the southwestern Mediterranean Basin. We implemented analyses to relate the genetic features of populations with their morph ratios.• We found greater frequencies of the S-morph in central populations and declining frequencies toward the periphery. This geographic pattern was not associated with the genetic structure of populations. Instead, we found two distinct genetic groups, mainly separated by the Strait of Gibraltar, with a mixture of morph ratios within each one. Overall, there was a weak genetic structure. Genetic diversity was greater in central and southern dimorphic populations than in northern L-monomorphic populations.• Altogether, our results do not support the hypothesis that the demographic history of populations can account for the observed geographical pattern of morph ratios in N. papyraceus. We suggest that adaptive processes shown in previous studies in the species are the main determinant of the existing variation in the morph composition of populations. © 2015 Botanical Society of America, Inc.

  3. A projection of lesser prairie chicken (Tympanuchus pallidicinctus) populations range-wide

    Science.gov (United States)

    Cummings, Jonathan W.; Converse, Sarah J.; Moore, Clinton T.; Smith, David R.; Nichols, Clay T.; Allan, Nathan L.; O'Meilia, Chris M.

    2017-08-09

    We built a population viability analysis (PVA) model to predict future population status of the lesser prairie-chicken (Tympanuchus pallidicinctus, LEPC) in four ecoregions across the species’ range. The model results will be used in the U.S. Fish and Wildlife Service's (FWS) Species Status Assessment (SSA) for the LEPC. Our stochastic projection model combined demographic rate estimates from previously published literature with demographic rate estimates that integrate the influence of climate conditions. This LEPC PVA projects declining populations with estimated population growth rates well below 1 in each ecoregion regardless of habitat or climate change. These results are consistent with estimates of LEPC population growth rates derived from other demographic process models. Although the absolute magnitude of the decline is unlikely to be as low as modeling tools indicate, several different lines of evidence suggest LEPC populations are declining.

  4. Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes

    DEFF Research Database (Denmark)

    Imamura, Minako; Takahashi, Atsushi; Yamauchi, Toshimasa

    2016-01-01

    Genome-wide association studies (GWAS) have identified more than 80 susceptibility loci for type 2 diabetes (T2D), but most of its heritability still remains to be elucidated. In this study, we conducted a meta-analysis of GWAS for T2D in the Japanese population. Combined data from discovery and ...

  5. High-Resolution Genome-Wide Linkage Mapping Identifies Susceptibility Loci for BMI in the Chinese Population

    DEFF Research Database (Denmark)

    Zhang, Dong Feng; Pang, Zengchang; Li, Shuxia

    2012-01-01

    linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis...

  6. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus.

    Directory of Open Access Journals (Sweden)

    Juan Wang

    Full Text Available Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE for 30 individuals from two populations. The nucleotide diversity (π for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001 and the putatively neutral SNPs (FST = 0.0347, P < 0.001. However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001. Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40% significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

  7. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands

    NARCIS (Netherlands)

    Schurink, A.; Wolc, A.; Ducro, B.J.; Frankena, K.; Garrick, D.J.; Dekkers, J.C.M.; Arendonk, van J.A.M.

    2012-01-01

    Background: Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite

  8. Population structure and genome-wide patterns of variation in Ireland and Britain.

    Science.gov (United States)

    O'Dushlaine, Colm T; Morris, Derek; Moskvina, Valentina; Kirov, George; Gill, Michael; Corvin, Aiden; Wilson, James F; Cavalleri, Gianpiero L

    2010-11-01

    Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

  9. Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

    DEFF Research Database (Denmark)

    Wu, Xiaoping; Fang, Ming; Liu, Lin

    2013-01-01

    Background: Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS for conformation traits of cattle is comparatively less. This study aims to use GWAS to find the candidates genes for body conformation traits.Re...

  10. The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations.

    Science.gov (United States)

    Derks, E M; Zwinderman, A H; Gamazon, E R

    2017-05-01

    Population divergence impacts the degree of population stratification in Genome Wide Association Studies. We aim to: (i) investigate type-I error rate as a function of population divergence (F ST ) in multi-ethnic (admixed) populations; (ii) evaluate the statistical power and effect size estimates; and (iii) investigate the impact of population stratification on the results of gene-based analyses. Quantitative phenotypes were simulated. Type-I error rate was investigated for Single Nucleotide Polymorphisms (SNPs) with varying levels of F ST between the ancestral European and African populations. Type-II error rate was investigated for a SNP characterized by a high value of F ST . In all tests, genomic MDS components were included to correct for population stratification. Type-I and type-II error rate was adequately controlled in a population that included two distinct ethnic populations but not in admixed samples. Statistical power was reduced in the admixed samples. Gene-based tests showed no residual inflation in type-I error rate.

  11. Comparison of Genome-Wide Association Methods in Analyses of Admixed Populations with Complex Familial Relationships

    DEFF Research Database (Denmark)

    Kadri, Naveen; Guldbrandtsen, Bernt; Sørensen, Peter

    2014-01-01

    ) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic......Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K...... and genomic relationships. In summary, in association studies using samples with both P and K, ancestries estimated using principal components or structured assignment were not sufficient to correct type-I errors. In such cases type-I errors may be controlled by use of linear mixed models with relationships...

  12. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

    Science.gov (United States)

    Baker, C S; Perry, A; Bannister, J L; Weinrich, M T; Abernethy, R B; Calambokidis, J; Lien, J; Lambertsen, R H; Ramírez, J U; Vasquez, O

    1993-01-01

    Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting. PMID:8367488

  13. A mixed model reduces spurious genetic associations produced by population stratification in genome-wide association studies.

    Science.gov (United States)

    Shin, Jimin; Lee, Chaeyoung

    2015-04-01

    Population stratification can produce spurious genetic associations in genome-wide association studies (GWASs). Mixed model methodology has been regarded useful for correcting population stratification. This study explored statistical power and false discovery rate (FDR) with the data simulated for dichotomous traits. Empirical FDRs and powers were estimated using fixed models with and without genomic control and using mixed models with and without reflecting loci linked to the candidate marker in genetic relationships. Population stratification with admixture degree ranged from 1% to 10% resulted in inflated FDRs from the fixed model analysis without genomic control and decreased power from the fixed model analysis with genomic control (Ppopulation stratification could not change FDR and power estimates from the mixed model analyses (P>0.05). We suggest that the mixed model methodology was useful to reduce spurious genetic associations produced by population stratification in GWAS, even with a high degree of admixture (10%). Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis).

    Science.gov (United States)

    Blancher, Antoine; Bonhomme, Maxime; Crouau-Roy, Brigitte; Terao, Keiji; Kitano, Takashi; Saitou, Naruya

    2008-01-01

    We studied the mitochondrial DNA (mtDNA) polymorphism of 304 Macaca fascicularis fascicularis (M. f. fascicularis) individuals, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius). By sequencing a 590-bp fragment in the hypervariable II region of the D-loop region, we defined 70 haplotypes. The homologous region was also characterized in 22 Chinese Macaca mulatta and 2 Macaca sylvanus. The phylogenetic analysis confirms the monophyly of M. f. fascicularis and defines 2 haplotype groups inside the M. f. fascicularis clade: one "insular," encompassing 6 Philippines, 2 Mauritius, and 31 Indonesian haplotypes, the other "continental" that contains all Indochinese and 6 Indonesian haplotypes. Continental and insular group divergence time was estimated to be approximately 10(6) years before present (BP). Among Indonesian haplotypes, some have a continental origin. This suggests either direct migration from mainland to Indonesia or that remnant lineages from an ancient population genetically close to the mainland (i.e., in the Sunda Shelf, Indonesia. The low nucleotide diversity in the Philippines population suggests a bottleneck following colonization by Indonesian individuals, around 110 000 years BP. mtDNA and further observations of nuclear genetic data corroborate the mixed origin (Indonesian/continental) hypothesis of Mauritius individuals and a population bottleneck.

  15. Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples.

    Directory of Open Access Journals (Sweden)

    Charleston W K Chiang

    2010-03-01

    Full Text Available As we move forward from the current generation of genome-wide association (GWA studies, additional cohorts of different ancestries will be studied to increase power, fine map association signals, and generalize association results to additional populations. Knowledge of genetic ancestry as well as population substructure will become increasingly important for GWA studies in populations of unknown ancestry. Here we propose genotyping pooled DNA samples using genome-wide SNP arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (AIMs in populations of unknown origin. We constructed DNA pools from African American, Native Hawaiian, Latina, and Jamaican samples and genotyped them using the Affymetrix 6.0 array. Aided by individual genotype data from the African American cohort, we established quality control filters to remove poorly performing SNPs and estimated allele frequencies for the remaining SNPs in each panel. We then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the International HapMap Consortium as reference panels, and identified AIMs unique to each population. In this study, we demonstrated that genotyping pooled DNA samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known AIMs. Furthermore, through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences (i.e., AIMs and that these AIMs are able to differentiate two closely related populations (HapMap JPT and CHB.

  16. Epidemiological and Genome-Wide Association Study of Gastritis or Gastric Ulcer in Korean Populations

    OpenAIRE

    Sumin Oh; Sejong Oh

    2014-01-01

    Gastritis is a major disease that has the potential to grow as gastric cancer. Gastric cancer is a very common cancer, and it is related to a very high mortality rate in Korea. This disease is known to have various reasons, including infection with Helicobacter pylori, dietary habits, tobacco, and alcohol. The incidence rate of gastritis has reported to differ between age, population, and gender. However, unlike other factors, there has been no analysis based on gender. So, we examined the hi...

  17. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands

    OpenAIRE

    Schurink, A.; Wolc, A.; Ducro, B.J.; Frankena, K.; Garrick, D.J.; Dekkers, J.C.M.; Arendonk, van, J.A.M.

    2012-01-01

    Background: Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Methods: Da...

  18. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands

    OpenAIRE

    Schurink, Anouk; Wolc, Anna; Ducro, Bart J; Frankena, Klaas; Garrick, Dorian J; Dekkers, Jack CM; van Arendonk, Johan AM

    2012-01-01

    Abstract Background Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Met...

  19. Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

    Energy Technology Data Exchange (ETDEWEB)

    McKown, Athena [University of British Columbia, Vancouver; Klapste, Jaroslav [University of British Columbia, Vancouver; Guy, Robert [University of British Columbia, Vancouver; Geraldes, Armando [University of British Columbia, Vancouver; Porth, Ilga [University of British Columbia, Vancouver; Hannemann, Jan [University of Victoria, Canada; Friedmann, Michael [University of British Columbia, Vancouver; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; Ehlting, Juergen [University of Victoria, Canada; Cronk, Quentin [University of British Columbia, Vancouver; El-Kassaby, Yousry [University of British Columbia, Vancouver; Mansfield, Shawn [University of British Columbia, Vancouver; Douglas, Carl [University of British Columbia, Vancouver

    2014-01-01

    To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

  20. Comparison of genome-wide association methods in analyses of admixed populations with complex familial relationships.

    Directory of Open Access Journals (Sweden)

    Naveen K Kadri

    Full Text Available Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P and family (K levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic markers. Linear models that ignored K were also tested. Correction for P was performed using principal component or structured association analysis. In analyses of simulated and real data, linear mixed models that corrected for K were able to control for type-I error, regardless of whether they also corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree and genomic relationships. In summary, in association studies using samples with both P and K, ancestries estimated using principal components or structured assignment were not sufficient to correct type-I errors. In such cases type-I errors may be controlled by use of linear mixed models with relationships derived from either pedigree or from genetic markers.

  1. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Directory of Open Access Journals (Sweden)

    Thais C de Oliveira

    2017-07-01

    Full Text Available The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences, Peru (PER, n = 23, Colombia (COL, n = 31, and Mexico (MEX, n = 19.We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4 as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092. Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically

  2. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    Directory of Open Access Journals (Sweden)

    Simon Boitard

    2016-03-01

    Full Text Available Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey, PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

  3. Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population.

    Directory of Open Access Journals (Sweden)

    Kejun Wang

    Full Text Available In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1, seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3, and one for average daily gain (COL27A1. Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

  4. Genome-wide association of lipid-lowering response to statins in combined study populations.

    Directory of Open Access Journals (Sweden)

    Mathew J Barber

    2010-03-01

    Full Text Available Statins effectively lower total and plasma LDL-cholesterol, but the magnitude of decrease varies among individuals. To identify single nucleotide polymorphisms (SNPs contributing to this variation, we performed a combined analysis of genome-wide association (GWA results from three trials of statin efficacy.Bayesian and standard frequentist association analyses were performed on untreated and statin-mediated changes in LDL-cholesterol, total cholesterol, HDL-cholesterol, and triglyceride on a total of 3932 subjects using data from three studies: Cholesterol and Pharmacogenetics (40 mg/day simvastatin, 6 weeks, Pravastatin/Inflammation CRP Evaluation (40 mg/day pravastatin, 24 weeks, and Treating to New Targets (10 mg/day atorvastatin, 8 weeks. Genotype imputation was used to maximize genomic coverage and to combine information across studies. Phenotypes were normalized within each study to account for systematic differences among studies, and fixed-effects combined analysis of the combined sample were performed to detect consistent effects across studies. Two SNP associations were assessed as having posterior probability greater than 50%, indicating that they were more likely than not to be genuinely associated with statin-mediated lipid response. SNP rs8014194, located within the CLMN gene on chromosome 14, was strongly associated with statin-mediated change in total cholesterol with an 84% probability by Bayesian analysis, and a p-value exceeding conventional levels of genome-wide significance by frequentist analysis (P = 1.8 x 10(-8. This SNP was less significantly associated with change in LDL-cholesterol (posterior probability = 0.16, P = 4.0 x 10(-6. Bayesian analysis also assigned a 51% probability that rs4420638, located in APOC1 and near APOE, was associated with change in LDL-cholesterol.Using combined GWA analysis from three clinical trials involving nearly 4,000 individuals treated with simvastatin, pravastatin, or atorvastatin, we

  5. Genome-wide association scans for idiopathic osteonecrosis of the femoral head in a Korean population.

    Science.gov (United States)

    Baek, Seung-Hoon; Kim, Kang-Il; Yoon, Kyung-Sik; Kim, Tae-Ho; Kim, Shin-Yoon

    2017-02-01

    Osteonecrosis of the femoral head (ONFH) is a multifactorial disease and is associated with genetic predisposition, and exposure to certain risk factors. In particular, idiopathic ONFH in twins and the clustering of cases in families have indicated that genetic factors are involved. However, the majority of cases of ONFH are sporadic and various studies have demonstrated that differences in the study design and/or the ethnic groups analyzed leads to different results. The present study performed one of the first genome‑wide association studies to identify genetic loci that may increase the risk of idiopathic ONFH. In total, 217 patients with idiopathic ONFH and 217 control samples, without ONFH, were genotyped using Axiom™ chips. Following quality control, 509,886 single‑nucleotide polymorphisms (SNPs) were included in the association analysis to identify genetic variants that may influence susceptibility to idiopathic ONFH. The lowest P‑value identified by the current study was for an association with rs220324 (P=3.57x10‑7), an SNP that is located near to the uromodulin‑like 1 gene region on chromosome 21q22.3, although none of the SNPs reached the traditional genome‑wide significance level of 5x10‑8. However, the DnaJ heat shock protein family (Hsp40) member C6 (DNAJC6) locus, a region between 65.37 and 65.67 Mb located on chromosome 1p31.3, harbored a cluster of SNPs that were associated with idiopathic ONFH at a significance level of P<1x10‑5. Four variants, rs10493374, rs12032616, rs17127529 and rs6679032, with marginal associations were located in and around the DNAJC6 locus and were in strong linkage disequilibrium with each other. In conclusion, the current study did not identify any SNPs that were associated with idiopathic ONFH at a genome‑wide significance level, however, the results suggest that future studies should investigate the effects of SNPs in the DNAJC6 gene on the idiopathic ONFH risk.

  6. Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations

    Science.gov (United States)

    Cardona, Alexia; Pagani, Luca; Antao, Tiago; Lawson, Daniel J.; Eichstaedt, Christina A.; Yngvadottir, Bryndis; Shwe, Ma Than Than; Wee, Joseph; Romero, Irene Gallego; Raj, Srilakshmi; Metspalu, Mait; Villems, Richard; Willerslev, Eske; Tyler-Smith, Chris; Malyarchuk, Boris A.; Derenko, Miroslava V.; Kivisild, Toomas

    2014-01-01

    Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture. PMID:24847810

  7. Genome-wide analysis of cold adaptation in indigenous Siberian populations.

    Directory of Open Access Journals (Sweden)

    Alexia Cardona

    Full Text Available Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66-69 Mb contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA and vascular smooth muscle contraction (PRKG1. By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

  8. Lithium in drinking water and the incidence of bipolar disorder: A nation-wide population-based study

    DEFF Research Database (Denmark)

    Kessing, Lars Vedel; Gerds, Thomas Alexander; Knudsen, Nikoline N.

    2017-01-01

    /bipolar disorder from 1995 to 2013 (N=14 820) and 10 age- and gender-matched controls from the Danish population (N= 140 311). Average drinking water lithium exposure was estimated for all study individuals. RESULTS: The median of the average lithium exposure did not differ between cases with a diagnosis of mania......OBJECTIVE: Animal data suggest that subtherapeutic doses, including micro doses, of lithium may influence mood, and lithium levels in drinking water have been found to correlate with the rate of suicide. It has never been investigated whether consumption of lithium may prevent the development...... of bipolar disorder (primary prophylaxis). In a nation-wide population-based study, we investigated whether long-term exposure to micro levels of lithium in drinking water correlates with the incidence of bipolar disorder in the general population, hypothesizing an inverse association in which higher long...

  9. Clinical Implications of Human Population Differences in Genome-wide Rates of Functional Genotypes

    Directory of Open Access Journals (Sweden)

    Ali eTorkamani

    2012-11-01

    Full Text Available There have been a number of recent successes in the use of whole genome sequencing and sophisticated bioinformatics techniques to identify pathogenic DNA sequence variants responsible for individual idiopathic congenital conditions. However, the success of this identification process is heavily influenced by the ancestry or genetic background of a patient with an idiopathic condition. This is so because potential pathogenic variants in a patient’s genome must be contrasted with variants in a reference set of genomes made up of other individuals’ genomes of the same ancestry as the patient. We explored the effect of ignoring the ancestries of both an individual patient and the individuals used to construct reference genomes. We pursued this exploration in two major steps. We first considered variation in the per-genome number and rates likely functional derived (i.e., non-ancestral, based on the chimp genome single nucleotide variants and small indels in 52 individual whole human genomes sampled from 10 different global populations. We took advantage of a suite of computational and bioinformatics techniques to predict the functional effect of over 24 million genomic variants, both coding and non-coding, across these genomes. We found that the typical human genome harbors ~5.5-6.1 million total derived variants, of which ~12,000 are likely to have a functional effect (~5000 coding and ~7000 non-coding. We also found that the rates of functional genotypes per the total number of genotypes in individual whole genomes differ dramatically between human populations. We then created tables showing how the use of comparator or reference genome panels comprised of genomes from individuals that do not have the same ancestral background as a patient can negatively impact pathogenic variant identification. Our results have important implications for clinical sequencing initiatives.

  10. Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

    Science.gov (United States)

    Fuchs, Florian; Pau, Gregoire; Kranz, Dominique; Sklyar, Oleg; Budjan, Christoph; Steinbrink, Sandra; Horn, Thomas; Pedal, Angelika; Huber, Wolfgang; Boutros, Michael

    2010-01-01

    Genetic screens for phenotypic similarity have made key contributions to associating genes with biological processes. With RNA interference (RNAi), highly parallel phenotyping of loss-of-function effects in cells has become feasible. One of the current challenges however is the computational categorization of visual phenotypes and the prediction of biological function and processes. In this study, we describe a combined computational and experimental approach to discover novel gene functions and explore functional relationships. We performed a genome-wide RNAi screen in human cells and used quantitative descriptors derived from high-throughput imaging to generate multiparametric phenotypic profiles. We show that profiles predicted functions of genes by phenotypic similarity. Specifically, we examined several candidates including the largely uncharacterized gene DONSON, which shared phenotype similarity with known factors of DNA damage response (DDR) and genomic integrity. Experimental evidence supports that DONSON is a novel centrosomal protein required for DDR signalling and genomic integrity. Multiparametric phenotyping by automated imaging and computational annotation is a powerful method for functional discovery and mapping the landscape of phenotypic responses to cellular perturbations. PMID:20531400

  11. Toxicity Assessment of Common Beans (Phaseolus vulgaris L.) Widely Consumed by Tunisian Population.

    Science.gov (United States)

    Nciri, Nader; Cho, Namjun; El Mhamdi, Faiçal; Ben Ismail, Hanen; Ben Mansour, Abderraouf; Sassi, Fayçal Haj; Ben Aissa-Fennira, Fatma

    2015-09-01

    This research aimed at assessing the content and the functional properties of phytohemagglutinin (PHA) in different varieties of beans widely consumed in Tunisia through soaking, cooking, autoclaving, germination, and their combinations. This study was carried out on three varieties of white beans grown in different localities of Tunisia, namely Twila, Coco, and Beldia, as well as on imported and local canned beans. All bean samples underwent biochemical and immunological evaluation by employing several techniques such as indirect competitive enzyme-linked immunosorbent assay (ELISA), hemagglutinating assay, Ouchterlony double immunodiffusion, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Biochemical and immunological analyses indicated that raw dry beans contained a considerable amount of proteins and PHAs. ELISA demonstrated that soaking, either in plain water or in alkaline solution, caused an increase in the concentration of PHA. A slight increase of PHA was produced equally by germination during 4 days in all bean varieties. Cooking or autoclaving of presoaked beans resulted in a complete disappearance of PHA. ELISA test also proved that both imported and local canned beans contained fingerprints of PHA. Hemagglutination assays showed that not only cooked and autoclaved presoaked beans lacked the ability to agglutinate red blood cells but also autoclaved unsoaked beans did. In agar gel immunodiffusion using rabbit anti-PHA serum, raw, soaked, cooked unsoaked, and sprouted beans gave precipitin arc reactions, indicating that PHA existed in immunoreactive form in the tested seeds. SDS-PAGE electrophoretograms showed protein isolates of Twila and Beldia beans to have different profiles through soaking, cooking, and autoclaving processes. This work revealed that the combination of soaking and cooking/autoclaving was the best way in reducing PHA content and its activity in all bean varieties when compared with germination.

  12. Genome-Wide Copy Number Variations Using SNP Genotyping in a Mixed Breed Swine Population.

    Directory of Open Access Journals (Sweden)

    Ralph T Wiedmann

    Full Text Available Copy number variations (CNVs are increasingly understood to affect phenotypic variation. This study uses SNP genotyping of trios of mixed breed swine to add to the catalog of known genotypic variation in an important agricultural animal. PorcineSNP60 BeadChip genotypes were collected from 1802 pigs that combined to form 1621 trios. These trios were from the crosses of 50 boars with 525 sows producing 1621 piglets. The pigs were part of a population that was a mix of ¼ Duroc, ½ Landrace and ¼ Yorkshire breeds. Merging the overlapping CNVs that were observed in two or more individuals to form CNV regions (CNVRs yielded 502 CNVRs across the autosomes. The CNVRs intersected genes, as defined by RefSeq, 84% of the time - 420 out of 502. The results of this study are compared and contrasted to other swine studies using similar and different methods of detecting CNVR. While progress is being made in this field, more work needs to be done to improve consistency and confidence in CNVR results.

  13. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases.

    Directory of Open Access Journals (Sweden)

    Roberto Amato

    Full Text Available Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or F(ST. We performed a genome-wide estimation of F(ST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of F(ST values between autosomes and heterochromosomes. When we compared the F(ST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of F(ST, while several pathways related to cell signalling, growth and morphogenesis showed high F(ST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.

  14. Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population.

    Directory of Open Access Journals (Sweden)

    Rafael Medeiros de Oliveira Silva

    Full Text Available The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA, 1,832 for backfat thickness (BF, and 1,830 for rump fat thickness (RF. A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS, which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.

  15. The Frequency of Granulocytes with Spontaneous Somatic Mutations: A Wide Distribution in a Normal Human Population

    Science.gov (United States)

    Peruzzi, Benedetta; Boni, Luca; Caporale, Roberto; Dolara, Piero; Notaro, Rosario; Luzzatto, Lucio

    2013-01-01

    Germ-line mutation rate has been regarded classically as a fundamental biological parameter, as it affects the prevalence of genetic disorders and the rate of evolution. Somatic mutation rate is also an important biological parameter, as it may influence the development and/or the course of acquired diseases, particularly of cancer. Estimates of this parameter have been previously obtained in few instances from dermal fibroblasts and lymphoblastoid cells. However, the methodology required has been laborious and did not lend itself to the analysis of large numbers of samples. We have previously shown that the X-linked gene PIG-A, since its product is required for glycosyl-phosphatidylinositol-anchored proteins to become surface bound, is a good sentinel gene for studying somatic mutations. We now show that by this approach we can accurately measure the proportion of PIG-A mutant peripheral blood granulocytes, which we call mutant frequency, ƒ. We found that the results are reproducible, with a variation coefficient (CV) of 45%. Repeat samples from 32 subjects also had a CV of 44%, indicating that ƒ is a relatively stable individual characteristic. From a study of 142 normal subjects we found that log ƒ is a normally distributed variable; ƒ variability spans a 80-fold range, from less than 1×10−6 to 37.5×10−6, with a median of 4.9×10−6. Unlike other techniques commonly employed in population studies, such as comet assay, this method can detect any kind of mutation, including point mutation, as long as it causes functional inactivation of PIG-A gene. Since the test is rapid and requires only a small sample of peripheral blood, this methodology will lend itself to investigating genetic factors that underlie the variation in the somatic mutation rate, as well as environmental factors that may affect it. It will be also possible to test whether ƒ is a determinant of the risk of cancer. PMID:23342069

  16. Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations.

    Science.gov (United States)

    Wu, Sijie; Tan, Jingze; Yang, Yajun; Peng, Qianqian; Zhang, Manfei; Li, Jinxi; Lu, Dongsheng; Liu, Yu; Lou, Haiyi; Feng, Qidi; Lu, Yan; Guan, Yaqun; Zhang, Zhaoxia; Jiao, Yi; Sabeti, Pardis; Krutmann, Jean; Tang, Kun; Jin, Li; Xu, Shuhua; Wang, Sijia

    2016-11-01

    Hair straightness/curliness is one of the most conspicuous features of human variation and is particularly diverse among populations. A recent genome-wide scan found common variants in the Trichohyalin (TCHH) gene that are associated with hair straightness in Europeans, but different genes might affect this phenotype in other populations. By sampling 2899 Han Chinese, we performed the first genome-wide scan of hair straightness in East Asians, and found EDAR (rs3827760) as the predominant gene (P = 4.67 × 10-16), accounting for 3.66 % of the total variance. The candidate gene approach did not find further significant associations, suggesting that hair straightness may be affected by a large number of genes with subtle effects. Notably, genetic variants associated with hair straightness in Europeans are generally low in frequency in Han Chinese, and vice versa. To evaluate the relative contribution of these variants, we performed a second genome-wide scan in 709 samples from the Uyghur, an admixed population with both eastern and western Eurasian ancestries. In Uyghurs, both EDAR (rs3827760: P = 1.92 × 10-12) and TCHH (rs11803731: P = 1.46 × 10-3) are associated with hair straightness, but EDAR (OR 0.415) has a greater effect than TCHH (OR 0.575). We found no significant interaction between EDAR and TCHH (P = 0.645), suggesting that these two genes affect hair straightness through different mechanisms. Furthermore, haplotype analysis indicates that TCHH is not subject to selection. While EDAR is under strong selection in East Asia, it does not appear to be subject to selection after the admixture in Uyghurs. These suggest that hair straightness is unlikely a trait under selection.

  17. An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding.

    Science.gov (United States)

    He, Jianbo; Meng, Shan; Zhao, Tuanjie; Xing, Guangnan; Yang, Shouping; Li, Yan; Guan, Rongzhan; Lu, Jiangjie; Wang, Yufeng; Xia, Qiuju; Yang, Bing; Gai, Junyi

    2017-11-01

    The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas ). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL × 1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was

  18. Populism

    OpenAIRE

    Abts, Koenraad; Van Kessel, Stijn

    2015-01-01

    Populism is a concept applied to a wide range of political movements and actors across the globe. There is, at the same time, considerable confusion about the attributes and manifestation of populism, as well as its impact on democracy. This contribution identifies the defining elements of the populist ideology and discusses the varieties in which populism manifests itself, for instance as a component of certain party families. We finally discuss various normative interpretations of populism,...

  19. Genome-wide analysis of Epstein-Barr virus identifies variants and genes associated with gastric carcinoma and population structure.

    Science.gov (United States)

    Yao, Youyuan; Xu, Miao; Liang, Liming; Zhang, Haojiong; Xu, Ruihua; Feng, Qisheng; Feng, Lin; Luo, Bing; Zeng, Yi-Xin

    2017-10-01

    Epstein-Barr virus is a ubiquitous virus and is associated with several human malignances, including the significant subset of gastric carcinoma, Epstein-Barr virus-associated gastric carcinoma. Some Epstein-Barr virus-associated diseases are uniquely prevalent in populations with different geographic origins. However, the features of the disease and geographically associated Epstein-Barr virus genetic variation as well as the roles that the variation plays in carcinogenesis and evolution remain unclear. Therefore, in this study, we sequenced 95 geographically distinct Epstein-Barr virus isolates from Epstein-Barr virus-associated gastric carcinoma biopsies and saliva of healthy donors to detect variants and genes associated with gastric carcinoma and population structure from a genome-wide spectrum. We demonstrated that Epstein-Barr virus revealed the population structure between North China and South China. In addition, we observed population stratification between Epstein-Barr virus strains from gastric carcinoma and healthy controls, indicating that certain Epstein-Barr virus subtypes are associated with different gastric carcinoma risks. We identified that the BRLF1, BBRF3, and BBLF2/BBLF3 genes had significant associations with gastric carcinoma. LMP1 and BNLF2a genes were strongly geographically associated genes in Epstein-Barr virus. Our study provides insights into the genetic basis of oncogenic Epstein-Barr virus for gastric carcinoma, and the genetic variants associated with gastric carcinoma can serve as biomarkers for oncogenic Epstein-Barr virus.

  20. Local Genealogies in a Linear Mixed Model for Genome-wide Association Mapping in Complex Pedigreed Populations

    DEFF Research Database (Denmark)

    Sahana, Goutam; Mailund, Thomas; Lund, Mogens Sandø

    2011-01-01

    Introduction: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS) is unified mixed model analysis (MMA). This approach is very flexible, can be applied to both family-based and population-based samples, and can be exten......Introduction: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS) is unified mixed model analysis (MMA). This approach is very flexible, can be applied to both family-based and population-based samples, and can...... be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called ‘GENMIX (genealogy based mixed model)’ which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. Subjects and Methods: We validated...... GENMIX using genotyping data of Danish Jersey cattle and simulated phenotype and compared to the MMA. We simulated scenarios for three levels of heritability (0.21, 0.34, and 0.64), seven levels of MAF (0.05, 0.10, 0.15, 0.20, 0.25, 0.35, and 0.45) and five levels of QTL effect (0.1, 0.2, 0.5, 0.7 and 1...

  1. Simulating range-wide population and breeding habitat dynamics for an endangered woodland warbler in the face of uncertainty

    Science.gov (United States)

    Adam Duarte,; Hatfield, Jeffrey; Todd M. Swannack,; Michael R. J. Forstner,; M. Clay Green,; Floyd W. Weckerly,

    2015-01-01

    Population viability analyses provide a quantitative approach that seeks to predict the possible future status of a species of interest under different scenarios and, therefore, can be important components of large-scale species’ conservation programs. We created a model and simulated range-wide population and breeding habitat dynamics for an endangered woodland warbler, the golden-cheeked warbler (Setophaga chrysoparia). Habitat-transition probabilities were estimated across the warbler's breeding range by combining National Land Cover Database imagery with multistate modeling. Using these estimates, along with recently published demographic estimates, we examined if the species can remain viable into the future given the current conditions. Lastly, we evaluated if protecting a greater amount of habitat would increase the number of warblers that can be supported in the future by systematically increasing the amount of protected habitat and comparing the estimated terminal carrying capacity at the end of 50 years of simulated habitat change. The estimated habitat-transition probabilities supported the hypothesis that habitat transitions are unidirectional, whereby habitat is more likely to diminish than regenerate. The model results indicated population viability could be achieved under current conditions, depending on dispersal. However, there is considerable uncertainty associated with the population projections due to parametric uncertainty. Model results suggested that increasing the amount of protected lands would have a substantial impact on terminal carrying capacities at the end of a 50-year simulation. Notably, this study identifies the need for collecting the data required to estimate demographic parameters in relation to changes in habitat metrics and population density in multiple regions, and highlights the importance of establishing a common definition of what constitutes protected habitat, what management goals are suitable within those protected

  2. Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies.

    Science.gov (United States)

    Newell, M A; Cook, D; Tinker, N A; Jannink, J-L

    2011-02-01

    The level of population structure and the extent of linkage disequilibrium (LD) can have large impacts on the power, resolution, and design of genome-wide association studies (GWAS) in plants. Until recently, the topics of LD and population structure have not been explored in oat due to the lack of a high-throughput, high-density marker system. The objectives of this research were to survey the level of population structure and the extent of LD in oat germplasm and determine their implications for GWAS. In total, 1,205 lines and 402 diversity array technology (DArT) markers were used to explore population structure. Principal component analysis and model-based cluster analysis of these data indicated that, for the lines used in this study, relatively weak population structure exists. To explore LD decay, map distances of 2,225 linked DArT marker pairs were compared with LD (estimated as r²). Results showed that LD between linked markers decayed rapidly to r² = 0.2 for marker pairs with a map distance of 1.0 centi-Morgan (cM). For GWAS, we suggest a minimum of one marker every cM, but higher densities of markers should increase marker-QTL association and therefore detection power. Additionally, it was found that LD was relatively consistent across the majority of germplasm clusters. These findings suggest that GWAS in oat can include germplasm with diverse origins and backgrounds. The results from this research demonstrate the feasibility of GWAS and related analyses in oat.

  3. Genome-wide association study of autistic-like traits in a general population study of young adults

    Directory of Open Access Journals (Sweden)

    Rachel Maree Jones

    2013-10-01

    Full Text Available Research has proposed that autistic-like traits in the general population lie on a continuum, with clinical Autism Spectrum Disorder (ASD representing the extreme end of this distribution. Inherent in this proposal is that biological mechanisms associated with clinical ASD may also underpin variation in autistic-like traits within the general population. A genome-wide association study using 2,462,046 single nucleotide polymorphisms (SNPs was undertaken for ASD in 965 individuals from the Western Australian Pregnancy Cohort (Raine Study. No SNP associations reached genome-wide significance (p < 5.0 x 10-8. However, investigations into nominal observed SNP associations (p < 1.0 x 10-5 add support to two positional candidate genes previously implicated in ASD aetiology, PRKCB1 and CBLN1.The rs198198 SNP (p = 9.587 x 10-6, is located within an intron of the protein kinase C, beta 1 (PRKCB1 gene on chromosome 16p11. The PRKCB1 gene has been previously reported in linkage and association studies for ASD, and its mRNA expression has been shown to be significantly down regulated in ASD cases compared with controls. The rs16946931 SNP (p = 1.78 x 10-6 is located in a region flanking the Cerebellin 1 (CBLN1 gene on chromosome 16q12.1. The CBLN1 gene is involved with synaptogenesis and is part of a gene family previously implicated in ASD. This GWA study is only the second to examine SNPs associated with autistic-like traits in the general population, and provides evidence to support roles for the PRKCB1 and CBLN1 genes in risk of clinical ASD.

  4. Ocean-wide Drivers of Migration Strategies and Their Influence on Population Breeding Performance in a Declining Seabird.

    Science.gov (United States)

    Fayet, Annette L; Freeman, Robin; Anker-Nilssen, Tycho; Diamond, Antony; Erikstad, Kjell E; Fifield, Dave; Fitzsimmons, Michelle G; Hansen, Erpur S; Harris, Mike P; Jessopp, Mark; Kouwenberg, Amy-Lee; Kress, Steve; Mowat, Stephen; Perrins, Chris M; Petersen, Aevar; Petersen, Ib K; Reiertsen, Tone K; Robertson, Gregory J; Shannon, Paula; Sigurðsson, Ingvar A; Shoji, Akiko; Wanless, Sarah; Guilford, Tim

    2017-12-18

    Which factors shape animals' migration movements across large geographical scales, how different migratory strategies emerge between populations, and how these may affect population dynamics are central questions in the field of animal migration [1] that only large-scale studies of migration patterns across a species' range can answer [2]. To address these questions, we track the migration of 270 Atlantic puffins Fratercula arctica, a red-listed, declining seabird, across their entire breeding range. We investigate the role of demographic, geographical, and environmental variables in driving spatial and behavioral differences on an ocean-basin scale by measuring puffins' among-colony differences in migratory routes and day-to-day behavior (estimated with individual daily activity budgets and energy expenditure). We show that competition and local winter resource availability are important drivers of migratory movements, with birds from larger colonies or with poorer local winter conditions migrating further and visiting less-productive waters; this in turn led to differences in flight activity and energy expenditure. Other behavioral differences emerge with latitude, with foraging effort and energy expenditure increasing when birds winter further north in colder waters. Importantly, these ocean-wide migration patterns can ultimately be linked with breeding performance: colony productivity is negatively associated with wintering latitude, population size, and migration distance, which demonstrates the cost of competition and migration on future breeding and the link between non-breeding and breeding periods. Our results help us to understand the drivers of animal migration and have important implications for population dynamics and the conservation of migratory species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Disaggregation of nation-wide dynamic population exposure estimates in The Netherlands: Applications of activity-based transport models

    Science.gov (United States)

    Beckx, Carolien; Int Panis, Luc; Uljee, Inge; Arentze, Theo; Janssens, Davy; Wets, Geert

    Traditional exposure studies that link concentrations with population data do not always take into account the temporal and spatial variations in both concentrations and population density. In this paper we present an integrated model chain for the determination of nation-wide exposure estimates that incorporates temporally and spatially resolved information about people's location and activities (obtained from an activity-based transport model) and about ambient pollutant concentrations (obtained from a dispersion model). To the best of our knowledge, it is the first time that such an integrated exercise was successfully carried out in a fully operational modus for all models under consideration. The evaluation of population level exposure in The Netherlands to NO 2 at different time-periods, locations, for different subpopulations (gender, socio-economic status) and during different activities (residential, work, transport, shopping) is chosen as a case-study to point out the new features of this methodology. Results demonstrate that, by neglecting people's travel behaviour, total average exposure to NO 2 will be underestimated by 4% and hourly exposure results can be underestimated by more than 30%. A more detailed exposure analysis reveals the intra-day variations in exposure estimates and the presence of large exposure differences between different activities (traffic > work > shopping > home) and between subpopulations (men > women, low socio-economic class > high socio-economic class). This kind of exposure analysis, disaggregated by activities or by subpopulations, per time of day, provides useful insight and information for scientific and policy purposes. It demonstrates that policy measures, aimed at reducing the overall (average) exposure concentration of the population may impact in a different way depending on the time of day or the subgroup considered. From a scientific point of view, this new approach can be used to reduce exposure misclassification.

  6. Estimation of Coast-Wide Population Trends of Marbled Murrelets in Canada Using a Bayesian Hierarchical Model.

    Directory of Open Access Journals (Sweden)

    Douglas F Bertram

    Full Text Available Species at risk with secretive breeding behaviours, low densities, and wide geographic range pose a significant challenge to conservation actions because population trends are difficult to detect. Such is the case with the Marbled Murrelet (Brachyramphus marmoratus, a seabird listed as 'Threatened' by the Species at Risk Act in Canada largely due to the loss of its old growth forest nesting habitat. We report the first estimates of population trend of Marbled Murrelets in Canada derived from a monitoring program that uses marine radar to detect birds as they enter forest watersheds during 923 dawn surveys at 58 radar monitoring stations within the six Marbled Murrelet Conservation Regions on coastal British Columbia, Canada, 1996-2013. Temporal trends in radar counts were analyzed with a hierarchical Bayesian multivariate modeling approach that controlled for variation in tilt of the radar unit and day of year, included year-specific deviations from the overall trend ('year effects', and allowed for trends to be estimated at three spatial scales. A negative overall trend of -1.6%/yr (95% credibility interval: -3.2%, 0.01% indicated moderate evidence for a coast-wide decline, although trends varied strongly among the six conservation regions. Negative annual trends were detected in East Vancouver Island (-9%/yr and South Mainland Coast (-3%/yr Conservation Regions. Over a quarter of the year effects were significantly different from zero, and the estimated standard deviation in common-shared year effects between sites within each region was about 50% per year. This large common-shared interannual variation in counts may have been caused by regional movements of birds related to changes in marine conditions that affect the availability of prey.

  7. Esophageal Cancer Epigenomics and Integrome Analysis of Genome-Wide Methylation and Expression in High Risk Northeast Indian Population.

    Science.gov (United States)

    Singh, Virendra; Singh, Laishram Chandreshwor; Vasudevan, Madavan; Chattopadhyay, Indranil; Borthakar, Bibhuti Bhusan; Rai, Avdhesh Kumar; Phukan, Rup Kumar; Sharma, Jagannath; Mahanta, Jagadish; Kataki, Amal Chandra; Kapur, Sujala; Saxena, Sunita

    2015-11-01

    Esophageal cancer is a major global health burden with a strong host-environment interaction component and epigenomics underpinnings that remain to be elucidated further. Certain populations such as the Northeast Indians suffer at a disproportionately higher rate from this devastating disease. Promoter methylation is correlated with transcriptional silencing of various genes in esophageal cancer. Very few studies on genome-wide methylation for esophageal cancer exist and yet, no one has carried out an integromics analysis of methylation and gene expression. In the present study, genome-wide methylation was measured in samples collected from the Northeast Indian population by Infinium 450k array, and integration of the methylation data was performed. To prepare a network of genes displaying enriched pathways, together with the list of genes exhibiting promoter hypermethylation or hypomethylation with inversely correlated expression, we performed an integrome analysis. We identified 23 Integrome network enriched genes with relevance to tumor progression and associated with the processes involved in metastasis such as cell adhesion, integrin signaling, cytoskeleton, and extracellular matrix organizations. These included four genes (PTK2, RND1, RND3, and UBL3) with promoter hypermethylation and downregulation, and 19 genes (SEMG2, CD97, CTNND2, CADM3, OMD, NEFM, FBN2, CTNNB1, DLX6, UGT2B4, CCDC80, PZP, SERPINA4, TNFSF13B, NPC1, COL1A1, TAC3, BMP8A, and IL22RA2) with promoter hypomethylation and upregulation. A Methylation Efficiency Index was further calculated for these genes; the top five gene with the highest index were COL1A1, TAC3, SERPINA4, TNFSF13B, and IL22RA2. In conclusion, we recommend that the circulatory proteins IL22RA2, TNFSF13B, SERPINA4, and TAC3 in serum of patients and disease-free healthy controls can be examined in the future as putative noninvasive biomarkers.

  8. Estimation of Coast-Wide Population Trends of Marbled Murrelets in Canada Using a Bayesian Hierarchical Model.

    Science.gov (United States)

    Bertram, Douglas F; Drever, Mark C; McAllister, Murdoch K; Schroeder, Bernard K; Lindsay, David J; Faust, Deborah A

    2015-01-01

    Species at risk with secretive breeding behaviours, low densities, and wide geographic range pose a significant challenge to conservation actions because population trends are difficult to detect. Such is the case with the Marbled Murrelet (Brachyramphus marmoratus), a seabird listed as 'Threatened' by the Species at Risk Act in Canada largely due to the loss of its old growth forest nesting habitat. We report the first estimates of population trend of Marbled Murrelets in Canada derived from a monitoring program that uses marine radar to detect birds as they enter forest watersheds during 923 dawn surveys at 58 radar monitoring stations within the six Marbled Murrelet Conservation Regions on coastal British Columbia, Canada, 1996-2013. Temporal trends in radar counts were analyzed with a hierarchical Bayesian multivariate modeling approach that controlled for variation in tilt of the radar unit and day of year, included year-specific deviations from the overall trend ('year effects'), and allowed for trends to be estimated at three spatial scales. A negative overall trend of -1.6%/yr (95% credibility interval: -3.2%, 0.01%) indicated moderate evidence for a coast-wide decline, although trends varied strongly among the six conservation regions. Negative annual trends were detected in East Vancouver Island (-9%/yr) and South Mainland Coast (-3%/yr) Conservation Regions. Over a quarter of the year effects were significantly different from zero, and the estimated standard deviation in common-shared year effects between sites within each region was about 50% per year. This large common-shared interannual variation in counts may have been caused by regional movements of birds related to changes in marine conditions that affect the availability of prey.

  9. Process Evaluation and Costing of a Multifaceted Population-Wide Intervention to Reduce Salt Consumption in Fiji.

    Science.gov (United States)

    Webster, Jacqui; Pillay, Arti; Suku, Arleen; Gohil, Paayal; Santos, Joseph Alvin; Schultz, Jimaima; Wate, Jillian; Trieu, Kathy; Hope, Silvia; Snowdon, Wendy; Moodie, Marj; Jan, Stephen; Bell, Colin

    2018-01-30

    This paper reports the process evaluation and costing of a national salt reduction intervention in Fiji. The population-wide intervention included engaging food industry to reduce salt in foods, strategic health communication and a hospital program. The evaluation showed a 1.4 g/day drop in salt intake from the 11.7 g/day at baseline; however, this was not statistically significant. To better understand intervention implementation, we collated data to assess intervention fidelity, reach, context and costs. Government and management changes affected intervention implementation, meaning fidelity was relatively low. There was no active mechanism for ensuring food companies adhered to the voluntary salt reduction targets. Communication activities had wide reach but most activities were one-off, meaning the overall dose was low and impact on behavior limited. Intervention costs were moderate (FJD $277,410 or $0.31 per person) but the strategy relied on multi-sector action which was not fully operationalised. The cyclone also delayed monitoring and likely impacted the results. However, 73% of people surveyed had heard about the campaign and salt reduction policies have been mainstreamed into government programs. Longer-term monitoring of salt intake is planned through future surveys and lessons from this process evaluation will be used to inform future strategies in the Pacific Islands and globally.

  10. Genome-wide interaction study of smoking behavior and non-small cell lung cancer risk in Caucasian population

    DEFF Research Database (Denmark)

    Li, Yafang; Xiao, Xiangjun; Han, Younghun

    2017-01-01

    Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. Both environmental and genetic risk factors contribute to lung carcinogenesis. We conducted a genome-wide interaction analysis between SNPs and smoking status (never vs ever smokers) in a European-descent population. We...... adopted a two-step analysis strategy in the discovery stage: we first conducted a case-only interaction analysis to assess the relationship between SNPs and smoking behavior using 13,336 NSCLC cases. Candidate SNPs with p-value less than 0.001 were further analyzed using a standard case...... of smoking with rs4751674 was identified in squamous cell lung carcinoma with an odds ratio of 0.58 and p-value of 8.12x10-7. This study is by far the largest genome-wide SNP-smoking interaction analysis reported for lung cancer. The three identified novel SNPs provide potential candidate biomarkers for lung...

  11. A genome-wide association study in large white and landrace pig populations for number piglets born alive.

    Directory of Open Access Journals (Sweden)

    Sarah Bergfelder-Drüing

    Full Text Available The number of piglets born alive (NBA per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3, Austria (1 and Switzerland (1. The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

  12. Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations.

    Science.gov (United States)

    Li, Liming; Wang, Yi; Yang, Shuping; Xia, Mingying; Yang, Yajun; Wang, Jiucun; Lu, Daru; Pan, Xingwei; Ma, Teng; Jiang, Pei; Yu, Ge; Zhao, Ziqin; Ping, Yuan; Zhou, Huaigu; Zhao, Xueying; Sun, Hui; Liu, Bing; Jia, Dongtao; Li, Chengtao; Hu, Rile; Lu, Hongzhou; Liu, Xiaoyang; Chen, Wenqing; Mi, Qin; Xue, Fuzhong; Su, Yongdong; Jin, Li; Li, Shilin

    2017-05-01

    The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3.6 million SNPs, for the application of personal identification. We optimized and validated FID panel using 729 Chinese individuals using a next generation sequencing (NGS) technology. We showed that the SNPs in the panel possess very high heterozygosity as well as low within- and among-continent differentiations, enabling FID panel exhibit discrimination power in both regional and worldwide populations, with the average match probabilities ranging from 4.77×10 -71 to 1.06×10 -64 across 54 world populations. With the advent of biomedical research, the SNPs connecting physical anthropological, physiological, behavioral and phenotypic traits will be eventually added to the forensic panels that will revolutionize criminal investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Lithium in drinking water and the incidence of bipolar disorder: A nation-wide population-based study.

    Science.gov (United States)

    Kessing, Lars V; Gerds, Thomas A; Knudsen, Nikoline N; Jørgensen, Lisbeth F; Kristiansen, Søren M; Voutchkova, Denitza; Ernstsen, Vibeke; Schullehner, Jörg; Hansen, Birgitte; Andersen, Per K; Ersbøll, Annette K

    2017-11-01

    Animal data suggest that subtherapeutic doses, including micro doses, of lithium may influence mood, and lithium levels in drinking water have been found to correlate with the rate of suicide. It has never been investigated whether consumption of lithium may prevent the development of bipolar disorder (primary prophylaxis). In a nation-wide population-based study, we investigated whether long-term exposure to micro levels of lithium in drinking water correlates with the incidence of bipolar disorder in the general population, hypothesizing an inverse association in which higher long-term lithium exposure is associated with lower incidences of bipolar disorder. We included longitudinal individual geographical data on municipality of residence, data from drinking water lithium measurements and time-specific data from all cases with a hospital contact with a diagnosis of mania/bipolar disorder from 1995 to 2013 (N=14 820) and 10 age- and gender-matched controls from the Danish population (N= 140 311). Average drinking water lithium exposure was estimated for all study individuals. The median of the average lithium exposure did not differ between cases with a diagnosis of mania/bipolar disorder (12.7 μg/L; interquartile range [IQR]: 7.9-15.5 μg/L) and controls (12.5 μg/L; IQR: 7.6-15.7 μg/L; P=.2). Further, the incidence rate ratio of mania/bipolar disorder did not decrease with higher long-term lithium exposure, overall, or within age categories (0-40, 41-60 and 61-100 years of age). Higher long-term lithium exposure from drinking water was not associated with a lower incidence of bipolar disorder. The association should be investigated in areas with higher lithium levels than in Denmark. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan.

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    Hsin-Chou Yang

    Full Text Available Young-onset hypertension has a stronger genetic component than late-onset counterpart; thus, the identification of genes related to its susceptibility is a critical issue for the prevention and management of this disease. We carried out a two-stage association scan to map young-onset hypertension susceptibility genes. The first-stage analysis, a genome-wide association study, analyzed 175 matched case-control pairs; the second-stage analysis, a confirmatory association study, verified the results at the first stage based on a total of 1,008 patients and 1,008 controls. Single-locus association tests, multilocus association tests and pair-wise gene-gene interaction tests were performed to identify young-onset hypertension susceptibility genes. After considering stringent adjustments of multiple testing, gene annotation and single-nucleotide polymorphism (SNP quality, four SNPs from two SNP triplets with strong association signals (-log(10(p>7 and 13 SNPs from 8 interactive SNP pairs with strong interactive signals (-log(10(p>8 were carefully re-examined. The confirmatory study verified the association for a SNP quartet 219 kb and 495 kb downstream of LOC344371 (a hypothetical gene and RASGRP3 on chromosome 2p22.3, respectively. The latter has been implicated in the abnormal vascular responsiveness to endothelin-1 and angiotensin II in diabetic-hypertensive rats. Intrinsic synergy involving IMPG1 on chromosome 6q14.2-q15 was also verified. IMPG1 encodes interphotoreceptor matrix proteoglycan 1 which has cation binding capacity. The genes are novel hypertension targets identified in this first genome-wide hypertension association study of the Han Chinese population.

  15. Population status of a cryptic top predator: an island-wide assessment of tigers in Sumatran rainforests.

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    Hariyo T Wibisono

    Full Text Available Large carnivores living in tropical rainforests are under immense pressure from the rapid conversion of their habitat. In response, millions of dollars are spent on conserving these species. However, the cost-effectiveness of such investments is poorly understood and this is largely because the requisite population estimates are difficult to achieve at appropriate spatial scales for these secretive species. Here, we apply a robust detection/non-detection sampling technique to produce the first reliable population metric (occupancy for a critically endangered large carnivore; the Sumatran tiger (Panthera tigris sumatrae. From 2007-2009, seven landscapes were surveyed through 13,511 km of transects in 394 grid cells (17×17 km. Tiger sign was detected in 206 cells, producing a naive estimate of 0.52. However, after controlling for an unequal detection probability (where p = 0.13±0.017; ±S.E., the estimated tiger occupancy was 0.72±0.048. Whilst the Sumatra-wide survey results gives cause for optimism, a significant negative correlation between occupancy and recent deforestation was found. For example, the Northern Riau landscape had an average deforestation rate of 9.8%/yr and by far the lowest occupancy (0.33±0.055. Our results highlight the key tiger areas in need of protection and have led to one area (Leuser-Ulu Masen being upgraded as a 'global priority' for wild tiger conservation. However, Sumatra has one of the highest global deforestation rates and the two largest tiger landscapes identified in this study will become highly fragmented if their respective proposed roads networks are approved. Thus, it is vital that the Indonesian government tackles these threats, e.g. through improved land-use planning, if it is to succeed in meeting its ambitious National Tiger Recovery Plan targets of doubling the number of Sumatran tigers by 2022.

  16. Population status of a cryptic top predator: an island-wide assessment of tigers in Sumatran rainforests.

    Science.gov (United States)

    Wibisono, Hariyo T; Linkie, Matthew; Guillera-Arroita, Gurutzeta; Smith, Joseph A; Sunarto; Pusparini, Wulan; Asriadi; Baroto, Pandu; Brickle, Nick; Dinata, Yoan; Gemita, Elva; Gunaryadi, Donny; Haidir, Iding A; Herwansyah; Karina, Indri; Kiswayadi, Dedy; Kristiantono, Decki; Kurniawan, Harry; Lahoz-Monfort, José J; Leader-Williams, Nigel; Maddox, Tom; Martyr, Deborah J; Maryati; Nugroho, Agung; Parakkasi, Karmila; Priatna, Dolly; Ramadiyanta, Eka; Ramono, Widodo S; Reddy, Goddilla V; Rood, Ente J J; Saputra, Doddy Y; Sarimudi, Ahmad; Salampessy, Adnun; Septayuda, Eka; Suhartono, Tonny; Sumantri, Ade; Susilo; Tanjung, Iswandri; Tarmizi; Yulianto, Koko; Yunus, Mohammad; Zulfahmi

    2011-01-01

    Large carnivores living in tropical rainforests are under immense pressure from the rapid conversion of their habitat. In response, millions of dollars are spent on conserving these species. However, the cost-effectiveness of such investments is poorly understood and this is largely because the requisite population estimates are difficult to achieve at appropriate spatial scales for these secretive species. Here, we apply a robust detection/non-detection sampling technique to produce the first reliable population metric (occupancy) for a critically endangered large carnivore; the Sumatran tiger (Panthera tigris sumatrae). From 2007-2009, seven landscapes were surveyed through 13,511 km of transects in 394 grid cells (17×17 km). Tiger sign was detected in 206 cells, producing a naive estimate of 0.52. However, after controlling for an unequal detection probability (where p = 0.13±0.017; ±S.E.), the estimated tiger occupancy was 0.72±0.048. Whilst the Sumatra-wide survey results gives cause for optimism, a significant negative correlation between occupancy and recent deforestation was found. For example, the Northern Riau landscape had an average deforestation rate of 9.8%/yr and by far the lowest occupancy (0.33±0.055). Our results highlight the key tiger areas in need of protection and have led to one area (Leuser-Ulu Masen) being upgraded as a 'global priority' for wild tiger conservation. However, Sumatra has one of the highest global deforestation rates and the two largest tiger landscapes identified in this study will become highly fragmented if their respective proposed roads networks are approved. Thus, it is vital that the Indonesian government tackles these threats, e.g. through improved land-use planning, if it is to succeed in meeting its ambitious National Tiger Recovery Plan targets of doubling the number of Sumatran tigers by 2022.

  17. Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations.

    Directory of Open Access Journals (Sweden)

    Sophie I Candille

    Full Text Available Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS. Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.

  18. Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations

    Science.gov (United States)

    Candille, Sophie I.; Absher, Devin M.; Beleza, Sandra; Bauchet, Marc; McEvoy, Brian; Garrison, Nanibaa’ A.; Li, Jun Z.; Myers, Richard M.; Barsh, Gregory S.; Tang, Hua; Shriver, Mark D.

    2012-01-01

    Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world. PMID:23118974

  19. A Cross-Sectional Survey of Population-Wide Wait Times for Patients Seeking Medical vs. Cosmetic Dermatologic Care.

    Science.gov (United States)

    Yadav, Geeta; Goldberg, Hanna R; Barense, Morgan D; Bell, Chaim M

    2016-01-01

    Though previous work has examined some aspects of the dermatology workforce shortage and access to dermatologic care, little research has addressed the effect of rising interest in cosmetic procedures on access to medical dermatologic care. Our objective was to determine the wait times for Urgent and Non-Urgent medical dermatologic care and Cosmetic dermatology services at a population level and to examine whether wait times for medical care are affected by offering cosmetic services. A population-wide survey of dermatology practices using simulated calls asking for the earliest appointment for a Non-Urgent, Urgent and Cosmetic service. Response rates were greater than 89% for all types of care. Wait times across all types of care were significantly different from each other (all P Cosmetic care was associated with the shortest wait times (3.0 weeks; Interquartile Range (IQR) = 0.4-3.4), followed by Urgent care (9.0 weeks; IQR = 2.1-12.9), then Non-Urgent Care (12.7 weeks; IQR = 4.4-16.4). Wait times for practices offering only Urgent care were not different from practices offering both Urgent and Cosmetic care (10.3 vs. 7.0 weeks). Longer wait times and greater variation for Urgent and Non-Urgent dermatologic care and shorter wait times and less variation for Cosmetic care. Wait times were significantly longer in regions with lower dermatologist density. Provision of Cosmetic services did not increase wait times for Urgent care. These findings suggest an overall dermatology workforce shortage and a need for a more streamlined referral system for dermatologic care.

  20. Identification of novel susceptibility Loci for kawasaki disease in a Han chinese population by a genome-wide association study.

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    Fuu-Jen Tsai

    Full Text Available Kawasaki disease (KD is an acute systemic vasculitis syndrome that primarily affects infants and young children. Its etiology is unknown; however, epidemiological findings suggest that genetic predisposition underlies disease susceptibility. Taiwan has the third-highest incidence of KD in the world, after Japan and Korea. To investigate novel mechanisms that might predispose individuals to KD, we conducted a genome-wide association study (GWAS in 250 KD patients and 446 controls in a Han Chinese population residing in Taiwan, and further validated our findings in an independent Han Chinese cohort of 208 cases and 366 controls. The most strongly associated single-nucleotide polymorphisms (SNPs detected in the joint analysis corresponded to three novel loci. Among these KD-associated SNPs three were close to the COPB2 (coatomer protein complex beta-2 subunit gene: rs1873668 (p = 9.52×10⁻⁵, rs4243399 (p = 9.93×10⁻⁵, and rs16849083 (p = 9.93×10⁻⁵. We also identified a SNP in the intronic region of the ERAP1 (endoplasmic reticulum amino peptidase 1 gene (rs149481, p(best = 4.61×10⁻⁵. Six SNPs (rs17113284, rs8005468, rs10129255, rs2007467, rs10150241, and rs12590667 clustered in an area containing immunoglobulin heavy chain variable regions genes, with p(best-values between 2.08×10⁻⁵ and 8.93×10⁻⁶, were also identified. This is the first KD GWAS performed in a Han Chinese population. The novel KD candidates we identified have been implicated in T cell receptor signaling, regulation of proinflammatory cytokines, as well as antibody-mediated immune responses. These findings may lead to a better understanding of the underlying molecular pathogenesis of KD.

  1. Phenotypes, genome wide markers and structured genetic populations; a means to understand economically important traits in beta vulgaris and to inform the process of germplasm enhancement

    Science.gov (United States)

    Although hybrid seed systems in beet have been widely adopted due to profitability and productivity, the population remains the operational unit of beet improvement and thus characterizing populations in terms of markers and phenotypes is critical for novel trait discovery and eventual deployment of...

  2. Procrastination, Distress and Life Satisfaction across the Age Range - A German Representative Community Study.

    Directory of Open Access Journals (Sweden)

    Manfred E Beutel

    Full Text Available Addressing the lack of population-based data the purpose of this representative study was to assess procrastination and its associations with distress and life satisfaction across the life span. A representative German community sample (1,350 women; 1,177 men between the ages of 14 and 95 years was examined by the short form of the General Procrastination Scale (GPS-K; 1 and standardized scales of perceived stress, depression, anxiety, fatigue and life satisfaction. As hypothesized, procrastination was highest in the youngest cohort (14-29 years. Only in the youngest and most procrastinating cohort (aged 14 to 29 years, men procrastinated more than women. As we had further hypothesized, procrastination was consistently associated with higher stress, more depression, anxiety, fatigue and reduced satisfaction across life domains, especially regarding work and income. Associations were also found with lack of a partnership and unemployment. Findings are discussed with regard to potential developmental and cohort effects. While procrastination appears to be a pervasive indicator for maladjustment, longitudinal analyses in high-risk samples (e.g. late adolescence, unemployment are needed to identify means and mechanisms of procrastinating.

  3. Procrastination, Distress and Life Satisfaction across the Age Range – A German Representative Community Study

    Science.gov (United States)

    2016-01-01

    Addressing the lack of population-based data the purpose of this representative study was to assess procrastination and its associations with distress and life satisfaction across the life span. A representative German community sample (1,350 women; 1,177 men) between the ages of 14 and 95 years was examined by the short form of the General Procrastination Scale (GPS-K; 1) and standardized scales of perceived stress, depression, anxiety, fatigue and life satisfaction. As hypothesized, procrastination was highest in the youngest cohort (14–29 years). Only in the youngest and most procrastinating cohort (aged 14 to 29 years), men procrastinated more than women. As we had further hypothesized, procrastination was consistently associated with higher stress, more depression, anxiety, fatigue and reduced satisfaction across life domains, especially regarding work and income. Associations were also found with lack of a partnership and unemployment. Findings are discussed with regard to potential developmental and cohort effects. While procrastination appears to be a pervasive indicator for maladjustment, longitudinal analyses in high-risk samples (e.g. late adolescence, unemployment) are needed to identify means and mechanisms of procrastinating. PMID:26871572

  4. Procrastination, Distress and Life Satisfaction across the Age Range - A German Representative Community Study.

    Science.gov (United States)

    Beutel, Manfred E; Klein, Eva M; Aufenanger, Stefan; Brähler, Elmar; Dreier, Michael; Müller, Kai W; Quiring, Oliver; Reinecke, Leonard; Schmutzer, Gabriele; Stark, Birgit; Wölfling, Klaus

    2016-01-01

    Addressing the lack of population-based data the purpose of this representative study was to assess procrastination and its associations with distress and life satisfaction across the life span. A representative German community sample (1,350 women; 1,177 men) between the ages of 14 and 95 years was examined by the short form of the General Procrastination Scale (GPS-K; 1) and standardized scales of perceived stress, depression, anxiety, fatigue and life satisfaction. As hypothesized, procrastination was highest in the youngest cohort (14-29 years). Only in the youngest and most procrastinating cohort (aged 14 to 29 years), men procrastinated more than women. As we had further hypothesized, procrastination was consistently associated with higher stress, more depression, anxiety, fatigue and reduced satisfaction across life domains, especially regarding work and income. Associations were also found with lack of a partnership and unemployment. Findings are discussed with regard to potential developmental and cohort effects. While procrastination appears to be a pervasive indicator for maladjustment, longitudinal analyses in high-risk samples (e.g. late adolescence, unemployment) are needed to identify means and mechanisms of procrastinating.

  5. Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans.

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    Giorgio Pistis

    Full Text Available The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5-10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approaches alternative to large meta analysis. GWAS (Genome Wide Association Study for red blood cell traits in a founder population cohort from Northern Italy identified a new locus for mean corpuscular hemoglobin concentration (MCHC in the TAF3 gene. The association was replicated in two cohorts (rs1887582, P = 4.25E-09. TAF3 encodes a transcription cofactor that participates in core promoter recognition complex, and is involved in zebrafish and mouse erythropoiesis. We show here that TAF3 is required for transcription of the SPTA1 gene, encoding alpha spectrin, one of the proteins that link the plasma membrane to the actin cytoskeleton. Mutations in SPTA1 are responsible for hereditary spherocytosis, a monogenic disorder of MCHC, as well as for the normal MCHC level. Based on our results, we propose that TAF3 is required for normal erythropoiesis in human and that it might have a role in controlling the ratio between hemoglobin (Hb and cell volume and in the dynamics of RBC maturation in healthy individuals. Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane.

  6. Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC.

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    Eui-Soo Kim

    Full Text Available Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI nematode fecal egg count (FEC data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log10 p=4.3 with Box-Cox transformed mean FEC (BC-MFEC. DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection.

  7. Pulsar population synthesis using palfa detections and pulsar search collaboratory discoveries including a wide DNS system and a nearby MSP

    Science.gov (United States)

    Swiggum, Joseph Karl

    Using the ensemble of detections from pulsar surveys, we can learn about the sizes and characteristics of underlying populations. In this thesis, I analyze results from the Pulsar Arecibo L-band Feed Array (PALFA) precursor and Green Bank Telescope 350 MHz Drift Scan surveys; I examine survey sensitivity to see how detections can inform pulsar population models, I look at new ways of including young scientists -- high school students -- in the discovery process and I present timing solutions for students' discoveries (including a nearby millisecond pulsar and a pulsar in a wide-orbit double neutron star system). The PALFA survey is on-going and uses the ALFA 7-beam receiver at 1400 MHz to search both inner and outer Galactic sectors visible from Arecibo (32° ?£? 77° and 168° ?£? 214°) close to the Galactic plane (|b| ? 5°) for pulsars. The PALFA precursor survey observed a subset of this region, (|b| ? 1°) and detected 45 pulsars, including one known millisecond pulsar (MSP) and 11 previously unknown, long-period (normal) pulsars. I assess the sensitivity of the PALFA precursor survey and use the number of normal pulsar and MSP detections to infer the size of each underlying Galactic population. Based on 44 normal pulsar detections and one MSP, we constrain each population size to 107,000+36,000-25,000 and 15,000 +85,000-6,000 respectively with 95% confidence. Based on these constraints, we predict yields for the full PALFA survey and find a deficiency in normal pulsar detections, possibly due to radio frequency interference and/or scintillation, neither of which are currently accounted for in population simulations. The GBT 350 MHz Drift Scan survey collected data in the summer of 2007 while the GBT was stationary, undergoing track replacement. Results discussed here come from ~20% of the survey data, which were processed and donated to the Pulsar Search Collaboratory (PSC). The PSC is a joint outreach program between WVU and NRAO, involving high school

  8. Genetic diversity and structuring across the range of a widely distributed ladybird: focus on rear?edge populations phenotypically divergent

    OpenAIRE

    Lecompte, ?milie; Bouanani, Mohand?Ameziane; Magro, Alexandra; Crouau?Roy, Brigitte

    2016-01-01

    Abstract Population genetics and phenotypic structures are often predicted to vary along the geographic range of a species. This phenomenon would be accentuated for species with large range areas, with discontinuities and marginal populations. We herein compare the genetic patterns of central populations of Coccinella septempunctata L. with those of two phenotypically differentiated populations considered as rear?edge populations and subspecies based on phenotype (Algeria and Japan). Accordin...

  9. Anthropometric indices for non-pregnant women of childbearing age differ widely among four low-middle income populations.

    Science.gov (United States)

    Hambidge, K Michael; Krebs, Nancy F; Garcés, Ana; Westcott, Jamie E; Figueroa, Lester; Goudar, Shivaprasad S; Dhaded, Sangappa; Pasha, Omrana; Aziz Ali, Sumera; Tshefu, Antoinette; Lokangaka, Adrien; Thorsten, Vanessa R; Das, Abhik; Stolka, Kristen; McClure, Elizabeth M; Lander, Rebecca L; Bose, Carl L; Derman, Richard J; Goldenberg, Robert L; Bauserman, Melissa

    2017-07-24

    Maternal stature and body mass indices (BMI) of non-pregnant women (NPW) of child bearing age are relevant to maternal and offspring health. The objective was to compare anthropometric indices of NPW in four rural communities in low- to low-middle income countries (LMIC). Anthropometry and maternal characteristics/household wealth questionnaires were obtained for NPW enrolled in the Women First Preconception Maternal Nutrition Trial. Body mass index (BMI, kg/m(2)) was calculated. Z-scores were determined using WHO reference data. A total of 7268 NPW participated in Equateur, DRC (n = 1741); Chimaltenango, Guatemala (n = 1695); North Karnataka, India (n = 1823); and Thatta, Sindh, Pakistan (n = 2009). Mean age was 23 y and mean parity 1.5. Median (P25-P75) height (cm) ranged from 145.5 (142.2-148.9) in Guatemala to 156.0 (152.0-160.0) in DRC. Median weight (kg) ranged from 44.7 (39.9-50.3) in India to 52.7 (46.9-59.8) in Guatemala. Median BMI ranged from 19.4 (17.6-21.9) in India to 24.9 (22.3-28.0) in Guatemala. Percent stunted (<-2SD height for age z-score) ranged from 13.9% in DRC to 80.5% in Guatemala; % underweight (BMI <18.5) ranged from 1.2% in Guatemala to 37.1% in India; % overweight/obese (OW, BMI ≥25.0) ranged from 5.7% in DRC to 49.3% in Guatemala. For all sites, indicators for higher SES and higher age were associated with BMI. Lower SES women were underweight more frequently and higher SES women were OW more frequently at all sites. Younger women tended to be underweight, while older women tended to be OW. Anthropometric data for NPW varied widely among low-income rural populations in four countries located on three different continents. Global comparisons of anthropometric measurements across sites using standard reference data serve to highlight major differences among populations of low-income rural NPW and assist in evaluating the rationale for and the design of optimal intervention trials. ClinicalTrials.gov # NCT01883193 (18 June 2013

  10. Red blood cell alloimmunization in pregnancy during the years 1996-2015 in Iceland: a nation-wide population study.

    Science.gov (United States)

    Bollason, Gunnar; Hjartardottir, Hulda; Jonsson, Thorbjorn; Gudmundsson, Sveinn; Kjartansson, Sveinn; Halldorsdottir, Anna Margret

    2017-11-01

    Red blood cell (RBC) alloimmunization during pregnancy is still a major problem. Historically, anti-D antibodies are most likely to cause severe hemolysis, but other antibodies are also important. In Iceland, postnatal RhIg prophylaxis was implemented in 1969, universal RBC antibody screening was implemented in 1978, but antenatal RhIg prophylaxis is not yet routine. This nation-wide population study gathered data on alloimmunized pregnancies in Iceland between 1996 and 2015. Blood bank alloimmunization data were linked to Icelandic Medical Birth Registry data. RBC antibodies were classified as either clinically significant or clinically nonsignificant. In total, 912 positive antibody screens from 87,437 births were identified (1.04% prevalence). The most frequent antibodies were anti-M (19.4%), anti-E (19.0%), and anti-D (12.5%). Anti-D prevalence among D-negative mothers was 1.1%. Icelandic Medical Birth Registry data were available for 881 (96.6%) pregnancies. In the clinically significant group (n = 474), anti-E (27%) and anti-D (20%) were most common, whereas anti-M was most frequent (53%) in the clinically nonsignificant group (n = 407). Mothers in the clinically significant group were older, more often multigravidae, had more abortions and stillbirths, and had shorter gestational length. Newborns in the clinically significant group were less healthy, had lower weight and Apgar scores, and required more treatment. Among specificities in the clinically significant group, anti-D antibodies were most strongly associated with severe hemolysis. In this study, the prevalence of alloimmunization was similar to that in previous reports. Of all clinically significant antibodies, anti-D was most strongly associated with severe hemolysis, requiring phototherapy or exchange transfusions. Our data emphasize the importance of implementing an antenatal prophylactic RhIg program in Iceland in the near future. © 2017 AABB.

  11. Genome-Wide Association Study of Orthostatic Hypotension and Supine-Standing Blood Pressure Changes in Two Korean Populations

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    Kyung-Won Hong

    2013-09-01

    Full Text Available Orthostatic hypotension (OH is defined by a 20-mm Hg difference of systolic blood pressure (dtSBP and/or a 10-mm Hg difference of diastolic blood pressure (dtDBP between supine and standing, and OH is associated with a failure of the cardiovascular reflex to maintain blood pressure on standing from a supine position. To understand the underlying genetic factors for OH traits (OH, dtSBP, and dtDBP, genome-wide association studies (GWASs using 333,651 single nucleotide polymorphisms (SNPs were conducted separately for two population-based cohorts, Ansung (n = 3,173 and Ansan (n = 3,255. We identified 8 SNPs (5 SNPs for dtSBP and 3 SNPs for dtDBP that were repeatedly associated in both the Ansung and Ansan cohorts and had p-values of <1 × 10-5 in the meta-analysis. Unfortunately, the SNPs of the OH case control GWAS did not pass our p-value criteria. Four of 8 SNPs were located in the intergenic region of chromosome 2, and the nearest gene (CTNNA2 was located at 1 Mb of distance. CTNNA2 is a linker between cadherin adhesion receptors and the actin cytoskeleton and is essential for stabilizing dendritic spines in rodent hippocampal neurons. Although there is no report about the function in blood pressure regulation, hippocampal neurons interact primarily with the autonomic nervous system and might be related to OH. The remaining SNPs, rs7098785 of dtSBP trait and rs6892553, rs16887217, and rs4959677 of dtDBP trait were located in the PIK3AP1 intron, ACTBL2-3' flanking, STAR intron, and intergenic region, respectively, but there was no clear functional link to blood pressure regulation.

  12. Local genealogies in a linear mixed model for genome-wide association mapping in complex pedigreed populations.

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    Goutam Sahana

    Full Text Available INTRODUCTION: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS is unified mixed model analysis (MMA. This approach is very flexible, can be applied to both family-based and population-based samples, and can be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called 'GENMIX (genealogy based mixed model' which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. SUBJECTS AND METHODS: We validated GENMIX using genotyping data of Danish Jersey cattle and simulated phenotype and compared to the MMA. We simulated scenarios for three levels of heritability (0.21, 0.34, and 0.64, seven levels of MAF (0.05, 0.10, 0.15, 0.20, 0.25, 0.35, and 0.45 and five levels of QTL effect (0.1, 0.2, 0.5, 0.7 and 1.0 in phenotypic standard deviation unit. Each of these 105 possible combinations (3 h(2 x 7 MAF x 5 effects of scenarios was replicated 25 times. RESULTS: GENMIX provides a better ranking of markers close to the causative locus' location. GENMIX outperformed MMA when the QTL effect was small and the MAF at the QTL was low. In scenarios where MAF was high or the QTL affecting the trait had a large effect both GENMIX and MMA performed similarly. CONCLUSION: In discovery studies, where high-ranking markers are identified and later examined in validation studies, we therefore expect GENMIX to enrich candidates brought to follow-up studies with true positives over false positives more than the MMA would.

  13. NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation.

    Science.gov (United States)

    Neuditschko, Markus; Khatkar, Mehar S; Raadsma, Herman W

    2012-01-01

    High-throughput sequencing and single nucleotide polymorphism (SNP) genotyping can be used to infer complex population structures. Fine-scale population structure analysis tracing individual ancestry remains one of the major challenges. Based on network theory and recent advances in SNP chip technology, we investigated an unsupervised network clustering method called Super Paramagnetic Clustering (Spc). When applied to whole-genome marker data it identifies the natural divisions of groups of individuals into population clusters without use of prior ancestry information. Furthermore, we optimised an analysis pipeline called NetView, a high-definition network visualization, starting with computation of genetic distance, followed clustering using Spc and finally visualization of clusters with Cytoscape. We compared NetView against commonly used methodologies including Principal Component Analyses (PCA) and a model-based algorithm, Admixture, on whole-genome-wide SNP data derived from three previously described data sets: simulated (2.5 million SNPs, 5 populations), human (1.4 million SNPs, 11 populations) and cattle (32,653 SNPs, 19 populations). We demonstrate that individuals can be effectively allocated to their correct population whilst simultaneously revealing fine-scale structure within the populations. Analyzing the human HapMap populations, we identified unexpected genetic relatedness among individuals, and population stratification within the Indian, African and Mexican samples. In the cattle data set, we correctly assigned all individuals to their respective breeds and detected fine-scale population sub-structures reflecting different sample origins and phenotypes. The NetView pipeline is computationally extremely efficient and can be easily applied on large-scale genome-wide data sets to assign individuals to particular populations and to reproduce fine-scale population structures without prior knowledge of individual ancestry. NetView can be used on any

  14. Genome-wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4

    OpenAIRE

    Ma, R. C. W.; Hu, C.; Tam, C. H.; Zhang, R.; Kwan, P.; Leung, T. F.; Thomas, G. N.; Go, M. J.; Hara, K.; Sim, X.; Ho, J. S. K.; Wang, C.; Li, H.; Lu, L.; Wang, Y.

    2013-01-01

    Aims/hypothesis Most genetic variants identified for type 2 diabetes have been discovered in European populations. We performed genome-wide association studies (GWAS) in a Chinese population with the aim of identifying novel variants for type 2 diabetes in Asians. Methods We performed a meta-analysis of three GWAS comprising 684 patients with type 2 diabetes and 955 controls of Southern Han Chinese descent. We followed up the top signals in two independent Southern Han Chinese cohorts (totall...

  15. Genetic variants associated with arsenic metabolism within human arsenic (+3 oxidation state) methyltransferase show wide variation across multiple populations.

    Science.gov (United States)

    Fujihara, Junko; Yasuda, Toshihiro; Kato, Hideaki; Yuasa, Isao; Panduro, Arturo; Kunito, Takashi; Takeshita, Haruo

    2011-02-01

    Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene in Mexican and German populations. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was assessed on healthy individuals: 38 Mestizo, 69 Nahuas, 50 Huicholes, and 32 Germans. All 18 SNPs were polymorphic in the German and Mexican populations. Of the three Mexican populations, a minor allele frequency was the highest in the Mestizo, followed by the Nahuas and Huicholes. In the German and three Mexican groups, haplotype #1(TATAGAAGTCTTCATGAC) was the most predominant. Seven haplotypes were newly found in the German and three Mexican populations. The D' values between SNP pairs were high in the German and Nahua populations; they had a similar pattern. The pattern of the Mestizo was more similar to the African than to the other Mexican populations. Huicholes had a moderate pattern of the African and German/Nahua populations. The network had three clusters. One originated in the African population and another may have originated in an Asian (Chinese and/or Japanese) population. The third one may have originated among Caucasians. This study is the first to demonstrate the existence of genetic heterogeneity in the distribution of 18 SNPs in AS3MT of German and Mexican populations.

  16. A New Measure for Assessing Executive Function across a Wide Age Range: Children and Adults Find "Happy-Sad" More Difficult than "Day-Night"

    Science.gov (United States)

    Lagattuta, Kristin Hansen; Sayfan, Liat; Monsour, Michael

    2011-01-01

    Two experiments examined 4- to 11-year-olds' and adults' performance (N = 350) on two variants of a Stroop-like card task: the "day-night task" (say "day" when shown a moon and "night" when shown a sun) and a new "happy-sad task" (say "happy" for a sad face and "sad" for a happy face). Experiment 1 featured colored cartoon drawings. In Experiment…

  17. A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

    Science.gov (United States)

    Khrunin, Andrey V.; Khokhrin, Denis V.; Filippova, Irina N.; Esko, Tõnu; Nelis, Mari; Bebyakova, Natalia A.; Bolotova, Natalia L.; Klovins, Janis; Nikitina-Zake, Liene; Rehnström, Karola; Ripatti, Samuli; Schreiber, Stefan; Franke, Andre; Macek, Milan; Krulišová, Veronika; Lubinski, Jan; Metspalu, Andres; Limborska, Svetlana A.

    2013-01-01

    Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations. PMID:23505534

  18. Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise.

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    Ljerka Lah

    Full Text Available The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena, in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs, derived from double digest restriction-site associated DNA sequencing (ddRAD-seq, as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA, and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

  19. EU protected area network did not prevent a country wide population decline in a threatened grassland bird

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    João P. Silva

    2018-01-01

    Full Text Available Background Few studies have assessed the effectiveness of the Protected Area networks on the conservation status of target species. Here, we assess the effectiveness of the Portuguese Natura 2000 (the European Union network of protected areas in maintaining a species included in the Annex I of the Bird Directive, namely the population of a priority farmland bird, the little bustard Tetrax tetrax. Methods We measured the effectiveness of the Natura 2000 by comparing population trends across time (2003–2006 and 2016 in 51 areas, 21 of which within 12 Special Protection Areas (SPA that were mostly designated for farmland bird conservation and another 30 areas without EU protection. Results Overall, the national population is estimated to have declined 49% over the last 10–14 years. This loss was found to be proportionally larger outside SPA (64% decline compared to losses within SPA (25% decline. However, the absolute male density decline was significantly larger within SPA . Discussion In spite of holding higher population densities and having prevented habitat loss, we conclude that Natura 2000 was not effective in buffering against the overall bustard population decline. Results show that the mere designation of SPA in farmland is not enough to secure species populations and has to be combined with agricultural policies and investment to maintain not only habitat availability but also habitat quality.

  20. Projecting range-wide sun bear population trends using tree cover and camera-trap bycatch data.

    Science.gov (United States)

    Scotson, Lorraine; Fredriksson, Gabriella; Ngoprasert, Dusit; Wong, Wai-Ming; Fieberg, John

    2017-01-01

    Monitoring population trends of threatened species requires standardized techniques that can be applied over broad areas and repeated through time. Sun bears Helarctos malayanus are a forest dependent tropical bear found throughout most of Southeast Asia. Previous estimates of global population trends have relied on expert opinion and cannot be systematically replicated. We combined data from 1,463 camera traps within 31 field sites across sun bear range to model the relationship between photo catch rates of sun bears and tree cover. Sun bears were detected in all levels of tree cover above 20%, and the probability of presence was positively associated with the amount of tree cover within a 6-km2 buffer of the camera traps. We used the relationship between catch rates and tree cover across space to infer temporal trends in sun bear abundance in response to tree cover loss at country and global-scales. Our model-based projections based on this "space for time" substitution suggested that sun bear population declines associated with tree cover loss between 2000-2014 in mainland southeast Asia were ~9%, with declines highest in Cambodia and lowest in Myanmar. During the same period, sun bear populations in insular southeast Asia (Malaysia, Indonesia and Brunei) were projected to have declined at a much higher rate (22%). Cast forward over 30-years, from the year 2000, by assuming a constant rate of change in tree cover, we projected population declines in the insular region that surpassed 50%, meeting the IUCN criteria for endangered if sun bears were listed on the population level. Although this approach requires several assumptions, most notably that trends in abundance across space can be used to infer temporal trends, population projections using remotely sensed tree cover data may serve as a useful alternative (or supplement) to expert opinion. The advantages of this approach is that it is objective, data-driven, repeatable, and it requires that all assumptions

  1. Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands

    Science.gov (United States)

    Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

    2016-01-01

    The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

  2. Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands.

    Science.gov (United States)

    Biljecki, Filip; Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

    2016-01-01

    The remote estimation of a region's population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach.

  3. Spatial genetic heterogeneity in populations of a newly invasive whitefly in china revealed by a nation-wide field survey.

    Science.gov (United States)

    Chu, Dong; Pan, Hui-Peng; Li, Xian-Chun; Guo, Dong; Tao, Yun-Li; Liu, Bai-Ming; Zhang, You-Jun

    2013-01-01

    Even though introductions of exotic species provide ready-made experiments of rapid evolution, few studies have examined the genetic structure of an exotic species shortly after its initial introduction and subsequent spread. To determine the genetic structure of its populations during the initial introduction, we investigated the invasive sweet potato whitefly (Bemisia tabaci Q, commonly known as B. tabaci biotype Q) in China, which was introduced in approximately 2003. A total of 619 B. tabaci Q individuals in 20 provinces throughout China were collected and analyzed using five microsatellite loci. The introduced populations of B. tabaci Q in China represent eight genetic clusters with different geographic distributions. The populations in Yunnan Province, where B. tabaci Q was first detected, are genetically different from the other populations in China. The introduced populations of B. tabaci Q in China have high spatial genetic heterogeneity. Additional research is required to determine whether the heterogeneity results from multiple introductions, rapid evolution following one or few introductions, or some combination of multiple introductions and rapid evolution. The heterogeneity, however, is inconsistent with a single introduction at Yunnan Province, where B. tabaci Q was first detected, followed by spread.

  4. Spatial genetic heterogeneity in populations of a newly invasive whitefly in china revealed by a nation-wide field survey.

    Directory of Open Access Journals (Sweden)

    Dong Chu

    Full Text Available BACKGROUND: Even though introductions of exotic species provide ready-made experiments of rapid evolution, few studies have examined the genetic structure of an exotic species shortly after its initial introduction and subsequent spread. To determine the genetic structure of its populations during the initial introduction, we investigated the invasive sweet potato whitefly (Bemisia tabaci Q, commonly known as B. tabaci biotype Q in China, which was introduced in approximately 2003. A total of 619 B. tabaci Q individuals in 20 provinces throughout China were collected and analyzed using five microsatellite loci. RESULTS: The introduced populations of B. tabaci Q in China represent eight genetic clusters with different geographic distributions. The populations in Yunnan Province, where B. tabaci Q was first detected, are genetically different from the other populations in China. CONCLUSION: The introduced populations of B. tabaci Q in China have high spatial genetic heterogeneity. Additional research is required to determine whether the heterogeneity results from multiple introductions, rapid evolution following one or few introductions, or some combination of multiple introductions and rapid evolution. The heterogeneity, however, is inconsistent with a single introduction at Yunnan Province, where B. tabaci Q was first detected, followed by spread.

  5. Impact of specific training and competition on myocardial structure and function in different age ranges of male handball players.

    Science.gov (United States)

    Agrebi, Brahim; Tkatchuk, Vladimir; Hlila, Nawel; Mouelhi, Emna; Belhani, Ali

    2015-01-01

    Handball activity involves cardiac changes and demands a mixture of both eccentric and concentric remodeling within the heart. This study seeks to explore heart performance and cardiac remodeling likely to define cardiac parameters which influence specific performance in male handball players across different age ranges. Forty three players, with a regular training and competitive background in handball separated into three groups aged on average 11.78 ± 0.41 for youth players aka "schools", "elite juniors" 15.99 ± 0.81 and "elite adults" 24.46 ± 2.63 years, underwent echocardiography and ECG examinations. Incremental ergocycle and specific field (SFT) tests have also been conducted. With age and regular training and competition, myocardial remodeling in different age ranges exhibit significant differences in dilatation's parameters between "schools" and "juniors" players, such as the end-diastolic diameter (LVEDD) and the end-systolic diameter of the left ventricle (LVESD), the root of aorta (Ao) and left atrial (LA), while significant increase is observed between "juniors" and "adults" players in the interventricular septum (IVS), the posterior wall thicknesses (PWT) and LV mass index. ECG changes are also noted but NS differences were observed in studied parameters. For incremental maximal test, players demonstrate a significant increase in duration and total work between "schools" and "juniors" and, in total work only, between "juniors" and "seniors". The SFT shows improvement in performance which ranged between 26.17 ± 1.83 sec to 31.23 ± 2.34 sec respectively from "seniors" to "schools". The cross-sectional approach used to compare groups with prior hypothesis that there would be differences in exercise performance and cardiac parameters depending on duration of prior handball practice, leads to point out the early cardiac remodeling within the heart as adaptive change. Prevalence of cardiac chamber dilation with less hypertrophy remodeling was found

  6. Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data

    DEFF Research Database (Denmark)

    Pinto, M Alice; Henriques, Dora; Chávez-Galarza, Julio

    2014-01-01

    The recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies...... to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide...... polymorphisms (SNPs), to assess genetic diversity and introgression levels in several protected populations of A. m. mellifera, which were then compared with samples collected from unprotected populations. MtDNA analysis of the protected populations revealed a single colony bearing a foreign haplotype, whereas...

  7. Prioritizing management actions for invasive populations using cost, efficacy, demography and expert opinion for 14 plant species world-wide.

    Science.gov (United States)

    Kerr, Natalie Z; Baxter, Peter W J; Salguero-Gómez, Roberto; Wardle, Glenda M; Buckley, Yvonne M

    2016-04-01

    Management of invasive populations is typically investigated case-by-case. Comparative approaches have been applied to single aspects of management, such as demography, with cost or efficacy rarely incorporated.We present an analysis of the ranks of management actions for 14 species in five countries that extends beyond the use of demography alone to include multiple metrics for ranking management actions, which integrate cost, efficacy and demography (cost-effectiveness) and managers' expert opinion of ranks. We use content analysis of manager surveys to assess the multiple criteria managers use to rank management strategies.Analysis of the matrix models for managed populations showed that all management actions led to reductions in population growth rate (λ), with a median 48% reduction in λ across all management units; however, only 66% of the actions led to declining populations (λ demography as important. 80% of managers identified off-target effects of management as important, which was not captured using any of the other metrics. Synthesis and applications. A multidimensional view of the benefits and costs of management options provides a range of single and integrated metrics. These rankings, and the relationships between them, can be used to assess management actions for invasive plants. The integrated cost-effectiveness approach goes well 'beyond demography' and provides additional information for managers; however, cost-effectiveness needs to be augmented with information on off-target effects and social impacts of management in order to provide greater benefits for on-the-ground management.

  8. Distribution of peak expiratory flow variability by age, gender and smoking habits in a random population sample aged 20-70 yrs

    NARCIS (Netherlands)

    Boezen, H M; Schouten, J. P.; Postma, D S; Rijcken, B

    1994-01-01

    Peak expiratory flow (PEF) variability can be considered as an index of bronchial lability. Population studies on PEF variability are few. The purpose of the current paper is to describe the distribution of PEF variability in a random population sample of adults with a wide age range (20-70 yrs),

  9. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    Science.gov (United States)

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  10. The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies.

    Science.gov (United States)

    Byrne, Enda M; McRae, Allan F; Zhao, Zhen-Zhen; Martin, Nicholas G; Montgomery, Grant W; Visscher, Peter M

    2008-11-01

    There is an increasing recognition of the potential role of variants in mitochondrial DNA and nuclear-encoded mitochondrial proteins in modifying disease risk. This has led to a rise in the number of mitochondrial association studies being undertaken. The unique inheritance pattern of mitochondria makes mitochondrial DNA variation susceptible to having geographical structure. Such a structure may have a dramatic impact on mitochondrial association studies, particularly in heterogeneous populations. By combining self-reported ancestry data and mitochondrial genotype data for a sample of 3839 individuals from 1037 Australian families, population substructure is tested by looking for evidence of differences in mitochondrial haplogroup and single nucleotide polymorphism (SNP) frequencies between different ancestral groups in Australia. In addition, the substructure within ancestral groups is tested by comparing the similarity of mates to randomly drawn pairs of individuals from the same ancestral group. It is shown that there are significant differences in the frequency of variants both between European and non-European groups, and within Europe. This agrees with previous studies of European mitochondrial variation. No evidence was found for structure within ancestral groups. These results have implications for future association studies in the Australian population, and other populations of heterogeneous ancestry.

  11. Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population.

    Directory of Open Access Journals (Sweden)

    Ligang Wang

    Full Text Available As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS in 605 pigs of the F2 generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC, body height (BH, body length (BL, cannon bone circumference (CBC, chest depth (CD, chest width (CW, rump circumference (RC, rump width (RW, scapula width (SW, and waist width (WW. A total of 138 SNPs (the most significant being MARC0033464 on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value= 4.15E-6. One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1-25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC and 9 SNPs on SSC7 (RC. Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1 in block 1 (495 kb, and one gene (SCUBE3 in block 3 (124 kb. Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses.

  12. Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2

    DEFF Research Database (Denmark)

    Haraldsdottir, Sigurdis; Rafnar, Thorunn; Frankel, Wendy L

    2017-01-01

    Lynch syndrome, caused by germline mutations in the mismatch repair genes, is associated with increased cancer risk. Here using a large whole-genome sequencing data bank, cancer registry and colorectal tumour bank we determine the prevalence of Lynch syndrome, associated cancer risks...... and pathogenicity of several variants in the Icelandic population. We use colorectal cancer samples from 1,182 patients diagnosed between 2000-2009. One-hundred and thirty-two (11.2%) tumours are mismatch repair deficient per immunohistochemistry. Twenty-one (1.8%) have Lynch syndrome while 106 (9.0%) have somatic...... hypermethylation or mutations in the mismatch repair genes. The population prevalence of Lynch syndrome is 0.442%. We discover a translocation disrupting MLH1 and three mutations in MSH6 and PMS2 that increase endometrial, colorectal, brain and ovarian cancer risk. We find thirteen mismatch repair variants...

  13. Prioritizing management actions for invasive populations using cost, efficacy, demography and expert opinion for 14 plant species world?wide

    OpenAIRE

    Kerr, N.Z.; Baxter, P. W. J.; Salguero-Gómez, R.; Wardle, G.M.; Buckley, Y.M.

    2016-01-01

    1. Management of invasive populations is typically investigated case-by-case. Comparative approaches have been applied to single aspects of management, such as demography, with cost or efficacy rarely incorporated.\\ud 2. We present an analysis of the ranks of management actions for 14 species in five countries that extends beyond the use of demography alone to include multiple metrics for ranking management actions, which integrate cost, efficacy and demography (cost-effectiveness) and manage...

  14. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme.

    Science.gov (United States)

    Delorme, Christine; Legravet, Nicolas; Jamet, Emmanuel; Hoarau, Caroline; Alexandre, Bolotin; El-Sharoud, Walid M; Darwish, Mohamed S; Renault, Pierre

    2017-02-02

    We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

    Science.gov (United States)

    Fuller, Zachary L; Niño, Elina L; Patch, Harland M; Bedoya-Reina, Oscar C; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M; Miller, Webb

    2015-07-10

    With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

  16. The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population.

    Science.gov (United States)

    Kanduri, Chakravarthi; Ukkola-Vuoti, Liisa; Oikkonen, Jaana; Buck, Gemma; Blancher, Christine; Raijas, Pirre; Karma, Kai; Lähdesmäki, Harri; Järvelä, Irma

    2013-12-01

    Here we characterized the genome-wide architecture of copy number variations (CNVs) in 286 healthy, unrelated Finnish individuals belonging to the MUSGEN study, where molecular background underlying musical aptitude and related traits are studied. By using Illumina HumanOmniExpress-12v.1.0 beadchip, we identified 5493 CNVs that were spread across 467 different cytogenetic regions, spanning a total size of 287.83 Mb (∼9.6% of the human genome). Merging the overlapping CNVs across samples resulted in 999 discrete copy number variable regions (CNVRs), of which ∼6.9% were putatively novel. The average number of CNVs per person was 20, whereas the average size of CNV per locus was 52.39 kb. Large CNVs (>1 Mb) were present in 4% of the samples. The proportion of homozygous deletions in this data set (∼12.4%) seemed to be higher when compared with three other populations. Interestingly, several CNVRs were significantly enriched in this sample set, whereas several others were totally depleted. For example, a CNVR at chr2p22.1 intersecting GALM was more common in this population (P=3.3706 × 10(-44)) than in African and other European populations. The enriched CNVRs, however, showed no significant association with music-related phenotypes. Moreover, the most common CNV locations in world's normal population cohorts (6q14.1, 11q11) were overrepresented in this population. Thus, the genome-wide CNV investigation in this Finnish sample set demonstrated features that are characteristic to isolated populations. Novel CNVRs and the functional implications of CNVs revealed in this study elucidate structural variation present in this population isolate, and may also serve as candidate gene loci for music-related traits.

  17. Longitudinal exome-wide association study to identify genetic susceptibility loci for hypertension in a Japanese population.

    Science.gov (United States)

    Yasukochi, Yoshiki; Sakuma, Jun; Takeuchi, Ichiro; Kato, Kimihiko; Oguri, Mitsutoshi; Fujimaki, Tetsuo; Horibe, Hideki; Yamada, Yoshiji

    2017-12-08

    Genome-wide association studies have identified various genetic variants associated with complex disorders. However, these studies have commonly been conducted in a cross-sectional manner. Therefore, we performed a longitudinal exome-wide association study (EWAS) in a Japanese cohort. We aimed to identify genetic variants that confer susceptibility to hypertension using ~244 000 single-nucleotide variants (SNVs) and physiological data from 6026 Japanese individuals who underwent annual health check-ups for several years. After quality control, the association of hypertension with SNVs was tested using a generalized estimating equation model. Finally, our longitudinal EWAS detected seven hypertension-related SNVs that passed strict criteria. Among these variants, six SNVs were densely located at 12q24.1, and an East Asian-specific motif (haplotype) 'CAAAA' comprising five derived alleles was identified. Statistical analyses showed that the prevalence of hypertension in individuals with the East Asian-specific haplotype was significantly lower than that in individuals with the common haplotype 'TGGGT'. Furthermore, individuals with the East Asian haplotype may be less susceptible to the adverse effects of smoking on hypertension. The longitudinal EWAS for the recessive model showed that a novel SNV, rs11917356 of COL6A5, was significantly associated with systolic blood pressure, and the derived allele at the SNV may have spread throughout East Asia in recent evolutionary time.

  18. Impact of specific training and competition on myocardial structure and function in different age ranges of male handball players.

    Directory of Open Access Journals (Sweden)

    Brahim Agrebi

    Full Text Available Handball activity involves cardiac changes and demands a mixture of both eccentric and concentric remodeling within the heart. This study seeks to explore heart performance and cardiac remodeling likely to define cardiac parameters which influence specific performance in male handball players across different age ranges. Forty three players, with a regular training and competitive background in handball separated into three groups aged on average 11.78 ± 0.41 for youth players aka "schools", "elite juniors" 15.99 ± 0.81 and "elite adults" 24.46 ± 2.63 years, underwent echocardiography and ECG examinations. Incremental ergocycle and specific field (SFT tests have also been conducted. With age and regular training and competition, myocardial remodeling in different age ranges exhibit significant differences in dilatation's parameters between "schools" and "juniors" players, such as the end-diastolic diameter (LVEDD and the end-systolic diameter of the left ventricle (LVESD, the root of aorta (Ao and left atrial (LA, while significant increase is observed between "juniors" and "adults" players in the interventricular septum (IVS, the posterior wall thicknesses (PWT and LV mass index. ECG changes are also noted but NS differences were observed in studied parameters. For incremental maximal test, players demonstrate a significant increase in duration and total work between "schools" and "juniors" and, in total work only, between "juniors" and "seniors". The SFT shows improvement in performance which ranged between 26.17 ± 1.83 sec to 31.23 ± 2.34 sec respectively from "seniors" to "schools". The cross-sectional approach used to compare groups with prior hypothesis that there would be differences in exercise performance and cardiac parameters depending on duration of prior handball practice, leads to point out the early cardiac remodeling within the heart as adaptive change. Prevalence of cardiac chamber dilation with less hypertrophy remodeling

  19. Impact of specific training and competition on myocardial structure and function in different age ranges of male handball players

    Science.gov (United States)

    Agrebi, Brahim; Tkatchuk, Vladimir; Hlila, Nawel; Mouelhi, Emna; Belhani, Ali

    2015-01-01

    Handball activity involves cardiac changes and demands a mixture of both eccentric and concentric remodeling within the heart. This study seeks to explore heart performance and cardiac remodeling likely to define cardiac parameters which influence specific performance in male handball players across different age ranges. Forty three players, with a regular training and competitive background in handball separated into three groups aged on average 11.78±0.41 for youth players aka “schools”, “elite juniors” 15.99±0.81 and “elite adults” 24.46±2.63 years, underwent echocardiography and ECG examinations. Incremental ergocycle and specific field (SFT) tests have also been conducted. With age and regular training and competition, myocardial remodeling in different age ranges exhibit significant differences in dilatation’s parameters between “schools” and “juniors” players, such as the end-diastolic diameter (LVEDD) and the end-systolic diameter of the left ventricle (LVESD), the root of aorta (Ao) and left atrial (LA), while significant increase is observed between “juniors” and “adults” players in the interventricular septum (IVS), the posterior wall thicknesses (PWT) and LV mass index. ECG changes are also noted but NS differences were observed in studied parameters. For incremental maximal test, players demonstrate a significant increase in duration and total work between “schools” and “juniors” and, in total work only, between “juniors” and “seniors”. The SFT shows improvement in performance which ranged between 26.17±1.83 sec to 31.23±2.34 sec respectively from “seniors” to “schools”. The cross-sectional approach used to compare groups with prior hypothesis that there would be differences in exercise performance and cardiac parameters depending on duration of prior handball practice, leads to point out the early cardiac remodeling within the heart as adaptive change. Prevalence of cardiac chamber dilation

  20. Costing of a State-Wide Population Based Cancer Awareness and Early Detection Campaign in a 2.67 Million Population of Punjab State in Northern India.

    Science.gov (United States)

    Thakur, Js; Prinja, Shankar; Jeet, Gursimer; Bhatnagar, Nidhi

    2016-01-01

    Punjab state is particularly reporting a rising burden of cancer. A 'door to door cancer awareness and early detection campaign' was therefore launched in the Punjab covering about 2.67 million population, wherein after initial training accredited social health activists (ASHAs) and other health staff conducted a survey for early detection of cancer cases based on a twelve point clinical algorithm. To ascertain unit cost for undertaking a population-based cancer awareness and early detection campaign. Data were collected using bottom-up costing methods. Full economic costs of implementing the campaign from the health system perspective were calculated. Options to meet the likely demand for project activities were further evaluated to examine their worth from the point of view of long-term sustainability. The campaign covered 97% of the state population. A total of 24,659 cases were suspected to have cancer and were referred to health facilities. At the state level, incidence and prevalence of cancer were found to be 90 and 216 per 100,000, respectively. Full economic cost of implementing the campaign in pilot district was USD 117,524. However, the financial cost was approximately USD 6,301. Start-up phase of campaign was more resource intensive (63% of total) than the implementation phase. The economic cost per person contacted and suspected by clinical algorithm was found to be USD 0.20 and USD 40 respectively. Cost per confirmed case under the campaign was 7,043 USD. The campaign was able to screen a reasonably large population. High to high economic cost points towards the fact that the opportunity cost of campaign put a significant burden on health system and other programs. However, generating awareness and early detection strategy adopted in this campaign seems promising in light of fact that organized screening is not in place in India and in many developing countries.

  1. [Study of a population-wide epidemic outbreak of mumps virus G1 in Jerez de la Frontera (Spain)].

    Science.gov (United States)

    González, Pascasio Peña; Barrios, José Almenara; Morales Serna, Juan Carlos

    2012-06-01

    To characterize the mumps outbreak, assess the effectiveness of vaccines and discuss prevention and control measures. Observational cross-sectional study of cases by person, place, and time. City Jerez de la Frontera and 8 Primary Care centres. A total of 116 cases of mumps were reported throughout seven months, with the last case in June 2008. age, sex, place of study or work, symptoms start date, clinical description, complications, and genotype of virus isolation, history and vaccination compositions. Calculation of total vaccine effectiveness. Active case finding and contact studies were performed on the families, work places and leisure areas. The mean age of the cases was 16.24 years(SD 10.6). The majority (68.96%) of the cases were children at school and 31.03% arose from family and work areas. Mumps vaccine coverage rates were above 90%. The complete vaccine effectiveness (2 doses); for those under 20 years-old it was: 99.84% (95% CI=99.77 - 99.89), being lower in schools with the highest attack rate, immunised with current vaccine from Jeryl Lynn strain: 71.01% (95% CI=55.85 80.97). Two doses of this strain were used in 13.79% of the cases. Susceptible populations were vaccinated at the start of the outbreak: 11,381 doses used in schools and 93 outside schools. An outbreak of mumps virus G 1 population with high rates of mumps vaccine coverage, with areas with low vaccine effectiveness with current vaccine. Mass vaccination of population has contributed to the resolution of the outbreak. Copyright © 2011 Elsevier España, S.L. All rights reserved.

  2. Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda: Rhabditoidea Provide Insights into Population Structure and Reproductive Life Cycles.

    Directory of Open Access Journals (Sweden)

    Taisei Kikuchi

    2016-12-01

    Full Text Available The helminth Strongyloides stercoralis, which is transmitted through soil, infects 30-100 million people worldwide. S. stercoralis reproduces sexually outside the host as well as asexually within the host, which causes a life-long infection. To understand the population structure and transmission patterns of this parasite, we re-sequenced the genomes of 33 individual S. stercoralis nematodes collected in Myanmar (prevalent region and Japan (non-prevalent region. We utilised a method combining whole genome amplification and next-generation sequencing techniques to detect 298,202 variant positions (0.6% of the genome compared with the reference genome. Phylogenetic analyses of SNP data revealed an unambiguous geographical separation and sub-populations that correlated with the host geographical origin, particularly for the Myanmar samples. The relatively higher heterozygosity in the genomes of the Japanese samples can possibly be explained by the independent evolution of two haplotypes of diploid genomes through asexual reproduction during the auto-infection cycle, suggesting that analysing heterozygosity is useful and necessary to infer infection history and geographical prevalence.

  3. Analysis of DNA variations in GSTA and GSTM gene clusters based on the results of genome-wide data from three Russian populations taken as an example

    Directory of Open Access Journals (Sweden)

    Filippova Irina N

    2012-10-01

    Full Text Available Abstract Background Extensive genome-wide analyses of many human populations, using microarrays containing hundreds of thousands of single-nucleotide polymorphisms, have provided us with abundant information about global genomic diversity. However, these data can also be used to analyze local variability in individual genomic regions. In this study, we analyzed the variability in two genomic regions carrying the genes of the GSTA and GSTM subfamilies, located on different chromosomes. Results Analysis of the polymorphisms in GSTA and GSTM gene clusters showed similarities in their allelic and haplotype diversities. These patterns were similar in three Russian populations and the CEU population of European origin. There were statistically significant differences in all the haploblocks of both the GSTM and GSTA regions when the Russian populations were compared with populations from China and Japan. Most haploblocks also differed between the Russians and Nigerians from Yoruba, but, some of them had similar allelic frequencies. Special attention was paid to SNP rs4986947 from the intron of the GSTA4 gene, which is represented in apes by an A nucleotide. In the Asian and African samples, it was represented only by a G allele, and both allelic variants (G/A occurred in the Russian and European populations. Conclusions The results obtained suggest the presence of common features in the evolutionary histories of the GSTA and GSTM gene regions, and that African subpopulations were involved differently in the formation of the European and Asian human lineages.

  4. Rhinos in the Parks: An Island-Wide Survey of the Last Wild Population of the Sumatran Rhinoceros.

    Directory of Open Access Journals (Sweden)

    Wulan Pusparini

    Full Text Available In the 200 years since the Sumatran rhinoceros was first scientifically described (Fisher 1814, the range of the species has contracted from a broad region in Southeast Asia to three areas on the island of Sumatra and one in Kalimantan, Indonesia. Assessing population and spatial distribution of this very rare species is challenging because of their elusiveness and very low population number. Using an occupancy model with spatial dependency, we assessed the fraction of the total landscape occupied by Sumatran rhinos over a 30,345-km2 survey area and the effects of covariates in the areas where they are known to occur. In the Leuser Landscape (surveyed in 2007, the model averaging result of conditional occupancy estimate was ψ(SE[ψ] = 0.151(0.109 or 2,371.47 km2, and the model averaging result of replicated level detection probability p(SE[p] = 0.252(0.267; in Way Kambas National Park--2008: ψ(SE[ψ] = 0.468(0.165 or 634.18 km2, and p(SE[p] = 0.138(0.571; and in Bukit Barisan Selatan National Park--2010: ψ(SE[ψ] = 0.322(0.049 or 819.67 km2, and p(SE[p] = 0.365(0.42. In the Leuser Landscape, rhino occurrence was positively associated with primary dry land forest and rivers, and negatively associated with the presence of a road. In Way Kambas, occurrence was negatively associated with the presence of a road. In Bukit Barisan Selatan, occurrence was negatively associated with presence of primary dryland forest and rivers. Using the probabilities of site occupancy, we developed spatially explicit maps that can be used to outline intensive protection zones for in-situ conservation efforts, and provide a detailed assessment of conserving Sumatran rhinos in the wild. We summarize our core recommendation in four points: consolidate small population, strong protection, determine the percentage of breeding females, and recognize the cost of doing nothing. To reduce the probability of poaching, here we present only the randomized location of site level

  5. Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

    Science.gov (United States)

    Bosse, Mirte; Megens, Hendrik-Jan; Madsen, Ole; Crooijmans, Richard P.M.A.; Ryder, Oliver A.; Austerlitz, Frédéric; Groenen, Martien A.M.; de Cara, M. Angeles R.

    2015-01-01

    Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs. PMID:26063737

  6. Incidence and survival of oropharyngeal cancer in Denmark: a nation-wide, population-based study from 1980 to 2014.

    Science.gov (United States)

    Jensen, Jakob Schmidt; Jensen, David Hebbelstrup; Grønhøj, Christian; Karnov, Kirstine Kim Schmidt; Nørregaard, Cecilie; Agander, Tina Klitmøller; Specht, Lena; von Buchwald, Christian

    2017-10-23

    Oropharyngeal carcinomas (OPCs) constitute a significant and increasing proportion of head and neck carcinomas and are an important global cause of morbidity and mortality. The purpose of this study was to determine trends in incidence and survival in OPC in the Danish population from 1980 to 2014. This study included all patients registered in the nationwide Danish Cancer Registry over the period 1980-2014. The age-adjusted incidence rates (AAIR) per 100,000, annual percentage change (APC) and average annual percent change (AAPC) were evaluated. Five-year relative survival (RS) was calculated with Cox regression analyses in relation to gender, anatomical location and histology. A total of 6555 patients (69% male) were included, with a median age at diagnosis of 60 years. The AAIR of patients with OPC increased from 0.815 per 100,000 in 1980 to 4.51 per 100,000 in 2014 with an AAPC of 5.3. The 5-year RS increased significantly from 33.1% over the period 1980-1984 to 58.5% (25.4% points) over the period 2010-2014. With no significant difference stratified for gender. Tumors located at the palatine tonsils (n = 3333) and salivary gland OPC (n = 90) had significantly better survival compared with other sub-locations and histology subtypes. In the APC model the birth cohort effect rate ratio increased until 1925 and then decreased until 1935 from which point it increased in the last cohorts. In this population-based study, we observed a significant increase in the incidence of OPCs and in the RS for OPC. We also identified a profound birth cohort effect on the incidence.

  7. Genome-Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations.

    Science.gov (United States)

    Fiedler, Jason D; Salsman, Evan; Liu, Yuan; Michalak de Jiménez, Monika; Hegstad, Justin B; Chen, Bingcan; Manthey, Frank A; Chao, Shiaoman; Xu, Steven; Elias, Elias M; Li, Xuehui

    2017-11-01

    Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. The aim of this study was to identify major quality trait quantitative trait loci (QTL) for marker-assisted selection (MAS) and to explore potential application of genomic selection (GS) in a durum wheat breeding program. In this study, genome-wide association mapping was conducted for five quality traits using 1184 lines from the North Dakota State University (NDSU) durum wheat breeding program. Several QTL associated with test weight, semolina color, and gluten strength were identified. Genomic selection models were developed and forward prediction accuracies of 0.27 to 0.66 were obtained for the five quality traits. Our results show the potential for grain and semolina quality traits to be selected more efficiently through MAS and GS with further refinement. Considerable opportunity exists to extend these techniques to other traits such as grain yield and agronomic characteristics, further improving breeding efficiency in durum cultivar development. Copyright © 2017 Crop Science Society of America.

  8. Occupational Injuries in Germany: Population-Wide National Survey Data Emphasize the Importance of Work-Related Factors.

    Directory of Open Access Journals (Sweden)

    Alexander Rommel

    Full Text Available Unintentional injuries cause much of the global mortality burden, with the workplace being a common accident setting. Even in high-income economies, occupational injury figures remain remarkably high. Because risk factors for occupational injuries are prone to confounding, the present research takes a comprehensive approach. To better understand the occurrence of occupational injuries, sociodemographic factors and work- and health-related factors are tested simultaneously. Thus, the present analysis aims to develop a comprehensive epidemiological model that facilitates the explanation of varying injury rates in the workplace. The representative phone survey German Health Update 2010 provides information on medically treated occupational injuries sustained in the year prior to the interview. Data were collected on sociodemographics, occupation, working conditions, health-related behaviors, and chronic diseases. For the economically active population (18-70 years, n = 14,041, the 12-month prevalence of occupational injuries was calculated with a 95% confidence interval (CI. Blockwise multiple logistic regression was applied to successively include different groups of variables. Overall, 2.8% (95% CI 2.4-3.2 of the gainfully employed population report at least one occupational injury (women: 0.9%; 95% CI 0.7-1.2; men: 4.3%; 95% CI 3.7-5.0. In the fully adjusted model, male gender (OR 3.16 and age 18-29 (OR 1.54, as well as agricultural (OR 5.40, technical (OR 3.41, skilled service (OR 4.24 or manual (OR 5.12, and unskilled service (OR 3.13 or manual (OR 4.97 occupations are associated with higher chances of occupational injuries. The same holds for frequent stressors such as heavy carrying (OR 1.78, working in awkward postures (OR 1.46, environmental stress (OR 1.48, and working under pressure (OR 1.41. Among health-related variables, physical inactivity (OR 1.47 and obesity (OR 1.73 present a significantly higher chance of occupational injuries

  9. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    María Muñoz-Amatriaín

    Full Text Available New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait. Different patterns of linkage disequilibrium (LD were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.

  10. Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Qingli Meng

    2017-04-01

    Full Text Available Objective The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods Using a panel of 54,148 single nucleotide polymorphisms (SNPs, we performed a genome-wide Association (GWA study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]. Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

  11. Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

    Science.gov (United States)

    Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat. PMID:27486464

  12. A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number.

    Science.gov (United States)

    Beissinger, Timothy M; Hirsch, Candice N; Vaillancourt, Brieanne; Deshpande, Shweta; Barry, Kerrie; Buell, C Robin; Kaeppler, Shawn M; Gianola, Daniel; de Leon, Natalia

    2014-03-01

    A genome-wide scan to detect evidence of selection was conducted in the Golden Glow maize long-term selection population. The population had been subjected to selection for increased number of ears per plant for 30 generations, with an empirically estimated effective population size ranging from 384 to 667 individuals and an increase of more than threefold in the number of ears per plant. Allele frequencies at >1.2 million single-nucleotide polymorphism loci were estimated from pooled whole-genome resequencing data, and FST values across sliding windows were employed to assess divergence between the population preselection and the population postselection. Twenty-eight highly divergent regions were identified, with half of these regions providing gene-level resolution on potentially selected variants. Approximately 93% of the divergent regions do not demonstrate a significant decrease in heterozygosity, which suggests that they are not approaching fixation. Also, most regions display a pattern consistent with a soft-sweep model as opposed to a hard-sweep model, suggesting that selection mostly operated on standing genetic variation. For at least 25% of the regions, results suggest that selection operated on variants located outside of currently annotated coding regions. These results provide insights into the underlying genetic effects of long-term artificial selection and identification of putative genetic elements underlying number of ears per plant in maize.

  13. Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability.

    Science.gov (United States)

    Jump, A S; Rico, L; Coll, M; Peñuelas, J

    2012-06-01

    Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied on to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase in up to 800% in comparison with the generally accepted maximum of 30-40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent or the Sp parameter. Consequently, we argue that greater standardization should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.

  14. Genome-Wide Association Analysis for Blood Lipid Traits Measured in Three Pig Populations Reveals a Substantial Level of Genetic Heterogeneity.

    Science.gov (United States)

    Yang, Hui; Huang, Xiaochang; Zeng, Zhijun; Zhang, Wanchang; Liu, Chenlong; Fang, Shaoming; Huang, Lusheng; Chen, Congying

    2015-01-01

    Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.

  15. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq.

    Science.gov (United States)

    Kang, Jingliang; Ma, Xiuhui; He, Shunping

    2017-06-06

    Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.

  16. Genome-Wide Association Analysis for Blood Lipid Traits Measured in Three Pig Populations Reveals a Substantial Level of Genetic Heterogeneity.

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    Hui Yang

    Full Text Available Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.

  17. Genome-wide QTL mapping for wheat processing quality parameters in a Gaocheng 8901/Zhoumai 16 recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Hui Jin

    2016-07-01

    Full Text Available Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.. In the present study, a recombinant inbred line (RIL population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA and Mixolab parameters using 90K and 660K single nucleotide polymorphism (SNP chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90K and 660K SNP assays spanned a total length of 4,121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6,596 new SNP markers were anchored to the bread wheat linkage map, with 1,046 and 5,550 markers from the 90K and 660K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP technique for improvement of processing quality in bread wheat.

  18. Weekend warrior physical activity pattern and common mental disorder: a population wide study of 108,011 British adults.

    Science.gov (United States)

    Hamer, Mark; Biddle, Stuart J H; Stamatakis, Emmanuel

    2017-07-14

    The dose-response association between physical activity (PA) and mental health is poorly described. We explored cross-sectional associations between physical activity and common mental disorder (psychological distress) in 'weekend warriors' who do all their exercise in one or two sessions per week. Adult participants (n = 108,011, age = 47 ± 17 yrs., 46.5% men) were recruited from general population household-based surveys (Health Survey for England and Scottish Health Survey) from 1994 to 2004. Data were pooled and analyzed using logistic regression models. Moderate to vigorous physical activity (MVPA) was self-reported and psychological distress was measured using the 12 item General Health Questionnaire (GHQ-12). Psychological distress (GHQ-12 > 3) was prevalent in 14.5% of the sample. In healthy participants an inverse association between PA and psychological distress was optimal at the PA guideline (150 mins/wk. MVPA or 75 min/wk. Vigorous PA) regardless of whether it was accumulated in one or two bouts per week "Weekend warrior" (odd ratio = 0.68, 95% CI, 0.63, 0.73) or as more frequent daily bouts (odd ratio = 0.68, 95% CI, 0.64, 0.72) in comparison to the inactive reference group. In participants with chronic health conditions an inverse association between PA and psychological distress was also evident at lower doses (one or two sessions of PA a week below PA guideline) (OR = 0.72, 95% CI, 0.68, 0.77). Undertaking vigorous intensity PA as part of the PA guideline conferred additional benefit in women (odds ratio = 0.87, 95% CI, 0.75, 1.00), but not men. Mental health benefits may be accrued through different PA patterns, thus individual approaches to prescribing exercise should be promoted.

  19. A Genome-Wide Association Study Identifies UTRN Gene Polymorphism for Restless Legs Syndrome in a Korean Population.

    Science.gov (United States)

    Cho, Chul-Hyun; Choi, Ji-Hye; Kang, Seung-Gul; Yoon, Ho-Kyoung; Park, Young-Min; Moon, Joung-Ho; Jung, Ki-Young; Han, Jin-Kyu; Shin, Hong-Bum; Noh, Hyun Ji; Koo, Yong Seo; Kim, Leen; Woo, Hyun Goo; Lee, Heon-Jeong

    2017-11-01

    Restless legs syndrome (RLS) is a highly heritable and common neurological sensorimotor disease disturbing sleep. The objective of study was to investigate significant gene for RLS by performing GWA and replication study in a Korean population. We performed a GWA study for RLS symptom group (n=325) and non-RLS group (n=2,603) from the Korea Genome Epidemiology Study. We subsequently performed a replication study in RLS and normal controls (227 RLS and 229 controls) to confirm the present GWA study findings as well as previous GWA study results. In the initial GWA study of RLS, we observed an association of rs11645604 (OR=1.531, p=1.18×10-6) in MPHOSPH6 on chromosome 16q23.3, rs1918752 (OR=0.6582, p=1.93×10-6) and rs9390170 (OR=0.6778, p=7.67×10-6) in UTRN on chromosome 6q24. From the replication samples, we found rs9390170 in UTRN (p=0.036) and rs3923809 and rs9296249 in BTBD9 (p=0.045, p=0.046, respectively) were significantly associated with RLS. Moreover, we found the haplotype polymorphisms of rs9357271, rs3923809, and rs9296249 (overall p=5.69×10-18) in BTBD9 was associated with RLS. From our sequential GWA and replication study, we could hypothesize rs9390170 polymorphism in UTRN is a novel genetic marker for susceptibility to RLS. Regarding with utrophin, which is encoded by UTRN, is preferentially expressed in the neuromuscular synapse and myotendinous junctions, we speculate that utrophin is involved in RLS, particularly related to the neuromuscular aspects.

  20. Genome-wide association study for levels of total serum IgE identifies HLA-C in a Japanese population.

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    Yohei Yatagai

    Full Text Available Most of the previously reported loci for total immunoglobulin E (IgE levels are related to Th2 cell-dependent pathways. We undertook a genome-wide association study (GWAS to identify genetic loci responsible for IgE regulation. A total of 479,940 single nucleotide polymorphisms (SNPs were tested for association with total serum IgE levels in 1180 Japanese adults. Fine-mapping with SNP imputation demonstrated 6 candidate regions: the PYHIN1/IFI16, MHC classes I and II, LEMD2, GRAMD1B, and chr13∶60576338 regions. Replication of these candidate loci in each region was assessed in 2 independent Japanese cohorts (n = 1110 and 1364, respectively. SNP rs3130941 in the HLA-C region was consistently associated with total IgE levels in 3 independent populations, and the meta-analysis yielded genome-wide significance (P = 1.07×10(-10. Using our GWAS results, we also assessed the reproducibility of previously reported gene associations with total IgE levels. Nine of 32 candidate genes identified by a literature search were associated with total IgE levels after correction for multiple testing. Our findings demonstrate that SNPs in the HLA-C region are strongly associated with total serum IgE levels in the Japanese population and that some of the previously reported genetic associations are replicated across ethnic groups.

  1. Impact of energy intake, physical activity, and population-wide weight loss on cardiovascular disease and diabetes mortality in Cuba, 1980-2005.

    Science.gov (United States)

    Franco, Manuel; Orduñez, Pedro; Caballero, Benjamín; Tapia Granados, José A; Lazo, Mariana; Bernal, José Luís; Guallar, Eliseo; Cooper, Richard S

    2007-12-15

    Cuba's economic crisis of 1989-2000 resulted in reduced energy intake, increased physical activity, and sustained population-wide weight loss. The authors evaluated the possible association of these factors with mortality trends. Data on per capita daily energy intake, physical activity, weight loss, and smoking were systematically retrieved from national and local surveys. National vital statistics from 1980-2005 were used to assess trends in mortality from diabetes, coronary heart disease, stroke, cancer, and all causes. The crisis reduced per capita daily energy intake from 2,899 calories to 1,863 calories. During the crisis period, the proportion of physically active adults increased from 30% to 67%, and a 1.5-unit shift in the body mass index distribution was observed, along with a change in the distribution of body mass index categories. The prevalence of obesity declined from 14% to 7%, the prevalence of overweight increased 1%, and the prevalence of normal weight increased 4%. During 1997-2002, there were declines in deaths attributed to diabetes (51%), coronary heart disease (35%), stroke (20%), and all causes (18%). An outbreak of neuropathy and a modest increase in the all-cause death rate among the elderly were also observed. These results suggest that population-wide measures designed to reduce energy stores, without affecting nutritional sufficiency, may lead to declines in diabetes and cardiovascular disease prevalence and mortality.

  2. Genome-wide association analysis on five isolated populations identifies variants of the HLA-DOA gene associated with white wine liking.

    Science.gov (United States)

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; Amin, Najaf; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia M; Toniolo, Daniela; Gasparini, Paolo

    2015-12-01

    Wine is the most popular alcoholic beverage around the world and because of its importance in society has been widely studied. Understanding what drives its flavor has been a quest for decades but much is still unknown and will be determined at least in part by individual taste preferences. Recently studies in the genetics of taste have uncovered the role of different genes in the determination of food preferences giving new insight on its physiology. In this context we have performed a genome-wide association study on red and white wine liking using three isolated populations collected in Italy, and replicated our results on two additional populations coming from the Netherland and Central Asia for a total of 3885 samples. We have found a significant association (P=2.1 × 10(-8)) between white wine liking and rs9276975:C>T a polymorphism in the HLA-DOA gene encoding a non-canonical MHC II molecule, which regulates other MHC II molecules. The same association was also found with red wine liking (P=8.3 × 10(-6)). Sex-separated analysis have also revealed that the effect of HLA-DOA is twice as large in women as compared to men suggesting an interaction between this polymorphism and gender. Our results are one of the first examples of genome-wide association between liking of a commonly consumed food and gene variants. Moreover, our results suggest a role of the MHC system in the determination of food preferences opening new insight in this field in general.

  3. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations.

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    Jingjing Liang

    2017-05-01

    Full Text Available Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genome-wide association studies comprised of 31,968 individuals of African ancestry, and validated our results with additional 54,395 individuals from multi-ethnic studies. These analyses identified nine loci with eleven independent variants which reached genome-wide significance (P < 1.25×10-8 for either systolic and diastolic blood pressure, hypertension, or for combined traits. Single-trait analyses identified two loci (TARID/TCF21 and LLPH/TMBIM4 and multiple-trait analyses identified one novel locus (FRMD3 for blood pressure. At these three loci, as well as at GRP20/CDH17, associated variants had alleles common only in African-ancestry populations. Functional annotation showed enrichment for genes expressed in immune and kidney cells, as well as in heart and vascular cells/tissues. Experiments driven by these findings and using angiotensin-II induced hypertension in mice showed altered kidney mRNA expression of six genes, suggesting their potential role in hypertension. Our study provides new evidence for genes related to hypertension susceptibility, and the need to study African-ancestry populations in order to identify biologic factors contributing to hypertension.

  4. Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus.

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    Eduardo P Cappa

    Full Text Available The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model ( UMM on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303 with 7,680 Diversity Array Technology (DArT markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S:G ratio, a key wood property trait. The two DArT markers associated with S:G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly

  5. The Use of Targeted Marker Subsets to Account for Population Structure and Relatedness in Genome-Wide Association Studies of Maize (Zea mays L.

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    Angela H. Chen

    2016-08-01

    Full Text Available A typical plant genome-wide association study (GWAS uses a mixed linear model (MLM that includes a trait as the response variable, a marker as an explanatory variable, and fixed and random effect covariates accounting for population structure and relatedness. Although effective in controlling for false positive signals, this model typically fails to detect signals that are correlated with population structure or are located in high linkage disequilibrium (LD genomic regions. This result likely arises from each tested marker being used to estimate population structure and relatedness. Previous work has demonstrated that it is possible to increase the power of the MLM by estimating relatedness (i.e., kinship with markers that are not located on the chromosome where the tested marker resides. To quantify the amount of additional significant signals one can expect using this so-called K_chr model, we reanalyzed Mendelian, polygenic, and complex traits in two maize (Zea mays L. diversity panels that have been previously assessed using the traditional MLM. We demonstrated that the K_chr model could find more significant associations, especially in high LD regions. This finding is underscored by our identification of novel genomic signals proximal to the tocochromanol biosynthetic pathway gene ZmVTE1 that are associated with a ratio of tocotrienols. We conclude that the K_chr model can detect more intricate sources of allelic variation underlying agronomically important traits, and should therefore become more widely used for GWAS. To facilitate the implementation of the K_chr model, we provide code written in the R programming language.

  6. Genome-wide estimation of heritability and its functional components for flowering, defense, ionomics, and developmental traits in a geographically diverse population of Arabidopsis thaliana.

    Science.gov (United States)

    Yang, Rong-Cai

    2017-07-01

    Narrow-sense heritability (portion of the total phenotypic variation attributable to additive genetic effect, h 2 ) is a critical parameter in plant breeding and genetics, but its estimation is difficult for populations with unknown pedigree information. This study applied a marker-based linear mixed model (LMM) analysis to estimate narrow-sense heritability and its seven functional components corresponding to SNPs in coding and noncoding regions for each of 107 flowering, defense, ionomics, and developmental traits in an Arabidopsis (Arabidopsis thaliana) population of 199 inbred lines with unknown genetic relatedness. Genetic relationship matrix (GRM) based on 214 051 SNPs and component GRMs based on seven subsets of SNPs were computed for LMM estimation of h 2 and functional components contributing to h 2 , respectively. The h 2 estimates for flowering traits were higher than those for defense, ionomics, and developmental traits, supporting a general view that the fitness-related traits have lower heritabilities than other traits. The function component owing to SNPs in coding (exon) regions was the least contributor to h 2 . Our LMM analysis provides an opportunity to gain a comprehensive view on heritability and its functional components for populations with unknown structure but with genome-wide DNA markers.

  7. The Impact of Marine Protected Areas on Reef-Wide Population Structure and Fishing-Induced Phenotypes in Coral-Reef Fishes

    Science.gov (United States)

    Fidler, Robert Young, III

    Overfishing and destructive fishing practices threaten the sustainability of fisheries worldwide. In addition to reducing population sizes, anthropogenic fishing effort is highly size-selective, preferentially removing the largest individuals from harvested stocks. Intensive, size-selective mortality induces widespread phenotypic shifts toward the predominance of smaller and earlier-maturing individuals. Fish that reach sexual maturity at smaller size and younger age produce fewer, smaller, and less viable larvae, severely reducing the reproductive capacity of exploited populations. These directional phenotypic alterations, collectively known as "fisheries-induced evolution" (FIE) are among the primary causes of the loss of harvestable fish biomass. Marine protected areas (MPAs) are one of the most widely utilized components of fisheries management programs around the world, and have been proposed as a potential mechanism by which the impacts of FIE may be mitigated. The ability of MPAs to buffer exploited populations against fishing pressure, however, remains debated due to inconsistent results across studies. Additionally, empirical evidence of phenotypic shifts in fishes within MPAs is lacking. This investigation addresses both of these issues by: (1) using a categorical meta-analysis of MPAs to standardize and quantify the magnitude of MPA impacts across studies; and (2) conducting a direct comparison of life-history phenotypes known to be influenced by FIE in six reef-fish species inside and outside of MPAs. The Philippines was used as a model system for analyses due to the country's significance in global marine biodiversity and reliance on MPAs as a fishery management tool. The quantitative impact of Philippine MPAs was assessed using a "reef-wide" meta-analysis. This analysis used pooled visual census data from 39 matched pairs of MPAs and fished reefs surveyed twice over a mean period of 3 years. In 17 of these MPAs, two additional surveys were conducted

  8. Assessment of heterogeneity between European Populations: a Baltic and Danish replication case-control study of SNPs from a recent European ulcerative colitis genome wide association study.

    Science.gov (United States)

    Andersen, Vibeke; Ernst, Anja; Sventoraityte, Jurgita; Kupcinskas, Limas; Jacobsen, Bent A; Krarup, Henrik B; Vogel, Ulla; Jonaitis, Laimas; Denapiene, Goda; Kiudelis, Gediminas; Balschun, Tobias; Franke, Andre

    2011-10-13

    Differences in the genetic architecture of inflammatory bowel disease between different European countries and ethnicities have previously been reported. In the present study, we wanted to assess the role of 11 newly identified UC risk variants, derived from a recent European UC genome wide association study (GWAS) (Franke et al., 2010), for 1) association with UC in the Nordic countries, 2) for population heterogeneity between the Nordic countries and the rest of Europe, and, 3) eventually, to drive some of the previous findings towards overall genome-wide significance. Eleven SNPs were replicated in a Danish sample consisting of 560 UC patients and 796 controls and nine missing SNPs of the German GWAS study were successfully genotyped in the Baltic sample comprising 441 UC cases and 1156 controls. The independent replication data was then jointly analysed with the original data and systematic comparisons of the findings between ethnicities were made. Pearson's χ2, Breslow-Day (BD) and Cochran-Mantel-Haenszel (CMH) tests were used for association analyses and heterogeneity testing. The rs5771069 (IL17REL) SNP was not associated with UC in the Danish panel. The rs5771069 (IL17REL) SNP was significantly associated with UC in the combined Baltic, Danish and Norwegian UC study sample driven by the Norwegian panel (OR = 0.89, 95% CI: 0.79-0.98, P = 0.02). No association was found between rs7809799 (SMURF1/KPNA7) and UC (OR = 1.20, 95% CI: 0.95-1.52, P = 0.10) or between UC and all other remaining SNPs. We had 94% chance of detecting an association for rs7809799 (SMURF1/KPNA7) in the combined replication sample, whereas the power were 55% or lower for the remaining SNPs.Statistically significant PBD was found for OR heterogeneity between the combined Baltic, Danish, and Norwegian panel versus the combined German, British, Belgian, and Greek panel (rs7520292 (P = 0.001), rs12518307 (P = 0.007), and rs2395609 (TCP11) (P = 0.01), respectively).No SNP reached genome-wide

  9. Replication and Relevance of Multiple Susceptibility Loci Discovered from Genome Wide Association Studies for Type 2 Diabetes in an Indian Population.

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    Nagaraja M Phani

    Full Text Available Several genetic variants for type 2 diabetes (T2D have been identified through genome wide association studies (GWAS from Caucasian population; however replication studies were not consistent across various ethnicities. Objective of the current study is to examine the possible correlation of 9 most significant GWAS single nucleotide polymorphisms (SNPs for T2D susceptibility as well as the interactive effect of these variants on the risk of T2D in an Indian population.Case-control cohorts of 1156 individuals were genotyped for 9 SNPs from an Indian population. Association analyses were performed using logistic regression after adjusting for covariates. Multifactor dimensionality reduction (MDR analysis was adopted to determine gene-gene interactions and discriminatory power of combined SNP effect was assessed by grouping individuals based on the number of risk alleles and by calculating area under the receiver-operator characteristic curve (AUC.We confirm the association of TCF7L2 (rs7903146 and SLC30A8 (rs13266634 with T2D. MDR analysis showed statistically significant interactions among four SNPs of SLC30A8 (rs13266634, IGF2BP2 (rs4402960, HHEX (rs1111875 and CDKN2A (rs10811661 genes. Cumulative analysis showed an increase in odds ratio against the baseline group of individuals carrying 5 to 6 risk alleles and discriminatory power of genetic test based on 9 variants showed higher AUC value when analyzed along with body mass index (BMI.These results provide a strong evidence for independent association between T2D and SNPs for in TCF7L2 and SLC30A8. MDR analysis demonstrates that independently non-significant variants may interact with one another resulting in increased disease susceptibility in the population tested.

  10. Incidence and Risk Factors for Deliberate Self-harm, Mental Illness, and Suicide Following Bariatric Surgery: A State-wide Population-based Linked-data Cohort Study.

    Science.gov (United States)

    Morgan, David J R; Ho, Kwok M

    2017-02-01

    Assess the incidence and determinants of hospitalization for deliberate self-harm and mental health disorders, and suicide after bariatric surgery. Limited recent literature suggests an increase in deliberate self-harm following bariatric surgery. A state-wide, population-based, self-matched, longitudinal cohort study over a 5-year period between 2007 and 2011. Utilizing the Western Australian Department of Health Data Linkage Unit records, all patients undergoing bariatric surgery (n = 12062) in Western Australia were followed for an average 30.4 months preoperatively and 40.6 months postoperatively. There were 110 patients (0.9%) hospitalized for deliberate self-harm, which was higher than the general population [incidence rate ratio (IRR) 1.47, 95% confidence interval (CI) 1.11-1.94, P = 0.005]. Compared with before surgery, there was no significant increase in deliberate self-harm hospitalizations (IRR 0.79, 95% CI 0.54-1.16; P = 0.206) and a reduction in overall mental illness related hospitalizations (IRR 0.76, 95% CI 0.63-0.91; P = 0.002) after surgery. Younger age, no private-health insurance cover, a history of hospitalizations due to depression before surgery, and gastrointestinal complications after surgery were predictors for deliberate self-harm hospitalizations after bariatric surgery. Three suicides occurred during the follow-up period, a rate comparable to the general population during the same time period (IRR 0.61, 95% CI 0.11-2.27, P = 0.444). Hospitalization for deliberate self-harm in bariatric patients was more common than the general population, but an increased incidence of deliberate self-harm after bariatric surgery was not observed. Hospitalization for depression before surgery and major postoperative gastrointestinal complications after bariatric surgery are potentially modifiable risk factors for deliberate self-harm after bariatric surgery.

  11. Influence of Genetic Variants in EGF and Other Genes on Hematological Traits in Korean Populations by a Genome-Wide Approach.

    Science.gov (United States)

    Kim, Yun Kyoung; Oh, Ji Hee; Kim, Young Jin; Hwang, Mi Yeong; Moon, Sanghoon; Low, Siew-Kee; Takahashi, Atsushi; Matsuda, Koichi; Kubo, Michiaki; Lee, Juyoung; Kim, Bong-Jo

    2015-01-01

    Hematological traits are important health indicators and are used as diagnostic clinical parameters for human disorders. Recently, genome-wide association studies (GWAS) identified many genetic loci associated with hematological traits in diverse ethnic groups. However, additional GWAS are necessary to elucidate the breadth of genetic variation and the underlying genetic architecture represented by hematological metrics. To identify additional genetic loci influencing hematological traits (such as hematocrit, hemoglobin concentration, white blood cell count, red blood cell count, and platelet count), we conducted GWAS and meta-analyses on data from 12,509 Korean individuals grouped into population-based cohorts. Of interest is EGF, a factor plays a role in the proliferation and differentiation of hematopoietic progenitor cells. We identified a novel EGF variant, which associated with platelet count in our study (P combined = 2.44 × 10(-15)). Our study also replicated 16 genetic associations related to five hematological traits with genome-wide significance (P influencing platelet count are distributed across several genes and have pleiotropic effects in coronary artery disease and dyslipidemia. Our findings may aid in elucidating molecular mechanisms underlying not only hematopoiesis but also inflammatory and cardiovascular diseases.

  12. An imputation-based genome-wide association study on traits related to male reproduction in a White Duroc × Erhualian F2 population.

    Science.gov (United States)

    Zhao, Xueyan; Zhao, Kewei; Ren, Jun; Zhang, Feng; Jiang, Chao; Hong, Yuan; Jiang, Kai; Yang, Qiang; Wang, Chengbin; Ding, Nengshui; Huang, Lusheng; Zhang, Zhiyan; Xing, Yuyun

    2016-05-01

    Boar reproductive traits are economically important for the pig industry. Here we conducted a genome-wide association study (GWAS) for 13 reproductive traits measured on 205 F2 boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F2 intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome-wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r(2) correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits. © 2015 Japanese Society of Animal Science.

  13. Genetic Influences on Political Ideologies: Twin Analyses of 19 Measures of Political Ideologies from Five Democracies and Genome-Wide Findings from Three Populations

    Science.gov (United States)

    Hatemi, Peter K.; Medland, Sarah E.; Klemmensen, Robert; Oskarrson, Sven; Littvay, Levente; Dawes, Chris; Verhulst, Brad; McDermott, Rose; Nørgaard, Asbjørn Sonne; Klofstad, Casey; Christensen, Kaare; Johannesson, Magnus; Magnusson, Patrik K.E.; Eaves, Lindon J.; Martin, Nicholas G.

    2014-01-01

    Almost forty years ago, evidence from large studies of adult twins and their relatives suggested that between 30-60% of the variance in social and political attitudes could be explained by genetic influences. However, these findings have not been widely accepted or incorporated into the dominant paradigms that explain the etiology of political ideology. This has been attributed in part to measurement and sample limitations, as well the relative absence of molecular genetic studies. Here we present results from original analyses of a combined sample of over 12,000 twins pairs, ascertained from nine different studies conducted in five democracies, sampled over the course of four decades. We provide evidence that genetic factors play a role in the formation of political ideology, regardless of how ideology is measured, the era, or the population sampled. The only exception is a question that explicitly uses the phrase “Left-Right”. We then present results from one of the first genome-wide association studies on political ideology using data from three samples: a 1990 Australian sample involving 6,894 individuals from 3,516 families; a 2008 Australian sample of 1,160 related individuals from 635 families and a 2010 Swedish sample involving 3,334 individuals from 2,607 families. No polymorphisms reached genome-wide significance in the meta-analysis. The combined evidence suggests that political ideology constitutes a fundamental aspect of one’s genetically informed psychological disposition, but as Fisher proposed long ago, genetic influences on complex traits will be composed of thousands of markers of very small effects and it will require extremely large samples to have enough power in order to identify specific polymorphisms related to complex social traits. PMID:24569950

  14. Genome-wide scan identifies variant in TNFSF13 associated with serum IgM in a healthy Chinese male population.

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    Ming Yang

    Full Text Available IgM provides a first line of defense during microbial infections. Serum IgM levels are detected routinely in clinical practice. And IgM is a genetically complex trait. We conducted a two-stage genome-wide association study (GWAS to identify genetic variants affecting serum IgM levels in a Chinese population of 3495, including 1999 unrelated subjects in the first stage and 1496 independent individuals in the second stage. Our data show that a common single nucleotide polymorphism (SNP, rs11552708 located in the TNFSF13 gene was significantly associated with IgM levels (p = 5.00×10(-7 in first stage, p = 1.34×10(-3 in second stage, and p = 4.22×10(-9 when combined. Besides, smoking was identified to be associated with IgM levels in both stages (P0.05. It is suggested that TNFSF13 may be a susceptibility gene affecting serum IgM levels in Chinese male population.

  15. Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame

    Science.gov (United States)

    Cui, Chengqi; Mei, Hongxian; Liu, Yanyang; Zhang, Haiyang; Zheng, Yongzhan

    2017-01-01

    The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype–genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 × 10-3, with averages of 1.0 × 10-4, 2.7 × 10-4, and 3.6 × 10-4 obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to ∼99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel. PMID:28729877

  16. First genome-wide association study in an Australian aboriginal population provides insights into genetic risk factors for body mass index and type 2 diabetes.

    Directory of Open Access Journals (Sweden)

    Denise Anderson

    Full Text Available A body mass index (BMI >22kg/m2 is a risk factor for type 2 diabetes (T2D in Aboriginal Australians. To identify loci associated with BMI and T2D we undertook a genome-wide association study using 1,075,436 quality-controlled single nucleotide polymorphisms (SNPs genotyped (Illumina 2.5M Duo Beadchip in 402 individuals in extended pedigrees from a Western Australian Aboriginal community. Imputation using the thousand genomes (1000G reference panel extended the analysis to 6,724,284 post quality-control autosomal SNPs. No associations achieved genome-wide significance, commonly accepted as P45,000 years ago. The top hit (rs10868204 Pgenotyped = 1.50x10-6; rs11140653 Pimputed_1000G = 2.90x10-7 for BMI lies 5' of NTRK2, the type 2 neurotrophic tyrosine kinase receptor for brain-derived neurotrophic factor (BDNF that regulates energy balance downstream of melanocortin-4 receptor (MC4R. PIK3C2G (rs12816270 Pgenotyped = 8.06x10-6; rs10841048 Pimputed_1000G = 6.28x10-7 was associated with BMI, but not with T2D as reported elsewhere. BMI also associated with CNTNAP2 (rs6960319 Pgenotyped = 4.65x10-5; rs13225016 Pimputed_1000G = 6.57x10-5, previously identified as the strongest gene-by-environment interaction for BMI in African-Americans. The top hit (rs11240074 Pgenotyped = 5.59x10-6, Pimputed_1000G = 5.73x10-6 for T2D lies 5' of BCL9 that, along with TCF7L2, promotes beta-catenin's transcriptional activity in the WNT signaling pathway. Additional hits occurred in genes affecting pancreatic (KCNJ6, KCNA1 and/or GABA (GABRR1, KCNA1 functions. Notable associations observed for genes previously identified at genome-wide significance in other populations included MC4R (Pgenotyped = 4.49x10-4 for BMI and IGF2BP2 Pimputed_1000G = 2.55x10-6 for T2D. Our results may provide novel functional leads in understanding disease pathogenesis in this Australian Aboriginal population.

  17. Genome-wide association study confirms lung cancer susceptibility loci on chromosomes 5p15 and 15q25 in an African-American population.

    Science.gov (United States)

    Zanetti, Krista A; Wang, Zhaoming; Aldrich, Melinda; Amos, Christopher I; Blot, William J; Bowman, Elise D; Burdette, Laurie; Cai, Qiuyin; Caporaso, Neil; Chung, Charles C; Gillanders, Elizabeth M; Haiman, Christopher A; Hansen, Helen M; Henderson, Brian E; Kolonel, Laurence N; Marchand, Loic Le; Li, Shengchao; McNeill, Lorna Haughton; Ryan, Bríd M; Schwartz, Ann G; Sison, Jennette D; Spitz, Margaret R; Tucker, Margaret; Wenzlaff, Angela S; Wiencke, John K; Wilkens, Lynne; Wrensch, Margaret R; Wu, Xifeng; Zheng, Wei; Zhou, Weiyin; Christiani, David; Palmer, Julie R; Penning, Trevor M; Rieber, Alyssa G; Rosenberg, Lynn; Ruiz-Narvaez, Edward A; Su, Li; Vachani, Anil; Wei, Yongyue; Whitehead, Alexander S; Chanock, Stephen J; Harris, Curtis C

    2016-08-01

    Genome-wide association studies (GWAS) of lung cancer have identified regions of common genetic variation with lung cancer risk in Europeans who smoke and never-smoking Asian women. This study aimed to conduct a GWAS in African Americans, who have higher rates of lung cancer despite smoking fewer cigarettes per day when compared with Caucasians. This population provides a different genetic architecture based on underlying African ancestry allowing the identification of new regions and exploration of known regions for finer mapping. We genotyped 1,024,001 SNPs in 1737 cases and 3602 controls in stage 1, followed by a replication phase of 20 SNPs (p<1.51×10(-5)) in an independent set of 866 cases and 796 controls in stage 2. In the combined analysis, we confirmed two loci to be associated with lung cancer that achieved the threshold of genome-wide significance: 15q25.1 marked by rs2036527 (p=1.3×10(-9); OR=1.32; 95% CI=1.20-1.44) near CHRNA5, and 5p15.33 marked by rs2853677 (p=2.8×10(-9); OR=1.28; 95% CI=1.18-1.39) near TERT. The association with rs2853677 is driven by the adenocarcinoma subtype of lung cancer (p=1.3×10(-8); OR=1.37; 95% CI=1.23-1.54). No SNPs reached genome-wide significance for either of the main effect models examining smoking - cigarettes per day and current or former smoker. Our study was powered to identify strong risk loci for lung cancer in African Americans; we confirmed results previously reported in African Americans and other populations for two loci near plausible candidate genes, CHRNA5 and TERT, on 15q25.1 and 5p15.33 respectively, are associated with lung cancer. Additional work is required to map and understand the biological underpinnings of the strong association of these loci with lung cancer risk in African Americans. Published by Elsevier Ireland Ltd.

  18. Genome-wide association study confirms lung cancer susceptibility loci on chromosome 5p15 and 15q25 in an African-American population

    Science.gov (United States)

    Zanetti, Krista A.; Wang, Zhaoming; Aldrich, Melinda; Amos, Christopher I.; Blot, William J.; Bowman, Elise D.; Burdette, Laurie; Cai, Quiyin; Caporaso, Neil; Chung, Charles C.; Gillanders, Elizabeth M.; Haiman, Christopher A.; Hansen, Helen M.; Henderson, Brian E.; Kolonel, Laurence N.; Le Marchand, Loic; Li, Shengchao; McNeill, Lorna Haughton; Ryan, Bríd M.; Schwartz, Ann G.; Sison, Jennette D.; Spitz, Margaret R.; Tucker, Margaret; Wenzlaff, Angela S.; Wiencke, John K.; Wilkens, Lynne; Wrensch, Margaret R.; Wu, Xifeng; Zheng, Wei; Zhou, Weiyin; Christiani, David; Palmer, Julie R.; Penning, Trevor M.; Rieber, Alyssa G.; Rosenberg, Lynn; Ruiz-Narvaez, Edward A.; Su, Li; Vachani, Anil; Wei, Yongyue; Whitehead, Alexander S.; Chanock, Stephen J.; Harris, Curtis C.

    2016-01-01

    Objectives Genome-wide association studies (GWAS) of lung cancer have identified regions of common genetic variation with lung cancer risk in Europeans who smoke and never-smoking Asian women. This study aimed to conduct a GWAS in African Americans, who have higher rates of lung cancer despite smoking fewer cigarettes per day when compared with Caucasians. This population provides a different genetic architecture based on underlying African ancestry allowing the identification of new regions and exploration of known regions for finer mapping. Materials and Methods We genotyped 1,024,001 SNPs in 1737 cases and 3602 controls in stage 1, followed by a replication phase of 20 SNPs (p<1.51×10−5) in an independent set of 866 cases and 796 controls in stage 2. Results and Conclusion In the combined analysis, we confirmed two loci to be associated with lung cancer that achieved the threshold of genome-wide significance: 15q25.1 marked by rs2036527 (p = 1.3 × 10−9; OR = 1.32; 95% CI = 1.20–1.44) near CHRNA5, and 5p15.33 marked by rs2853677 (p = 2.8 × 10−9; OR = 1.28; 95% CI = 1.18–1.39) near TERT. The association with rs2853677 is driven by the adenocarcinoma subtype of lung cancer (p = 1.3 × 10−8; OR = 1.37; 95% CI = 1.23–1.54). No SNPs reached genome-wide significance for either of the main effect models examining smoking - cigarettes per day and current or former smoker. Our study was powered to identify strong risk loci for lung cancer in African Americans; we confirmed results previously reported in African Americans and other populations for two loci near plausible candidate genes, CHRNA5 and TERT, on 15q25.1 and 5p15.33 respectively, are associated with lung cancer. Additional work is required to map and understand the biological underpinnings of the strong association of these loci with lung cancer risk in African Americans. PMID:27393504

  19. Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population.

    Science.gov (United States)

    Liu, Xianxian; Xiong, Xinwei; Yang, Jie; Zhou, Lisheng; Yang, Bin; Ai, Huashui; Ma, Huanban; Xie, Xianhua; Huang, Yixuan; Fang, Shaoming; Xiao, Shijun; Ren, Jun; Ma, Junwu; Huang, Lusheng

    2015-05-12

    Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population. Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations. We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several

  20. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database.

    Science.gov (United States)

    Glenn, Travis C; Lance, Stacey L; McKee, Anna M; Webster, Bonnie L; Emery, Aidan M; Zerlotini, Adhemar; Oliveira, Guilherme; Rollinson, David; Faircloth, Brant C

    2013-10-17

    Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences

  1. Hyperthyroidism incidence fluctuates widely in and around pregnancy and is at variance with some other autoimmune diseases: a Danish population-based study.

    Science.gov (United States)

    Andersen, Stine Linding; Olsen, Jørn; Carlé, Allan; Laurberg, Peter

    2015-03-01

    Hyperthyroidism in women of reproductive age is predominantly caused by Graves' disease. Pregnancy associated changes in the immune system may influence the onset of disease, but population-based incidence rates in and around pregnancy have not been reported. The objective of the study was to estimate the incidence of maternal hyperthyroidism (defined by redeemed prescription of antithyroid drugs) in and around pregnancy and to compare this with the incidence of other autoimmune diseases such as rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). This was a population-based cohort study. The study used the Danish nationwide registers. The participants were women who gave birth to singleton liveborn children in Denmark from 1999 to 2008 (n = 403,958). Incidence rates (IR) of maternal hyperthyroidism during a 4-year period beginning 2 years before and ending 2 years after the date when the mother was giving birth for the first time in the study period were measured. Altogether 3673 women (0.9%) were identified with an onset of hyperthyroidism from 1997 to 2010, and the overall IR of maternal hyperthyroidism was 65.0/100,000/year. The IR of hyperthyroidism in and around pregnancy varied widely and was high in the first 3 months of pregnancy [incidence rate ratio (IRR) vs the remaining study period: 1.50 (95% CI 1.09-2.06)), very low in the last 3 months of pregnancy (0.26 (0.15-0.44)], and reached the highest level 7-9 months postpartum [3.80 (2.88-5.02)]. The incidence variation in and around pregnancy was different for RA and IBD. These are the first population-based data on the incidence of hyperthyroidism in and around pregnancy. The incidence of hyperthyroidism was high in early pregnancy and postpartum, whereas such particular pattern was not observed for other diseases of autoimmune origin.

  2. HIV-Associated Anemia After 96 Weeks on Therapy: Determinants Across Age Ranges in Uganda and Zimbabwe

    Science.gov (United States)

    Walker, A. Sarah; Ssali, Francis; Musiime, Victor; Kiweewa, Francis; Kityo, Cissy; Salata, Robert; Mugyenyi, Peter

    2014-01-01

    Abstract Given the detrimental effects of HIV-associated anemia on morbidity, we determined factors associated with anemia after 96 weeks of antiretroviral therapy (ART) across age groups. An HIV-positive cohort (n=3,580) of children age 5–14, reproductive age adults 18–49, and older adults ≥50 from two randomized trials in Uganda and Zimbabwe were evaluated from initiation of therapy through 96 weeks. We conducted logistic and multinomial regression to evaluate common and differential determinants for anemia at 96 weeks on therapy. Prior to initiation of ART, the prevalence of anemia (age 5–11 age adults (OR 2.60, 95% CI 1.44–4.70, p=0.002). Reproductive age females had a significantly higher odds of anemia compared to men at week 96 (OR 2.56, 95% CI 1.92–3.40, page group (p=0.001). Other common factors associated with anemia included low body mass index (BMI) and microcytosis; greater increases in CD4 count to week 96 were protective. Thus, while ART significantly reduced the prevalence of anemia at 96 weeks, 13% of the population continued to be anemic. Specific groups, such as reproductive age females and older adults, have a greater odds of anemia and may guide clinicians to pursue further evaluation and management. PMID:24506102

  3. Genome wide linkage study, using a 250K SNP map, of Plasmodium falciparum infection and mild malaria attack in a Senegalese population.

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    Jacqueline Milet

    Full Text Available Multiple factors are involved in the variability of host's response to P. falciparum infection, like the intensity and seasonality of malaria transmission, the virulence of parasite and host characteristics like age or genetic make-up. Although admitted nowadays, the involvement of host genetic factors remains unclear. Discordant results exist, even concerning the best-known malaria resistance genes that determine the structure or function of red blood cells. Here we report on a genome-wide linkage and association study for P. falciparum infection intensity and mild malaria attack among a Senegalese population of children and young adults from 2 to 18 years old. A high density single nucleotide polymorphisms (SNP genome scan (Affimetrix GeneChip Human Mapping 250K-nsp was performed for 626 individuals: i.e. 249 parents and 377 children out of the 504 ones included in the follow-up. The population belongs to a unique ethnic group and was closely followed-up during 3 years. Genome-wide linkage analyses were performed on four clinical and parasitological phenotypes and association analyses using the family based association tests (FBAT method were carried out in regions previously linked to malaria phenotypes in literature and in the regions for which we identified a linkage peak. Analyses revealed three strongly suggestive evidences for linkage: between mild malaria attack and both the 6p25.1 and the 12q22 regions (empirical p-value=5x10(-5 and 9x10(-5 respectively, and between the 20p11q11 region and the prevalence of parasite density in asymptomatic children (empirical p-value=1.5x10(-4. Family based association analysis pointed out one significant association between the intensity of plasmodial infection and a polymorphism located in ARHGAP26 gene in the 5q31-q33 region (p-value=3.7x10(-5. This study identified three candidate regions, two of them containing genes that could point out new pathways implicated in the response to malaria infection

  4. Phenome-wide association study (PheWAS for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE Network.

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    Sarah A Pendergrass

    Full Text Available Using a phenome-wide association study (PheWAS approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships. This PheWAS drew on five population-based studies representing four major racial/ethnic groups (European Americans (EA, African Americans (AA, Hispanics/Mexican-Americans, and Asian/Pacific Islanders in PAGE, each site with measurements for multiple traits, associated laboratory measures, and intermediate biomarkers. A total of 83 single nucleotide polymorphisms (SNPs identified by genome-wide association studies (GWAS were genotyped across two or more PAGE study sites. Comprehensive tests of association, stratified by race/ethnicity, were performed, encompassing 4,706 phenotypes mapped to 105 phenotype-classes, and association results were compared across study sites. A total of 111 PheWAS results had significant associations for two or more PAGE study sites with consistent direction of effect with a significance threshold of p<0.01 for the same racial/ethnic group, SNP, and phenotype-class. Among results identified for SNPs previously associated with phenotypes such as lipid traits, type 2 diabetes, and body mass index, 52 replicated previously published genotype-phenotype associations, 26 represented phenotypes closely related to previously known genotype-phenotype associations, and 33 represented potentially novel genotype-phenotype associations with pleiotropic effects. The majority of the potentially novel results were for single PheWAS phenotype-classes, for example, for CDKN2A/B rs1333049 (previously associated with type 2 diabetes in EA a PheWAS association was identified for hemoglobin levels in AA. Of note, however, GALNT2 rs2144300 (previously associated with high

  5. Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network.

    Science.gov (United States)

    Pendergrass, Sarah A; Brown-Gentry, Kristin; Dudek, Scott; Frase, Alex; Torstenson, Eric S; Goodloe, Robert; Ambite, Jose Luis; Avery, Christy L; Buyske, Steve; Bůžková, Petra; Deelman, Ewa; Fesinmeyer, Megan D; Haiman, Christopher A; Heiss, Gerardo; Hindorff, Lucia A; Hsu, Chu-Nan; Jackson, Rebecca D; Kooperberg, Charles; Le Marchand, Loic; Lin, Yi; Matise, Tara C; Monroe, Kristine R; Moreland, Larry; Park, Sungshim L; Reiner, Alex; Wallace, Robert; Wilkens, Lynn R; Crawford, Dana C; Ritchie, Marylyn D

    2013-01-01

    Using a phenome-wide association study (PheWAS) approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE) network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships. This PheWAS drew on five population-based studies representing four major racial/ethnic groups (European Americans (EA), African Americans (AA), Hispanics/Mexican-Americans, and Asian/Pacific Islanders) in PAGE, each site with measurements for multiple traits, associated laboratory measures, and intermediate biomarkers. A total of 83 single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) were genotyped across two or more PAGE study sites. Comprehensive tests of association, stratified by race/ethnicity, were performed, encompassing 4,706 phenotypes mapped to 105 phenotype-classes, and association results were compared across study sites. A total of 111 PheWAS results had significant associations for two or more PAGE study sites with consistent direction of effect with a significance threshold of pSNP, and phenotype-class. Among results identified for SNPs previously associated with phenotypes such as lipid traits, type 2 diabetes, and body mass index, 52 replicated previously published genotype-phenotype associations, 26 represented phenotypes closely related to previously known genotype-phenotype associations, and 33 represented potentially novel genotype-phenotype associations with pleiotropic effects. The majority of the potentially novel results were for single PheWAS phenotype-classes, for example, for CDKN2A/B rs1333049 (previously associated with type 2 diabetes in EA) a PheWAS association was identified for hemoglobin levels in AA. Of note, however, GALNT2 rs2144300 (previously associated with high-density lipoprotein cholesterol levels in EA) had

  6. A colorectal cancer susceptibility new variant at 4q26 in the Spanish population identified by genome-wide association analysis.

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    Luis M Real

    Full Text Available BACKGROUND: Non-hereditary colorectal cancer (CRC is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome-wide association studies (GWAS are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population. RESULTS: A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNPs from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10(-8, and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10(-11. Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599, 8q24 (rs10505477, 8q24.21(rs6983267, 11q13.4 (rs3824999 and 14q22.2 (rs4444235. CONCLUSIONS: Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses.

  7. A Colorectal Cancer Susceptibility New Variant at 4q26 in the Spanish Population Identified by Genome-Wide Association Analysis

    Science.gov (United States)

    Real, Luis M.; Ruiz, Agustín; Gayán, Javier; González-Pérez, Antonio; Sáez, María E.; Ramírez-Lorca, Reposo; Morón, Francisco J.; Velasco, Juan; Marginet-Flinch, Ruth; Musulén, Eva; Carrasco, José M.; Moreno-Rey, Concha; Vázquez, Enrique; Chaves-Conde, Manuel; Moreno-Nogueira, Jose A.; Hidalgo-Pascual, Manuel; Ferrero-Herrero, Eduardo; Castellví-Bel, Sergi; Castells, Antoni; Fernandez-Rozadilla, Ceres; Ruiz-Ponte, Clara; Carracedo, Angel; González, Beatriz; Alonso, Sergio; Perucho, Manuel

    2014-01-01

    Background Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome–wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population. Results A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNP)s from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10−8), and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10−11). Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599), 8q24 (rs10505477), 8q24.21(rs6983267), 11q13.4 (rs3824999) and 14q22.2 (rs4444235). Conclusions Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses. PMID:24978480

  8. The RAISE Coalition: Lessons Learned From a Multisector Coalition Used to Implement High-impact Population-Wide Strategies in Cleveland, Ohio.

    Science.gov (United States)

    Arista, Pedro; Vue, Cathy; Byun, Michael; Choi, Ashley; Chin, Kathy Ko

    2017-01-01

    Recent public health initiatives include policy, systems, and environmental (PSE) strategies with the aim of improving community health. These high-impact, population-wide strategies provide opportunities for multisector coalitions to engage and inform the implementation process to ultimately reach underrepresented communities, like Asian Americans and Pacific Islanders (AAPIs). The purpose of this article is to discuss (1) the objectives of "Reaching Asian Americans through Innovative and Supportive Engagement," (RAISE) a multisector coalition (2) describe the process in which the coalition was engaged in, and (3) share lessons learned that can inform future partnerships with various sectors that reach AAPI communities that are highly diverse and in geographically dispersed areas. Asian Services In Action, a community-based organization in Cleveland, Ohio recruited 10 member organizations to participate in a multisector coalition to identify, plan and implement a PSE strategy reaching AAPIs. Key lessons learned include: the need to navigate competing priorities for member organizations; the value in creating a space where racial/ethnic diversity and cultural adaption are discussed; and the importance of creating a shared learning community for coalition members. As the public health landscape shifts toward effectively improving community health through PSE strategies, it is vital that multisector coalitions are included to potentially have the greatest impact in health overall and to increase community engagement and buy-in.

  9. Genome-Wide Study of Percent Emphysema on Computed Tomography in the General Population. The Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study

    Science.gov (United States)

    Manichaikul, Ani; Hoffman, Eric A.; Smolonska, Joanna; Gao, Wei; Cho, Michael H.; Baumhauer, Heather; Budoff, Matthew; Austin, John H. M.; Washko, George R.; Carr, J. Jeffrey; Kaufman, Joel D.; Pottinger, Tess; Powell, Charles A.; Wijmenga, Cisca; Zanen, Pieter; Groen, Harry J. M.; Postma, Dirkje S.; Wanner, Adam; Rouhani, Farshid N.; Brantly, Mark L.; Powell, Rhea; Smith, Benjamin M.; Rabinowitz, Dan; Raffel, Leslie J.; Hinckley Stukovsky, Karen D.; Crapo, James D.; Beaty, Terri H.; Hokanson, John E.; Silverman, Edwin K.; Dupuis, Josée; O’Connor, George T.; Boezen, H. Marike; Rich, Stephen S.

    2014-01-01

    Rationale: Pulmonary emphysema overlaps partially with spirometrically defined chronic obstructive pulmonary disease and is heritable, with moderately high familial clustering. Objectives: To complete a genome-wide association study (GWAS) for the percentage of emphysema-like lung on computed tomography in the Multi-Ethnic Study of Atherosclerosis (MESA) Lung/SNP Health Association Resource (SHARe) Study, a large, population-based cohort in the United States. Methods: We determined percent emphysema and upper-lower lobe ratio in emphysema defined by lung regions less than −950 HU on cardiac scans. Genetic analyses were reported combined across four race/ethnic groups: non-Hispanic white (n = 2,587), African American (n = 2,510), Hispanic (n = 2,113), and Chinese (n = 704) and stratified by race and ethnicity. Measurements and Main Results: Among 7,914 participants, we identified regions at genome-wide significance for percent emphysema in or near SNRPF (rs7957346; P = 2.2 × 10−8) and PPT2 (rs10947233; P = 3.2 × 10−8), both of which replicated in an additional 6,023 individuals of European ancestry. Both single-nucleotide polymorphisms were previously implicated as genes influencing lung function, and analyses including lung function revealed independent associations for percent emphysema. Among Hispanics, we identified a genetic locus for upper-lower lobe ratio near the α-mannosidase–related gene MAN2B1 (rs10411619; P = 1.1 × 10−9; minor allele frequency [MAF], 4.4%). Among Chinese, we identified single-nucleotide polymorphisms associated with upper-lower lobe ratio near DHX15 (rs7698250; P = 1.8 × 10−10; MAF, 2.7%) and MGAT5B (rs7221059; P = 2.7 × 10−8; MAF, 2.6%), which acts on α-linked mannose. Among African Americans, a locus near a third α-mannosidase–related gene, MAN1C1 (rs12130495; P = 9.9 × 10−6; MAF, 13.3%) was associated with percent emphysema. Conclusions: Our results suggest that some genes previously identified as

  10. New variants near RHOJ and C2, HLA-DRA region and susceptibility to endometriosis in the Polish population-The genome-wide association study.

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    Sobalska-Kwapis, Marta; Smolarz, Beata; Słomka, Marcin; Szaflik, Tomasz; Kępka, Ewa; Kulig, Bartosz; Siewierska-Górska, Anna; Polak, Grzegorz; Romanowicz, Hanna; Strapagiel, Dominik; Szyłło, Krzysztof

    2017-10-01

    Endometriosis is a common gynaecological disease, associated with severe pelvic pain and reduced fertility; however, molecular mechanisms remain largely unknown. Genome-wide association studies (GWAS) are able to identify genetic loci, which can play significant role during endometriosis development. The study aimed at localisation of new genes and chromosomal loci, the nucleotide variants of which determine the level of susceptibility to endometriosis. Blood samples from 171 patients with endometriosis were used as material for studies. The patients were recruited to the study at the Department of Operative Gynaecology of the Institute of the Polish Mother's Memorial Hospital in Lodz. A control group (n=2934) came from the POPULOUS collection registered at Biobank Lab, Department of Molecular Biophysics, University of Lodz. DNA of the patients with endometriosis was compared with DNA of women free from that disease, the comparison being supported by GWAS. Genome-wide significant correlation was identified between one new, not previously described, single nucleotide polymorphism (SNP), rs10129516, localised on chromosome 14 in intergenic region between PARP1P2 and RHOJ genes (p=1.44×10 -10 , OR=3.104, 95% CI=2.329-4.136) and endometriosis. We have also identified significant association with endometriosis of 18 SNPs localised on chromosome 6 in position range 31883957 - 32681631 (C2 and HLA-DRA genes region) with the lowest observed p value for rs644045 in C2 gene (p=2.04×10 -8 , OR=1.955, 95% CI=1.541-2.480). Reported GWAS identified the novel loci associated with endometriosis in Polish women, not previously reported. The most interesting observation shown in our study are regions associated with susceptibility to endometriosis of loci located near C2, HLA-DRA and RHOJ genes. of that study did not correspond to previously published data about polymorphism in that regions and further evaluations are necessary in groups with higher numbers of patients to explain

  11. Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population

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    Ai Huashui

    2009-02-01

    Full Text Available Abstract Background Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL for three traits related to teat number including the total teat number (TTN, the teat number at the left (LTN and right (RTN sides in a large scale White Duroc × Erhualian resource population. Results A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12. Conclusion The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small

  12. Bladder Morbidity and Hepatic Fibrosis in Mixed Schistosoma haematobium and S. mansoni Infections: A Population-Wide Study in Northern Senegal

    Science.gov (United States)

    Meurs, Lynn; Mbow, Moustapha; Vereecken, Kim; Menten, Joris; Mboup, Souleymane; Polman, Katja

    2012-01-01

    Background The global distribution map of schistosomiasis shows a large overlap of Schistosoma haematobium- and S. mansoni-endemic areas in Africa. Yet, little is known about the consequences of mixed Schistosoma infections for the human host. A recent study in two neighboring co-endemic communities in Senegal indicated that infection intensities of both species were higher in mixed than in single infections. Here, we investigated the relationship between mixed Schistosoma infections and morbidity in the same population. So far, this has only been studied in children. Methods Schistosoma infection was assessed by microscopy. Schistosoma-specific morbidity was assessed by ultrasound according to WHO guidelines. Multivariable logistic regression models were used to identify independent risk factors for morbidity. Principal Findings Complete parasitological and morbidity data were obtained from 403 individuals. Schistosoma haematobium-specific bladder morbidity was observed in 83% and S. mansoni-specific hepatic fibrosis in 27% of the participants. Bladder morbidity was positively associated with S. haematobium infection intensity (OR = 1.9 (95% CI 1.3–2.9) for a 10-fold increase in intensity). Moreover, people with mixed infections tended to have less bladder morbidity than those with single S. haematobium infections (OR = 0.3 (95% CI 0.1–1.1)). This effect appeared to be related to ectopic S. mansoni egg elimination in urine. Hepatic fibrosis on the other hand was not related to S. mansoni infection intensity (OR = 0.9 (95% CI 0.6–1.3)), nor to mixed infections (OR = 1.0 (95% CI 0.7–1.7)). Conclusions/Significance This is the first population-wide study on the relationship between mixed Schistosoma infections and morbidity. Mixed infections did not increase the risk of S. mansoni-associated morbidity. They even tended to reduce the risk of S. haematobium-associated morbidity, suggesting a protective effect of S. mansoni infection on bladder

  13. Genome-wide association study for lactation characteristics, milk yield and age at first calving in a Thai multibreed dairy cattle population

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    Pimchanok Yodklaew

    2017-06-01

    Full Text Available A genome-wide association study was performed for milk yield per lactation (MY, initial yield (IY, peak yield (PY, persistency (PS and age at first calving (AFC in a Thai multibreed dairy cattle population. The dataset contained 1305 first-lactation cows raised on 188 farms located in Central, Northeastern and Southern Thailand. Cows were genotyped with GeneSeek Genomic Profiler low-density bead chips (8810 single nucleotide polymorphism [SNP]; n = 1255 and with high-density bead chips (76,883 SNP; n = 50. The single SNP association analyses utilized 8096 SNPs in common between the low and high density GeneSeek chips. The mixed model contained the fixed effects of contemporary group, fraction of non-Holstein breeds, age at first calving and gene content, and the random effects of animal and residual. Computations were done with the QXPAK.5 software. The number of SNPs associated with MY, IY, PY, PS and AFC at the significant threshold level of p < 0.00001 were 75, 102, 145, 74 and 24, respectively. Of the 366 SNP markers significantly associated with the studied traits, 54 (14.75% were associated with two traits and 312 (85.25% with only one trait, and all but one of the 54 SNPs associated with two traits affected MY and lactation characteristics. Genetic improvement of Thai dairy cows for lactation characteristics, milk yield and age at first calving could be aided by selecting animals with the SNP markers found to be highly associated with genes influencing these traits.

  14. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits.

    Science.gov (United States)

    Casiró, S; Velez-Irizarry, D; Ernst, C W; Raney, N E; Bates, R O; Charles, M G; Steibel, J P

    2017-02-01

    Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL

  15. Aedes albopictus: it's invasion, expansion of range, and the use of an area wide management project to control its population in the USA.

    Science.gov (United States)

    Aedes albopictus invaded the U.S.A. between 1983-85. It has become a widely distributed nuisance pest. A n ARS-sponsored 5 year Area Wide Pest Management cooperative program between USDA-ARS, Mosquito and Fly Research Unit (Florida), Rutgers University (New Jersey) and Brandeis University (Massach...

  16. Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs

    Science.gov (United States)

    Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we exami...

  17. The Association of Type 2 Diabetes Loci Identified in Genome-Wide Association Studies with Metabolic Syndrome and Its Components in a Chinese Population with Type 2 Diabetes.

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    Xiaomu Kong

    Full Text Available Metabolic syndrome (MetS is prevalent in type 2 diabetes (T2D patients. The comorbidity of MetS and T2D increases the risk of cardiovascular complications. The aim of the present study was to determine the T2D-related genetic variants that contribute to MetS-related components in T2D patients of Chinese ancestry. We successfully genotyped 25 genome wide association study validated T2D-related single nucleotide polymorphisms (SNPs among 5,169 T2D individuals and 4,560 normal glycemic controls recruited from the Chinese National Diabetes and Metabolic Disorders Study (DMS. We defined MetS in this population using the harmonized criteria (2009 combined with the Chinese criteria for abdominal obesity. The associations between SNPs and MetS-related components, as well as the associations between SNPs and risk for T2D with or without MetS, were subjected to logistic regression analysis adjusted for age and sex. Results showed that the T2D risk alleles of rs243021 located near BCL11A, rs10830963 in MTNR1B, and rs2237895 in KCNQ1 were related to a lower risk for abdominal obesity in T2D patients (rs243021: 0.92 (0.84, 1.00, P = 4.42 × 10-2; rs10830963: 0.92 (0.85, 1.00, P = 4.07 × 10-2; rs2237895: 0.89 (0.82, 0.98, P = 1.29 × 10-2. The T2D risk alleles of rs972283 near KLF14 contributed to a higher risk of elevated blood pressure (1.10 (1.00, 1.22, P = 4.48 × 10-2, while the T2D risk allele of rs7903146 in TCF7L2 was related to a lower risk for elevated blood pressure (0.74 (0.61, 0.90, P = 2.56 × 10-3. The T2D risk alleles of rs972283 near KLF14 and rs11634397 near ZFAND6 were associated with a higher risk for elevated triglycerides (rs972283: 1.11 (1.02, 1.24, P = 1.46 × 10-2; rs11634397: 1.14 (1.00, 1.29, P = 4.66 × 10-2, while the T2D risk alleles of rs780094 in GCKR and rs7903146 in TCF7L2 were related to a lower risk of elevated triglycerides (rs780094: 0.86 (0.80, 0.93, P = 1.35 × 10-4; rs7903146: 0.82 (0.69, 0.98, P = 3.18 × 10-2. The

  18. Population-wide weight loss and regain in relation to diabetes burden and cardiovascular mortality in Cuba 1980-2010: repeated cross sectional surveys and ecological comparison of secular trends.

    Science.gov (United States)

    Franco, Manuel; Bilal, Usama; Orduñez, Pedro; Benet, Mikhail; Morejón, Alain; Caballero, Benjamín; Kennelly, Joan F; Cooper, Richard S

    2013-04-09

    To evaluate the associations between population-wide loss and gain in weight with diabetes prevalence, incidence, and mortality, as well as cardiovascular and cancer mortality trends, in Cuba over a 30 year interval. Repeated cross sectional surveys and ecological comparison of secular trends. Cuba and the province of Cienfuegos, from 1980 to 2010. Measurements in Cienfuegos included a representative sample of 1657, 1351, 1667, and 1492 adults in 1991, 1995, 2001, and 2010, respectively. National surveys included a representative sample of 14 304, 22 851, and 8031 participants in 1995, 2001, and 2010, respectively. Changes in smoking, daily energy intake, physical activity, and body weight were tracked from 1980 to 2010 using national and regional surveys. Data for diabetes prevalence and incidence were obtained from national population based registries. Mortality trends were modelled using national vital statistics. Rapid declines in diabetes and heart disease accompanied an average population-wide loss of 5.5 kg in weight, driven by an economic crisis in the mid-1990s. A rebound in population weight followed in 1995 (33.5% prevalence of overweight and obesity) and exceeded pre-crisis levels by 2010 (52.9% prevalence). The population-wide increase in weight was immediately followed by a 116% increase in diabetes prevalence and 140% increase in diabetes incidence. Six years into the weight rebound phase, diabetes mortality increased by 49% (from 9.3 deaths per 10 000 people in 2002 to 13.9 deaths per 10 000 people in 2010). A deceleration in the rate of decline in mortality from coronary heart disease was also observed. In relation to the Cuban experience in 1980-2010, there is an association at the population level between weight reduction and death from diabetes and cardiovascular disease; the opposite effect on the diabetes and cardiovascular burden was seen on population-wide weight gain.

  19. Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel

    Science.gov (United States)

    Inoue, K; Monroe, E M; Elderkin, C L; Berg, D J

    2014-01-01

    Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure throughout its range. Mitochondrial DNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in most populations; however, all populations have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them. PMID:24149656

  20. Drought tolerance and growth in populations of a wide-ranging tree species indicate climate change risks for the boreal north.

    Science.gov (United States)

    Montwé, David; Isaac-Renton, Miriam; Hamann, Andreas; Spiecker, Heinrich

    2016-02-01

    Choosing drought-tolerant planting stock in reforestation programs may help adapt forests to climate change. To inform such reforestation strategies, we test lodgepole pine (Pinus contorta Doug. ex Loud. var latifolia Englm.) population response to drought and infer potential benefits of a northward transfer of seeds from drier, southern environments. The objective is addressed by combining dendroecological growth analysis with long-term genetic field trials. Over 500 trees originating from 23 populations across western North America were destructively sampled in three experimental sites in southern British Columbia, representing a climate warming scenario. Growth after 32 years from provenances transferred southward or northward over long distances was significantly lower than growth of local populations. All populations were affected by a severe natural drought event in 2002. The provenances from the most southern locations showed the highest drought tolerance but low productivity. Local provenances were productive and drought tolerant. Provenances from the boreal north showed lower productivity and less drought tolerance on southern test sites than all other sources, implying that maladaptation to drought may prevent boreal populations from taking full advantage of more favorable growing conditions under projected climate change. © 2015 John Wiley & Sons Ltd.

  1. RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

    Science.gov (United States)

    Benestan, Laura; Gosselin, Thierry; Perrier, Charles; Sainte-Marie, Bernard; Rochette, Rémy; Bernatchez, Louis

    2015-07-01

    Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species' range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species' natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT  = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST  = 0.00185; CI: 0.0007-0.0021, P-value < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST . Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid 'high-grading bias', 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence. © 2015 John Wiley & Sons Ltd.

  2. A genome-wide association study for diabetic retinopathy in a Japanese population: potential association with a long intergenic non-coding RNA.

    Directory of Open Access Journals (Sweden)

    Takuya Awata

    Full Text Available Elucidation of the genetic susceptibility factors for diabetic retinopathy (DR is important to gain insight into the pathogenesis of DR, and may help to define genetic risk factors for this condition. In the present study, we conducted a three-stage genome-wide association study (GWAS to identify DR susceptibility loci in Japanese patients, which comprised a total of 837 type 2 diabetes patients with DR (cases and 1,149 without DR (controls. From the stage 1 genome-wide scan of 446 subjects (205 cases and 241 controls on 614,216 SNPs, 249 SNPs were selected for the stage 2 replication in 623 subjects (335 cases and 288 controls. Eight SNPs were further followed up in a stage 3 study of 297 cases and 620 controls. The top signal from the present association analysis was rs9362054 in an intron of RP1-90L14.1 showing borderline genome-wide significance (Pmet = 1.4×10(-7, meta-analysis of stage 1 and stage 2, allele model. RP1-90L14.1 is a long intergenic non-coding RNA (lincRNA adjacent to KIAA1009/QN1/CEP162 gene; CEP162 plays a critical role in ciliary transition zone formation before ciliogenesis. The present study raises the possibility that the dysregulation of ciliary-associated genes plays a role in susceptibility to DR.

  3. Genome-wide mapping of spike-related and agronomic traits in a common wheat population derived from a supernumerary parent and an elite parent

    Science.gov (United States)

    In wheat (Triticum aestivum L), exotic genotypes express a broad range of spike-related traits and could be used as a source of new genes to enrich the germplasm for wheat breeding programs. In the present study, a population of 163 recombinant inbred lines derived from a cross between an elite line...

  4. Barriers to cross-fertilization between populations of a widely dispersed polychaete species are unlikely to have arisen through gametic compatibility arms-races.

    Science.gov (United States)

    Styan, Craig A; Kupriyanova, Elena; Havenhand, Jon N

    2008-12-01

    Although there are theoretical reasons to suspect that gametic incompatibility may develop readily among populations of broadcast spawning marine invertebrates, there have been very few studies documenting geographic patterns of interpopulation incompatibility for any species. To address this we determined how successfully individuals of the intertidal serpulid polychaete, Galeolaria caespitosa, can cross-fertilize within and among populations from across temperate Australia. Fertilization assays revealed asymmetrical differences between very distantly located populations from different coasts, with near-complete incompatibility between eggs from Sydney with sperm from Adelaide, but the reverse cross (Adelaide eggs, Sydney sperm) was reasonably compatible. Although that pattern was congruent with a clear difference in Cytochrome B sequences between worms on the south and east coasts of Australia, we also detected some indication of interpopulation incompatibility within the genetic grouping on east coast, between two populations separated by only 220 km. We then assessed whether commonly proposed gametic compatibility arms-races could account for these patterns. Our results suggest reduced gametic compatibility may reduce a female's maximum fertilization potential, resulting in a cost to this potential mechanism for reducing polyspermy. Consequently, the apparently rapid development of reproductive barriers here seems unlikely to have been driven by arms-races involving sexual conflict over fertilization rate.

  5. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

    DEFF Research Database (Denmark)

    Besenbacher, Søren; Liu, Siyang; Gonzalez-Izarzugaza, Jose Maria

    2015-01-01

    Building a population-specific catalogue of single nucleotide variants (SNVs), indels andstructural variants (SVs) with frequencies, termed a national pan-genome, is critical forfurther advancing clinical and public health genetics in large cohorts. Here we report a Danishpan-genome obtained from...

  6. Open Access Resources for Genome Wide Association Studies (GWAS) in rice (Oryza sativa) illustrate the power of population-specific mapping

    Science.gov (United States)

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. New sources of genetic variation are key to enhancing the productivity, sustainability and resilience of crop varieties and agricultural systems that...

  7. Health-related quality of life in inflammatory bowel disease in a European-wide population-based cohort 10 years after diagnosis

    DEFF Research Database (Denmark)

    Huppertz-Hauss, Gert; Høivik, Marte Lie; Langholz, Ebbe

    2015-01-01

    countries were invited to a follow-up visit 10 years after their diagnosis of IBD. We assessed their clinical and demographic data, including the generic HRQoL questionnaire short form health survey-36. Countrywise comparison with the background population was performed with z-scores using the Cohen...

  8. Effects of flow regimes altered by dams on survival, population declines, and range-wide losses of California river-breeding frogs.

    Science.gov (United States)

    Kupferberg, Sarah J; Palen, Wendy J; Lind, Amy J; Bobzien, Steve; Catenazzi, Alessandro; Drennan, Joe; Power, Mary E

    2012-06-01

    Widespread alteration of natural hydrologic patterns by large dams combined with peak demands for power and water delivery during summer months have resulted in frequent aseasonal flow pulses in rivers of western North America. Native species in these ecosystems have evolved with predictable annual flood-drought cycles; thus, their likelihood of persistence may decrease in response to disruption of the seasonal synchrony between stable low-flow conditions and reproduction. We evaluated whether altered flow regimes affected 2 native frogs in California and Oregon (U.S.A.) at 4 spatial and temporal extents. We examined changes in species distribution over approximately 50 years, current population density in 11 regulated and 16 unregulated rivers, temporal trends in abundance among populations occupying rivers with different hydrologic histories, and within-year patterns of survival relative to seasonal hydrology. The foothill yellow-legged frog (Rana boylii), which breeds only in flowing water, is more likely to be absent downstream of large dams than in free-flowing rivers, and breeding populations are on average 5 times smaller in regulated rivers than in unregulated rivers. Time series data (range = 8 - 19 years) from 5 populations of yellow-legged frogs and 2 populations of California red-legged frogs (R. draytonii) across a gradient of natural to highly artificial timing and magnitude of flooding indicate that variability of flows in spring and summer is strongly correlated with high mortality of early life stages and subsequent decreases in densities of adult females. Flow management that better mimics natural flow timing is likely to promote persistence of these species and others with similar phenology. ©2012 Society for Conservation Biology.

  9. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

    Science.gov (United States)

    Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

    2017-08-01

    Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

  10. Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study.

    Science.gov (United States)

    Panni, Tommaso; Mehta, Amar J; Schwartz, Joel D; Baccarelli, Andrea A; Just, Allan C; Wolf, Kathrin; Wahl, Simone; Cyrys, Josef; Kunze, Sonja; Strauch, Konstantin; Waldenberger, Melanie; Peters, Annette

    2016-07-01

    Epidemiological studies have reported associations between particulate matter (PM) concentrations and cancer and respiratory and cardiovascular diseases. DNA methylation has been identified as a possible link but so far it has only been analyzed in candidate sites. We studied the association between DNA methylation and short- and mid-term air pollution exposure using genome-wide data and identified potential biological pathways for additional investigation. We collected whole blood samples from three independent studies-KORA F3 (2004-2005) and F4 (2006-2008) in Germany, and the Normative Aging Study (1999-2007) in the United States-and measured genome-wide DNA methylation proportions with the Illumina 450k BeadChip. PM concentration was measured daily at fixed monitoring stations and three different trailing averages were considered and regressed against DNA methylation: 2-day, 7-day and 28-day. Meta-analysis was performed to pool the study-specific results. Random-effect meta-analysis revealed 12 CpG (cytosine-guanine dinucleotide) sites as associated with PM concentration (1 for 2-day average, 1 for 7-day, and 10 for 28-day) at a genome-wide Bonferroni significance level (p ≤ 7.5E-8); 9 out of these 12 sites expressed increased methylation. Through estimation of I2 for homogeneity assessment across the studies, 4 of these sites (annotated in NSMAF, C1orf212, MSGN1, NXN) showed p > 0.05 and I2 F3, KORA F4, and the Normative Aging Study. Environ Health Perspect 124:983-990; http://dx.doi.org/10.1289/ehp.1509966.

  11. Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)

    OpenAIRE

    Henriques, Dora; Chavez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. Alice

    2012-01-01

    The black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental be...

  12. Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure

    Directory of Open Access Journals (Sweden)

    Solbach Werner

    2007-10-01

    Full Text Available Abstract Background Chlamydophila pneumoniae is an obligate intracellular bacterium that replicates in a biphasic life cycle within eukaryotic host cells. Four published genomes revealed an identity of > 99 %. This remarkable finding raised questions about the existence of distinguishable genotypes in correlation with geographical and anatomical origin. Results We studied the genetic diversity of C. pneumoniae by analysing synonymous single nucleotide polymorphisms (sSNPs that are under reduced selection pressure. We conducted an in silico analysis of the four sequenced genomes, chose 232 representative sSNPs and analysed the loci in 38 C. pneumoniae isolates. We identified 15 different genotypes that were separated in four major clusters. Clusters were not associated with anatomical or geographical origin. However, animal lineages are basal on the C. pneumomiae phylogeny, suggesting a recent transmission to humans through successive bottlenecks some 150,000 years ago. A lack of detectable variation in 17 isolates emphasizes the extraordinary genetic conservation of this species and the high clonality of the population. Moreover, the largest cluster, which encompasses 80% of all analysed strains, is an extremely young clade, that went through an important population expansion some 3,300 years ago. Conclusion sSNPs have proven useful as a sensitive marker to gain new insights into genetic diversity, population structure and evolutionary history of C. pneumoniae.

  13. Mortality due to traumatic spinal cord injuries in Europe: a cross-sectional and pooled analysis of population-wide data from 22 countries.

    Science.gov (United States)

    Majdan, Marek; Plancikova, Dominika; Nemcovska, Eva; Krajcovicova, Lenka; Brazinova, Alexandra; Rusnak, Martin

    2017-07-03

    Traumatic spinal cord injuries (TSCI) pose a significant burden globally, while existing epidemiological data-especially on population mortality-are limited. The aim of this study was to calculate the age-standardized population mortality rates attributable to TSCI in 22 European countries, along with the pooled age-standardized mortality rate attributable to TSCI in Europe. A descriptive cross-sectional epidemiological study was conducted. Crude and age-standardized mortality rates attributable to TSCI for the year 2012 for 22 European countries were compared using data from death certificates provided by Eurostat. Pooled age-standardized mortality rates were calculated using the random effects model, and overall number of cases were estimated by extrapolating our findings to the populations of EU and Europe (48 countries), in 2012. A total of 1840 TSCI-related deaths were identified, of which 1084 (59%) were males. The pooled age-standardized TSCI-related mortality rate of 6.7 per million (95% CI: 5.2 to 8.2) overall, 9.4 (95% CI: 7.3 to 11.5) for males, and 4.5 (95% CI: 3.4 to 5.6) for females. Extrapolating our results, 3152 (95% CI: 2441 to 3915) deaths would occur in 2012 in the EU-28 and 4570 (95% CI: 3538 to 5675) deaths in the whole Europe. TSCI-related deaths contributed by 2% (95% CI: 1.8% to 2.2%) to the overall injury related mortality. 61% of fatal TSCI were located in the cervical spine area. To our knowledge, this is the largest study that reports TSCI-related population-based mortalities to date which brings valuable information that can inform further research or prevention strategies. Our study presents a comprehensive and large-scale overview of TSCI-related population mortality in Europe. With an estimated toll of nearly five thousand lives that could be potentially saved by prevention, our findings confirm TSCI as an important cause of injury related deaths in Europe. Further action towards harmonization of case ascertainment and towards

  14. Tensile properties of the hip joint ligaments are largely variable and age-dependent - An in-vitro analysis in an age range of 14-93 years.

    Science.gov (United States)

    Schleifenbaum, Stefan; Prietzel, Torsten; Hädrich, Carsten; Möbius, Robert; Sichting, Freddy; Hammer, Niels

    2016-10-03

    Hip joint stability is maintained by the surrounding ligaments, muscles, and the atmospheric pressure exerted via these structures. It is unclear whether the ligaments are capable of preventing dislocation solely due to their tensile properties, and to what extent they undergo age-related changes. This study aimed to obtain stress-strain data of the hip ligaments over a large age range. Stress-strain data of the iliofemoral (IL), ischiofemoral (IS) and pubofemoral ligament (PF) were obtained from cadavers ranging between 14 and 93 years using a highly standardized setting. Maximum strains were compared to the distances required for dislocation. Elastic modulus was 24.4 (IL), 22.4 (IS) and 24.9N/mm(2) (PF) respectively. Maximum strain was 84.5%, 86.1%, 72.4% and ultimate stress 10.0, 7.7 and 6.5N/mm(2) for the IL, IS and PF respectively. None of these values varied significantly between ligaments or sides. The IS' elastic modulus was higher and maximum strain lower in males. Lower elastic moduli of the PF and higher maximum strains for the IS and PF were revealed in the ≥55 compared to the ligaments are largely variable. The IS and PF change age-dependently. Though the hip ligaments contribute to hip stability, the IS and cranial IL may not prevent dislocation due to their elasticity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Genome-wide discovery of single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in deep-sea mussels: Potential use in population genomics and cross-species application

    Science.gov (United States)

    Xu, Ting; Sun, Jin; Lv, Jia; Kayama Watanabe, Hiromi; Li, Tianqi; Zou, Weiwen; Rouse, Greg W.; Wang, Shi; Qian, Pei-Yuan; Bao, Zhenmin; Qiu, Jian-Wen

    2017-03-01

    The present study aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for the deep-sea mussel Bathymodiolus platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) sequencing, assess the potential use of SNPs in detecting fine-sale population genetic structure and signatures of divergent selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781,720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified by 2b-RAD for 28 B. platifrons individuals collected from a seep and a vent population. Among these SNPs, nine outliers showed significant evidence for divergent selection, and their positions in the genes or scaffolds were identified. The FST estimated based on the putative neutral SNPs was low (0.0126) indicating the two B. platifrons populations having a high genetic connectivity. However, the permutation test detected significant differences (Pgenome survey sequencing and 2b-RAD to rapidly generate genomic resources for use in fine-scale population genetic studies, and various cross-species applications.

  16. Genome-wide association study identifies 22 new loci for body dimension and body weight traits in a White Duroc×Erhualian F2 intercross population.

    Science.gov (United States)

    Ji, Jiuxiu; Zhou, Lisheng; Guo, Yuanmei; Huang, Lusheng; Ma, Junwu

    2017-08-01

    Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. A genome-wide association study (GWAS) on body dimension and body weight traits was performed in a White Duroc×Erhualian F2 intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs) and the phenotypes. In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs) on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level (5×10-4), three QTLs exceeded the genome-wide significance threshold (1.15×10-6). Except the one on Sus scrofa chromosome (SSC) 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes' role and further identifying causative variants underlying these loci.

  17. Genome-wide association study identifies 22 new loci for body dimension and body weight traits in a White Duroc×Erhualian F intercross population

    Directory of Open Access Journals (Sweden)

    Jiuxiu Ji

    2017-08-01

    Full Text Available Objective Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. Methods A genome-wide association study (GWAS on body dimension and body weight traits was performed in a White Duroc×Erhualian F2 intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs and the phenotypes. Results In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level (5×10−4, three QTLs exceeded the genome-wide significance threshold (1.15×10−6. Except the one on Sus scrofa chromosome (SSC 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. Conclusion The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes’ role and further identifying causative variants underlying these loci.

  18. Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume

    Directory of Open Access Journals (Sweden)

    Kaifeng Ma

    2018-01-01

    Full Text Available Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP and methylation-sensitive amplified polymorphism (MSAP techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80% was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77% was higher than the relative full methylation level (14.03%. The epigenetic diversity (I∗ = 0.575, h∗ = 0.393 was higher than the genetic diversity (I = 0.484, h = 0.319. The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.

  19. Prevalence of risk factors for acquiring measles during the 2011 outbreak in Quebec and impact of the province-wide school-based vaccination campaign on population immunity.

    Science.gov (United States)

    Billard, Marie-Noëlle; De Serres, Gaston; Gariépy, Marie-Claude; Boulianne, Nicole; Toth, Eveline; Landry, Monique; Skowronski, Danuta M

    2017-01-01

    A large measles outbreak occurred in Quebec, Canada, in 2011. Although nearly two-thirds of the cases occurred in only two health districts, a mass vaccination campaign targeting all Quebec elementary and high school students without valid two-dose history was undertaken to prevent future outbreaks. We compared rates of non-vaccination and age at first measles vaccine dose among students in the two most-affected districts and the rest of the province and estimated the improvement in overall student measles immunity due to the mass school-based vaccination campaign. Data were extracted from the provincial vaccination registry for students in kindergarten to grade 11 during the 2011/2012 school year. A telephone survey was conducted in three sub-groups: students whose first measles vaccine dose recorded in the vaccination registry was received during the 2011 school vaccination campaign; students with no dose recorded in the registry whose parents refused receipt during the school campaign; and students with no dose recorded in the registry and no information about parental consent/refusal during the school campaign. Neither the prevalence of being non-vaccinated nor a younger age at first pediatric dose were higher in the two most-affected districts versus the rest of the province. The school campaign vaccinated nearly 8% of all students including 7% who previously received at least one dose. Before the outbreak, 3% of students were not vaccinated and one-third of these (1%/3%) were vaccinated during the campaign. The campaign likely increased the absolute school population immunity by just 1.7%. The concentration of measles cases in the two most-affected health districts during the large Quebec outbreak is not explained by more students who were unvaccinated or who had received their first vaccine dose at a younger age. The vaccination campaign reached one-third of unvaccinated students and only marginally improved population immunity.

  20. Genome-wide sequencing and an open reading frame analysis of dichlorodiphenyltrichloroethane (DDT susceptible (91-C and resistant (91-R Drosophila melanogaster laboratory populations.

    Directory of Open Access Journals (Sweden)

    Laura D Steele

    Full Text Available The Drosophila melanogaster 91-R and 91-C strains are of common origin, however, 91-R has been intensely selected for dichlorodiphenyltrichloroethane (DDT resistance over six decades while 91-C has been maintained as the non-selected control strain. These fly strains represent a unique genetic resource to understand the accumulation and fixation of mutations under laboratory conditions over decades of pesticide selection. Considerable research has been done to investigate the differential expression of genes associated with the highly DDT resistant strain 91-R, however, with the advent of whole genome sequencing we can now begin to develop an in depth understanding of the genomic changes associated with this intense decades-long xenobiotic selection pressure. Here we present the first whole genome sequencing analysis of the 91-R and 91-C fly strains to identify genome-wide structural changes within the open reading frames. Between-strain changes in allele frequencies revealed a higher percent of new alleles going to fixation for the 91-R strain, as compared to 91-C (P<0.0001. These results suggest that resistance to DDT in the 91-R laboratory strain could potentially be due primarily to new mutations, as well as being polygenic rather than the result of a few major mutations, two hypotheses that remain to be tested.

  1. Genome-wide sequencing and an open reading frame analysis of dichlorodiphenyltrichloroethane (DDT) susceptible (91-C) and resistant (91-R) Drosophila melanogaster laboratory populations.

    Science.gov (United States)

    Steele, Laura D; Muir, William M; Seong, Keon Mook; Valero, M Carmen; Rangesa, Madhumitha; Sun, Weilin; Clark, John M; Coates, Brad; Pittendrigh, Barry R

    2014-01-01

    The Drosophila melanogaster 91-R and 91-C strains are of common origin, however, 91-R has been intensely selected for dichlorodiphenyltrichloroethane (DDT) resistance over six decades while 91-C has been maintained as the non-selected control strain. These fly strains represent a unique genetic resource to understand the accumulation and fixation of mutations under laboratory conditions over decades of pesticide selection. Considerable research has been done to investigate the differential expression of genes associated with the highly DDT resistant strain 91-R, however, with the advent of whole genome sequencing we can now begin to develop an in depth understanding of the genomic changes associated with this intense decades-long xenobiotic selection pressure. Here we present the first whole genome sequencing analysis of the 91-R and 91-C fly strains to identify genome-wide structural changes within the open reading frames. Between-strain changes in allele frequencies revealed a higher percent of new alleles going to fixation for the 91-R strain, as compared to 91-C (PDDT in the 91-R laboratory strain could potentially be due primarily to new mutations, as well as being polygenic rather than the result of a few major mutations, two hypotheses that remain to be tested.

  2. Genetic parameters of measures and population-wide infrared predictions of 92 traits describing the fine composition and technological properties of milk in Italian Simmental cattle.

    Science.gov (United States)

    Bonfatti, V; Vicario, D; Lugo, A; Carnier, P

    2017-07-01

    The objectives of this study were to estimate, for the Italian Simmental cattle population, genetic parameters for 92 traits and their infrared predictions (IP) and to investigate the genetic relationship between measured traits (MT) and IP. Data for milk fat fatty acid composition (n = 1,040), detailed protein composition (n = 3,337), lactoferrin (n = 558), pH (n = 3,438), coagulation properties (n = 3,266), curd yield and composition obtained by a micro-cheese making procedure (n = 1,177), and content of Ca, P, Mg, and K (n = 689) were obtained using reference laboratory analysis. Infrared prediction for all the investigated traits was performed using 143,198 spectra records belonging to 17,619 Italian Simmental cows. (Co)variance components for MT and their IP were estimated in a set of bivariate animal model REML analyses and genetic correlations between MT and IP were estimated using all IP obtained at the population level. A significant positive relationship was observed between the coefficient of determination of the infrared prediction models and the phenotypic and genetic variation of the IP. The decrease in the estimated genetic variance of IP compared with MT was on average 64%. For traits exhibiting calibration models with coefficients of determination in cross-validation (R2CV) greater than 0.9, the decrease in the genetic variance ranged from approximately 20 to 50%. Most traits (88 out of 92) exhibited lower heritability estimates for IP than for the corresponding MT. The estimated genetic correlations between IP and MT (ra) were in general very high. A positive relationship (r = 0.57) between R2CV of calibration models and the estimated ra has been detected. For calibration models exhibiting R2CV higher than 0.75, ra were greater than 0.9. The variability in the estimated correlations increased when R2CV decreased, and for calibration models of moderate predictive ability, estimates of ra ranged from 0.2 to 1. Genetic parameter estimates suggested

  3. Family load estimates of schizophrenia and associated risk factors in a nation-wide population study of former child and adolescent patients up to forty years of age.

    Science.gov (United States)

    Helenius, Dorte; Munk-Jørgensen, Povl; Steinhausen, Hans-Christoph

    2012-08-01

    This nation-wide register-based study investigates the family load of schizophrenia (SZ) across three generations in affected families compared to control families. Furthermore the study compares the family load in case vs. control families considering the age of onset of the disorder in the cases. In addition, the study addresses the impact of certain socio-demographic risk factors, i.e. sex, region of residence, year of birth, month of birth, and maternal and paternal age at birth. A total of N=2020 child and adolescent psychiatric cases born between 1969 and 1985 registered in the Danish Central Psychiatric Register (DCPR) before the age of 18 developed SZ before the age of 40. N=5982 controls without any psychiatric diagnosis before age 18 were matched for age, sex, and residential region. Psychiatric diagnoses were also obtained on the first-degree relatives, i.e. parents, siblings, and offspring as a part of the Danish Three Generation Study (3GS). A family load was obtained by using various mixed regression models. SZ did occur more often in case than in control families. Having a mother, father or a sibling with the disorder was proven to be a risk factor. The year of birth, the region of residence, and paternal age at birth (≥ 35) were associated with SZ. However, the family load was not dependent on age of onset of the case-proband. Furthermore, case relatives did not develop SZ earlier than control relatives. These findings based on a very large and representative dataset provide further and solid evidence for the high family aggregation of SZ. The year of birth, the region of residence, and paternal age at birth play an additional role in the development of the disorder. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. A common thermal niche among geographically diverse populations of the widely distributed tree species Eucalyptus tereticornis: No evidence for adaptation to climate-of-origin.

    Science.gov (United States)

    Drake, John E; Vårhammar, Angelica; Kumarathunge, Dushan; Medlyn, Belinda E; Pfautsch, Sebastian; Reich, Peter B; Tissue, David T; Ghannoum, Oula; Tjoelker, Mark G

    2017-12-01

    Impacts of climate warming depend on the degree to which plants are constrained by adaptation to their climate-of-origin or exhibit broad climatic suitability. We grew cool-origin, central and warm-origin provenances of Eucalyptus tereticornis in an array of common temperature environments from 18 to 35.5°C to determine if this widely distributed tree species consists of geographically contrasting provenances with differentiated and narrow thermal niches, or if provenances share a common thermal niche. The temperature responses of photosynthesis, respiration, and growth were equivalent across the three provenances, reflecting a common thermal niche despite a 2,200 km geographic distance and 13°C difference in mean annual temperature at seed origin. The temperature dependence of growth was primarily mediated by changes in leaf area per unit plant mass, photosynthesis, and whole-plant respiration. Thermal acclimation of leaf, stem, and root respiration moderated the increase in respiration with temperature, but acclimation was constrained at high temperatures. We conclude that this species consists of provenances that are not differentiated in their thermal responses, thus rejecting our hypothesis of adaptation to climate-of-origin and suggesting a shared thermal niche. In addition, growth declines with warming above the temperature optima were driven by reductions in whole-plant leaf area and increased respiratory carbon losses. The impacts of climate warming will nonetheless vary across the geographic range of this and other such species, depending primarily on each provenance's climate position on the temperature response curves for photosynthesis, respiration, and growth. © 2017 John Wiley & Sons Ltd.

  5. Body mass index and breast cancer: analysis of a nation-wide population-based prospective cohort study on 1 393 985 Taiwanese women.

    Science.gov (United States)

    Chen, M-J; Wu, W Y-Y; Yen, A M-F; Fann, J C-Y; Chen, S L-S; Chiu, S Y-H; Chen, H-H; Chiou, S-T

    2016-03-01

    Asian women have a younger age at onset of breast cancer and a lower body mass index (BMI) than Western women. The link between obesity and risk of breast cancer in Asian women is still elusive. We aimed to investigate the effect of BMI on the risk of incident breast cancer in Taiwanese women. A total of 1,393,985 women who had been cancer-free before recruitment and attended a nation-wide Taiwanese breast cancer-screening program between 1999 and 2009 were enrolled using a prospective cohort study. Obesity and other relevant variables (such as menopause status and other biochemical markers) were collected through in-person interviews, anthropometric measurements and blood samples at first screen. Incident breast cancers during follow-up were ascertained through the linkage of the cohort with the National Cancer Registry and the National Death Certification System. A total of 6969 and 7039 incident breast cancer cases were identified among women enrolled before and after menopause, respectively. Compared with a BMI range of 18.5-23.9 kg m(-)(2), the incremental level of BMI in the enrolled women before menopause revealed a lack of statistically significant association with the risk of incident breast cancer (adjusted hazard ratio=0.94, 0.98, 1.02, 1.01 and 0.82 for BMI women after menopause led to a statistically significant incremental increase in the risk of breast cancer (adjusted hazard ratio=0.78, 1.19, 1.31, 1.53 and 1.65 for BMI breast cancer after menopause in Taiwanese women.

  6. Traumatic Stress during Population-wide Exposure to Trauma in Israel: Gender as a Moderator of the Effects of Marital Status and Social Support.

    Science.gov (United States)

    Israel-Cohen, Yael; Kaplan, Oren

    2016-12-01

    The 'tend-and-befriend' approach (Taylor et al., ) posits that in times of stress, women in particular may tend to their loved ones and seek out social support as a coping mechanism. Two corollaries of this model are that when confronted with a situation of extreme stress, marriage may be more of a protective factor for men, as central beneficiaries of their wives 'tending' or nurturing response, and social support from a wider network may be more of a protective factor for women, as part of women's 'befriending' response to stress. Using a sample of 508 Israelis (M = 47 years; 48% women) under the real condition of a population under missile attacks, we investigated the latter two corollaries of the tend-and-befriend model, hypothesizing that marriage would buffer against symptoms of traumatic stress for men in particular and that social support would buffer against symptoms of traumatic stress for women in particular. Our findings revealed gender differences affirming both hypotheses and offering interpretive evidence in support of the tend-and-befriend model based on a gender-informed field study of responses to traumatic stress in real time. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  7. [What potential do geographic information systems have for population-wide health monitoring in Germany? : Perspectives and challenges for the health monitoring of the Robert Koch Institute].

    Science.gov (United States)

    Thißen, Martin; Niemann, Hildegard; Varnaccia, Gianni; Rommel, Alexander; Teti, Andrea; Butschalowsky, Hans; Manz, Kristin; Finger, Jonas David; Kroll, Lars Eric; Ziese, Thomas

    2017-12-01

    Geographic information systems (GISs) are computer-based systems with which geographical data can be recorded, stored, managed, analyzed, visualized and provided. In recent years, they have become an integral part of public health research. They offer a broad range of analysis tools, which enable innovative solutions for health-related research questions. An analysis of nationwide studies that applied geographic information systems underlines the potential this instrument bears for health monitoring in Germany. Geographic information systems provide up-to-date mapping and visualization options to be used for national health monitoring at the Robert Koch Institute (RKI). Furthermore, objective information on the residential environment as an influencing factor on population health and on health behavior can be gathered and linked to RKI survey data at different geographic scales. Besides using physical information, such as climate, vegetation or land use, as well as information on the built environment, the instrument can link socioeconomic and sociodemographic data as well as information on health care and environmental stress to the survey data and integrate them into concepts for analyses. Therefore, geographic information systems expand the potential of the RKI to present nationwide, representative and meaningful health-monitoring results. In doing so, data protection regulations must always be followed. To conclude, the development of a national spatial data infrastructure and the identification of important data sources can prospectively improve access to high quality data sets that are relevant for the health monitoring.

  8. Cardiovascular Disease and Type 2 Diabetes Risk Across Occupational Groups and Industry in a State Wide Study of an Australian Working Population.

    Science.gov (United States)

    Kelsall, Helen Louise; Fernando, Palamandadige Harsha Suranga; Gwini, Stella May; Sim, Malcolm Ross

    2017-11-13

    To investigate prevalence of type 2 diabetes (diabetes) and cardiovascular disease (CVD) risk in occupational and industry groups in a large, diverse working population. 500,000 Victorian workers undertook health checks including lifestyle, anthropometric and biomedical cardiovascular risk factor assessment. 5-year diabetes (AUSDRISK) and absolute CVD risk were estimated. High diabetes and CVD risk was increased in many occupational groups and industries relative to managers and Professional/Scientific/Technical Services respectively. Significantly more blue collar workers had high diabetes risk (males prevalence ratio PR 1.19 (95% CI 1.17-1.20); females 1.34 (1.30-1.38)), high CVD risk (males 1.45 (1.37-1.53); females 1.48 (1.17-1.88), and risk factors including smoking (males 2.26 (2.22-2.30); females 2.20 (2.13-2.27), compared with white collar workers. Targeting occupational and industry groups within sustainable workplace programs could assist in reducing chronic diseases, lowering sickness absence and improving productivity.

  9. Absence of socioeconomic inequalities in access to good-quality breast cancer treatment within a population-wide screening programme in Turin (Italy).

    Science.gov (United States)

    Zengarini, Nicolás; Ponti, Antonio; Tomatis, Mariano; Casella, Denise; Giordano, Livia; Mano, Maria P; Segnan, Nereo; Whitehead, Margaret; Costa, Giuseppe; Spadea, Teresa

    2016-11-01

    Several studies suggest that population-based breast cancer screening programmes might help reduce social inequalities in breast cancer survival both by increasing early diagnosis and by improving access to effective treatments. To start disentangling the two effects, we evaluated social inequalities in quality of treatment of screen-detected breast cancer in the city of Turin (Italy). Combining data from the Audit System on Quality of Breast Cancer Treatment and the Turin Longitudinal Study, we analysed 2700 cases in the screening target age class 50-69 diagnosed in the period 1995-2008. We selected 10 indicators of the pathway of care, relative to timeliness and appropriateness of diagnosis and treatment, and three indicators of socioeconomic position: education, occupational status and housing characteristics. For each indicator of care, relative risks of failure were estimated by robust Poisson regression models, controlling for calendar period of diagnosis, size of tumour and activity volume of the surgery units. The principal predictor of failure of the good care indicators was the calendar period of diagnosis, with a general improvement with time in the quality of diagnosis and treatment, followed by size of the tumour and volume of activity. Socioeconomic indicators show only a marginal independent effect on timeliness indicators. The observed associations of quality indicators with socioeconomic characteristics are lower than expected, suggesting a possible role of the screening programme in reducing disparities in the access to good-quality treatments thanks to its capability to enter screen-detected women into a protected pathway of care.

  10. ANALYZING STAR CLUSTER POPULATIONS WITH STOCHASTIC MODELS: THE HUBBLE SPACE TELESCOPE/WIDE FIELD CAMERA 3 SAMPLE OF CLUSTERS IN M83

    Energy Technology Data Exchange (ETDEWEB)

    Fouesneau, Morgan; Lancon, Ariane [Observatoire astronomique and CNRS UMR 7550, Universite de Strasbourg, Strasbourg (France); Chandar, Rupali [Department of Physics and Astronomy, University of Toledo, Toledo, OH (United States); Whitmore, Bradley C., E-mail: morgan.fouesneau@astro.u-strasbg.fr [Space Telescope Science Institute, Baltimore, MD (United States)

    2012-05-01

    The majority of clusters in the universe have masses well below 10{sup 5} M{sub Sun }. Hence, their integrated fluxes and colors can be affected by the presence or absence of a few bright stars introduced by stochastic sampling of the stellar mass function. Specific methods are being developed to extend the analysis of cluster energy distributions into the low-mass regime. In this paper, we apply such a method to real observations of star clusters, in the nearby spiral galaxy M83. We reassess the ages and masses of a sample of 1242 clusters for which UBVIH{alpha} fluxes were obtained from observations with the Wide Field Camera 3 instrument on board the Hubble Space Telescope. Synthetic clusters with known properties are used to characterize the limitations of the method (valid range and resolution in age and mass, method artifacts). The ensemble of color predictions of the discrete cluster models are in good agreement with the distribution of observed colors. We emphasize the important role of the H{alpha} data in the assessment of the fraction of young objects, particularly in breaking the age-extinction degeneracy that hampers an analysis based on UBVI data only. We find the mass distribution of the cluster sample to follow a power law of index -2.1 {+-} 0.2, and the distribution of ages a power law of index -1.0 {+-} 0.2 for log (M/ M{sub Sun }) > 3.5, and ages between 10{sup 7} and 10{sup 9} yr. An extension of our main method, which makes full use of the probability distributions of age and mass obtained for the individual clusters of the sample, is explored. It produces similar power-law slopes and will deserve further investigation. Although the properties derived for individual clusters significantly differ from those obtained with traditional, non-stochastic models in about 30% of the objects, the first-order aspect of the age and mass distributions is similar to those obtained previously for this M83 sample in the range of overlap of the studies. We

  11. The incidence of inguinal hernia and associated risk factors of incarceration in pediatric inguinal hernia: a nation-wide longitudinal population-based study.

    Science.gov (United States)

    Chang, S-J; Chen, J Y-C; Hsu, C-K; Chuang, F-C; Yang, S S-D

    2016-08-01

    This study uses a national database to evaluate the incidence of inguinal hernia and associated risk factors of incarcerated hernia in children from birth to 15 years of age. The study selected children born from 1997 to 2005 from a randomly selected cohort of 1,000,000 from an insured population of 23 million. We regarded children that were classified with code 550 and hernia surgery in accordance to the International Classification of Diseases, 9th Revision, as having inguinal hernia. We used the 2 chi-square test and logistic regression modeling for statistical analyses. In total, 79,794 children (41,767 male and 38,027 female) were enrolled in the study. The cumulative incidence of inguinal hernia in males and females from birth to 15 years old were 6.62 and 0.74 %, respectively (p inguinal hernia was at 0 years of age for males and 5 years of age for females. The ratio of unilateral vs. bilateral repair was 5.54:1. Females tend to have more bilateral inguinal hernia than males (25.4 vs. 12.9 %, p hernia occurred in 4.19 % children with inguinal hernia without significant gender discrepancy. Approximately 40 % of incarcerated hernia underwent hernia repair immediately after visiting the emergent department. In patients who presented with reducible hernia, we did not find significant correlation between waiting time to hernia repair and occurrence of incarceration. The cumulative incidence of inguinal hernia from birth to 15 years of age was 6.62 and 0.74 % in males and females, respectively. Incarceration was not related to prematurity or the waiting time for surgery.

  12. An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line.

    Science.gov (United States)

    Kim, Myung-Chul; Kim, Na-Yon; Seo, Yu-Ri; Kim, Yongbaek

    2016-01-01

    Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity.

  13. A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B

    DEFF Research Database (Denmark)

    Yamauchi, Toshimasa; Hara, Kazuo; Maeda, Shiro

    2010-01-01

    associations in UBE2E2 on chromosome 3 and in C2CD4A-C2CD4B on chromosome 15 at genome-wide significant levels (rs7612463 in UBE2E2, combined P = 2.27 × 10¿¿; rs7172432 in C2CD4A-C2CD4B, combined P = 3.66 × 10¿¿). The association of these two loci with T2D was replicated in other east Asian populations....... In the European populations, the C2CD4A-C2CD4B locus was significantly associated with T2D, and a combined analysis of all populations gave P = 8.78 × 10¿¹4, whereas the UBE2E2 locus did not show association to T2D. In conclusion, we identified two new loci at UBE2E2 and C2CD4A-C2CD4B associated...

  14. Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers

    Science.gov (United States)

    Chen, Wu; Hou, Lu; Zhang, Zhiyong; Pang, Xiaoming; Li, Yingyue

    2017-01-01

    Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube. PMID:28458680

  15. Alcohol problems and all-cause mortality in men and women: predictive capacity of a clinical screening tool in a 21-year follow-up of a large, UK-wide, general population-based survey.

    Science.gov (United States)

    Batty, G David; Hunt, Kate; Emslie, Carol; Lewars, Heather; Gale, Catharine R

    2009-04-01

    While the relation between alcohol consumption and mortality has been well explored, little is known about the link between alcohol problems and mortality in general population-based studies, particularly among women. This was the objective of the present study In this prospective cohort study, 5333 non-abstaining individuals (2539 women) from the UK-wide Health and Lifestyle Survey (aged 42.9 years at study induction) completed the CAGE questionnaire of alcohol problems and participated in a medical examination in 1984/1985; they were then followed up for mortality experience until 2005. Alcohol problems at baseline were less common in women (2.4%) than in men (7.8%). A total of 21 years of follow-up gave rise to 1201 deaths. Elevated rates of mortality were evident in persons reporting symptoms of alcohol problems in comparison to those who did not. In gender-stratified analyses, alcohol problems were more strongly associated with mortality risk in women (age-adjusted hazards ratio: 2.25; 95% confidence interval: 1.22-4.12) than in men (1.49; 1.12-1.99), although this effect modification was not statistically significant (P value for interaction=0.125). Controlling for a range of covariates--including socioeconomic position, co-morbidity (somatic and psychiatric), and alcohol intake--had essentially no impact on these associations. The CAGE questionnaire may have some utility in routine health assessments in the general population.

  16. Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations; significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes (FIND) Research Group

    Science.gov (United States)

    Malhotra, Alka; Igo, Robert P.; Thameem, Farook; Kao, W.H. Linda; Abboud, Hanna E.; Adler, Sharon G.; Arar, Nedal H.; Bowden, Donald W.; Duggirala, Ravindranath; Freedman, Barry I.; Goddard, Katrina A.B.; Ipp, Eli; Iyengar, Sudha K.; Kimmel, Paul L.; Knowler, William C.; Kohn, Orly; Leehey, David; Meoni, Lucy A.; Nelson, Robert G.; Nicholas, Susanne B.; Parekh, Rulan S.; Rich, Stephen S.; Chen, Yii-Der I.; Saad, Mohammed F.; Scavini, Marina; Schelling, Jeffrey R.; Sedor, John R.; Shah, Vallabh O.; Taylor, Kent D.; Thornley-Brown, Denyse; Zager, Philip G.; Horvath, Amanda; Hanson, Robert L.

    2009-01-01

    Background Previous studies have shown that, in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations. Methods Phenotypic and genotypic data were obtained from African American (AA; total number of individuals (N)=1004), American Indian (AI; N=883), European American (EA; N=537), and Mexican American (MA; N=1634) individuals from the Family Investigation of Nephropathy and Diabetes. Nonparametric linkage analysis, using an average of 4,404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM. Results Statistically significant evidence for linkage was observed on chromosomes 4q21.1 (LOD=3.13; genome-wide p=0.04) in AA. In addition, a total of eleven regions showed suggestive evidence for linkage (estimated at LOD>1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD=2.02) and 22q12.3 (LOD=2.38) in AA, 2p11.1 (LOD=2.23) in AI, 6p12.3 (LOD=2.77) in EA, and 13q21.1 (LOD=2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD>1.71 have been identified in previously published studies. Conclusions The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA, 6p in EA, 2p in AI, and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population. PMID:19795399

  17. Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations-significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes Research Group.

    Science.gov (United States)

    Malhotra, Alka; Igo, Robert P; Thameem, Farook; Kao, W H Linda; Abboud, Hanna E; Adler, Sharon G; Arar, Nedal H; Bowden, Donald W; Duggirala, Ravindranath; Freedman, Barry I; Goddard, Katrina A B; Ipp, Eli; Iyengar, Sudha K; Kimmel, Paul L; Knowler, William C; Kohn, Orly; Leehey, David; Meoni, Lucy A; Nelson, Robert G; Nicholas, Susanne B; Parekh, Rulan S; Rich, Stephen S; Chen, Yii-Der I; Saad, Mohammed F; Scavini, Marina; Schelling, Jeffrey R; Sedor, John R; Shah, Vallabh O; Taylor, Kent D; Thornley-Brown, Denyse; Zager, Philip G; Horvath, Amanda; Hanson, Robert L

    2009-11-01

    Previous studies have shown that in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations. Phenotypic and genotypic data were obtained from African American (AA; total number of individuals [N] = 1004), American Indian (AI; N = 883), European American (EA; N = 537), and Mexican American (MA; N = 1634) individuals from the Family Investigation of Nephropathy and Diabetes. Non-parametric linkage analysis, using an average of 4404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM. Statistically significant evidence for linkage was observed on chromosome 4q21.1 (LOD = 3.13; genome-wide p = 0.04) in AA. In addition, a total of 11 regions showed suggestive evidence for linkage (estimated at LOD > 1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD = 2.02) and 22q12.3 (LOD = 2.38) in AA, 2p11.1 (LOD = 2.23) in AI, 6p12.3 (LOD = 2.77) in EA, and 13q21.1 (LOD = . 2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD > 1.71 have been identified in previously published studies. The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA; 6p in EA; 2p in AI; and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population.

  18. The non-synonymous Arg230Cys variant (R230C) of the ATP-binding cassette transporter A1 is associated with low HDL cholesterol concentrations in Mexican adults: a population based nation wide study.

    Science.gov (United States)

    Aguilar-Salinas, Carlos A; Canizales-Quinteros, Samuel; Rojas-Martínez, Rosalba; Mehta, Roopa; Rodriguez-Guillén, Rosario; Ordoñez-Sanchez, María Luisa; Riba, Laura; Tusié-Luna, María Teresa

    2011-05-01

    To search for an association between the non-synonymous Arg230Cys variant (R230C) of the ATP-binding cassette transporter A1 and low HDL cholesterol levels in a Mexican, population-based nation wide survey. The 2000 National Health Survey is a cross sectional study that included individuals from 400 cities. All individuals who had a 9-12-h fasted blood sample and a DNA sample were selected (n = 1729). These cases were randomly distributed; no bias was detected for sex, education, region or socioeconomic status. The R230C variant was genotyped using TaqMan assays. In individuals with the R230C/C230C genotypes (39.03 mg/dl (36.63-41.43)) lower HDL-C levels (p cholesterol levels between alleles was 5.73 ± 1.4 mg/dl. The magnitude of the effect was significantly greater in males. The C230 allele of ABCA1 was associated with an increased risk for hypoalphalipoproteinemia (OR 1.66 (95%CI 1.08-2.54), p effect of waist circumference and gender, was 12.2% (95%CI 1.4-24.2%). The non-synonymous Arg230Cys variant of ABCA1 is associated with low levels of HDL cholesterol levels in Mexican adults. The HDL cholesterol lowering effect of the variant is greater in males. The size of the effect is greater compared to that reported for other ABCA1 variants. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  19. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

    Science.gov (United States)

    Wheeler, Eleanor; Leong, Aaron; Yao, Jie; Hong, Jaeyoung; Chu, Audrey Y.; Zhang, Weihua; Wang, Xu; Maruthur, Nisa M.; Porneala, Bianca C.; Jia, Yucheng; Kabagambe, Edmond K.; Chang, Li-Ching; Chen, Wei-Min; Elks, Cathy E.; Fan, Qiao; Giulianini, Franco; Go, Min Jin; Hottenga, Jouke-Jan; Hu, Yao; Jackson, Anne U.; Kanoni, Stavroula; Kleber, Marcus E.; Lu, Yingchang; Mahajan, Anubha; Marzi, Carola; Nalls, Mike A.; Nolte, Ilja M.; Rose, Lynda M.; Rybin, Denis V.; Shi, Yuan; Stram, Daniel O.; Tan, Shu Pei; Zhao, Wanting; Goel, Anuj; Martinez Larrad, Maria Teresa; Radke, Dörte; Salo, Perttu; van Iperen, Erik P. A.; Abecasis, Goncalo; Afaq, Saima; Bertoni, Alain G.; Bonnefond, Amelie; Böttcher, Yvonne; Chen, Chien-Hsiun; Cho, Yoon Shin; Garvey, W. Timothy; Gieger, Christian; Goodarzi, Mark O.; Grallert, Harald; Hamsten, Anders; Hartman, Catharina A.; Hsiung, Chao Agnes; Igase, Michiya; Isono, Masato; Khor, Chiea-Chuen; Kiess, Wieland; Kohara, Katsuhiko; Lee, Juyoung; Lehne, Benjamin; Li, Huaixing; Liu, Jianjun; Lobbens, Stephane; Luan, Jian'an; Lyssenko, Valeriya; Meitinger, Thomas; Miki, Tetsuro; Moon, Sanghoon; Mulas, Antonella; Müller-Nurasyid, Martina; Nagaraja, Ramaiah; Nauck, Matthias; Pankow, James S.; Polasek, Ozren; Prokopenko, Inga; Rasmussen-Torvik, Laura; Rathmann, Wolfgang; Rich, Stephen S.; Robertson, Neil R.; Roden, Michael; Roussel, Ronan; Rudan, Igor; Scott, Robert A.; Scott, William R.; Sennblad, Bengt; Siscovick, David S.; Strauch, Konstantin; Sun, Liang; Taylor, Kent D.; Teo, Yik-Ying; Tham, Yih Chung; Tönjes, Anke; Willemsen, Gonneke; Wilsgaard, Tom; Egan, Josephine; Hovingh, G. Kees; Jula, Antti; Kumari, Meena; Njølstad, Inger; Serrano Ríos, Manuel; Stumvoll, Michael; Watkins, Hugh; Aung, Tin; Blüher, Matthias; Boehnke, Michael; Bornstein, Stefan R.; Chambers, John C.; Chasman, Daniel I.; Chen, Yii-Der Ida; Chen, Yduan-Tsong; Cheng, Ching-Yu; Deloukas, Panos; Evans, Michele K.; Fornage, Myriam; Froguel, Philippe; Groop, Leif; Gross, Myron D.; Harris, Tamara B.; Hayward, Caroline; Ingelsson, Erik; Kato, Norihiro; Kim, Bong-Jo; Koh, Woon-Puay; Kooner, Jaspal S.; Körner, Antje; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lin, Xu; Liu, Yongmei; Loos, Ruth J. F.; März, Winfried; Pedersen, Nancy L.; Ridker, Paul M.; Saleheen, Danish; Saltevo, Juha; Schwarz, Peter EH.; Sheu, Wayne H. H.; Snieder, Harold; Spector, Timothy D.; Tabara, Yasuharu; Tuomilehto, Jaakko; Wilson, James G.; Wolffenbuttel, Bruce H. R.; Wu, Jer-Yuarn; Zonderman, Alan B.; Soranzo, Nicole; Guo, Xiuqing; Roberts, David J.; Florez, Jose C.; Tai, E-Shyong; Selvin, Elizabeth; Rotter, Jerome I.

    2017-01-01

    Background Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely biological action as erythrocytic (also associated with erythrocyte traits) or glycemic (associated with other glucose-related traits). In this study, we tested the hypotheses that, in a very large scale GWAS, we would identify more genetic variants associated with HbA1c and that HbA1c variants implicated in erythrocytic biology would affect the diagnostic accuracy of HbA1c. We therefore expanded the number of HbA1c-associated loci and tested the effect of genetic risk-scores comprised of erythrocytic or glycemic variants on incident diabetes prediction and on prevalent diabetes screening performance. Throughout this multiancestry study, we kept a focus on interancestry differences in HbA1c genetics performance that might influence race-ancestry differences in health outcomes. Methods & findings Using genome-wide association meta-analyses in up to 159,940 individuals from 82 cohorts of European, African, East Asian, and South Asian ancestry, we identified 60 common genetic variants associated with HbA1c. We classified variants as implicated in glycemic, erythrocytic, or unclassified biology and tested whether additive genetic scores of erythrocytic variants (GS-E) or glycemic variants (GS-G) were associated with higher T2D incidence in multiethnic longitudinal cohorts (N = 33,241). Nineteen glycemic and 22 erythrocytic variants were associated with HbA1c at genome-wide significance. GS-G was associated with higher T2D risk (incidence OR = 1.05, 95% CI 1.04–1.06, per HbA1c-raising allele, p = 3 × 10−29); whereas GS-E was not (OR = 1.00, 95% CI 0.99–1.01, p = 0.60). In Europeans and Asians, erythrocytic variants in aggregate had only modest effects on the diagnostic

  20. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis.

    Directory of Open Access Journals (Sweden)

    Eleanor Wheeler

    2017-09-01

    Full Text Available Glycated hemoglobin (HbA1c is used to diagnose type 2 diabetes (T2D and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely biological action as erythrocytic (also associated with erythrocyte traits or glycemic (associated with other glucose-related traits. In this study, we tested the hypotheses that, in a very large scale GWAS, we would identify more genetic variants associated with HbA1c and that HbA1c variants implicated in erythrocytic biology would affect the diagnostic accuracy of HbA1c. We therefore expanded the number of HbA1c-associated loci and tested the effect of genetic risk-scores comprised of erythrocytic or glycemic variants on incident diabetes prediction and on prevalent diabetes screening performance. Throughout this multiancestry study, we kept a focus on interancestry differences in HbA1c genetics performance that might influence race-ancestry differences in health outcomes.Using genome-wide association meta-analyses in up to 159,940 individuals from 82 cohorts of European, African, East Asian, and South Asian ancestry, we identified 60 common genetic variants associated with HbA1c. We classified variants as implicated in glycemic, erythrocytic, or unclassified biology and tested whether additive genetic scores of erythrocytic variants (GS-E or glycemic variants (GS-G were associated with higher T2D incidence in multiethnic longitudinal cohorts (N = 33,241. Nineteen glycemic and 22 erythrocytic variants were associated with HbA1c at genome-wide significance. GS-G was associated with higher T2D risk (incidence OR = 1.05, 95% CI 1.04-1.06, per HbA1c-raising allele, p = 3 × 10-29; whereas GS-E was not (OR = 1.00, 95% CI 0.99-1.01, p = 0.60. In Europeans and Asians, erythrocytic variants in aggregate had only modest effects on the diagnostic accuracy of HbA1c. Yet, in

  1. Health Care Wide Hazards

    Science.gov (United States)

    ... Scope | Glossary | References | Site Map | Credits Hospital eTool Administration Central Supply Clinical Services Dietary Emergency Engineering Healthcare Wide Hazards Heliport Housekeeping ICU Laboratory Laundry ...

  2. A significant association between rs8067378 at 17q12 and invasive cervical cancer originally identified by a genome-wide association study in Han Chinese is replicated in a Japanese population.

    Science.gov (United States)

    Miura, Kiyonori; Mishima, Hiroyuki; Yasunami, Michio; Kaneuchi, Masanori; Kitajima, Michio; Abe, Shuhei; Higashijima, Ai; Fuchi, Naoki; Miura, Shoko; Yoshiura, Koh-Ichiro; Masuzaki, Hideaki

    2016-09-01

    In this study, associations between invasive cervical cancer and four cervical cancer susceptibility loci (rs13117307 at 4q12, rs8067378 at 17q12, and rs4282438 and rs9277952 at 6p21.32) in the Han Chinese population were investigated in a Japanese population. Human leukocyte antigen (HLA)-DPB1 alleles were also investigated for their association with cervical cancer risk in the Japanese population. After receiving written informed consent, 214 unrelated Japanese women with invasive cervical cancer and 288 cancer-free Japanese women were recruited, and DNA samples were obtained (study protocol approved by Institutional Review Board of Nagasaki University). Of the four single-nucleotide polymorphisms, rs8067378 showed a significant association with invasive cervical cancer (P=0.0071). Under a recessive model, the minor allele G of rs8067378 contributed to the risk of invasive cervical cancer (odds ratio=2.92, 95% confidence interval=1.40-6.36; P=0.0021). No association was detected between HLA-DPB1 alleles and cervical cancer risk in the Japanese population. In conclusion, we show for the first time, to the best of our knowledge, that an association between increased risk of invasive cervical cancer and rs8067378 in the Han Chinese population is replicated in a Japanese population. In addition, Japanese women with the GG genotype of rs8067378 are a candidate high-risk group for invasive cervical carcinoma.

  3. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations : A transethnic genome-wide meta-analysis

    NARCIS (Netherlands)

    Wheeler, Eleanor; Leong, Aaron; Liu, Ching-Ti; Hivert, Marie-France; Strawbridge, Rona J; Podmore, Clara; Li, Man; Yao, Jie; Sim, Xueling; Hong, Jaeyoung; Chu, Audrey Y; Zhang, Weihua; Wang, Xu; Chen, Peng; Maruthur, Nisa M; Porneala, Bianca C; Sharp, Stephen J; Jia, Yucheng; Kabagambe, Edmond K; Chang, Li-Ching; Chen, Wei-Min; Elks, Cathy E; Evans, Daniel S; Fan, Qiao; Giulianini, Franco; Go, Min Jin; Hottenga, Jouke-Jan; Hu, Yao; Jackson, Anne U; Kanoni, Stavroula; Kim, Young Jin; Kleber, Marcus E; Ladenvall, Claes; Lecoeur, Cecile; Lim, Sing-Hui; Lu, Yingchang; Mahajan, Anubha; Marzi, Carola; Nalls, Mike A; Navarro, Pau; Nolte, Ilja M; Rose, Lynda M; Rybin, Denis V; Sanna, Serena; Shi, Yuan; Stram, Daniel O; Takeuchi, Fumihiko; Tan, Shu Pei; van der Most, Peter J; Van Vliet-Ostaptchouk, Jana V.; Wong, Andrew; Yengo, Loic; Zhao, Wanting; Goel, Anuj; Martinez Larrad, Maria Teresa; Radke, Dörte; Salo, Perttu; Tanaka, Toshiko; van Iperen, Erik P A; Abecasis, Goncalo; Afaq, Saima; Alizadeh, Behrooz Z; Bertoni, Alain G; Bonnefond, Amelie; Böttcher, Yvonne; Bottinger, Erwin P; Campbell, Harry; Carlson, Olga D; Chen, Chien-Hsiun; Cho, Yoon Shin; Garvey, W Timothy; Gieger, Christian; Goodarzi, Mark O; Grallert, Harald; Hamsten, Anders; Hartman, Catharina A; Herder, Christian; Hsiung, Chao Agnes; Huang, Jie; Igase, Michiya; Isono, Masato; Katsuya, Tomohiro; Khor, Chiea-Chuen; Kiess, Wieland; Kohara, Katsuhiko; Kovacs, Peter; Lee, Juyoung; Lee, Wen-Jane; Lehne, Benjamin; Li, Huaixing; Liu, Jianjun; Lobbens, Stephane; Luan, Jian'an; Lyssenko, Valeriya; Meitinger, Thomas; Miki, Tetsuro; Miljkovic, Iva; Moon, Sanghoon; Mulas, Antonella; Müller, Gabriele; Müller-Nurasyid, Martina; Nagaraja, Ramaiah; Nauck, Matthias; Pankow, James S; Polasek, Ozren; Prokopenko, Inga; Ramos, Paula S; Rasmussen-Torvik, Laura; Rathmann, Wolfgang; Rich, Stephen S; Robertson, Neil R; Roden, Michael; Roussel, Ronan; Rudan, Igor; Scott, Robert A; Scott, William R; Sennblad, Bengt; Siscovick, David S; Strauch, Konstantin; Sun, Liang; Swertz, Morris; Tajuddin, Salman M; Taylor, Kent D; Teo, Yik-Ying; Tham, Yih Chung; Tönjes, Anke; Wareham, Nicholas J; Willemsen, Gonneke; Wilsgaard, Tom; Hingorani, Aroon D; Egan, Josephine; Ferrucci, Luigi; Hovingh, G Kees; Jula, Antti; Kivimaki, Mika; Kumari, Meena; Njølstad, Inger; Palmer, Colin N A; Serrano Ríos, Manuel; Stumvoll, Michael; Watkins, Hugh; Aung, Tin; Blüher, Matthias; Boehnke, Michael; Boomsma, Dorret I; Bornstein, Stefan R; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der Ida; Chen, Yduan-Tsong; Cheng, Ching-Yu; Cucca, Francesco; de Geus, Eco J C; Deloukas, Panos; Evans, Michele K; Fornage, Myriam; Friedlander, Yechiel; Froguel, Philippe; Groop, Leif; Gross, Myron D; Harris, Tamara B; Hayward, Caroline; Heng, Chew-Kiat; Ingelsson, Erik; Kato, Norihiro; Kim, Bong-Jo; Koh, Woon-Puay; Kooner, Jaspal S; Körner, Antje; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lin, Xu; Liu, Yongmei; Loos, Ruth J F; Magnusson, Patrik K E; März, Winfried; McCarthy, Mark I; Oldehinkel, Albertine J; Ong, Ken K; Pedersen, Nancy L; Pereira, Mark A; Peters, Annette; Ridker, Paul M; Sabanayagam, Charumathi; Sale, Michele; Saleheen, Danish; Saltevo, Juha; Schwarz, Peter Eh; Sheu, Wayne H H; Snieder, Harold; Spector, Timothy D; Tabara, Yasuharu; Tuomilehto, Jaakko; van Dam, Rob M; Wilson, James G; Wilson, James F; Wolffenbuttel, Bruce H R; Wong, Tien Yin; Wu, Jer-Yuarn; Yuan, Jian-Min; Zonderman, Alan B; Soranzo, Nicole; Guo, Xiuqing; Roberts, David J; Florez, Jose C; Sladek, Robert; Dupuis, Josée; Morris, Andrew P; Tai, E-Shyong; Selvin, Elizabeth; Rotter, Jerome I; Langenberg, Claudia; Barroso, Inês; Meigs, James B

    2017-01-01

    Background Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely

  4. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations : A transethnic genome-wide meta-analysis

    NARCIS (Netherlands)

    Wheeler, Eleanor; Leong, Aaron; Liu, Ching-Ti; Hivert, Marie-France; Strawbridge, Rona J; Podmore, Clara; Li, Man; Yao, Jie; Sim, Xueling; Hong, Jaeyoung; Chu, Audrey Y; Zhang, Weihua; Wang, Xu; Chen, Peng; Maruthur, Nisa M; Porneala, Bianca C; Sharp, Stephen J; Jia, Yucheng; Kabagambe, Edmond K; Chang, Li-Ching; Chen, Wei-Min; Elks, Cathy E; Evans, Daniel S; Fan, Qiao; Giulianini, Franco; Go, Min Jin; Hottenga, Jouke-Jan; Hu, Yao; Jackson, Anne U; Kanoni, Stavroula; Kim, Young Jin; Kleber, Marcus E; Ladenvall, Claes; Lecoeur, Cecile; Lim, Sing-Hui; Lu, Yingchang; Mahajan, Anubha; Marzi, Carola; Nalls, Mike A; Navarro, Pau; Nolte, Ilja M; Rose, Lynda M; Rybin, Denis V; Sanna, Serena; Shi, Yuan; Stram, Daniel O; Takeuchi, Fumihiko; Tan, Shu Pei; van der Most, Peter J; van Vliet-Ostaptchouk, Jana V; Wong, Andrew; Yengo, Loic; Zhao, Wanting; Goel, Anuj; Martinez Larrad, Maria Teresa; Radke, Dörte; Salo, Perttu; Tanaka, Toshiko; van Iperen, Erik P A; Abecasis, Goncalo; Afaq, Saima; Alizadeh, Behrooz Z; Bertoni, Alain G; Bonnefond, Amelie; Böttcher, Yvonne; Bottinger, Erwin P; Campbell, Harry; Carlson, Olga D; Chen, Chien-Hsiun; Cho, Yoon Shin; Garvey, W Timothy; Gieger, Christian; Goodarzi, Mark O; Grallert, Harald; Hamsten, Anders; Hartman, Catharina A; Herder, Christian; Hsiung, Chao Agnes; Huang, Jie; Igase, Michiya; Isono, Masato; Katsuya, Tomohiro; Khor, Chiea-Chuen; Kiess, Wieland; Kohara, Katsuhiko; Kovacs, Peter; Lee, Juyoung; Lee, Wen-Jane; Lehne, Benjamin; Li, Huaixing; Liu, Jianjun; Lobbens, Stephane; Luan, Jian'an; Lyssenko, Valeriya; Meitinger, Thomas; Miki, Tetsuro; Miljkovic, Iva; Moon, Sanghoon; Mulas, Antonella; Müller, Gabriele; Müller-Nurasyid, Martina; Nagaraja, Ramaiah; Nauck, Matthias; Pankow, James S; Polasek, Ozren; Prokopenko, Inga; Ramos, Paula S; Rasmussen-Torvik, Laura J; Rathmann, Wolfgang; Rich, Stephen S; Robertson, Neil R; Roden, Michael; Roussel, Ronan; Rudan, Igor; Scott, Robert A; Scott, William R; Sennblad, Bengt; Siscovick, David S; Strauch, Konstantin; Sun, Shan-Liang; Swertz, Morris a.; Tajuddin, Salman M; Taylor, Kent D; Teo, Yik-Ying; Tham, Yih Chung; Tönjes, Anke; Wareham, Nicholas J; Willemsen, Gonneke; Wilsgaard, Tom; Hingorani, Aroon D; Egan, Josephine; Ferrucci, Luigi; Hovingh, G. Kees; Jula, Antti; Kivimaki, Mika; Kumari, Meena; Njølstad, Inger; Palmer, Colin N A; Serrano Ríos, Manuel; Stumvoll, Michael; Watkins, Hugh; Aung, Tin; Blüher, Matthias; Boehnke, Michael; Boomsma, Dorret I; Bornstein, Stefan R; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der Ida; Chen, Yduan-Tsong; Cheng, Ching-Yu; Cucca, Francesco; de Geus, Eco J C; Deloukas, Panos; Evans, Michele K; Fornage, Myriam; Friedlander, Yechiel; Froguel, Philippe; Groop, Leif; Gross, Myron D; Harris, Tamara B; Hayward, Caroline; Heng, Chew-Kiat; Ingelsson, Erik; Kato, Norihiro; Kim, Bong-Jo; Koh, Woon-Puay; Kooner, Jaspal S; Körner, Antje; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lin, Xu; Liu, YongMei; Loos, Ruth J F; Magnusson, Patrik K E; März, Winfried; McCarthy, Mark I; Oldehinkel, Albertine J; Ong, Ken K; Pedersen, Nancy L; Pereira, Mark A; Peters, Annette; Ridker, Paul M; Sabanayagam, Charumathi; Sale, Michele; Saleheen, Danish; Saltevo, Juha; Schwarz, Peter Eh; Sheu, Wayne H H; Snieder, Harold; Spector, Timothy D; Tabara, Yasuharu; Tuomilehto, Jaakko; van Dam, Rob M; Wilson, James G; Wilson, James F; Wolffenbuttel, Bruce H R; Wong, Tien Yin; Wu, Jer-Yuarn; Yuan, Jian-Min; Zonderman, Alan B; Soranzo, Nicole; Guo, Xiuqing; Roberts, David J; Florez, Jose C; Sladek, Robert; Dupuis, Josée; Morris, Andrew P; Tai, E Shyong; Selvin, Elizabeth; Rotter, Jerome I; Langenberg, Claudia; Barroso, Inês; Meigs, James B

    BACKGROUND: Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely

  5. Wide-Gap Chalcopyrites

    CERN Document Server

    Siebentritt, Susanne

    2006-01-01

    Chalcopyrites, in particular those with a wide band gap, are fascinating materials in terms of their technological potential in the next generation of thin-film solar cells and in terms of their basic material properties. They exhibit uniquely low defect formation energies, leading to unusual doping and phase behavior and to extremely benign grain boundaries. This book collects articles on a number of those basic material properties of wide-gap chalcopyrites, comparing them to their low-gap cousins. They explore the doping of the materials, the electronic structure and the transport through interfaces and grain boundaries, the formation of the electric field in a solar cell, the mechanisms and suppression of recombination, the role of inhomogeneities, and the technological role of wide-gap chalcopyrites.

  6. Ultra wide band antennas

    CERN Document Server

    Begaud, Xavier

    2013-01-01

    Ultra Wide Band Technology (UWB) has reached a level of maturity that allows us to offer wireless links with either high or low data rates. These wireless links are frequently associated with a location capability for which ultimate accuracy varies with the inverse of the frequency bandwidth. Using time or frequency domain waveforms, they are currently the subject of international standards facilitating their commercial implementation. Drawing up a complete state of the art, Ultra Wide Band Antennas is aimed at students, engineers and researchers and presents a summary of internationally recog

  7. Jihadism, Narrow and Wide

    DEFF Research Database (Denmark)

    Sedgwick, Mark

    2015-01-01

    The term “jihadism” is popular, but difficult. It has narrow senses, which are generally valuable, and wide senses, which may be misleading. This article looks at the derivation and use of “jihadism” and of related terms, at definitions provided by a number of leading scholars, and at media usage...

  8. World wide biomass resources

    NARCIS (Netherlands)

    Faaij, A.P.C.

    2012-01-01

    In a wide variety of scenarios, policy strategies, and studies that address the future world energy demand and the reduction of greenhouse gas emissions, biomass is considered to play a major role as renewable energy carrier. Over the past decades, the modern use of biomass has increased

  9. Identification of FAM13A gene associated with the ratio of FEV1 to FVC in Korean population by genome-wide association studies including gene-environment interactions.

    Science.gov (United States)

    Kim, Soriul; Kim, Hyun; Cho, Namhan; Lee, Seung Ku; Han, Bok-Ghee; Sull, Jae Woong; Jee, Sun Ha; Shin, Chol

    2015-03-01

    Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial disease. Although smoking is a main risk factor for obstructive impairment, not all smokers develop this critical disease. We conducted a genome-wide association study to identify the association between genetic variants and pulmonary function and also examined how these variants relate to lung impairment in accordance with smoking behaviors. Using two community-based cohorts, the Ansan cohort (n=4319) and the Ansung cohort (n=3674), in the Korean Genome Epidemiology Study, we analyzed the association between genetic variants (single-nucleotide polymorphisms and haplotypes) and the ratio of FEV1 to FVC (FEV1/FVC) using multivariate linear regression models. Similar analyses were conducted after stratification by smoking status. Four genome-wide significant signals in the FAM13A gene (the strongest signal at rs2609264, P=1.76 × 10(-7) in a combined set) were associated with FEV1/FVC. For the association with ratio, the effect size in the CTGA haplotype (risk haplotype) was -0.57% (s.e., 0.11; P=2.10 × 10(-7)) as compared with the TCAG haplotype (reference haplotype) in a combined set. There was also a significant interaction of FAM13A haplotypes with heavy smoking on FEV1/FVC (P for interaction=0.028). We confirmed the previously reported association of FAM13A in 4q22.1 with pulmonary function. The FAM13A haplotypes also interacted with heavy smoking to affect the risk of reduced pulmonary function.

  10. Using Genome-Wide SNPs to Detect Structure in High-Diversity and Low-Divergence Populations of Severely Impacted Eastern Tropical Pacific Spinner (Stenella longirostris And Pantropical Spotted Dolphins (S. attenuata

    Directory of Open Access Journals (Sweden)

    Matthew Steven Leslie

    2016-12-01

    Full Text Available Millions of spinner (Stenella longirostris and pantropical spotted dolphins (Stenella attenuata died since the 1960’s as bycatch in tuna nets in the eastern tropical Pacific Ocean. Despite three decades of protection, they show little-to-no sign of recovery (although recent fisheries-independent abundance estimates are not available. In efforts to establish biologically meaningful management boundaries for recovery, endemic subspecies and multiple stocks have been proposed. However, genetic differentiation among most of these units has been difficult to identify, possibly due to low statistical power stemming from large historical abundances, ongoing gene flow, and recent divergence. We tested for genetic structure at multiple hierarchical levels by analyzing the largest dataset to date brought to bear on these questions. Single nucleotide polymorphisms (SNPs were collected from nuclear DNA regions associated with the restriction enzyme site PstI from 72 spinner dolphins and 58 pantropical spotted dolphins using genotype-by-sequencing (GBS. Our results support the current subspecies for both species and indicate stock-level separation for Tres Marias spinner dolphins and the two offshore pantropical spotted dolphin stocks in this area. Although bycatch has been reduced a small fraction of pre-protection levels, incidental mortality continues to impact these populations. Our results are important for the ongoing management and recovery of these highly-impacted pelagic dolphins in the eastern tropical Pacific Ocean.

  11. Candidate Gene Identification of Feed Efficiency and Coat Color Traits in a C57BL/6J × Kunming F2 Mice Population Using Genome-Wide Association Study

    Directory of Open Access Journals (Sweden)

    Yuanxin Miao

    2017-01-01

    Full Text Available Feed efficiency (FE is a very important trait in livestock industry. Identification of the candidate genes could be of benefit for the improvement of FE trait. Mouse is used as the model for many studies in mammals. In this study, the candidate genes related to FE and coat color were identified using C57BL/6J (C57 × Kunming (KM F2 mouse population. GWAS results showed that 61 and 2 SNPs were genome-wise suggestive significantly associated with feed conversion ratio (FCR and feed intake (FI traits, respectively. Moreover, the Erbin, Msrb2, Ptf1a, and Fgf10 were considered as the candidate genes of FE. The Lpl was considered as the candidate gene of FI. Further, the coat color trait was studied. KM mice are white and C57 ones are black. The GWAS results showed that the most significant SNP was located at chromosome 7, and the closely linked gene was Tyr. Therefore, our study offered useful target genes related to FE in mice; these genes may play similar roles in FE of livestock. Also, we identified the major gene of coat color in mice, which would be useful for better understanding of natural mutation of the coat color in mice.

  12. Wide Band Artificial Pulsar

    Science.gov (United States)

    Parsons, Zackary

    2017-01-01

    The Wide Band Artificial Pulsar (WBAP) is an instrument verification device designed and built by the National Radio Astronomy Observatory (NRAO) in Green Bank, West Virgina. The site currently operates the Green Bank Ultimate Pulsar Processing Instrument (GUPPI) and the Versatile Green Bank Astronomical Spectrometer (VEGAS) digital backends for their radio telescopes. The commissioning and continued support for these sophisticated backends has demonstrated a need for a device capable of producing an accurate artificial pulsar signal. The WBAP is designed to provide a very close approximation to an actual pulsar signal. This presentation is intended to provide an overview of the current hardware and software implementations and to also share the current results from testing using the WBAP.

  13. Mile wide, inch deep?

    Science.gov (United States)

    Carlowicz, Michael

    Compared to their counterparts in other nations, American grade school students learn a lot less about a lot more. According to a new report entitled A Splintered Vision: An Investigation of U.S. Science and Mathematics Education, a student in the United States is expected to absorb information about a wide array of topics in a school year, yet he or she is seldom given the opportunity to explore any one topic in depth. The report was funded by the National Science Foundation (NSF) and is part of the Third International Mathematics and Science Study (TIMSS), a five-year project to compare teaching and student achievement in 45 countries.Before they reach high school, American students will have covered more topics than 75% of the students in other countries; yet in many cases, they will have been taught some of the same topics several years in a row. Researchers also criticized conventional U.S. education standards for being unfocused and aimed at the lowest common denominator. They noted that most American textbooks make minimal demands on students and they represent “a limited notion” of what should be discussed in “basic” texts.

  14. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. II: Multivariate spike and slab priors for marker effects and derivation of approximate Bayes and fractional Bayes factors for the complete family of models.

    Science.gov (United States)

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

    2017-03-21

    This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes. This paper extends this family of models by considering multivariate spike and slab conditional priors for marker allele substitution effects and contains derivations of approximate Bayes factors and fractional Bayes factors to compare models from part I and those developed here with their null versions. These null versions correspond to simpler models ignoring heterogeneity of populations, but still accounting for randomness of genotypes. For each marker loci, the spike component of priors corresponded to point mass at 0 in R S , where S is the number of populations, and the slab component was a S-variate Gaussian distribution, independent conditional priors were assumed. For the Gaussian components, covariance matrices were assumed to be either the same for all markers or different for each marker. For null models, the priors were simply univariate versions of these finite mixture distributions. Approximate algebraic expressions for Bayes factors and fractional Bayes factors were found using the Laplace approximation. Using the simulated datasets described in part I, these models were implemented and compared with models derived in part I using measures of predictive performance based on squared Pearson correlations, Deviance Information Criterion, Bayes factors, and fractional Bayes factors. The extensions presented here enlarge our family of genome-wide prediction models making it more flexible in the

  15. Wide-Bandgap Semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Chinthavali, M.S.

    2005-11-22

    With the increase in demand for more efficient, higher-power, and higher-temperature operation of power converters, design engineers face the challenge of increasing the efficiency and power density of converters [1, 2]. Development in power semiconductors is vital for achieving the design goals set by the industry. Silicon (Si) power devices have reached their theoretical limits in terms of higher-temperature and higher-power operation by virtue of the physical properties of the material. To overcome these limitations, research has focused on wide-bandgap materials such as silicon carbide (SiC), gallium nitride (GaN), and diamond because of their superior material advantages such as large bandgap, high thermal conductivity, and high critical breakdown field strength. Diamond is the ultimate material for power devices because of its greater than tenfold improvement in electrical properties compared with silicon; however, it is more suited for higher-voltage (grid level) higher-power applications based on the intrinsic properties of the material [3]. GaN and SiC power devices have similar performance improvements over Si power devices. GaN performs only slightly better than SiC. Both SiC and GaN have processing issues that need to be resolved before they can seriously challenge Si power devices; however, SiC is at a more technically advanced stage than GaN. SiC is considered to be the best transition material for future power devices before high-power diamond device technology matures. Since SiC power devices have lower losses than Si devices, SiC-based power converters are more efficient. With the high-temperature operation capability of SiC, thermal management requirements are reduced; therefore, a smaller heat sink would be sufficient. In addition, since SiC power devices can be switched at higher frequencies, smaller passive components are required in power converters. Smaller heat sinks and passive components result in higher-power-density power converters

  16. Supporting a population wide reduction of salt consumption in Costa ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    health in low- and middle-income countries. NCDP funds research focusing on the main risk factors for NCDs: tobacco use, unhealthy diet, alcohol misuse, and physical inactivity. The challenge. High salt diets are a major cause of raised blood pressure, which increases the risk for cardiovascular and kidney disease.

  17. Europe-wide dampening of population cycles in keystone herbivores

    Czech Academy of Sciences Publication Activity Database

    Cornulier, T.; Yoccoz, N. G.; Bretagnolle, V.; Brommer, J. E.; Butet, A.; Ecke, F.; Elston, D. A.; Framstad, E.; Henttonen, H.; Hornfeldt, B.; Huitu, O.; Imholt, C.; Ims, R. A.; Jacob, J.; Jedrzejewska, B.; Millon, A.; Petty, S. J.; Pietiainen, H.; Tkadlec, Emil; Zub, K.; Lambin, X.

    2013-01-01

    Roč. 340, č. 6128 (2013), s. 63-66 ISSN 0036-8075 Institutional support: RVO:68081766 Keywords : grey-sided vole * density-dependence * lemming cycles Subject RIV: EG - Zoology Impact factor: 31.477, year: 2013

  18. Femoral morphology and epiphyseal growth plate changes of the hip during maturation: MR assessments in a 1-year follow-up on a cross-sectional asymptomatic cohort in the age range of 9-17 years

    Energy Technology Data Exchange (ETDEWEB)

    Kienle, Karl-Philipp [University of Bern, Department of Orthopedic Surgery, Bern (Switzerland); University of Bern, Inselspital, Bern, Department of Orthopaedic Surgery, Erlangen (Germany); Keck, Johannes; Siebenrock, Klaus-Arno; Mamisch, Tallal Charles [University of Bern, Department of Orthopedic Surgery, Bern (Switzerland); Werlen, Stefan [Department of Radiology, Sonnenhof Clinic, Bern (Switzerland); Kim, Young-Jo [Harvard Medical School, Department of Orthopaedic Surgery, Children' s Hospital, Boston, MA (United States)

    2012-11-15

    The goal of this prospective study was to characterize the morphology and physeal changes of the femoral head during maturation using MRI in a population-based group of asymptomatic volunteers. Sixty-four pupils (127 hips) of 331 pupils from a primary and high school were asked to take part in this study and were willing to participate. 3T MRI of the hip was obtained at baseline and 1-year follow-up. With these images, we analyzed the femoral morphology and epiphyseal changes related to age, status of the physis, and location on the femur. The radius of the femoral head and neck increased with age, as expected, (p < 0.001). The epiphyseal extension increased significantly with age (p < 0.05), but epiphyseal tilt and alpha angle showed no differences (p > 0.05). Building groups by using the epiphyseal status, we found that the epiphyseal extension had the highest changes in the ''open'' group and almost stopped in the ''closed'' group. The tilt angle did not change significantly (p > 0.05). Significant smaller alpha-angles were found in the ''closed'' group, however, these were in a normal range in all of them. Correlated to the position, the highest alpha-angle values were located in anterior-superior and superior-anterior position. Our data can be used as normative values, which can be compared to patients or cohorts with certain risk factors (e.g., professional athletes), this will offer the chance to detect and understand pathological changes. (orig.)

  19. Wide boundaries of microbial life as due to anabiosis

    Science.gov (United States)

    Abyzov, S. A.; Mulyukin, A. L.; Mitskevich, I. N.; Ivanov, M. V.

    Gaining more insights to the boundaries in which microbial life can exist came from comprehensive studies of various especially extreme terrestrial environments They differ in their origin age temperature salinity energy flux and many other factors that are of paramount importance for life sustenance Microbiological studies of ancient Antarctic glaciers gave experimentally substantiated information on time and the lowest boundary of temperature in which viable pro- and eukaryotic microbial cells survived Noticeably the total number of viable microorganisms that are present in Antarctic ice horizons with temperature varying from -50 oC to -2 4 oC and the age range from 0 2 to 500 thousands of years The existence of microbial cells in so widely ranging temperature and age is regarded as due to super-long anabiosis Theoretically there is no difference between microorganisms that existed in the anabiotic state for tens of hundreds to millennia of years if they faced to low temperatures Hence wide boundaries of microbial life are associated to the state of anabiosis and this is true not only for deep cold environments such as Antarctic glaciers Indeed sensational findings of viable microorganisms in a variety of terrestrial ancient objects extend our knowledge of life boundaries Revelations of ancient microbial cells especially in those habitats where the number of microorganisms is very low unavoidably concerns the problem of authentication Therefore it is great importance to develop and use the methods that exclude contamination of studied samples by

  20. System Wide Information Management (SWIM)

    Science.gov (United States)

    Hritz, Mike; McGowan, Shirley; Ramos, Cal

    2004-01-01

    This viewgraph presentation lists questions regarding the implementation of System Wide Information Management (SWIM). Some of the questions concern policy issues and strategies, technology issues and strategies, or transition issues and strategies.

  1. Wide spectrum microwave pulse measurement

    Energy Technology Data Exchange (ETDEWEB)

    King, R.J.

    1986-01-01

    Various techniques are postulated as diagnostics for wide band microwave pulses. The diagnostics include determinations of both the instantaneous amplitude and the frequency content of one-shot pulses. 6 refs., 11 figs. (WRF)

  2. Wide-Field Plate Database

    Science.gov (United States)

    Tsvetkov, M. K.; Stavrev, K. Y.; Tsvetkova, K. P.; Semkov, E. H.; Mutatov, A. S.

    The Wide-Field Plate Database (WFPDB) and the possibilities for its application as a research tool in observational astronomy are presented. Currently the WFPDB comprises the descriptive data for 400 000 archival wide field photographic plates obtained with 77 instruments, from a total of 1 850 000 photographs stored in 269 astronomical archives all over the world since the end of last century. The WFPDB is already accessible for the astronomical community, now only in batch mode through user requests sent by e-mail. We are working on on-line interactive access to the data via INTERNET from Sofia and parallel from the Centre de Donnees Astronomiques de Strasbourg. (Initial information can be found on World Wide Web homepage URL http://www.wfpa.acad.bg.) The WFPDB may be useful in studies of a variety of astronomical objects and phenomena, andespecially for long-term investigations of variable objects and for multi-wavelength research. We have analysed the data in the WFPDB in order to derive the overall characteristics of the totality of wide-field observations, such as the sky coverage, the distributions by observation time and date, by spectral band, and by object type. We have also examined the totality of wide-field observations from point of view of their quality, availability and digitisation. The usefulness of the WFPDB is demonstrated by the results of identification and investigation of the photometrical behaviour of optical analogues of gamma-ray bursts.

  3. Oxytocin treatment in pediatric populations

    Directory of Open Access Journals (Sweden)

    Adrienne Elise Taylor

    2014-10-01

    Full Text Available The role of endogenous oxytocin as neuromodulator of birth, lactation and social behaviors is well-recognized. Moreover, the use of oxytocin as a facilitator of social and other behaviors is becoming more and more accepted. Many positive effects have been attributed to intranasal oxytocin administration in animals and humans; with current research highlighting encouraging advances in its potential for use in mental health disorders. The new frontier will be investigating the effective use of oxytocin in pediatric populations. Limited animal data is available on this. Large-scale human studies focusing on autism are currently under way, but many other possibilities seem to lie in the future. However, we need to know more about the risks and effects of repeated use on the developing brain and body. This paper will provide an overview of the current understanding of the role of endogenous oxytocin and its related neuropeptide systems in influencing behaviors, in particular attachment, and will review a the literature on the use of intranasal oxytocin in young animals, children (age range birth-12 years and adolescents (age range 13-19 years, b the expected benefits and risks based on the current research, and c the risks of oxytocin in children with severe psychopathology and early life trauma. The paper will conclude with a clinical perspective on these findings

  4. Medication-wide association studies

    NARCIS (Netherlands)

    P.B. Ryan (Patrick); D. Madigan (David); P.E. Stang (Paul); M.J. Schuemie (Martijn); G. Hripcsak (G.)

    2013-01-01

    textabstractUndiscovered side effects of drugs can have a profound effect on the health of the nation, and electronic health-care databases offer opportunities to speed up the discovery of these side effects. We applied a "medication-wide association study" approach that combined multivariate

  5. The Ooty Wide Field Array

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Astrophysics and Astronomy; Volume 38; Issue 1. The Ooty Wide Field Array. C. R. Subrahmanya P. K. Manoharan Jayaram N. Chengalur. Review Article Volume 38 Issue 1 March 2017 Article ID ... Keywords. Cosmology: large scale structure of Universe; intergalactic medium; diffuse radiation.

  6. Wide Bandgap Extrinsic Photoconductive Switches

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, James S. [State Univ. of New York (SUNY), Plattsburgh, NY (United States); Univ. of California, Davis, CA (United States)

    2012-01-20

    Photoconductive semiconductor switches (PCSS) have been investigated since the late 1970s. Some devices have been developed that withstand tens of kilovolts and others that switch hundreds of amperes. However, no single device has been developed that can reliably withstand both high voltage and switch high current. Yet, photoconductive switches still hold the promise of reliable high voltage and high current operation with subnanosecond risetimes. Particularly since good quality, bulk, single crystal, wide bandgap semiconductor materials have recently become available. In this chapter we will review the basic operation of PCSS devices, status of PCSS devices and properties of the wide bandgap semiconductors 4H-SiC, 6H-SiC and 2H-GaN.

  7. Wide and High Additive Manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Post, Brian K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roschli, Alex C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-03-01

    The goal of this project is to develop and demonstrate the enabling technologies for Wide and High Additive Manufacturing (WHAM). WHAM will open up new areas of U.S. manufacturing for very large tooling in support of the transportation and energy industries, significantly reducing cost and lead time. As with Big Area Additive Manufacturing (BAAM), the initial focus is on the deposition of composite materials.

  8. Wide Bandgap Extrinsic Photoconductive Switches

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, James S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-07-03

    Semi-insulating Gallium Nitride, 4H and 6H Silicon Carbide are attractive materials for compact, high voltage, extrinsic, photoconductive switches due to their wide bandgap, high dark resistance, high critical electric field strength and high electron saturation velocity. These wide bandgap semiconductors are made semi-insulating by the addition of vanadium (4H and 6HSiC) and iron (2H-GaN) impurities that form deep acceptors. These deep acceptors trap electrons donated from shallow donor impurities. The electrons can be optically excited from these deep acceptor levels into the conduction band to transition the wide bandgap semiconductor materials from a semi-insulating to a conducting state. Extrinsic photoconductive switches with opposing electrodes have been constructed using vanadium compensated 6H-SiC and iron compensated 2H-GaN. These extrinsic photoconductive switches were tested at high voltage and high power to determine if they could be successfully used as the closing switch in compact medical accelerators.

  9. Measuring transcutaneous bilirubin: a comparative analysis of three devices on a multiracial population

    Science.gov (United States)

    2012-01-01

    Background Hyperbilirubinemia can lead to potentially irreversible bilirubin-induced neurotoxicity. Transcutaneous bilirubin (TcB) determination has become a valuable aid in non invasive screening of neonatal jaundice. The aim of this study is to compare the performance of three most widespread transcutaneous bilirubinometers on a multiracial population of term and late pre-term neonates. Methods Bilirubin concentration was determined using traditional photometric determination and transcutaneously with Bilicheck, BiliMed and JM-103, in random order. Total serum bilirubin (TSB) was determined over a wide concentration range (15,8–0,7 mg/dl) with a mean of 9,5 mg/dl. Related TcB values using Bilicheck (TcB-BC), BiliMed (TcB-BM), and JM-103 (TcB-JM) are reported in Table 1. Results A multiracial population of 289 neonates was enrolled with a gestational age ranging from 35 to 41 weeks; birth weight ranging from 1800to 4350 grams; hours of life ranging from 4 to 424. In the total study population correlation analysis using Pearson coefficients showed good results for Bilicheck (r = 0.86) and JM-103 (r = 0.85) but poor for BiliMed (r = 0,70). Similar results were found for the non-Caucasian neonates subgroup. Bilicheck and JM-103 had a greater area under the curve than BiliMed when TSB =14 mg/dl was chosen as a threshold value both for the total study population and the non-Caucasian subgroup. Conclusions Bilicheck and JM-103, but not BiliMed, are equally reliable screening tools for hyperbilirubinemia in our multiracial neonatal population. PMID:22697173

  10. Vestibular rehabilitation using a wide field of view virtual environment.

    Science.gov (United States)

    Sparto, P J; Furman, J M; Whitney, S L; Hodges, L F; Redfern, M S

    2004-01-01

    This paper presents a theoretical justification for using a wide field of view (FOV) virtual reality display system for use in vestibular rehabilitation. A wide FOV environment offers some unique features that may be beneficial to vestibular rehabilitation. Primarily, optic flow information extracted from the periphery may be critical for recalibrating the sensory processes used by people with vestibular disorders. If this hypothesis is correct, then wide FOV systems will have an advantage over narrow field of view input devices such as head mounted or desktop displays. Devices that we have incorporated into our system that are critical for monitoring improvement in this clinical population will also be described.

  11. Community wide interventions for increasing physical activity.

    Science.gov (United States)

    Baker, Philip R A; Francis, Daniel P; Soares, Jesus; Weightman, Alison L; Foster, Charles

    2015-01-05

    Multi-strategic community wide interventions for physical activity are increasingly popular but their ability to achieve population level improvements is unknown. To evaluate the effects of community wide, multi-strategic interventions upon population levels of physical activity. We searched the Cochrane Public Health Group Segment of the Cochrane Register of Studies,The Cochrane Library, MEDLINE, MEDLINE in Process, EMBASE, CINAHL, LILACS, PsycINFO, ASSIA, the British Nursing Index, Chinese CNKI databases, EPPI Centre (DoPHER, TRoPHI), ERIC, HMIC, Sociological Abstracts, SPORT Discus, Transport Database and Web of Science (Science Citation Index, Social Sciences Citation Index, Conference Proceedings Citation Index). We also scanned websites of the EU Platform on Diet, Physical Activity and Health; Health-Evidence.org; the International Union for Health Promotion and Education; the NIHR Coordinating Centre for Health Technology (NCCHTA); the US Centre for Disease Control and Prevention (CDC) and NICE and SIGN guidelines. Reference lists of all relevant systematic reviews, guidelines and primary studies were searched and we contacted experts in the field. The searches were updated to 16 January 2014, unrestricted by language or publication status. Cluster randomised controlled trials, randomised controlled trials, quasi-experimental designs which used a control population for comparison, interrupted time-series studies, and prospective controlled cohort studies were included. Only studies with a minimum six-month follow up from the start of the intervention to measurement of outcomes were included. Community wide interventions had to comprise at least two broad strategies aimed at physical activity for the whole population. Studies which randomised individuals from the same community were excluded. At least two review authors independently extracted the data and assessed the risk of bias. Each study was assessed for the setting, the number of included components

  12. The LOFT wide field monitor

    DEFF Research Database (Denmark)

    Brandt, Søren; Hernanz, M.; Alvarez, L.

    2012-01-01

    be able to address fundamental questions about strong gravity in the vicinity of black holes and the equation of state of nuclear matter in neutron stars. The prime goal of the WFM will be to detect transient sources to be observed by the LAD. However, with its wide field of view and good energy...... to the community of ~100 gamma ray burst positions per year with a ~1 arcmin location accuracy within 30 s of the burst. This paper provides an overview of the design, configuration, and capabilities of the LOFT WFM instrument....

  13. Wide Field Imager for Athena

    Science.gov (United States)

    Meidinger, Norbert; Nandra, Kirpal; Rau, Arne; Plattner, Markus; WFI proto-Consortium

    2015-09-01

    The Wide Field Imager focal plane instrument on ATHENA will combine unprecedented survey power through its large field of view of 40 arcmin with a high count-rate capability (> 1 Crab). The energy resolution of the silicon sensor is state-of-the-art in the energy band of interest from 0.1 keV to 15 keV. At energy of 6 keV for example, the full width at half maximum of the line shall be not worse than 150 eV until the end of the mission. The performance is accomplished by a set of DEPFET active pixel sensor matrices with a pixel size well suited to the angular resolution of 5 arc sec (on-axis) of the mirror system.Each DEPFET pixel is a combined detector-amplifier structure with a MOSFET integrated onto a fully depleted 450 micron thick silicon bulk. Two different types of DEPFET sensors are planned for the WFI instrument: A set of large-area sensors to cover the physical size of 14 cm x 14 cm in the focal plane and a single gateable DEPFET sensor matrix optimized for the high count rate capability of the instrument. An overview will be given about the presently developed instrument concept and design, the status of the technology development, and the expected performance. An outline of the project organization, the model philosophy as well as the schedule will complete the presentation about the Wide Field Imager for Athena.

  14. Review Single nucleotide polymorphism in genome-wide ...

    African Journals Online (AJOL)

    Genome-wide patterns of variation across individuals provide most powerful source of data for uncovering the history of migration, expansion, and adaptation of the human population. The arrival of new technologies that type more than millions of the single nucleotide polymorphisms (SNPs) in a single experiment has ...

  15. Power analysis for genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Klein Robert J

    2007-08-01

    Full Text Available Abstract Background Genome-wide association studies are a promising new tool for deciphering the genetics of complex diseases. To choose the proper sample size and genotyping platform for such studies, power calculations that take into account genetic model, tag SNP selection, and the population of interest are required. Results The power of genome-wide association studies can be computed using a set of tag SNPs and a large number of genotyped SNPs in a representative population, such as available through the HapMap project. As expected, power increases with increasing sample size and effect size. Power also depends on the tag SNPs selected. In some cases, more power is obtained by genotyping more individuals at fewer SNPs than fewer individuals at more SNPs. Conclusion Genome-wide association studies should be designed thoughtfully, with the choice of genotyping platform and sample size being determined from careful power calculations.

  16. Juvenile resilience and adult longevity explain residual populations of the Andean wax palm Ceroxylon quindiuense after deforestation.

    Directory of Open Access Journals (Sweden)

    María José Sanín

    Full Text Available Wax palms are an important element of the cloud forests in the tropical Andes. Despite heavy deforestation, the density of adults seems to be similar in deforested pastures as in forests. We aimed to infer the mechanisms responsible for this apparent resilience in pastures and we tested two hypotheses to explain it: 1 adult palms survived in pastures because they were spared from logging, and 2 adults occurred in pastures through the resilience of large juvenile rosettes, which survived through subterranean meristems and later developed into adults. For this purpose, we characterized the demographic structure of C. quindiuense in a total of 122 plots of 400 m(2 in forests and pastures at two sites with contrasted land use histories in Colombia and Peru. Additionally, we implemented growth models that allowed us to estimate the age of individuals at four sites. These data were combined with information collected from local land managers in order to complete our knowledge on the land use history at each site. At two sites, the presence of old individuals up to 169 years and a wide age range evidenced that, at least, a portion of current adults in pastures were spared from logging at the time of deforestation. However, at the two other sites, the absence of older adults in pastures and the narrow age range of the populations indicated that individuals came exclusively from rosette resilience. These interpretations were consistent with the land use history of sites. In consequence, the combination of the two hypotheses (spared individuals and rosette resilience explained patterns of C. quindiuense in pastures on a regional scale. Regeneration through subterranean meristems in palms is an important, yet overlooked mechanism of resilience, which occurs in a number of palm species and deserves being integrated in the conceptual framework of disturbance ecology.

  17. Wide spectral band beam analysis

    Science.gov (United States)

    Aharon, Oren

    2015-03-01

    The reality in laser beam profiling is that measurements are performed over a wide spectrum of wavelengths and power ranges. Many applications use multiple laser wavelengths with very different power levels, a fact which dictates a need for a better measuring tool. Rapid progress in the fiber laser area has increased the demand for lasers in the wavelength range of 900 - 1030 nm, while the telecommunication market has increased the demand for wavelength range of 1300nm - 1600 nm, on the other hand the silicone chip manufacturing and mass production requirements tend to lower the laser wavelength towards the 190nm region. In many cases there is a need to combine several lasers together in order to perform a specific task. A typical application is to combine one visible laser for pointing, with a different laser for material processing with a very different wavelength and power level. The visible laser enables accurate pointing before the second laser is operated. The beam profile of the intensity distribution is an important parameter that indicates how a laser beam will behave in an application. Currently a lab, where many different lasers are used, will find itself using various laser beam profilers from several vendors with different specifications and accuracies. It is the propose of this article to present a technological breakthrough in the area of detectors, electronics and optics allowing intricate measurements of lasers with different wavelength and with power levels that vary many orders of magnitude by a single beam profiler.

  18. Wide area continuous offender monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Hoshen, J. [Lucent Technologies (United States); Drake, G. [New Mexico Dept. of Corrections, Santa Fe, NM (United States); Spencer, D. [Sandia National Labs., Albuquerque, NM (United States)

    1996-11-01

    The corrections system in the U.S. is supervising over five million offenders. This number is rising fast and so are the direct and indirect costs to society. To improve supervision and reduce the cost of parole and probation, first generation home arrest systems were introduced in 1987. While these systems proved to be helpful to the corrections system, their scope is rather limited because they only cover an offender at a single location and provide only a partial time coverage. To correct the limitations of first-generation systems, second-generation wide area continuous electronic offender monitoring systems, designed to monitor the offender at all times and locations, are now on the drawing board. These systems use radio frequency location technology to track the position of offenders. The challenge for this technology is the development of reliable personal locator devices that are small, lightweight, with long operational battery life, and indoors/outdoors accuracy of 100 meters or less. At the center of a second-generation system is a database that specifies the offender`s home, workplace, commute, and time the offender should be found in each. The database could also define areas from which the offender is excluded. To test compliance, the system would compare the observed coordinates of the offender with the stored location for a given time interval. Database logfiles will also enable law enforcement to determine if a monitored offender was present at a crime scene and thus include or exclude the offender as a potential suspect.

  19. Unit 148 - World Wide Web Basics

    OpenAIRE

    148, CC in GIScience; Yeung, Albert K.

    2000-01-01

    This unit explains the characteristics and the working principles of the World Wide Web as the most important protocol of the Internet. Topics covered in this unit include characteristics of the World Wide Web; using the World Wide Web for the dissemination of information on the Internet; and using the World Wide Web for the retrieval of information from the Internet.

  20. Population Research.

    Science.gov (United States)

    National Inst. of Child Health and Human Development (NIH), Bethesda, MD.

    The scope of population research as carried on by the National Institute of Child Health and Human Development (NICHD) is set forth in this booklet. Population problems of the world, United States, and the individual are considered along with international population policies based on voluntary family planning programs. NICHD goals for biological…

  1. Stature Estimation Based On Lower Limb Dimensions in the Malaysian Population

    OpenAIRE

    F. M. Nor; N. Abdullah; Al-M. Mustapa; L. Q. Wen; N. A. Faisal; D. A. A. Ahmad Nazari

    2013-01-01

    Estimation of stature is an important step in developing a biological profile for human identification. It may provide a valuable indicator for unknown individual in a population. The aim of this study was to analyses the relationship between stature and lower limb dimensions in the Malaysian population. The sample comprised 100 corpses, which included 69 males and 31 females between age ranges of 20 to 90 years old. The parameters measured were stature, thigh length, lower leg length, leg le...

  2. Prevalence of problematic cell phone use in an adult population in Spain as assessed by the Mobile Phone Problem Use Scale (MPPUS)

    Science.gov (United States)

    de-Sola, José; Talledo, Hernán; Rubio, Gabriel

    2017-01-01

    Problematic cell phone use has alarmingly increased in industrialized countries in the past 10 years. For many perpetrators, it can turn into a behavioural addiction, although this is not a recognized medical condition. Although there are many tools for evaluating this use, one of the most widely used tools is the Mobile Phone Problematic Use Scale (MPPUS), which we test on a representative sample of the population in Spain to obtain an estimate of the prevalence of problematic cell phone use in our midst. The age range consists of 16–65 years, with 1,126 surveys conducted. In this population, we verify that the reliability and internal consistency of the MPPUS (α = 0.939) are maintained. Additionally, the construct validity, considering the derived factors (Abuse and Dependence, Craving and Loss of Control, and Dependence on the Social Environment) are aligned with other research and with diverse external criteria of addiction. We establish four categories of users (Casual, Regular, At Risk, and Problematic) and obtain a prevalence of 15.4% among At Risk Users and 5.1% among Problematic Users. This finding implies a total of 20.5% of Users with Problems. A binary logistic regression analysis shows that age, gender, level of education, and daily cell phone use predict problematic cell phone use. The results, based on multiple criteria, show that such problematic use shares features of recognized addictions, affecting large segments of the population and not only adolescents. PMID:28771626

  3. Prevalence of problematic cell phone use in an adult population in Spain as assessed by the Mobile Phone Problem Use Scale (MPPUS.

    Directory of Open Access Journals (Sweden)

    José de-Sola

    Full Text Available Problematic cell phone use has alarmingly increased in industrialized countries in the past 10 years. For many perpetrators, it can turn into a behavioural addiction, although this is not a recognized medical condition. Although there are many tools for evaluating this use, one of the most widely used tools is the Mobile Phone Problematic Use Scale (MPPUS, which we test on a representative sample of the population in Spain to obtain an estimate of the prevalence of problematic cell phone use in our midst. The age range consists of 16-65 years, with 1,126 surveys conducted. In this population, we verify that the reliability and internal consistency of the MPPUS (α = 0.939 are maintained. Additionally, the construct validity, considering the derived factors (Abuse and Dependence, Craving and Loss of Control, and Dependence on the Social Environment are aligned with other research and with diverse external criteria of addiction. We establish four categories of users (Casual, Regular, At Risk, and Problematic and obtain a prevalence of 15.4% among At Risk Users and 5.1% among Problematic Users. This finding implies a total of 20.5% of Users with Problems. A binary logistic regression analysis shows that age, gender, level of education, and daily cell phone use predict problematic cell phone use. The results, based on multiple criteria, show that such problematic use shares features of recognized addictions, affecting large segments of the population and not only adolescents.

  4. Prevalence of problematic cell phone use in an adult population in Spain as assessed by the Mobile Phone Problem Use Scale (MPPUS).

    Science.gov (United States)

    de-Sola, José; Talledo, Hernán; Rodríguez de Fonseca, Fernando; Rubio, Gabriel

    2017-01-01

    Problematic cell phone use has alarmingly increased in industrialized countries in the past 10 years. For many perpetrators, it can turn into a behavioural addiction, although this is not a recognized medical condition. Although there are many tools for evaluating this use, one of the most widely used tools is the Mobile Phone Problematic Use Scale (MPPUS), which we test on a representative sample of the population in Spain to obtain an estimate of the prevalence of problematic cell phone use in our midst. The age range consists of 16-65 years, with 1,126 surveys conducted. In this population, we verify that the reliability and internal consistency of the MPPUS (α = 0.939) are maintained. Additionally, the construct validity, considering the derived factors (Abuse and Dependence, Craving and Loss of Control, and Dependence on the Social Environment) are aligned with other research and with diverse external criteria of addiction. We establish four categories of users (Casual, Regular, At Risk, and Problematic) and obtain a prevalence of 15.4% among At Risk Users and 5.1% among Problematic Users. This finding implies a total of 20.5% of Users with Problems. A binary logistic regression analysis shows that age, gender, level of education, and daily cell phone use predict problematic cell phone use. The results, based on multiple criteria, show that such problematic use shares features of recognized addictions, affecting large segments of the population and not only adolescents.

  5. Mexico's population policy turnaround.

    Science.gov (United States)

    Nagel, J S

    1978-12-01

    Until 1972 Mexico's officials seemed to believe that the annual population growth rate of 3.5% was not really a problem as long as the economic development rate could be kept ahead of the population growth rate. The General Law of Population of 1947 was actually promoting population growth. It was only during the 1960s that elite opinion shifted, and privately funded family planning programs became increasingly active. By 1972 the population had reached 54 million, from 20 million in 1940. President Echevarria, till then a traditional pronatalist, announced in 1972 the creation of a national family planning program, and, in 1974, the creation of a national population council. Since then the Mexican government has embarked on ambitious programs of mass communication and sex education to make the population receptive to its new attitudes. The plans have worked: by mid-1979 estimates put the population growth rate at 2.9%, within sight of the 2.5% target set for 1982 by new president Lopez Portillo. According to a survey conducted by the National Fertility Survey, by late 1976 41.50% of Mexican women of childbearing age were practicing contraception. Within the 41.50% of active contraceptors, 14.9% use the pill, and 7.8% the IUD. New channels of information and of contraceptive delivery are being explored to reach Mexico's widely scattered rural population, and to bring the average family size down to 2 children from the average of 6.5 children per woman for 1973-1975. The government goal is of a 1% population increase by the year 2000.

  6. Apolipoprotein E phenotype is not related to late-life depression in a population-based sample

    NARCIS (Netherlands)

    Schmand, B.; Hooijer, C.; Jonker, C.; Lindeboom, J.; Havekes, L.M.

    1998-01-01

    Apolipoprotein E (ApoE) allele frequencies were examined in a population-based sample (n = 475; age range 65-84 years; Amsterdam Study of the Elderly). The relation of ApoE ε4 with dementia and with various types of late-life depression was studied. Depression was measured with the Geriatric Mental

  7. Passive Range of Motion in a Population-Based Sample of Children with Spastic Cerebral Palsy Who Walk

    Science.gov (United States)

    McDowell, Brona C.; Salazar-Torres, Jose J.; Kerr, Claire; Cosgrove, Aidan P.

    2012-01-01

    -While passive range of motion (PROM) is commonly used to inform decisions on therapeutic management, knowledge of PROM of children with spastic cerebral palsy (CP) is limited. A population-based sample of 178 children with spastic CP (110 male; unilateral, n = 94; bilateral, n = 84; age range 4-17 years) and 68 typically developing children (24…

  8. GWAMA: software for genome-wide association meta-analysis

    Directory of Open Access Journals (Sweden)

    Mägi Reedik

    2010-05-01

    Full Text Available Abstract Background Despite the recent success of genome-wide association studies in identifying novel loci contributing effects to complex human traits, such as type 2 diabetes and obesity, much of the genetic component of variation in these phenotypes remains unexplained. One way to improving power to detect further novel loci is through meta-analysis of studies from the same population, increasing the sample size over any individual study. Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies. Results We have developed flexible, open-source software for the meta-analysis of genome-wide association studies. The software incorporates a variety of error trapping facilities, and provides a range of meta-analysis summary statistics. The software is distributed with scripts that allow simple formatting of files containing the results of each association study and generate graphical summaries of genome-wide meta-analysis results. Conclusions The GWAMA (Genome-Wide Association Meta-Analysis software has been developed to perform meta-analysis of summary statistics generated from genome-wide association studies of dichotomous phenotypes or quantitative traits. Software with source files, documentation and example data files are freely available online at http://www.well.ox.ac.uk/GWAMA.

  9. Genome-wide detection of selection and other evolutionary forces

    DEFF Research Database (Denmark)

    Xu, Zhuofei; Zhou, Rui

    2015-01-01

    As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed...... of an animal pathogen. The evolutionary analysis of the protein-coding part of the genomes will provide a wide spectrum oof genetic variations that play potential roles in adaptive evolution of bacteria....

  10. Wide Bandgap Semiconductors for Energy Efficiency and Renewable Energy Applications /

    OpenAIRE

    Yang, Muchuan

    2014-01-01

    Energy has emerged to be a global concern as the world confronts the challenges of population growth, climate change, economic recovery, energy affordability. To overcome the energy crisis, people need to work with both hands: use one hand to make a transition from fossil fuels to clean, renewable energy and the other hand to cut down energy consumption by developing energy efficient devices and systems. In this dissertation, I focus my research to tackle these problems using wide bandgap sem...

  11. Range-wide success of red-cockaded woodpecker translocations.

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, John W; Costa, Ralph

    2004-12-31

    Edwards, John W.; Costa, Ralph. 2004. Range-wide success of red-cockaded woodpecker translocations. In: Red-cockaded woodpecker; Road to Recovery. Proceedings of the 4th Red-cockaded woodpecker Symposium. Ralph Costa and Susan J. Daniels, eds. Savannah, Georgia. January, 2003. Chapter 6. Translocation. Pp 307-311. Abstract: Red-cockaded woodpeckers (Picoides borealis) have declined range-wide during the past century, suffering from habitat loss and the effects of fire exclusion in older southern pine forests. Red-cockaded woodpecker translocations are a potentially important tool in conservation efforts to reestablish red-cockaded woodpeckers in areas from which they have been extirpated. Currently, translocations are critical in ongoing efforts to save and restore the many existing small populations. We examined the effects of demographic and environmental factors on the range-wide success of translocations between 1989 and 1995.

  12. Population Blocks.

    Science.gov (United States)

    Smith, Martin H.

    1992-01-01

    Describes an educational game called "Population Blocks" that is designed to illustrate the concept of exponential growth of the human population and some potential effects of overpopulation. The game material consists of wooden blocks; 18 blocks are painted green (representing land), 7 are painted blue (representing water); and the remaining…

  13. Wolf population dynamics

    Science.gov (United States)

    Fuller, Todd K.; Mech, L. David; Cochrane, Jean Fitts; Mech, L. David; Boitani, Luigi

    2003-01-01

    A large, dark wolf poked his nose out of the pines in Yellowstone National Park as he thrust a broad foot deep into the snow and plowed ahead. Soon a second animal appeared, then another, and a fourth. A few minutes later, a pack of thirteen lanky wolves had filed out of the pines and onto the open hillside.Wolf packs are the main social units of a wolf population. As numbers of wolves in packs change, so too, then, does the wolf population (Rausch 1967). Trying to understand the factors and mechanisms that affect these changes is what the field of wolf population dynamics is all about. In this chapter, we will explore this topic using two main approaches: (1) meta-analysis using data from studies from many areas and periods, and (2) case histories of key long-term studies. The combination presents a good picture – a picture, however, that is still incomplete. We also caution that the data sets summarized in the analyses represent snapshots of wolf population dynamics under widely varying conditions and population trends, and that the figures used are usually composites or averages. Nevertheless, they should allow generalizations that provide important insight into wolf population dynamics.

  14. Genome wide selection in Citrus breeding.

    Science.gov (United States)

    Gois, I B; Borém, A; Cristofani-Yaly, M; de Resende, M D V; Azevedo, C F; Bastianel, M; Novelli, V M; Machado, M A

    2016-10-17

    Genome wide selection (GWS) is essential for the genetic improvement of perennial species such as Citrus because of its ability to increase gain per unit time and to enable the efficient selection of characteristics with low heritability. This study assessed GWS efficiency in a population of Citrus and compared it with selection based on phenotypic data. A total of 180 individual trees from a cross between Pera sweet orange (Citrus sinensis Osbeck) and Murcott tangor (Citrus sinensis Osbeck x Citrus reticulata Blanco) were evaluated for 10 characteristics related to fruit quality. The hybrids were genotyped using 5287 DArT_seq TM (diversity arrays technology) molecular markers and their effects on phenotypes were predicted using the random regression - best linear unbiased predictor (rr-BLUP) method. The predictive ability, prediction bias, and accuracy of GWS were estimated to verify its effectiveness for phenotype prediction. The proportion of genetic variance explained by the markers was also computed. The heritability of the traits, as determined by markers, was 16-28%. The predictive ability of these markers ranged from 0.53 to 0.64, and the regression coefficients between predicted and observed phenotypes were close to unity. Over 35% of the genetic variance was accounted for by the markers. Accuracy estimates with GWS were lower than those obtained by phenotypic analysis; however, GWS was superior in terms of genetic gain per unit time. Thus, GWS may be useful for Citrus breeding as it can predict phenotypes early and accurately, and reduce the length of the selection cycle. This study demonstrates the feasibility of genomic selection in Citrus.

  15. [Population education].

    Science.gov (United States)

    Niang, M

    1992-12-01

    Africa has the highest population growth rate in the world (3%). It has 650 million people (about 900 million in 2000). Rapid population growth has serious consequences which, if not addressed, will be disastrous. This worrisome situation has led some governments to adopt demographic policies to slow down population growth. The UN Economic, Scientific and Cultural Organization (UNESCO) recommends that schools provide population education. Various population conferences have popularized population education in schools among African countries. UNESCO began its regional program on population education in Africa in 1969. National family life and population education (FL/PE) projects have increased from 4 in 1970 to 32 in 1990 (17 in French- and Portuguese-speaking Africa and 5 in English-speaking Africa). These projects teach students about the links between demographic problems and socioeconomic factors and contemporary culture. They aim for total development of the individual and improvement of the quality of life for the individual, family, and community. Topics covered in FL/PE are birth rate; fertility; health; and maternal, infant, and child mortality; unwanted pregnancy; illegal abortion; sexually transmitted diseases; rural-urban migration; and urbanization. Benin introduced FL/PE at all levels of its education system while Senegal, Guinea, Mauritania, and Zaire introduced it to only the primary and secondary school levels. Some countries teach FL/PE as one discipline while most countries (e.g., Senegal) have integrated it into other disciplines (e.g., geography). FL/PE should begin in primary schools because they have the most students and prepare students for middle schools, which provide FL/PE. Elementary education in Senegal is being overhauled to introduce current major problems bit by bit. Senegal also wants to incorporate FL/PE into literacy and adult education programs. Integration of FL/PE into other disciplines should be encouraged.

  16. State machine replication for wide area networks

    OpenAIRE

    Mao, Yanhua

    2010-01-01

    State machine replication is the most general approach for providing highly available services with strong consistency guarantees. This dissertation studies protocols for implementing replicated state machines for wide area networks. First it demonstrates the challenges by comparing two protocols designed for local area networks in a cluster-based wide-area setting and shows that existing protocols designed for local area networks do not perform well in wide-area settings. A generic rotating ...

  17. Wide-Field Imaging Using Nitrogen Vacancies

    Science.gov (United States)

    Englund, Dirk Robert (Inventor); Trusheim, Matthew Edwin (Inventor)

    2017-01-01

    Nitrogen vacancies in bulk diamonds and nanodiamonds can be used to sense temperature, pressure, electromagnetic fields, and pH. Unfortunately, conventional sensing techniques use gated detection and confocal imaging, limiting the measurement sensitivity and precluding wide-field imaging. Conversely, the present sensing techniques do not require gated detection or confocal imaging and can therefore be used to image temperature, pressure, electromagnetic fields, and pH over wide fields of view. In some cases, wide-field imaging supports spatial localization of the NVs to precisions at or below the diffraction limit. Moreover, the measurement range can extend over extremely wide dynamic range at very high sensitivity.

  18. Genome-wide landscapes of human local adaptation in Asia.

    Directory of Open Access Journals (Sweden)

    Wei Qian

    Full Text Available Genetic studies of human local adaptation have been facilitated greatly by recent advances in high-throughput genotyping and sequencing technologies. However, few studies have investigated local adaptation in Asian populations on a genome-wide scale and with a high geographic resolution. In this study, taking advantage of the dense population coverage in Southeast Asia, which is the part of the world least studied in term of natural selection, we depicted genome-wide landscapes of local adaptations in 63 Asian populations representing the majority of linguistic and ethnic groups in Asia. Using genome-wide data analysis, we discovered many genes showing signs of local adaptation or natural selection. Notable examples, such as FOXQ1, MAST2, and CDH4, were found to play a role in hair follicle development and human cancer, signal transduction, and tumor repression, respectively. These showed strong indications of natural selection in Philippine Negritos, a group of aboriginal hunter-gatherers living in the Philippines. MTTP, which has associations with metabolic syndrome, body mass index, and insulin regulation, showed a strong signature of selection in Southeast Asians, including Indonesians. Functional annotation analysis revealed that genes and genetic variants underlying natural selections were generally enriched in the functional category of alternative splicing. Specifically, many genes showing significant difference with respect to allele frequency between northern and southern Asian populations were found to be associated with human height and growth and various immune pathways. In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome.

  19. Population Analysis: Communicating in Context

    Science.gov (United States)

    Rajulu, Sudhakar; Thaxton, Sherry

    2008-01-01

    Providing accommodation to a widely varying user population presents a challenge to engineers and designers. It is often even difficult to quantify who is accommodated and who is not accommodated by designs, especially for equipment with multiple critical anthropometric dimensions. An approach to communicating levels of accommodation referred to as population analysis applies existing human factors techniques in novel ways. This paper discusses the definition of population analysis as well as major applications and case studies. The major applications of population analysis consist of providing accommodation information for multivariate problems and enhancing the value of feedback from human-in-the-loop testing. The results of these analyses range from the provision of specific accommodation percentages of the user population to recommendations of design specifications based on quantitative data. Such feedback is invaluable to designers and results in the design of products that accommodate the intended user population.

  20. Age gradients in the stellar populations of massive star forming regions based on a new stellar chronometer

    Energy Technology Data Exchange (ETDEWEB)

    Getman, Konstantin V.; Feigelson, Eric D.; Kuhn, Michael A.; Broos, Patrick S.; Townsley, Leisa K.; Luhman, Kevin L. [Department of Astronomy and Astrophysics, 525 Davey Laboratory, Pennsylvania State University, University Park, PA 16802 (United States); Naylor, Tim [School of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL (United Kingdom); Povich, Matthew S. [Department of Physics and Astronomy, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768 (United States); Garmire, Gordon P. [Huntingdon Institute for X-ray Astronomy, LLC, 10677 Franks Road, Huntingdon, PA 16652 (United States)

    2014-06-01

    A major impediment to understanding star formation in massive star-forming regions (MSFRs) is the absence of a reliable stellar chronometer to unravel their complex star formation histories. We present a new estimation of stellar ages using a new method that employs near-infrared (NIR) and X-ray photometry, Age {sub JX} . Stellar masses are derived from X-ray luminosities using the L{sub X} -M relation from the Taurus cloud. J-band luminosities are compared to mass-dependent pre-main-sequence (PMS) evolutionary models to estimate ages. Age {sub JX} is sensitive to a wide range of evolutionary stages, from disk-bearing stars embedded in a cloud to widely dispersed older PMS stars. The Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) project characterizes 20 OB-dominated MSFRs using X-ray, mid-infrared, and NIR catalogs. The Age {sub JX} method has been applied to 5525 out of 31,784 MYStIX Probable Complex Members. We provide a homogeneous set of median ages for over 100 subclusters in 15 MSFRs; median subcluster ages range between 0.5 Myr and 5 Myr. The important science result is the discovery of age gradients across MYStIX regions. The wide MSFR age distribution appears as spatially segregated structures with different ages. The Age {sub JX} ages are youngest in obscured locations in molecular clouds, intermediate in revealed stellar clusters, and oldest in distributed populations. The NIR color index J – H, a surrogate measure of extinction, can serve as an approximate age predictor for young embedded clusters.

  1. Wireless Wide Area Networks for School Districts.

    Science.gov (United States)

    Nair, Prakash

    This paper considers a basic question that many schools districts face in attempting to develop affordable, expandable district-wide computer networks that are resistant to obsolescence: Should these wide area networks (WANs) employ wireless technology, stick to venerable hard-wired solutions, or combine both. This publication explores the…

  2. Michelson wide-field stellar interferometry

    NARCIS (Netherlands)

    Montilla, I.

    2004-01-01

    The main goal of this thesis is to develop a system to permit wide field operation of Michelson Interferometers. A wide field of view is very important in applications such as the observation of extended or multiple objects, the fringe acquisition and/ or tracking on a nearby unresolved object, and

  3. Two Objections to Wide-Scoping

    NARCIS (Netherlands)

    Evers, Daan

    2011-01-01

    Wide-scopers argue that the detachment of intuitively false ‘ought’ claims from hypothetical imperatives is blocked because ‘ought’ takes wide, as opposed to narrow, scope. I present two arguments against this view. The first questions the premise that natural language conditionals are true just in

  4. Management van World-Wide Web Servers

    NARCIS (Netherlands)

    van Hengstum, F.P.H.; Pras, Aiko

    1996-01-01

    Het World Wide Web is een populaire Internet toepassing waarmee het mogelijk is documenten aan willekeurige Internet gebruikers aan te bieden. Omdat hiervoor nog geen voorzieningen zijn getroffen, was het tot voor kort niet goed mogelijk het World Wide Web op afstand te beheren. De Universiteit

  5. Innovation in Science Education - World-Wide.

    Science.gov (United States)

    Baez, Albert V.

    The purpose of this book is to promote improvements in science education, world-wide, but particularly in developing countries. It is addressed to those in positions to make effective contributions to the improvement of science education. The world-wide role of science education, the goals of innovative activities, past experience in efforts to…

  6. Consistency in the World Wide Web

    DEFF Research Database (Denmark)

    Thomsen, Jakob Grauenkjær

    Tim Berners-Lee envisioned that computers will behave as agents of humans on the World Wide Web, where they will retrieve, extract, and interact with information from the World Wide Web. A step towards this vision is to make computers capable of extracting this information in a reliable...... and consistent way. In this dissertation we study steps towards this vision by showing techniques for the specication, the verication and the evaluation of the consistency of information in the World Wide Web. We show how to detect certain classes of errors in a specication of information, and we show how...... the World Wide Web, in order to help perform consistent evaluations of web extraction techniques. These contributions are steps towards having computers reliable and consistently extract information from the World Wide Web, which in turn are steps towards achieving Tim Berners-Lee's vision. ii...

  7. Population dynamics

    Directory of Open Access Journals (Sweden)

    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  8. Prioritising range-wide scientific monitoring of the Cape fur seal in ...

    African Journals Online (AJOL)

    The range of the Cape fur seal Arctocephalus pusillus pusillus population largely coincides with the region of the cold, nutrient-rich Benguela Current Large Marine Ecosystem (BCLME) adjoining the west coast of South Africa, Namibia and Angola. Range-wide scientific monitoring of the seal population was initiated in the ...

  9. Age of Sexual Consent Law in Canada: Population-Based Evidence for Law and Policy

    OpenAIRE

    Miller, Bonnie B.; Cox, David N.; Saewyc, Elizabeth M.

    2010-01-01

    This study evaluated the implications of the 2008 increase in age for sexual consent in Canada using a population health survey of Canadian adolescents. Government rationales for the increase asserted younger adolescents were more likely to experience sexual exploitation and engage in risky sexual behaviour than adolescents 16 and older. Using data from sexually experienced adolescents in the 2008 British Columbia Adolescent Health Survey (BC AHS, N=6,262; age range 12 – 19; 52% female), anal...

  10. Genome-wide association studies and resting heart rate

    DEFF Research Database (Denmark)

    Oskari Kilpeläinen, Tuomas

    2016-01-01

    Genome-wide association studies (GWASs) have revolutionized the search for genetic variants regulating resting heart rate. In the last 10 years, GWASs have led to the identification of at least 21 novel heart rate loci. These discoveries have provided valuable insights into the mechanisms...... and pathways that regulate heart rate and link heart rate to cardiovascular morbidity and mortality. GWASs capture majority of genetic variation in a population sample by utilizing high-throughput genotyping chips measuring genotypes for up to several millions of SNPs across the genome in thousands...... of individuals. This allows the identification of the strongest heart rate associated signals at genome-wide level. While GWASs provide robust statistical evidence of the association of a given genetic locus with heart rate, they are only the starting point for detailed follow-up studies to locate the causal...

  11. Populism in High School Textbooks

    Science.gov (United States)

    Peiser, Andrew C.

    1973-01-01

    The purpose of this study was to determine whether one area of United States history--Populism and Populists--is accurately presented in nine widely used current American history high school textbooks. Another objective was to devise a system that could be used to make such a determination for any history text. (Author)

  12. The World Wide Web of War

    National Research Council Canada - National Science Library

    Smith, Craig A

    2006-01-01

    Modern communications, combined with the near instantaneous publication of information on the World Wide Web, are providing the means to dramatically affect the pursuit, conduct, and public opinion of war on both sides...

  13. Wide Bandgap Nanostructured Space Photovoltaics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Firefly, in collaboration with Rochester Institute of Technology, proposes an STTR program for the development of a wide-bandgap GaP-based space solar cell capable...

  14. Final Range Wide Environmental Impact Statement

    National Research Council Canada - National Science Library

    Botdorf, Charles

    2001-01-01

    This Final Range Wide Environmental Impact Statement presents the impacts associated with the direct, indirect, and cumulative effects of mission diversification and changes to land use for Yuma Proving Ground, Arizona...

  15. Susceptibility to Chronic Mucus Hypersecretion, a Genome Wide Association Study

    DEFF Research Database (Denmark)

    Dijkstra, A. E.; Smolonska, J.; van den Berge, M.

    2014-01-01

    of smokers develops CMH. A plausible explanation for this phenomenon is a predisposing genetic constitution. Therefore, we performed a genome wide association (GWA) study of CMH in Caucasian populations. Methods: GWA analysis was performed in the NELSON-study using the Illumina 610 array, followed...... of SATB1 (4.3610 29) in lung tissue. Presence of CMH was associated with increased SATB1 mRNA expression in bronchial biopsies from COPD patients. SATB1 expression was induced during differentiation of primary human bronchial epithelial cells in culture. Conclusions: Our findings, that SNP rs6577641...

  16. A high mean-HbA1c value 3-15 months after diagnosis of type 1 diabetes in childhood is related to metabolic control, macroalbuminuria, and retinopathy in early adulthood--a pilot study using two nation-wide population based quality registries.

    Science.gov (United States)

    Samuelsson, Ulf; Steineck, Isabelle; Gubbjornsdottir, Soffia

    2014-05-01

    Intensive treatment of patients with type 1 diabetes delays the onset of long-term complications. On the basis of the information from two nation-wide quality registers, we investigated to which extent HbA1c values 3-15 months after diagnosis in childhood are related to metabolic control, albuminuria, and retinopathy in early adulthood. In Sweden, physicians register all children and adolescents with type 1 diabetes mellitus in the Swedish Pediatric Quality Registry. After 18 yr of age, people with diabetes are followed by the Swedish National Diabetes Register. We identified 1543 children and adolescents with a mean age of 13.9 yr at diagnosis and a mean duration of type 1 diabetes mellitus of 7.1 yr. Children and adolescents with poor metabolic control (mean HbA1c ≥ 70 mmol/mol (8.6 %)) adjacent to diagnosis had a significantly higher mean HbA1c value years later as adults than did patients with a good metabolic control [metabolic group. Patients with a high mean HbA1c 3-15 months after diagnosis had significantly more often macroalbuminuria and retinopathy in early adulthood. Metabolic control adjacent to the diagnosis of type 1 diabetes in childhood or adolescence can predict metabolic control in early adulthood. It is therefore very important that pediatric diabetes teams identify key factors for successful early metabolic control. Actively using quality registries may be one such factor. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. AA, assembly of wide bending magnet

    CERN Multimedia

    CERN PhotoLab

    1980-01-01

    The very particular lattice of the AA required 2 types of dipoles (bending magnets; BST, short and wide; BLG, long and narrow). The wide ones had a steel length of 2.71 m, a "good field" width of 0.564 m, and a weight of about 75 t. Here we see the copper coils being hoisted onto the lower half of a BST. See also 7811105, 8006050. For a BLG, see 8001044.

  18. AA, wide quadrupole on measurement stand

    CERN Multimedia

    CERN PhotoLab

    1981-01-01

    Please look up 8101024 first. Shims and washers on the wide quadrupoles (QFW, QDW; located in the lattice where dispersion was large) served mostly for corrections of those lattice parameters which were a function of momentum. After mounting shims and washers, the quadrupoles were measured to determine their magnetic centre and to catalogue the effect of washer constellations. Raymond Brown is busy measuring a wide quad.

  19. Emergency Medicine for medical students world wide!

    DEFF Research Database (Denmark)

    Perinpam, Larshan; Thi Huynh, Anh-Nhi

    2015-01-01

    A guest blog from Larshan Perinpam (President of ISAEM) and Anh-Nhi Thi Huynh (Vice president of external affairs, ISAEM) - http://blogs.bmj.com/emj/2015/04/17/emergency-medicine-for-medical-students-world-wide/......A guest blog from Larshan Perinpam (President of ISAEM) and Anh-Nhi Thi Huynh (Vice president of external affairs, ISAEM) - http://blogs.bmj.com/emj/2015/04/17/emergency-medicine-for-medical-students-world-wide/...

  20. Wooden Model of Wide AA Bending Magnet

    CERN Multimedia

    CERN PhotoLab

    1978-01-01

    The very particular lattice of the AA required 2 types of dipoles (bending magnets: BLG, long and narrow; BST, short and wide). The wide ones had a steel length of 2.71 m, a "good field" width of 0.564 m, and a weight of about 75 t. Here we see a wooden model, built in 1978, to gain dimensional experience with such a monster.

  1. IOT Overview: Wide-Field Imaging

    Science.gov (United States)

    Selman, F. J.

    The Wide Field Imager (WFI) instrument at La Silla has been the workhorse of wide-field imaging instruments at ESO for several years. In this contribution I will summarize the issues relating to its productivity for the community both in terms of the quality and quantity of data that has come out of it. Although only surveys of limited scope have been completed using WFI, it is ESO's stepping-stone to the new generation of survey telescopes.

  2. Spatial and temporal variation in the range-wide cyclic dynamics of greater sage-grouse.

    Science.gov (United States)

    Row, Jeffrey R; Fedy, Bradley C

    2017-10-19

    Periodic changes in abundance, or population cycles, are common in a variety of species and is one of the most widely studied ecological phenomena. The strength of, and synchrony between population cycles can vary across time and space and understanding these patterns can provide insight into the mechanisms generating population cycles and their variability within and among species. Here, we used wavelet and spectral analysis on a range-wide dataset of abundance for the greater sage-grouse (Centrocercus urophasianus) to test for regional differences in temporal cyclicity. Overall, we found that most populations (11 of 15) were cyclic at some point in a 50-year time series (1965-2015), but the patterns varied over both time and space. Several peripheral populations demonstrated amplitude dampening or loss of cyclicity following population lows in the mid-1990s. Populations through the core of the range in the Great and Wyoming Basins had more consistent cyclic dynamics, but period length appeared to shorten from 10-12 to 6-8 years. In one time period, where cyclicity was greatest overall, increased pairwise population synchrony was correlated with cycle intensity. Our work represents a comprehensive range-wide assessment of cyclic dynamics and revealed substantial variation in temporal and spatial trends of cyclic dynamics across populations.

  3. Stickleback Population

    Directory of Open Access Journals (Sweden)

    Ulrika Candolin

    2012-01-01

    Full Text Available Human-induced eutrophication has increased offspring production in a population of threespine stickleback Gasterosteus aculeatus in the Baltic Sea. Here, we experimentally investigated the effects of an increased density of juveniles on behaviours that influence survival and dispersal, and, hence, population growth—habitat choice, risk taking, and foraging rate. Juveniles were allowed to choose between two habitats that differed in structural complexity, in the absence and presence of predators and conspecific juveniles. In the absence of predators or conspecifics, juveniles preferred the more complex habitat. The preference was further enhanced in the presence of a natural predator, a perch Perca fluviatilis (behind a transparent Plexiglas wall. However, an increased density of conspecifics relaxed the predator-enhanced preference for the complex habitat and increased the use of the open, more predator-exposed habitat. Foraging rate was reduced under increased perceived predation risk. These results suggest that density-dependent behaviours can cause individuals to choose suboptimal habitats where predation risk is high and foraging rate low. This could contribute to the regulation of population growth in eutrophicated areas where offspring production is high.

  4. Population geography.

    Science.gov (United States)

    Nash, A

    1994-03-01

    Population geographers are involved in contemporary policy issues, the production of quality work, and successful communication of research findings. This article reviewed some contributions population geographers have made to the understanding of the geographic impact of aging and the consequences of migration. Geographers have come late to the study of aging and have focused primarily on four main policy issues: 1) fertility decline, 2) housing demography, 3) aged patterns of housing and migration, and 4) government policy. Fertility decline research has highlighted information diffusion theories for fertility decline by researchers such as Zelinsky, Skeldon, and Noin. Changes in attitudes and the removal on constraints has been examined by Woods. Residential mobility studies have been the focus of researchers such as Gober, Moore, and Clark, and Myers. Regional labor markets and the movement of the "baby boom" through the life course have been examined by Miron, Plane and Rogerson, and Clout, who studied the empty nesters and the movement out of suburbia. Private residential housing has increased for the elderly in England and Wales (Hamnett and Mullings), and seasonal migration of Minnesotans results in lost sales revenues and high health and social costs for those too ill to travel (Craig). Geographers have not accomplished a significant thrust into the literature on demographic aging. Contributions to the transnational and international literature have resulted in internal migration studies by Clout on "counterurbanization" in northwestern industrial Europe, while Fielding, Baltensperger, Marchand and Scott, and Jones have examined the continuing rural-urban migration. The loss of urban population has been associated with inner city problems, the impact of labor supply and market demand, and the revenue and health care consequences in the work of Champion, Gibson, and Champion and Illeris, and Craig. Impacts are felt differently by geographic location, and

  5. Indian populations

    CERN Multimedia

    Spahni,J

    1974-01-01

    Le Prof. J.C. Spahni qui a parcouru les Andes, Vénezuela etc. parle de ses expériences et connaissances qu'il a vécu au cours des 14 ans parmi les populations indiennes de la Cordillière des Andes. Il a ramené des objets artisanals indiens lesquels l'auditoire peut acquérir. L'introduction-conférence est suivi d'un film, commenté par lui-même; après l'entracte il y un débat-dialogue avec le public.

  6. Genome-wide association study of Tourette Syndrome

    Science.gov (United States)

    Scharf, Jeremiah M.; Yu, Dongmei; Mathews, Carol A.; Neale, Benjamin M.; Stewart, S. Evelyn; Fagerness, Jesen A; Evans, Patrick; Gamazon, Eric; Edlund, Christopher K.; Service, Susan; Tikhomirov, Anna; Osiecki, Lisa; Illmann, Cornelia; Pluzhnikov, Anna; Konkashbaev, Anuar; Davis, Lea K; Han, Buhm; Crane, Jacquelyn; Moorjani, Priya; Crenshaw, Andrew T.; Parkin, Melissa A.; Reus, Victor I.; Lowe, Thomas L.; Rangel-Lugo, Martha; Chouinard, Sylvain; Dion, Yves; Girard, Simon; Cath, Danielle C; Smit, Jan H; King, Robert A.; Fernandez, Thomas; Leckman, James F.; Kidd, Kenneth K.; Kidd, Judith R.; Pakstis, Andrew J.; State, Matthew; Herrera, Luis Diego; Romero, Roxana; Fournier, Eduardo; Sandor, Paul; Barr, Cathy L; Phan, Nam; Gross-Tsur, Varda; Benarroch, Fortu; Pollak, Yehuda; Budman, Cathy L.; Bruun, Ruth D.; Erenberg, Gerald; Naarden, Allan L; Lee, Paul C; Weiss, Nicholas; Kremeyer, Barbara; Berrío, Gabriel Bedoya; Campbell, Desmond; Silgado, Julio C. Cardona; Ochoa, William Cornejo; Restrepo, Sandra C. Mesa; Muller, Heike; Duarte, Ana V. Valencia; Lyon, Gholson J; Leppert, Mark; Morgan, Jubel; Weiss, Robert; Grados, Marco A.; Anderson, Kelley; Davarya, Sarah; Singer, Harvey; Walkup, John; Jankovic, Joseph; Tischfield, Jay A.; Heiman, Gary A.; Gilbert, Donald L.; Hoekstra, Pieter J.; Robertson, Mary M.; Kurlan, Roger; Liu, Chunyu; Gibbs, J. Raphael; Singleton, Andrew; Hardy, John; Strengman, Eric; Ophoff, Roel; Wagner, Michael; Moessner, Rainald; Mirel, Daniel B.; Posthuma, Danielle; Sabatti, Chiara; Eskin, Eleazar; Conti, David V.; Knowles, James A.; Ruiz-Linares, Andres; Rouleau, Guy A.; Purcell, Shaun; Heutink, Peter; Oostra, Ben A.; McMahon, William; Freimer, Nelson; Cox, Nancy J.; Pauls, David L.

    2012-01-01

    Tourette Syndrome (TS) is a developmental disorder that has one of the highest familial recurrence rates among neuropsychiatric diseases with complex inheritance. However, the identification of definitive TS susceptibility genes remains elusive. Here, we report the first genome-wide association study (GWAS) of TS in 1285 cases and 4964 ancestry-matched controls of European ancestry, including two European-derived population isolates, Ashkenazi Jews from North America and Israel, and French Canadians from Quebec, Canada. In a primary meta-analysis of GWAS data from these European ancestry samples, no markers achieved a genome-wide threshold of significance (p<5 × 10−8); the top signal was found in rs7868992 on chromosome 9q32 within COL27A1 (p=1.85 × 10−6). A secondary analysis including an additional 211 cases and 285 controls from two closely-related Latin-American population isolates from the Central Valley of Costa Rica and Antioquia, Colombia also identified rs7868992 as the top signal (p=3.6 × 10−7 for the combined sample of 1496 cases and 5249 controls following imputation with 1000 Genomes data). This study lays the groundwork for the eventual identification of common TS susceptibility variants in larger cohorts and helps to provide a more complete understanding of the full genetic architecture of this disorder. PMID:22889924

  7. Digital demodulator for wide bandwidth SAR

    DEFF Research Database (Denmark)

    Jørgensen, Jørn Hjelm

    2000-01-01

    A novel approach to the design of efficient digital quadrature demodulators for wide bandwidth SAR systems is described. Efficiency is obtained by setting the intermediate frequency to 1/4 the ADC sampling frequency. One channel is made filter-free by synchronizing the local oscillator with the o......A novel approach to the design of efficient digital quadrature demodulators for wide bandwidth SAR systems is described. Efficiency is obtained by setting the intermediate frequency to 1/4 the ADC sampling frequency. One channel is made filter-free by synchronizing the local oscillator...

  8. Wooden Model of Wide AA Bending Magnet

    CERN Multimedia

    CERN PhotoLab

    1978-01-01

    The very particular lattice of the AA required 2 types of dipoles (bending magnets: BLG, long and narrow; BST, short and wide). A wide one had a steel length of 2.71 m, a "good field" width of 0.564 m, and a weight of about 75 t. A wooden model was build in 1978, to gain dimensional experience. Here, Peter Zettwoch, one of the largest men at CERN at that time, is putting a hand in the mouth of the wooden BST monster.

  9. Significance of genome-wide association studies in molecular anthropology.

    Science.gov (United States)

    Gupta, Vipin; Khadgawat, Rajesh; Sachdeva, Mohinder Pal

    2009-12-01

    The successful advent of a genome-wide approach in association studies raises the hopes of human geneticists for solving a genetic maze of complex traits especially the disorders. This approach, which is replete with the application of cutting-edge technology and supported by big science projects (like Human Genome Project; and even more importantly the International HapMap Project) and various important databases (SNP database, CNV database, etc.), has had unprecedented success in rapidly uncovering many of the genetic determinants of complex disorders. The magnitude of this approach in the genetics of classical anthropological variables like height, skin color, eye color, and other genome diversity projects has certainly expanded the horizons of molecular anthropology. Therefore, in this article we have proposed a genome-wide association approach in molecular anthropological studies by providing lessons from the exemplary study of the Wellcome Trust Case Control Consortium. We have also highlighted the importance and uniqueness of Indian population groups in facilitating the design and finding optimum solutions for other genome-wide association-related challenges.

  10. Genome-Wide Association of Heroin Dependence in Han Chinese.

    Directory of Open Access Journals (Sweden)

    Gursharan Kalsi

    Full Text Available Drug addiction is a costly and recurring healthcare problem, necessitating a need to understand risk factors and mechanisms of addiction, and to identify new biomarkers. To date, genome-wide association studies (GWAS for heroin addiction have been limited; moreover they have been restricted to examining samples of European and African-American origin due to difficulty of recruiting samples from other populations. This is the first study to test a Han Chinese population; we performed a GWAS on a homogeneous sample of 370 Han Chinese subjects diagnosed with heroin dependence using the DSM-IV criteria and 134 ethnically matched controls. Analysis using the diagnostic criteria of heroin dependence yielded suggestive evidence for association between variants in the genes CCDC42 (coiled coil domain 42; p = 2.8x10-7 and BRSK2 (BR serine/threonine 2; p = 4.110-6. In addition, we found evidence for risk variants within the ARHGEF10 (Rho guanine nucleotide exchange factor 10 gene on chromosome 8 and variants in a region on chromosome 20q13, which is gene-poor but has a concentration of mRNAs and predicted miRNAs. Gene-based association analysis identified genome-wide significant association between variants in CCDC42 and heroin addiction. Additionally, when we investigated shared risk variants between heroin addiction and risk of other addiction-related and psychiatric phenotypes using polygenic risk scores, we found a suggestive relationship with variants predicting tobacco addiction, and a significant relationship with variants predicting schizophrenia. Our genome wide association study of heroin dependence provides data in a novel sample, with functionally plausible results and evidence of genetic data of value to the field.

  11. Microsatellite data analysis for population genetics

    Science.gov (United States)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  12. Mental health in war-affected populations

    NARCIS (Netherlands)

    Scholte, W.F.

    2013-01-01

    This book addresses mental health problems in populations in nonwestern war-affected regions, and methods to mitigate these problems through interventions focusing on social reintegration. It describes a number of studies among war-affected populations in widely different areas: refugees from the

  13. School-Wide Discipline and Classroom Ecology.

    Science.gov (United States)

    Marr, Mary Beth; Audette, Bob; White, Richard; Ellis, Edward; Algozzine, Bob

    2002-01-01

    Shortages of teachers with specialized skills, coupled with increased difficulty accommodating students with problem behaviors in general education classrooms, create pressures for performance and accountability in schools. Describes improvements in classroom ecology after implementation of a school-wide discipline model. These outcomes were…

  14. Re-Framing the World Wide Web

    Science.gov (United States)

    Black, August

    2011-01-01

    The research presented in this dissertation studies and describes how technical standards, protocols, and application programming interfaces (APIs) shape the aesthetic, functional, and affective nature of our most dominant mode of online communication, the World Wide Web (WWW). I examine the politically charged and contentious battle over browser…

  15. AA, wide quadrupole on measurement stand

    CERN Multimedia

    CERN PhotoLab

    1981-01-01

    Please look up 8101024 and 8103203 first. Wide quadrupole (QFW, QDW) with end-shims and shimming washers on the measurement stand. With the measurement coil one measured the harmonics of the magnetic field, determined the magnetic centre, and catalogued the effect of washer constellations.

  16. Enterprise-Wide Process & Performance Excellence:

    DEFF Research Database (Denmark)

    Edgeman, Rick; Kristensen, Kai; Eskildsen, Jacob Kjær

    2013-01-01

    Program value proposition, content, organization, and strategy are elaborated herein. This elaboration is the result of careful study of business and social trends, along with careful listening to collaborating enterprises. It is in this latter sense that the Enterprise-Wide Process & Performance...

  17. Inbreeding in genome-wide selection

    NARCIS (Netherlands)

    Daetwyler, H.D.; Villanueva, B.; Bijma, P.; Woolliams, J.A.

    2007-01-01

    Traditional selection methods, such as sib and best linear unbiased prediction (BLUP) selection, which increased genetic gain by increasing accuracy of evaluation have also led to an increased rate of inbreeding per generation (¿FG). This is not necessarily the case with genome-wide selection, which

  18. Welcome to the World-Wide Web.

    Science.gov (United States)

    Davis, Philip

    1995-01-01

    World Wide Web (WWW) is a multimedia, globally distributed, client/server information system based on hypertext. WWW browser software (Mosaic, Cello, and Samba) allows users to navigate hypertext documents via the Internet. Libraries are taking advantage of the fact that hypertext linked documents can be easily and inexpensively shared. (JMV)

  19. Happy 20th Birthday, World Wide Web!

    CERN Multimedia

    2009-01-01

    On 13 March CERN celebrated the 20th anniversary of the World Wide Web. Check out the video interview with Web creator Tim Berners-Lee and find out more about the both the history and future of the Web. To celebrate CERN also launched a brand new website, CERNland, for kids.

  20. Internet and The World Wide Web

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 2. Internet and The World Wide Web. Neelima Shrikhande. General Article Volume 2 Issue 2 February 1997 pp 64-74. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/002/02/0064-0074 ...

  1. The LOFT wide field monitor simulator

    DEFF Research Database (Denmark)

    Donnarumma, I.; Evangelista, Y.; Campana, R.

    2012-01-01

    We present the simulator we developed for the Wide Field Monitor (WFM) aboard the Large Observatory For Xray Timing (LOFT) mission, one of the four ESA M3 candidate missions considered for launch in the 2022–2024 timeframe. The WFM is designed to cover a large FoV in the same bandpass as the Larg...

  2. Proteome-Wide Quantitation by SILAC

    DEFF Research Database (Denmark)

    Rigbolt, Kristoffer T G; Blagoev, Blagoy

    2010-01-01

    Ongoing improvements in instrumentation, fractionation techniques, and enrichment procedures have dramatically increased the coverage of the proteome achievable via LC-MS/MS-based methodologies, opening the call for approaches to quantitatively assess differences at a proteome-wide scale. Stable...

  3. So Wide a Web, So Little Time.

    Science.gov (United States)

    McConville, David; And Others

    1996-01-01

    Discusses new trends in the World Wide Web. Highlights include multimedia; digitized audio-visual files; compression technology; telephony; virtual reality modeling language (VRML); open architecture; and advantages of Java, an object-oriented programming language, including platform independence, distributed development, and pay-per-use software.…

  4. Manual Colostomy Reversals Following Wide Colorectal Resections ...

    African Journals Online (AJOL)

    Manual Colostomy Reversals Following Wide Colorectal Resections at Poorly Equipped Surgical Facilities. EBFK Odimba, M Nthele, M Mbambiko. Abstract. Background: The decision for colostomy reversal is usually not easy and often reflects patient's desire, fully analyzed and agreed by the surgeon. The unavailability of ...

  5. Genome wide association identifies novel loci involved in fungal communication.

    Science.gov (United States)

    Palma-Guerrero, Javier; Hall, Charles R; Kowbel, David; Welch, Juliet; Taylor, John W; Brem, Rachel B; Glass, N Louise

    2013-01-01

    Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power

  6. Genome-wide association study of pathological gambling.

    Science.gov (United States)

    Lang, M; Leménager, T; Streit, F; Fauth-Bühler, M; Frank, J; Juraeva, D; Witt, S H; Degenhardt, F; Hofmann, A; Heilmann-Heimbach, S; Kiefer, F; Brors, B; Grabe, H-J; John, U; Bischof, A; Bischof, G; Völker, U; Homuth, G; Beutel, M; Lind, P A; Medland, S E; Slutske, W S; Martin, N G; Völzke, H; Nöthen, M M; Meyer, C; Rumpf, H-J; Wurst, F M; Rietschel, M; Mann, K F

    2016-08-01

    Pathological gambling is a behavioural addiction with negative economic, social, and psychological consequences. Identification of contributing genes and pathways may improve understanding of aetiology and facilitate therapy and prevention. Here, we report the first genome-wide association study of pathological gambling. Our aims were to identify pathways involved in pathological gambling, and examine whether there is a genetic overlap between pathological gambling and alcohol dependence. Four hundred and forty-five individuals with a diagnosis of pathological gambling according to the Diagnostic and Statistical Manual of Mental Disorders were recruited in Germany, and 986 controls were drawn from a German general population sample. A genome-wide association study of pathological gambling comprising single marker, gene-based, and pathway analyses, was performed. Polygenic risk scores were generated using data from a German genome-wide association study of alcohol dependence. No genome-wide significant association with pathological gambling was found for single markers or genes. Pathways for Huntington's disease (P-value=6.63×10(-3)); 5'-adenosine monophosphate-activated protein kinase signalling (P-value=9.57×10(-3)); and apoptosis (P-value=1.75×10(-2)) were significant. Polygenic risk score analysis of the alcohol dependence dataset yielded a one-sided nominal significant P-value in subjects with pathological gambling, irrespective of comorbid alcohol dependence status. The present results accord with previous quantitative formal genetic studies which showed genetic overlap between non-substance- and substance-related addictions. Furthermore, pathway analysis suggests shared pathology between Huntington's disease and pathological gambling. This finding is consistent with previous imaging studies. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  7. Population genetic analysis and genome-wide association study of patellar luxation in a Thai population of Pomeranian dogs

    NARCIS (Netherlands)

    Wangdee, C.; Leegwater, P.A.J.; Heuven, H.C.M.; Steenbeek, van F.G.; Techakumphu, M.; Hazewinkel, H.A.W.

    2017-01-01

    The genetics of patellar luxation (PL) were investigated in Pomeranian dogs presented at the Small Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University. A cohort of 339 Pomeranian dogs, part of a four-generation pedigree of 842 Pomeranians, was screened for PL from 2006 to

  8. Population genetic analysis and genome-wide association study of patellar luxation in a Thai population of Pomeranian dogs

    NARCIS (Netherlands)

    Wangdee, C; Leegwater, P A J|info:eu-repo/dai/nl/074236539; Heuven, H C M|info:eu-repo/dai/nl/314417818; van Steenbeek, F G|info:eu-repo/dai/nl/314417958; Techakumphu, M; Hazewinkel, H A W|info:eu-repo/dai/nl/070975760

    The genetics of patellar luxation (PL) were investigated in Pomeranian dogs presented at the Small Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University. A cohort of 339 Pomeranian dogs, part of a four-generation pedigree of 842 Pomeranians, was screened for PL from 2006 to 2013.

  9. Population Genetics with Fluctuating Population Sizes

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2017-05-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuation-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  10. Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata.

    Science.gov (United States)

    Mattila, Tiina M; Tyrmi, Jaakko; Pyhäjärvi, Tanja; Savolainen, Outi

    2017-10-01

    The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Wide field imaging problems in radio astronomy

    Science.gov (United States)

    Cornwell, T. J.; Golap, K.; Bhatnagar, S.

    2005-03-01

    The new generation of synthesis radio telescopes now being proposed, designed, and constructed face substantial problems in making images over wide fields of view. Such observations are required either to achieve the full sensitivity limit in crowded fields or for surveys. The Square Kilometre Array (SKA Consortium, Tech. Rep., 2004), now being developed by an international consortium of 15 countries, will require advances well beyond the current state of the art. We review the theory of synthesis radio telescopes for large fields of view. We describe a new algorithm, W projection, for correcting the non-coplanar baselines aberration. This algorithm has improved performance over those previously used (typically an order of magnitude in speed). Despite the advent of W projection, the computing hardware required for SKA wide field imaging is estimated to cost up to $500M (2015 dollars). This is about half the target cost of the SKA. Reconfigurable computing is one way in which the costs can be decreased dramatically.

  12. Athena Wide Field Imager key science drivers

    Science.gov (United States)

    Rau, Arne; Nandra, Kirpal; Aird, James; Comastri, Andrea; Dauser, Thomas; Merloni, Andrea; Pratt, Gabriel W.; Reiprich, Thomas H.; Fabian, Andy C.; Georgakakis, Antonis; Güdel, Manuel; RóŻańska, Agata; Sanders, Jeremy S.; Sasaki, Manami; Vaughan, Simon; Wilms, Jörn; Meidinger, Norbert

    2016-07-01

    The Wide Field Imager (WFI) is one of two instruments for the Advanced Telescope for High-ENergy Astrophysics (Athena). In this paper we summarise three of the many key science objectives for the WFI { the formation and growth of supermassive black holes, non-gravitational heating in clusters of galaxies, and spin measurements of stellar mass black holes { and describe their translation into the science requirements and ultimately instrument requirements. The WFI will be designed to provide excellent point source sensitivity and grasp for performing wide area surveys, surface brightness sensitivity, survey power, and absolute temperature and density calibration for in-depth studies of the outskirts of nearby clusters of galaxies and very good high-count rate capability, throughput, and low pile-up, paired with very good spectral resolution, for detailed explorations of bright Galactic compact objects.

  13. The Wide Field Imager for Athena

    Science.gov (United States)

    Rau, A.; Nandra, K.; Meidinger, N.; Plattner, M.

    2017-10-01

    The Wide Field Imager (WFI) is one of the two scientific instruments of Athena, ESA's next large X-ray Observatory with launch in 2028. The instrument will provide two defining capabilities to the mission sensitive wide-field imaging spectroscopy and excellent high-count rate performance. It will do so with the use of two separate detectors systems, the Large Detector Array (LDA) optimized for its field of view (40'×40') with a 100 fold survey speed increase compared to existing X-ray missions, and the Fast Detector (FD) tweaked for high throughput and low pile-up for point sources as bright as the Crab. In my talk I will present the key performance parameters of the instrument and their links to the scientific goals of Athena and summarize the status of the ongoing development activities.

  14. Chapter 11: Genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    William S Bush

    Full Text Available Genome-wide association studies (GWAS have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS.

  15. Wide bandgap matrix switcher, amplifier and oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Sampayan, Stephen

    2016-08-16

    An electronic device comprising an optical gate, an electrical input an electrical output and a wide bandgap material positioned between the electrical input and the electrical output to control an amount of current flowing between the electrical input and the electrical output in response to a stimulus received at the optical gate can be used in wideband telecommunication applications in transmission of multi-channel signals.

  16. Requirements for company-wide management

    Science.gov (United States)

    Southall, J. W.

    1980-01-01

    Computing system requirements were developed for company-wide management of information and computer programs in an engineering data processing environment. The requirements are essential to the successful implementation of a computer-based engineering data management system; they exceed the capabilities provided by the commercially available data base management systems. These requirements were derived from a study entitled The Design Process, which was prepared by design engineers experienced in development of aerospace products.

  17. 256-slice wide-detector computed tomography.

    Science.gov (United States)

    2007-11-01

    This article provides opinions and predictions about an emerging technology-256-slice wide-detector computed tomography-to help healthcare facilities decide whether the technology is worth tracking and when it might be ready for adoption. We believe 256-slice CT is worth monitoring based on its predicted clinical and business impact. We consider it unlikely, however, that more than a few select facilities will begin adopting this technology within the next three years.

  18. A Genome-Wide Perspective on Metabolism

    DEFF Research Database (Denmark)

    Rauch, Alexander; Mandrup, Susanne

    2015-01-01

    number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes...... are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level....

  19. Epigenome-Wide Association Study of Wellbeing.

    Science.gov (United States)

    Baselmans, Bart M L; van Dongen, Jenny; Nivard, Michel G; Lin, Bochao D; Zilhão, Nuno R; Boomsma, Dorret I; Bartels, Meike

    2015-12-01

    Wellbeing (WB) is a major topic of research across several scientific disciplines, partly driven by its strong association with psychological and mental health. Twin-family studies have found that both genotype and environment play an important role in explaining the variance in WB. Epigenetic mechanisms, such as DNA methylation, regulate gene expression, and may mediate genetic and environmental effects on WB. Here, for the first time, we apply an epigenome-wide association study (EWAS) approach to identify differentially methylated sites associated with individual differences in WB. Subjects were part of the longitudinal survey studies of the Netherlands Twin Register (NTR) and participated in the NTR biobank project between 2002 and 2011. WB was assessed by a short inventory that measures satisfaction with life (SAT). DNA methylation was measured in whole blood by the Illumina Infinium HumanMethylation450 BeadChip (HM450k array) and the association between WB and DNA methylation level was tested at 411,169 autosomal sites. Two sites (cg10845147, p = 1.51 * 10(-8) and cg01940273, p = 2.34 * 10(-8)) reached genome-wide significance following Bonferonni correction. Four more sites (cg03329539, p = 2.76* 10(-7); cg09716613, p = 3.23 * 10(-7); cg04387347, p = 3.95 * 10(-7); and cg02290168, p = 5.23 * 10(-7)) were considered to be genome-wide significant when applying the widely used criterion of a FDR q value system categories among higher-ranking methylation sites. Overall, these results provide a first insight into the epigenetic mechanisms associated with WB and lay the foundations for future work aiming to unravel the biological mechanisms underlying a complex trait like WB.

  20. Community relations via the World Wide Web

    Energy Technology Data Exchange (ETDEWEB)

    Gossman, D.G.; Gossman, S.E. [Gossman Consulting, Inc., Hampshire, IL (United States)

    1998-12-31

    The Internet or world wide web provides an unprecedented opportunity to communicate with the public and improve community relations. By providing a Virtual Plant Tour{trademark} and important environmental plans and reports on line, industry can short circuit the rumor mill and provide information to the local community, regulatory officials, and the world at large. Audience, content, maintenance, design considerations and costs are all examined.

  1. Stochastic population theories

    CERN Document Server

    Ludwig, Donald

    1974-01-01

    These notes serve as an introduction to stochastic theories which are useful in population biology; they are based on a course given at the Courant Institute, New York, in the Spring of 1974. In order to make the material. accessible to a wide audience, it is assumed that the reader has only a slight acquaintance with probability theory and differential equations. The more sophisticated topics, such as the qualitative behavior of nonlinear models, are approached through a succession of simpler problems. Emphasis is placed upon intuitive interpretations, rather than upon formal proofs. In most cases, the reader is referred elsewhere for a rigorous development. On the other hand, an attempt has been made to treat simple, useful models in some detail. Thus these notes complement the existing mathematical literature, and there appears to be little duplication of existing works. The authors are indebted to Miss Jeanette Figueroa for her beautiful and speedy typing of this work. The research was supported by the Na...

  2. Novel ultrasonic bone densitometry based on two longitudinal waves: significant correlation with pQCT measurement values and age-related changes in trabecular bone density, cortical thickness, and elastic modulus of trabecular bone in a normal Japanese population.

    Science.gov (United States)

    Sai, H; Iguchi, G; Tobimatsu, T; Takahashi, K; Otani, T; Horii, K; Mano, I; Nagai, I; Iio, H; Fujita, T; Yoh, K; Baba, H

    2010-10-01

    A reference database for trabecular bone density, cortical thickness, and elastic modulus of trabecular bone for a novel ultrasonic bone densitometry system (LD-100) based on two longitudinal waves (fast and slow) was determined over a wide age range in a normal Japanese population. A novel ultrasonic bone densitometry system (LD-100 system) was applied to create a reference database for trabecular bone density (TBD), cortical thickness (CoTh), and elastic modulus of trabecular bone (EMTb) for this device over a wide age range in a normal Japanese population. In a comparative study between LD-100 and peripheral quantitative computed tomography (pQCT) systems, 52 individuals were examined by both systems at the same radius simultaneously. To create a reference database, a total of 2,380 healthy subjects (1,179 men, 1,201 women), ages 18-99 years, were examined using the LD-100 system. Highly significant correlations between the LD-100 and pQCT systems were found in TBD (r = 0.877, p < 0.001) and CoTh (r = 0.723, p < 0.001). For the reference database, peak values of TBD, CoTh, and EMTb were observed at 30-34 years (255.09 mg/cm(3)), 20-24 years (5.23 mm), and 20-24 years (4.09 GPa) in men, and at 25-29 years (209.24 mg/cm(3)), 25-29 years (3.98 mm), and 20-24 years (3.33 GPa) in women, respectively. The TBD fell significantly (p < 0.05) beginning at 55-59 years in both sexes, with a relatively rapid decrease in women. The CoTh showed a significant decrease beginning at 40-44 years in men and 50-54 years in women. The EMTb showed a significant decrease beginning at 40-44 years in men and 55-59 years in women. The LD-100 system is a useful bone densitometry device and the database of age-related changes in TBD, CoTh, and EMTb established in this study will provide fundamental data for future studies related to bone status.

  3. Population, Population Density, and Technological Change

    OpenAIRE

    Klasen, Stephan; Nestmann, Thorsten

    2004-01-01

    In a model on population and endogenous technological change, Kremer combines a short-run Malthusian scenario where income determines the population that can be sustained, with the Boserupian insight that greater population spurs technological change and can therefore lift a country out of its Malthusian trap. We show that a more realistic version of the model, which combines population and population density, allows deeper insights into these processes. The incorporation of population densit...

  4. Implementation of a Population-wide Program to Reduce Salt and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    consumer awareness about salt and its health effects; and, - standardized and regulated nutrition labeling. For example, some food categories, processed, ... Production bananière durable et recours aux pesticides au Costa Rica. La production de bananes aux fins d'exportation est une activité économique importante du ...

  5. Collecting Genetic Samples in Population Wide (Panel) Surveys: Feasibility, Nonresponse and Selectivity

    OpenAIRE

    Matthias Schonlau; Martin Reuter; Juergen Schupp; Christian Montag; Bernd Weber; Thomas Dohmen; Nico A. Siegel; Uwe Sunde; Wagner, Gert G.; Armin Falk

    2010-01-01

    "Collecting biomarkers as part of general purpose surveys offers scientists - and social scientists in particular - the ability to study biosocial phenomena, e.g. the relation between genes and human behavior. The authors explore the feasibility of collecting buccal cells for genetic analyses with normal interviewers as part of a pretest for the German Socio-economic Panel Study (SOEP) using a probability sample. They introduce a new non-invasive technique for collecting cell material for gen...

  6. Determinants of Generic vs. Brand Drug Choice: Evidence from Population-wide Danish Data

    DEFF Research Database (Denmark)

    Skipper, Niels; Vejlin, Rune Majlund

    When prescription medications go off patent, vastly cheaper generic drugs usually enters the market. However, the original brand medication often maintains non-negligible market shares. This paper investigates whether demand for branded medications in post-patent markets is patient- or doctor...... of brand drug use are unobserved patient characteristics and price effects, while observed and unobserved doctor characteristics in general explain only 0.7 % of the variation in drug choice. This is suggestive evidence that the doctors in the Danish setting with no incentives to push expensive brand drugs...

  7. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations.

    Science.gov (United States)

    Stopnisek, Nejc; Bodenhausen, Natacha; Frey, Beat; Fierer, Noah; Eberl, Leo; Weisskopf, Laure

    2014-06-01

    Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Incongruous consultation behaviour: results from a UK-wide population survey

    Directory of Open Access Journals (Sweden)

    Elliott Alison M

    2012-03-01

    Full Text Available Abstract Background Symptom characteristics are strong drivers of care seeking. Despite this, incongruous consultation behaviour occurs and has implications for both individuals and health-care services. The aim of this study was to determine how frequently incongruous consultation behaviour occurs, to examine whether it is more common for certain types of symptoms and to identify the factors associated with being an incongruous consulter. Methods An age and sex stratified random sample of 8,000 adults was drawn from twenty UK general practices. A postal questionnaire was used to collect detailed information on the presence and characteristics of 25 physical and psychological symptoms, actions taken to manage the symptoms, general health, attitudes to symptom management and demographic/socio-economic details. Two types of incongruous consultation behaviour were examined: i consultation with a GP for symptoms self-rated as low impact and ii no consultation with a GP for symptoms self-rated as high impact. Results A fifth of all symptoms experienced resulted in consultation behaviour which was incongruous based on respondents' own rating of the symptoms' impact. Low impact consultations were not common, although symptoms indicative of a potentially serious condition resulted in a higher proportion of low impact consultations. High impact non-consultations were more common, although there was no clear pattern in the type of associated symptoms. Just under half of those experiencing symptoms in the previous two weeks were categorised as an incongruous consulter (low impact consulter: 8.3%, high impact non-consulter: 37.1%. Employment status, having a chronic condition, poor health, and feeling that reassurance or advice from a health professional is important were associated with being a low impact consulter. Younger age, employment status, being an ex-smoker, poor health and feeling that not wasting the GPs time is important were associated with being a high impact non-consulter. Conclusions This is one of the first studies to examine incongruous consultation behaviour for a range of symptoms. High impact non-consultations were common and may have important health implications, particularly for symptoms indicative of serious disease. More research is now needed to examine incongruous consultation behaviour and its impact on both the public's health and health service use.

  9. Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

    DEFF Research Database (Denmark)

    Jensen, Anders Boeck; Moseley, Pope; Oprea, Tudor

    2014-01-01

    . We use the entire spectrum of diseases and convert 14.9 years of registry data on 6.2 million patients into 1,171 significant trajectories. We group these into patterns centred on a small number of key diagnoses such as chronic obstructive pulmonary disease (COPD) and gout, which are central...

  10. World Wide Webs: Crossing the Digital Divide through Promotion of Public Access

    Science.gov (United States)

    Coetzee, Liezl

    “As Bill Gates and Steve Case proclaim the global omnipresence of the Internet, the majority of non-Western nations and 97 per cent of the world's population remain unconnected to the net for lack of money, access, or knowledge. This exclusion of so vast a share of the global population from the Internet sharply contradicts the claims of those who posit the World Wide Web as a ‘universal' medium of egalitarian communication.” (Trend 2001:2)

  11. Range-wide patterns of greater sage-grouse persistence

    Science.gov (United States)

    Aldridge, C.L.; Nielsen, S.E.; Beyer, H.L.; Boyce, M.S.; Connelly, J.W.; Knick, S.T.; Schroeder, M.A.

    2008-01-01

    Aim: Greater sage-grouse (Centrocercus urophasianus), a shrub-steppe obligate species of western North America, currently occupies only half its historical range. Here we examine how broad-scale, long-term trends in landscape condition have affected range contraction. Location: Sagebrush biome of the western USA. Methods: Logistic regression was used to assess persistence and extirpation of greater sage-grouse range based on landscape conditions measured by human population (density and population change), vegetation (percentage of sagebrush habitat), roads (density of and distance to roads), agriculture (cropland, farmland and cattle density), climate (number of severe and extreme droughts) and range periphery. Model predictions were used to identify areas where future extirpations can be expected, while also explaining possible causes of past extirpations. Results: Greater sage-grouse persistence and extirpation were significantly related to sagebrush habitat, cultivated cropland, human population density in 1950, prevalence of severe droughts and historical range periphery. Extirpation of sage-grouse was most likely in areas having at least four persons per square kilometre in 1950, 25% cultivated cropland in 2002 or the presence of three or more severe droughts per decade. In contrast, persistence of sage-grouse was expected when at least 30 km from historical range edge and in habitats containing at least 25% sagebrush cover within 30 km. Extirpation was most often explained (35%) by the combined effects of peripherality (within 30 km of range edge) and lack of sagebrush cover (less than 25% within 30 km). Based on patterns of prior extirpation and model predictions, we predict that 29% of remaining range may be at risk. Main Conclusions: Spatial patterns in greater sage-grouse range contraction can be explained by widely available landscape variables that describe patterns of remaining sagebrush habitat and loss due to cultivation, climatic trends, human

  12. The advent of genome-wide association studies for bacteria.

    Science.gov (United States)

    Chen, Peter E; Shapiro, B Jesse

    2015-06-01

    Significant advances in sequencing technologies and genome-wide association studies (GWAS) have revealed substantial insight into the genetic architecture of human phenotypes. In recent years, the application of this approach in bacteria has begun to reveal the genetic basis of bacterial host preference, antibiotic resistance, and virulence. Here, we consider relevant differences between bacterial and human genome dynamics, apply GWAS to a global sample of Mycobacterium tuberculosis genomes to highlight the impacts of linkage disequilibrium, population stratification, and natural selection, and finally compare the traditional GWAS against phyC, a contrasting method of mapping genotype to phenotype based upon evolutionary convergence. We discuss strengths and weaknesses of both methods, and make suggestions for factors to be considered in future bacterial GWAS. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. EHR-based phenome wide association study in pancreatic cancer.

    Science.gov (United States)

    Adamusiak, Tomasz; Shimoyama, Mary

    2014-01-01

    Pancreatic cancer is one of the most common causes of cancer-related deaths in the United States, it is difficult to detect early and typically has a very poor prognosis. We present a novel method of large-scale clinical hypothesis generation based on phenome wide association study performed using Electronic Health Records (EHR) in a pancreatic cancer cohort. The study population consisted of 1,154 patients diagnosed with malignant neoplasm of pancreas seen at The Froedtert & The Medical College of Wisconsin academic medical center between the years 2004 and 2013. We evaluated death of a patient as the primary clinical outcome and tested its association with the phenome, which consisted of over 2.5 million structured clinical observations extracted out of the EHR including labs, medications, phenotypes, diseases and procedures. The individual observations were encoded in the EHR using 6,617 unique ICD-9, CPT-4, LOINC, and RxNorm codes. We remapped this initial code set into UMLS concepts and then hierarchically expanded to support generalization into the final set of 10,164 clinical concepts, which formed the final phenome. We then tested all possible pairwise associations between any of the original 10,164 concepts and death as the primary outcome. After correcting for multiple testing and folding back (generalizing) child concepts were appropriate, we found 231 concepts to be significantly associated with death in the study population. With the abundance of structured EHR data, phenome wide association studies combined with knowledge engineering can be a viable method of rapid hypothesis generation.

  14. WIRELESS MINE-WIDE TELECOMMUNICATIONS TECHNOLOGY

    Energy Technology Data Exchange (ETDEWEB)

    Zvi H. Meiksin

    2004-03-01

    A comprehensive mine-wide, two-way wireless voice and data communication system for the underground mining industry was developed. The system achieves energy savings through increased productivity and greater energy efficiency in meeting safety requirements within mines. The mine-wide system is comprised of two interfaced subsystems: a through-the-earth communications system and an in-mine communications system. The mine-wide system permits two-way communication among underground personnel and between underground and surface personnel. The system was designed, built, and commercialized. Several systems are in operation in underground mines in the United States. The use of these systems has proven they result in considerable energy savings. A system for tracking the location of vehicles and people within the mine was also developed, built and tested successfully. Transtek's systems are being used by the National Institute of Occupational Safety and Health (NIOSH) in their underground mine rescue team training program. This project also resulted in a spin-off rescue team lifeline and communications system. Furthermore, the project points the way to further developments that can lead to a GPS-like system for underground mines allowing the use of autonomous machines in underground mining operations, greatly reducing the amount of energy used in these operations. Some products developed under this program are transferable to applications in fields other than mining. The rescue team system is applicable to use by first responders to natural, accidental, or terrorist-caused building collapses. The in-mine communications system can be installed in high-rise buildings providing in-building communications to security and maintenance personnel as well as to first responders.

  15. Promoting and supporting PBL interests world wide

    DEFF Research Database (Denmark)

    Enemark, Stig; Kolmos, Anette; Moesby, Egon

    2006-01-01

    of projects world wide focusing on institutional change toward a more student centred, project organised, and problem based approach to learning. The Centre is also establishing a UCPBL Global Network on Problem Based Learning in order to facilitate better access to and co-operation within the PBL area.......-Based Learning (PBL) in Engineering Education, an increasing number of universities and engineering schools throughout the world are seeking consultancy and cooperation with Aalborg University. The establishment of UCPBL is therefore a timely opportunity to merge the efforts into one organisational structure...

  16. The Wide Field Imager Instrument for Athena

    OpenAIRE

    Meidinger, Norbert; Eder, Josef; Eraerds, Tanja; Nandra, Kirpal; Pietschner, Daniel; Plattner, Markus; Rau, Arne; Strecker, Rafael

    2017-01-01

    The WFI (Wide Field Imager) instrument is planned to be one of two complementary focal plane cameras on ESA's next X-ray observatory Athena. It combines unprecedented survey power through its large field of view of 40 amin x 40 amin together with excellent count rate capability (larger than 1 Crab). The energy resolution of the silicon sensor is state-of-the-art in the energy band of interest from 0.2 keV to 15 keV, e.g. the full width at half maximum of a line at 7 keV will be better than 17...

  17. Regional water scarcity -- a widely neglected challenge.

    Science.gov (United States)

    Falkenmark, M

    1993-01-01

    Most of the world's population growth is taking place in developing countries. Thus, it is important to address the problem of meeting the subsequent growing demand for food. Fresh water and food are required for sustaining human life. To produce food requires considerable amounts of water. Water-scarce countries have 5 obstacles: period wet and dry seasons, most of the year is dry, recurrent droughts, erodible or impenetrable soils resulting in desiccation, and low recharge of aquifers and rivers. These conditions hinder their ability to become self-reliant in food production. Developing countries need to adopt an approach to water supply problems of finding how much water moves in and out of the ground and of the atmosphere and then determine how to best benefit from it, specifically an integrated approach to land and water. Decision makers must consider that forestry and land use practices affect the runoff of water. For example, tree growth and crop production consume rainwater, including returning water to the atmosphere via photosynthesis, leaving less water to recharge aquifers and rivers. Water takes on soluble pollutants as it moves through the environment and the atmosphere. Water storage is needed in arid areas, but construction of dams and reservoirs stirs conflict between human rights of local people adversely affected by construction and those of the people in drought-prone areas who would benefit from this construction. Population growth in urban areas requires bringing more water from ever more distant sources, reducing the amount needed for irrigation. For example, Coimbatore district in India is diverting irrigation water from the Bhavani River system to support industrial growth, Further, the untreated waste of growing urban populations jeopardizes the groundwater and rivers. Inadequate rural development is fueling the population explosion in urban areas. Countries need to take actions to improve rural living conditions, such as job creation and

  18. Genome-wide patterns of nucleotide polymorphism in domesticated rice.

    Directory of Open Access Journals (Sweden)

    Ana L Caicedo

    2007-09-01

    Full Text Available Domesticated Asian rice (Oryza sativa is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i selectively neutral population bottleneck model, (ii bottleneck plus migration model, (iii multiple selective sweeps model, and (iv bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.

  19. A Pooled Genome-Wide Association Study of Asperger Syndrome.

    Directory of Open Access Journals (Sweden)

    Varun Warrier

    Full Text Available Asperger Syndrome (AS is a neurodevelopmental condition characterized by impairments in social interaction and communication, alongside the presence of unusually repetitive, restricted interests and stereotyped behaviour. Individuals with AS have no delay in cognitive and language development. It is a subset of Autism Spectrum Conditions (ASC, which are highly heritable and has a population prevalence of approximately 1%. Few studies have investigated the genetic basis of AS. To address this gap in the literature, we performed a genome-wide pooled DNA association study to identify candidate loci in 612 individuals (294 cases and 318 controls of Caucasian ancestry, using the Affymetrix GeneChip Human Mapping version 6.0 array. We identified 11 SNPs that had a p-value below 1x10-5. These SNPs were independently genotyped in the same sample. Three of the SNPs (rs1268055, rs7785891 and rs2782448 were nominally significant, though none remained significant after Bonferroni correction. Two of our top three SNPs (rs7785891 and rs2782448 lie in loci previously implicated in ASC. However, investigation of the three SNPs in the ASC genome-wide association dataset from the Psychiatric Genomics Consortium indicated that these three SNPs were not significantly associated with ASC. The effect sizes of the variants were modest, indicating that our study was not sufficiently powered to identify causal variants with precision.

  20. A Pooled Genome-Wide Association Study of Asperger Syndrome.

    Science.gov (United States)

    Warrier, Varun; Chakrabarti, Bhismadev; Murphy, Laura; Chan, Allen; Craig, Ian; Mallya, Uma; Lakatošová, Silvia; Rehnstrom, Karola; Peltonen, Leena; Wheelwright, Sally; Allison, Carrie; Fisher, Simon E; Baron-Cohen, Simon

    2015-01-01

    Asperger Syndrome (AS) is a neurodevelopmental condition characterized by impairments in social interaction and communication, alongside the presence of unusually repetitive, restricted interests and stereotyped behaviour. Individuals with AS have no delay in cognitive and language development. It is a subset of Autism Spectrum Conditions (ASC), which are highly heritable and has a population prevalence of approximately 1%. Few studies have investigated the genetic basis of AS. To address this gap in the literature, we performed a genome-wide pooled DNA association study to identify candidate loci in 612 individuals (294 cases and 318 controls) of Caucasian ancestry, using the Affymetrix GeneChip Human Mapping version 6.0 array. We identified 11 SNPs that had a p-value below 1x10-5. These SNPs were independently genotyped in the same sample. Three of the SNPs (rs1268055, rs7785891 and rs2782448) were nominally significant, though none remained significant after Bonferroni correction. Two of our top three SNPs (rs7785891 and rs2782448) lie in loci previously implicated in ASC. However, investigation of the three SNPs in the ASC genome-wide association dataset from the Psychiatric Genomics Consortium indicated that these three SNPs were not significantly associated with ASC. The effect sizes of the variants were modest, indicating that our study was not sufficiently powered to identify causal variants with precision.

  1. Genome-wide association study of working memory brain activation.

    Science.gov (United States)

    Blokland, Gabriëlla A M; Wallace, Angus K; Hansell, Narelle K; Thompson, Paul M; Hickie, Ian B; Montgomery, Grant W; Martin, Nicholas G; McMahon, Katie L; de Zubicaray, Greig I; Wright, Margaret J

    2017-05-01

    In a population-based genome-wide association (GWA) study of n-back working memory task-related brain activation, we extracted the average percent BOLD signal change (2-back minus 0-back) from 46 regions-of-interest (ROIs) in functional MRI scans from 863 healthy twins and siblings. ROIs were obtained by creating spheres around group random effects analysis local maxima, and by thresholding a voxel-based heritability map of working memory brain activation at 50%. Quality control for test-retest reliability and heritability of ROI measures yielded 20 reliable (r>0.7) and heritable (h(2)>20%) ROIs. For GWA analysis, the cohort was divided into a discovery (n=679) and replication (n=97) sample. No variants survived the stringent multiple-testing-corrected genome-wide significance threshold (pmemory. Variants identified here may be relevant to (the susceptibility to) common disorders affecting brain function. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Population demographics of two local South Carolina mourning dove populations

    Science.gov (United States)

    McGowan, D.P.; Otis, D.L.

    1998-01-01

    The mourning dove (Zenaida macroura) call-count index had a significant (P 2,300 doves and examined >6,000 individuals during harvest bag checks. An age-specific band recovery model with time- and area-specific recovery rates, and constant survival rates, was chosen for estimation via Akaike's Information Criterion (AIC), likelihood ratio, and goodness-of-fit criteria. After-hatching-year (AHY) annual survival rate was 0.359 (SE = 0.056), and hatching-year (HY) annual survival rate was 0.118 (SE = 0.042). Average estimated recruitment per adult female into the prehunting season population was 3.40 (SE = 1.25) and 2.32 (SE = 0.46) for the 2 study areas. Our movement data support earlier hypotheses of nonmigratory breeding and harvested populations in South Carolina. Low survival rates and estimated population growth rate in the study areas may be representative only of small-scale areas that are heavily managed for dove hunting. Source-sink theory was used to develop a model of region-wide populations that is composed of source areas with positive growth rates and sink areas of declining growth. We suggest management of mourning doves in the Southeast might benefit from improved understanding of local population dynamics, as opposed to regional-scale population demographics.

  3. Genome-wide association study of antisocial personality disorder.

    Science.gov (United States)

    Rautiainen, M-R; Paunio, T; Repo-Tiihonen, E; Virkkunen, M; Ollila, H M; Sulkava, S; Jolanki, O; Palotie, A; Tiihonen, J

    2016-09-06

    The pathophysiology of antisocial personality disorder (ASPD) remains unclear. Although the most consistent biological finding is reduced grey matter volume in the frontal cortex, about 50% of the total liability to developing ASPD has been attributed to genetic factors. The contributing genes remain largely unknown. Therefore, we sought to study the genetic background of ASPD. We conducted a genome-wide association study (GWAS) and a replication analysis of Finnish criminal offenders fulfilling DSM-IV criteria for ASPD (N=370, N=5850 for controls, GWAS; N=173, N=3766 for controls and replication sample). The GWAS resulted in suggestive associations of two clusters of single-nucleotide polymorphisms at 6p21.2 and at 6p21.32 at the human leukocyte antigen (HLA) region. Imputation of HLA alleles revealed an independent association with DRB1*01:01 (odds ratio (OR)=2.19 (1.53-3.14), P=1.9 × 10(-5)). Two polymorphisms at 6p21.2 LINC00951-LRFN2 gene region were replicated in a separate data set, and rs4714329 reached genome-wide significance (OR=1.59 (1.37-1.85), P=1.6 × 10(-9)) in the meta-analysis. The risk allele also associated with antisocial features in the general population conditioned for severe problems in childhood family (β=0.68, P=0.012). Functional analysis in brain tissue in open access GTEx and Braineac databases revealed eQTL associations of rs4714329 with LINC00951 and LRFN2 in cerebellum. In humans, LINC00951 and LRFN2 are both expressed in the brain, especially in the frontal cortex, which is intriguing considering the role of the frontal cortex in behavior and the neuroanatomical findings of reduced gray matter volume in ASPD. To our knowledge, this is the first study showing genome-wide significant and replicable findings on genetic variants associated with any personality disorder.

  4. WFIRST: Simulating the Wide-Field Sky

    Science.gov (United States)

    Peeples, Molly; WFIRST Wide Field Imager Simulations Working Group

    2018-01-01

    As astronomy’s first high-resolution wide-field multi-mode instrument, simulated data will play a vital role in the planning for and analysis of data from WFIRST’s WFI (Wide Field Imager) instrument. Part of the key to WFIRST’s scientific success lies in our ability to push the systematics limit, but in order to do so, the WFI pipeline will need to be able to measure and take out said systematics. The efficacy of this pipeline can only be verified with large suites of synthetic data; these data must include both the range of astrophysical sky scenes (from crowded starfields to high-latitude grism data observations) and the systematics from the detector and telescope optics the WFI pipeline aims to mitigate. We summarize here(1) the status of current and planned astrophysical simulations in support of the WFI,(2) the status of current WFI instrument simulators and requirements on future generations thereof, and(3) plans, methods, and requirements on interfacing astrophysical simulations and WFI instrument simulators.

  5. Population policies and development.

    Science.gov (United States)

    Stamper, B M

    1984-01-01

    This article critically examines 4 conceptual frameworks for Third World population policies: the family planning approach, beyond family planning measures, the development hypothesis and transition theory, and the distributive hypothesis and fertility. Although family planning is a basic human right and can lead to lower levels of population and improved maternal-child health, this approach alone does not always have a meaningful demographic impact. If high fertility is economically rational from the family viewpoint, the demand for family planning services will remain marginal. Other policies seek to go beyond the family planning approach and to directly influence the demand for reproductive control through provision of old age support, monetary incentives for reduced fertility or stringent and coercive measures. However, such policies can have adverse distributional effects and directly penalize the children of large families. The demographic transition theory lacks a measurable and specifiable causation mechanism, giving it little predictive value. It may be that economic growth increases fertility in the short run and reduces fertility only over the long run through indirect effects. The key issue is how the rate of growth is distributed across the population. The development and demographic transition hypothesis focuses mainly on aggregate economic and social measures rather than on their underlying distributions. The distributive hypothesis implies policies that promote a greater level of investment in human capital, with a wide distributional emphasis. Diffused investment in human capital is believed to indirectly influence the desire to control fertility. It is concluded that all 4 conceptual frameworks for analyzing fertility-related policies for the Third World are inadequate or seriously flawed. They are not pragmatic, do not identify or assign weights to the crucial causal variables, fail to specify thresholds or critical minimum levels, discount

  6. Organism and population-level ecological models for ...

    Science.gov (United States)

    Ecological risk assessment typically focuses on animal populations as endpoints for regulatory ecotoxicology. Scientists at USEPA are developing models for animal populations exposed to a wide range of chemicals from pesticides to emerging contaminants. Modeled taxa include aquatic and terrestrial invertebrates, fish, amphibians, and birds, and employ a wide range of methods, from matrix-based projection models to mechanistic bioenergetics models and spatially explicit population models. not applicable

  7. Population growth rates in perfect contraceptive populations.

    Science.gov (United States)

    Udry, J R; Bauman, K E; Chase, C L

    1973-07-01

    Abstract Eventually, world population must cease to grow. In many countries attempts are made to decrease population growth by providing family planning services to all who want to prevent pregnancies. In this paper we use the concept 'perfect contraceptive population',(1) - a population in which no unwanted births occur - to derive estimates of the maximum contribution that prevention of unwanted births might make toward attaining a zero rate of natural increase in population.

  8. Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation

    Directory of Open Access Journals (Sweden)

    Robersy Sanchez

    2016-06-01

    Full Text Available Cytosine DNA methylation (CDM is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1 the amount of information gained/lost with the CDM changes I R and (2 the uncertainty of not observing a SNP L C R . We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to verify this hypothesis. Results support the hypothesis by the existence of discriminatory information (DI patterns of CDM able to discriminate between individuals and between individual subpopulations. The statistical analyses revealed a strong association between the topologies of the structured population of Arabidopsis ecotypes based on I R and on LCR, respectively. A statistical-physical relationship between I R and L C R was also found. Results to date imply that the genome-wide distribution of CDM changes is not only part of the biological signal created by the methylation regulatory machinery, but ensures the stability of the DNA molecule, preserving the integrity of the genetic message under continuous stress from thermal fluctuations in the cell environment.

  9. Assessing Predictive Properties of Genome-Wide Selection in Soybeans.

    Science.gov (United States)

    Xavier, Alencar; Muir, William M; Rainey, Katy Martin

    2016-08-09

    Many economically important traits in plant breeding have low heritability or are difficult to measure. For these traits, genomic selection has attractive features and may boost genetic gains. Our goal was to evaluate alternative scenarios to implement genomic selection for yield components in soybean (Glycine max L. merr). We used a nested association panel with cross validation to evaluate the impacts of training population size, genotyping density, and prediction model on the accuracy of genomic prediction. Our results indicate that training population size was the factor most relevant to improvement in genome-wide prediction, with greatest improvement observed in training sets up to 2000 individuals. We discuss assumptions that influence the choice of the prediction model. Although alternative models had minor impacts on prediction accuracy, the most robust prediction model was the combination of reproducing kernel Hilbert space regression and BayesB. Higher genotyping density marginally improved accuracy. Our study finds that breeding programs seeking efficient genomic selection in soybeans would best allocate resources by investing in a representative training set. Copyright © 2016 Xavie et al.

  10. Global fertility and population trends.

    Science.gov (United States)

    Bongaarts, John

    2015-01-01

    Over the past several decades, the world and most countries have undergone unprecedented demographic change. The most obvious example of this change is the rise in human numbers, and there are also important trends in fertility, family structure, mortality, migration, urbanization, and population aging. This paper summarizes past trends and projections in fertility and population. After reaching 2.5 billion in 1950, the world population grew rapidly to 7.2 billion in 2013 and the projections expect this total to be 10.9 billion by 2100. World regions differ widely in their demographic trends, with rapid population growth and high fertility continuing in the poorest countries, particularly in sub-Saharan Africa, while population decline, population aging, and very low fertility are now a key concern in many developed countries. These trends have important implications for human welfare and are of interest to policy makers. The conclusion comments briefly on policy options to address these adverse trends. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  11. Genome-wide meta-analysis identifies new susceptibility loci for migraine

    DEFF Research Database (Denmark)

    Anttila, Verneri; Winsvold, Bendik S; Gormley, Padhraig

    2013-01-01

    Migraine is the most common brain disorder, affecting approximately 14% of the adult population, but its molecular mechanisms are poorly understood. We report the results of a meta-analysis across 29 genome-wide association studies, including a total of 23,285 individuals with migraine (cases) an...

  12. A Genome Wide Genotyping Study To Find Candidate Genes That Influence Varroa-Sensitive Hygiene (VSH)

    Science.gov (United States)

    Varroa parasitism of honey bees is widely considered by apicultural researchers to be the greatest threat to beekeeping. Varroa-sensitive hygiene (VSH) is one of two identified behaviors that are highly important for controlling the growth of Varroa mite populations in bee hives. Bees exhibiting th...

  13. Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

    NARCIS (Netherlands)

    Ciani, Elena; Lasagna, Emiliano; D'Andrea, Mariasilvia; Alloggio, Ingrid; Marroni, Fabio; Ceccobelli, Simone; Delgado Bermejo, Juan V; Sarti, Francesca M; Kijas, James; Lenstra, Johannes A; Pilla, Fabio

    2015-01-01

    BACKGROUND: Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In

  14. Novel loci associated with usual sleep duration: The CHARGE Consortium Genome-Wide Association Study

    NARCIS (Netherlands)

    Gottlieb, D.J.; Hek, K.; Chen, T.H.; Watson, N.F.; Eiriksdottir, G.; Byrne, E.M.; Cornelis, M.; Warby, S.C.; Bandinelli, S.; Cherkas, L.; Evans, D.S.; Grabe, H.J.; Lahti, J.; Li, M.; Lehtimaki, T.; Lumley, T.; Marciante, K.D.; Pérusse, L.; Psaty, B.M.; Robbins, J.; Tranah, G.J.; Vink, J.M.; Wilk, J.B.; Stafford, J.M.; Bellis, C.; Biffar, R.; Bouchard, C.; Cade, B.; Curhan, G.C.; Eriksson, J.G.; Ewert, R.; Ferrucci, L.; Fulop, T.; Gehrman, P.R.; Goodloe, R.; Harris, T.B.; Heath, A.C.; Hernandez, D.G.; Hofman, A.; Hottenga, J.J.; Hunter, D.J.; Jensen, M.K.; Johnson, A.D.; Kahonen, M.; Kao, L.; Kraft, P.; Larkin, E.K.; Lauderdale, D.S.; Luik, A.I.; Medici, M.; Montgomery, G.W.; Palotie, A.; Patel, S.R.; Pistis, G.; Porcu, E.; Quaye, L.; Raitakari, O.; Redline, S.; Rimm, E.B.; Rotter, J.I.; Smith, A.V.; Spector, T.D.; Teumer, A.; Uitterlinden, A.G.; Vohl, M.C.; Widen, E.; Willemsen, G.; Young, T.; Zhang, X.; Liu, Y.; Blangero, J.; Boomsma, D.I.; Gudnason, V.; Hu, F.; Mangino, M.; Martin, N.G.; O'Connor, G.T.; Stone, K.L.; Tanaka, T.; Viikari, J.; Gharib, S.A.; Punjabi, N.M.; Raikkonen, K.; Völzke, H.; Mignot, E.; Tiemeier, H.

    2015-01-01

    Usual sleep duration is a heritable trait correlated with psychiatric morbidity, cardiometabolic disease and mortality, although little is known about the genetic variants influencing this trait. A genome-wide association study (GWAS) of usual sleep duration was conducted using 18 population-based

  15. A genome-wide association search for type 2 diabetes genes in African Americans

    DEFF Research Database (Denmark)

    Palmer, Nicholette D; McDonough, Caitrin W; Hicks, Pamela J

    2012-01-01

    African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wid...

  16. Genome wide association study identifies KCNMA1 contributing to human obesity

    DEFF Research Database (Denmark)

    Jiao, Hong; Arner, Peter; Hoffstedt, Johan

    2011-01-01

    Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a minor fraction of the total genetic variation expected to be present in the population...

  17. Toward wide-angle microvision sensors.

    Science.gov (United States)

    Koppal, Sanjeev J; Gkioulekas, Ioannis; Young, Travis; Park, Hyunsung; Crozier, Kenneth B; Barrows, Geoffrey L; Zickler, Todd

    2013-12-01

    Achieving computer vision on microscale devices is a challenge. On these platforms, the power and mass constraints are severe enough for even the most common computations (matrix manipulations, convolution, etc.) to be difficult. This paper proposes and analyzes a class of miniature vision sensors that can help overcome these constraints. These sensors reduce power requirements through template-based optical convolution, and they enable a wide field-of-view within a small form through a refractive optical design. We describe the tradeoffs between the field-of-view, volume, and mass of these sensors and we provide analytic tools to navigate the design space. We demonstrate milliscale prototypes for computer vision tasks such as locating edges, tracking targets, and detecting faces. Finally, we utilize photolithographic fabrication tools to further miniaturize the optical designs and demonstrate fiducial detection onboard a small autonomous air vehicle.

  18. Genome-Wide Association Studies of Cancer

    Science.gov (United States)

    Stadler, Zsofia K.; Thom, Peter; Robson, Mark E.; Weitzel, Jeffrey N.; Kauff, Noah D.; Hurley, Karen E.; Devlin, Vincent; Gold, Bert; Klein, Robert J.; Offit, Kenneth

    2010-01-01

    Knowledge of the inherited risk for cancer is an important component of preventive oncology. In addition to well-established syndromes of cancer predisposition, much remains to be discovered about the genetic variation underlying susceptibility to common malignancies. Increased knowledge about the human genome and advances in genotyping technology have made possible genome-wide association studies (GWAS) of human diseases. These studies have identified many important regions of genetic variation associated with an increased risk for human traits and diseases including cancer. Understanding the principles, major findings, and limitations of GWAS is becoming increasingly important for oncologists as dissemination of genomic risk tests directly to consumers is already occurring through commercial companies. GWAS have contributed to our understanding of the genetic basis of cancer and will shed light on biologic pathways and possible new strategies for targeted prevention. To date, however, the clinical utility of GWAS-derived risk markers remains limited. PMID:20585100

  19. [Wide QRS tachycardia preceded by pacemaker spikes].

    Science.gov (United States)

    Romero, M; Aranda, A; Gómez, F J; Jurado, A

    2014-04-01

    The differential diagnosis and therapeutic management of wide QRS tachycardia preceded by pacemaker spike is presented. The pacemaker-mediated tachycardia, tachycardia fibrillo-flutter in patients with pacemakers, and runaway pacemakers, have a similar surface electrocardiogram, but respond to different therapeutic measures. The tachycardia response to the application of a magnet over the pacemaker could help in the differential diagnosis, and in some cases will be therapeutic, as in the case of a tachycardia-mediated pacemaker. Although these conditions are diagnosed and treated in hospitals with catheterization laboratories using the application programmer over the pacemaker, patients presenting in primary care clinic and emergency forced us to make a diagnosis and treat the haemodynamically unstable patient prior to referral. Copyright © 2012 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España. All rights reserved.

  20. Wide-angle energy-momentum spectroscopy

    CERN Document Server

    Dodson, Christopher M; Li, Dongfang; Zia, Rashid

    2014-01-01

    Light emission is defined by its distribution in energy, momentum, and polarization. Here, we demonstrate a method that resolves these distributions by means of wide-angle energy-momentum spectroscopy. Specifically, we image the back focal plane of a microscope objective through a Wollaston prism to obtain polarized Fourier-space momentum distributions, and disperse these two-dimensional radiation patterns through an imaging spectrograph without an entrance slit. The resulting measurements represent a convolution of individual radiation patterns at adjacent wavelengths, which can be readily deconvolved using any well-defined basis for light emission. As an illustrative example, we use this technique with the multipole basis to quantify the intrinsic emission rates for electric and magnetic dipole transitions in europium-doped yttrium oxide (Eu$^{3+}$:Y$_{2}$O$_{3}$) and chromium-doped magnesium oxide (Cr$^{3+}$:MgO). Once extracted, these rates allow us to reconstruct the full, polarized, two-dimensional radi...

  1. World Wide Web Metasearch Clustering Algorithm

    Directory of Open Access Journals (Sweden)

    Adina LIPAI

    2008-01-01

    Full Text Available As the storage capacity and the processing speed of search engine is growing to keep up with the constant expansion of the World Wide Web, the user is facing an increasing list of results for a given query. A simple query composed of common words sometimes have hundreds even thousands of results making it practically impossible for the user to verify all of them, in order to identify a particular site. Even when the list of results is presented to the user ordered by a rank, most of the time it is not sufficient support to help him identify the most relevant sites for his query. The concept of search result clustering was introduced as a solution to this situation. The process of clustering search results consists of building up thematically homogenous groups from the initial list results provided by classic search tools, and using up characteristics present within the initial results, without any kind of predefined categories.

  2. World-Wide Web the information universe

    CERN Document Server

    Berners-Lee, Tim; Groff, Jean-Francois; Pollermann, Bernd

    1992-01-01

    Purpose - The World-Wide Web (W-3) initiative is a practical project designed to bring a global information universe into existence using available technology. This paper seeks to describe the aims, data model, and protocols needed to implement the "web" and to compare them with various contemporary systems. Design/methodology/approach - Since Vannevar Bush's article, men have dreamed of extending their intellect by making their collective knowledge available to each individual by using machines. Computers provide us two practical techniques for human-knowledge interface. One is hypertext, in which links between pieces of text (or other media) mimic human association of ideas. The other is text retrieval, which allows associations to be deduced from the content of text. The W-3 ideal world allows both operations and provides access from any browsing platform. Findings - Various server gateways to other information systems have been produced, and the total amount of information available on the web is...

  3. Teacher Reviews of Widely Used Physics Textbooks

    Science.gov (United States)

    2011-05-01

    Holt Physics (Serway & Faughn), Physics Principles and Problems (Zitzewitz), Conceptual Physics (Hewitt), and Physics: Principles with Applications (Giancoli) were the most widely used textbooks for regular high school physics courses during the 2008-09 academic year. Holt Physics and Zitzewitz were each used by about one-third of the teachers responding to our Nationwide Survey of High School Physics Teachers. Hewitt's text was used by approximately one-fourth of the teachers who responded, and 6% of the respondents reported using Giancoli. We also asked the respondents to tell us how well the text worked for the course. The good news is that well over 80% of the teachers find that all four of these texts work quite well or somewhat well for teaching regular physics.

  4. Wide-Stopband Aperiodic Phononic Filters

    Science.gov (United States)

    Rostem, Karwan; Chuss, David; Denis, K. L.; Wollack, E. J.

    2016-01-01

    We demonstrate that a phonon stopband can be synthesized from an aperiodic structure comprising a discrete set of phononic filter stages. Each element of the set has a dispersion relation that defines a complete bandgap when calculated under a Bloch boundary condition. Hence, the effective stopband width in an aperiodic phononic filter (PnF) may readily exceed that of a phononic crystal with a single lattice constant or a coherence scale. With simulations of multi-moded phononic waveguides, we discuss the effects of finite geometry and mode-converting junctions on the phonon transmission in PnFs. The principles described may be utilized to form a wide stopband in acoustic and surface wave media. Relative to the quantum of thermal conductance for a uniform mesoscopic beam, a PnF with a stopband covering 1.6-10.4 GHz is estimated to reduce the thermal conductance by an order of magnitude at 75 mK.

  5. Plant Wide Assessment for SIFCO Industries, Inc.

    Energy Technology Data Exchange (ETDEWEB)

    Kelly Kissock, Arvind Thekdi et. al.

    2005-07-06

    Sifco Industries carreid out a plant wide energy assessment under a collaborative program with the U.S. Department of Energy during October 2004 to September 2005. During the year, personnel from EIS, E3M, DPS, BuyCastings.Com, and Sifco plant facilities and maintenance personnel, as a team collected energy use, construction, process, equipment and operational information about the plant. Based on this information, the team identified 13 energy savings opportunities. Near term savings opportunities have a total potential savings of about $1,329,000 per year and a combined simple payback of about 11 months. Implementation of these recommendations would reduce CO2 emissions by about 16,000,000 pounds per year, which would reduce overall plant CO2 emissions by about 45%. These totals do not include another $830,000 per year in potential savings with an estimated 9-month payback, from converting the forging hammers from steam to compressed air.

  6. Self-reported oral health of a metropolitan homeless population in Australia: comparisons with population-level data.

    Science.gov (United States)

    Parker, E J; Jamieson, L M; Steffens, M A; Cathro, P; Logan, R M

    2011-09-01

    There is limited information on self-perceived oral health of homeless populations. This study quantified self-reported oral health among a metropolitan homeless adult population and compared against a representative sample of the metropolitan adult population obtained from the National Survey of Adult Oral Health. A total of 248 homeless participants (age range 17-78 years, 79% male) completed a self-report questionnaire. Data for an age-matched, representative sample of metropolitan-dwelling adults were obtained from Australia's second National Survey of Adult Oral Health. Percentage responses and 95% confidence intervals were calculated, with non-overlapping 95% confidence intervals used to identify statistically significant differences between the two groups. Homeless adults reported poorer oral health than their age-matched general population counterparts. Twice as many homeless adults reported visiting a dentist more than a year ago and that their usual reason for dental attendance was for a dental problem. The proportion of homeless adults with a perceived need for fillings or extractions was also twice that of their age-matched general population counterparts. Three times as many homeless adults rated their oral health as 'fair' or 'poor'. A significantly greater proportion of homeless adults in an Australian metropolitan location reported poorer oral health compared with the general metropolitan adult population. © 2011 Australian Dental Association.

  7. Magnetopause reconnection across wide local time

    Directory of Open Access Journals (Sweden)

    M. W. Dunlop

    2011-09-01

    Full Text Available During April to July 2007 a combination of 10 spacecraft provided simultaneous monitoring of the dayside magnetopause across a wide range of local times. The array of four Cluster spacecraft, separated at large distances (10 000 km, were traversing the dawn-side magnetopause at high and low latitudes; the five THEMIS spacecraft were often in a 4 + 1 grouped configuration, traversing the low latitude, dusk-side magnetosphere, and the Double star, TC-1 spacecraft was in an equatorial orbit between the local times of the THEMIS and Cluster orbits. We show here a number of near simultaneous conjunctions of all 10 spacecraft at the magnetopause. One conjunction identifies an extended magnetic reconnection X-line, tilted in the low latitude, sub-solar region, which exists together with active anti-parallel reconnection sites extending to locations on the dawn-side flank. Oppositely moving FTE's are observed on all spacecraft, consistent with the initially strong IMF By conditions and the comparative locations of the spacecraft both dusk-ward and dawn-ward of noon. Comparison with other conjunctions of magnetopause crossings, which are also distributed over wide local times, supports the result that reconnection activity may occur at many sites simultaneously across the sub-solar and flank magnetopause, but linked to the large scale (extended configuration of the merging line; broadly depending on IMF orientation. The occurrence of MR therefore inherently follows a "component" driven scenario irrespective of the guide field conditions. Some conjunctions allow the global magnetopause response to IMF changes to be observed and the distribution of spacecraft can directly confirm its shape, motion and deformation at local noon, dawn and dusk-side, simultaneously.

  8. Magnetopause reconnection across wide local time

    Directory of Open Access Journals (Sweden)

    M. W. Dunlop

    2011-09-01

    Full Text Available During April to July 2007 a combination of 10 spacecraft provided simultaneous monitoring of the dayside magnetopause across a wide range of local times. The array of four Cluster spacecraft, separated at large distances (10 000 km, were traversing the dawn-side magnetopause at high and low latitudes; the five THEMIS spacecraft were often in a 4 + 1 grouped configuration, traversing the low latitude, dusk-side magnetosphere, and the Double star, TC-1 spacecraft was in an equatorial orbit between the local times of the THEMIS and Cluster orbits. We show here a number of near simultaneous conjunctions of all 10 spacecraft at the magnetopause. One conjunction identifies an extended magnetic reconnection X-line, tilted in the low latitude, sub-solar region, which exists together with active anti-parallel reconnection sites extending to locations on the dawn-side flank. Oppositely moving FTE's are observed on all spacecraft, consistent with the initially strong IMF By conditions and the comparative locations of the spacecraft both dusk-ward and dawn-ward of noon. Comparison with other conjunctions of magnetopause crossings, which are also distributed over wide local times, supports the result that reconnection activity may occur at many sites simultaneously across the sub-solar and flank magnetopause, but linked to the large scale (extended configuration of the merging line; broadly depending on IMF orientation. The occurrence of MR therefore inherently follows a "component" driven scenario irrespective of the guide field conditions. Some conjunctions allow the global magnetopause response to IMF changes to be observed and the distribution of spacecraft can directly confirm its shape, motion and deformation at local noon, dawn and dusk-side, simultaneously.

  9. Effective Population Size of Korean Populations

    Directory of Open Access Journals (Sweden)

    Leeyoung Park

    2014-12-01

    Full Text Available Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China and JPT (Japanese in Tokyo, Japan of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

  10. Effective population size of korean populations.

    Science.gov (United States)

    Park, Leeyoung

    2014-12-01

    Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

  11. Genetic diversity in the modern horse illustrated from genome-wide SNP data.

    Directory of Open Access Journals (Sweden)

    Jessica L Petersen

    Full Text Available Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds. This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

  12. Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

    Science.gov (United States)

    Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; M. Wade, Claire; McCue, Molly E.

    2013-01-01

    Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. PMID:23383025

  13. Origin of Boundary Populations in Medaka (Oryzias latipes Species Complex).

    Science.gov (United States)

    Takehana, Yusuke; Sakai, Masato; Narita, Takanori; Sato, Tadashi; Naruse, Kiyoshi; Sakaizumi, Mitsuru

    2016-04-01

    The Japanese wild population of the medaka fish (Oryzias latipes species complex) comprises two genetically distinct groups, the Northern and the Southern Populations, with boundary populations having a unique genotype. It is thought that the boundary populations have been formed through introgressive hybridization between the two groups, because they are fixed with the Northern alleles at two allozymic loci, with the Southern alleles at two other loci, and have a unique allele at one locus. In this study, we examined the genetic population structure of the boundary populations using genome-wide single nucleotide polymorphism (SNP) data. Most SNPs of the Toyooka population, a typical boundary population, were shared with the Northern Population, some were shared with the Southern Population, and the remaining SNPs were unique to this population, suggesting that the boundary populations originated and diverged from the Northern Population. Further analyses of different populations using SNPs at eight genomic loci indicated that the boundary populations at different locations share similar genomic constitutions, and can be genetically distinguished from typical Northern Populations by unique SNPs. In addition, the boundary populations in the Maruyama River Basin had Northern mitochondrial DNA (mtDNA), while others, from the Fukuda and Kishida River Basins and from the Kumihama Bay area, had Southern mtDNA. These findings suggested that the boundary populations originated from the Northern Population, and then their genomes diverged as a result of geographical isolation, followed by mtDNA introgression from the Southern Population that occurred independently in some populations.

  14. Seroprevalence of antibody against diphtheria among the population in Khon Kaen province, Thailand.

    Science.gov (United States)

    Bansiddhi, Hataichanok; Vuthitanachot, Viboonsuk; Vuthitanachot, Chanpim; Prachayangprecha, Slinporn; Theamboonlers, Apiradee; Poovorawan, Yong

    2015-03-01

    To assess diphtheria immunity in the northeastern region of Thailand, a seroepidemiological survey was undertaken in 2011 from 516 healthy individuals (age range 2-87 years) in Khon Kaen province. Diphtheria antitoxin levels were measured by enzyme-linked immunosorbent assay and titers of ≥0.1 IU/mL were considered to be protective antitoxin levels. Among the studied population, 94.8% have fully protective levels. The younger population (age range 2-19 years) has higher diphtheria immunity with seroprotection rates of 96.8% to 97.9%, compared with the adult population. The proportion of protective diphtheria antitoxin levels declines to 88.3% to 91.9% in the middle-aged group (20-50 years), and appeared to be higher again in the older age-group (50-70 years). To avoid epidemic spreading, promoting immunization booster programs will be helpful, especially among the adult population (20-50 years). Finally, this study may serve as a valuable guide in deciding exactly which age-groups should be targeted by such an effort. © 2012 APJPH.

  15. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax

    Science.gov (United States)

    Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A.; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

    2015-01-01

    Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2–0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be

  16. Traffic Flow Wide-Area Surveillance system

    Energy Technology Data Exchange (ETDEWEB)

    Allgood, G.O.; Ferrell, R.K.; Kercel, S.W.; Abston, R.A.

    1994-09-01

    Traffic management can be thought of as a stochastic queuing process where the serving time at one of its control points is dynamically linked to the global traffic pattern, which is, in turn, dynamically linked to the control point. For this closed-loop system to be effective, the traffic management system must sense and interpret a large spatial projection of data originating from multiple sensor suites. This concept is the basis for the development of a Traffic Flow Wide-Area Surveillance (TFWAS) system. This paper presents the results of a study by Oak Ridge National Laboratory to define the operational specifications and characteristics, to determine the constraints, and to examine the state of technology of a TFWAS system in terms of traffic management and control. In doing so, the functions and attributes of a TFWAS system are mapped into an operational structure consistent with the Intelligent Vehicle Highway System (IVHS) concept and the existing highway infrastructure. This mapping includes identifying candidate sensor suites and establishing criteria, requirements, and performance measures by which these systems can be graded in their ability and practicality to meet the operational requirements of a TFWAS system. In light of this, issues such as system integration, applicable technologies, impact on traffic management and control, and public acceptance are addressed.

  17. Neurology of widely embedded free will.

    Science.gov (United States)

    de Jong, Bauke M

    2011-01-01

    Free will is classically attributed to the prefrontal cortex. In clinical neurology, prefrontal lesions have consistently been shown to cause impairment of internally driven action and increased reflex-like behaviour. Recently, parietal contributions to both free selection at early stages of sensorimotor transformations and perception of specifically self-intended movements were demonstrated in the healthy brain. Such findings generated the concept that 'free will' is not a function restricted to the prefrontal cortex but is more widely embedded in the brain, indeed including the parietal cortex. In this paper, a systematic re-interpretation of parietal symptoms, such as apraxia and reduced sense of agency, is given with reference to the consequences of reduced freedom of selection at early stages of sensorimotor transformation. Failed selection between possible movement options is argued to represent an intrinsic characteristic of apraxia. Paradoxical response facilitation supports this view. Perception of self-intended movement corresponds with a sense of agency. Impaired parietal distinction between predicted and perceived movement sensations may thus equal a restricted repertoire for selection between possible movement options of which intention is attributed to either oneself, others or an alien hand. Sense of agency, and thus perception of free will, logically fits a model of the parietal cortex as a neuronal interface between the internal drive to reach a goal and a body scheme required to select possible effectors for motor preparation. Copyright © 2011 Elsevier Srl. All rights reserved.

  18. Bitcoin – the World-Wide Currency

    Directory of Open Access Journals (Sweden)

    Shuba Olena А.

    2017-11-01

    Full Text Available The article is aimed at researching bitcoin, the digital currency. It has been found that Bitcoin is a cryptocurrency, that is, the virtual money, which has no material equivalent. The history of creation and development of cryptocurrency was reviewed. There is a reduction in volatility, which guarantees the security of currency, as well as the increase in currency volume and the inability to estimate the profitability of bitcoins. The dynamics of the value of digital currency in US dollars over recent years has been analyzed. Improvement of attitude of many countries to the considered cryptocurrency, in particular the USA, Germany, Spain, Canada, Australia, Israel and Scandinavian countries has been identified. The reasons of Ukraine’s interest in Bitcoin have been considered. Possibilities of creation of cryptocurrency on the territory of Ukraine have been analyzed, i.e. cost of electricity for mining, the legal status of mining firms, and the attitude of the National Bank of Ukraine to the digital currency. It has been concluded that the recognition of Bitcoin by the world countries in the future will allow it to be granted the status of world-wide currency.

  19. A wide field of view plasma spectrometer

    Science.gov (United States)

    Skoug, R. M.; Funsten, H. O.; Möbius, E.; Harper, R. W.; Kihara, K. H.; Bower, J. S.

    2016-07-01

    We present a fundamentally new type of space plasma spectrometer, the wide field of view plasma spectrometer, whose field of view is > 1.25π ster using fewer resources than traditional methods. The enabling component is analogous to a pinhole camera with an electrostatic energy-angle filter at the image plane. Particle energy-per-charge is selected with a tunable bias voltage applied to the filter plate relative to the pinhole aperture plate. For a given bias voltage, charged particles from different directions are focused by different angles to different locations. Particles with appropriate locations and angles can transit the filter plate and are measured using a microchannel plate detector with a position-sensitive anode. Full energy and angle coverage are obtained using a single high-voltage power supply, resulting in considerable resource savings and allowing measurements at fast timescales. We present laboratory prototype measurements and simulations demonstrating the instrument concept and discuss optimizations of the instrument design for application to space measurements.

  20. Traffic flow wide-area surveillance system

    Science.gov (United States)

    Allgood, Glenn O.; Ferrell, Regina K.; Kercel, Stephen W.; Abston, Ruth A.

    1995-01-01

    Traffic management can be thought of as a stochastic queuing process where the serving time at one of its control points is dynamically linked to the global traffic pattern, which is, in turn, dynamically linked to the control point. For this closed-loop system to be effective, the traffic management system must sense and interpret a large spatial projection of data originating from multiple sensor suites. This concept is the basis for the development of a traffic flow wide-area surveillance (TFWAS) system. This paper presents the results of a study by Oak Ridge National Laboratory to define the operational specifications and characteristics, to determine the constraints, and to examine the state of technology of a TFWAS system in terms of traffic management and control. In doing so, the functions and attributes of a TFWAS system are mapped into an operational structure consistent with the Intelligent Vehicle Highway System (IVHS) concept and the existing highway infrastructure. This mapping includes identifying candidate sensor suites and establishing criteria, requirements, and performance measures by which these systems can be graded in their ability and practicality to meet the operational requirements of a TFWAS system. In light of this, issues such as system integration, applicable technologies, impact on traffic management and control, and public acceptance are addressed.

  1. Faciocardiorenal syndrome: a wide clinical spectrum?

    Science.gov (United States)

    Brambila Tapia, A J L; Vásquez Velásque, A I; González Mercado, M G; Macías Chumacera, A; Gutierrez-Amavizca, B E; Lara Aguilar, R A; Pérez Juárez, Canton R; Moreno Andrade, A; Figuera, L E

    2012-01-01

    Faciocardiorenal syndrome (FCRS), also named Eastman-Bixler syndrome, is an apparent autosomal recessive entity, characterized by endocardial fibroelastosis, unusual facial appearance, renal defects and mental retardation. We report a 7 months male patient, with the diagnosis of endocardial fibroelastosis, an abnormal facial appearance (arched eyebrows, broad nasal root, long philtrum and microretrognathia) and psychomotor delay. Associated anomalies were: plagiocephaly, broad halluces, nail hypoplasia, cryptorchidism, diastasis recti, and adducted thumbs. Focal seizures in the mouth were also observed. The radiographs revealed advanced bone age and metaphyseal widening of femur and tibia. FCRS has an unknown etiology with only three reported cases so far (since 1977). We report a patient with the main features of FCRS but without the renal component, suggesting that this entity can present a wide clinical spectrum. Based on these findings and on the few previously reported cases with a highly variable phenotype when compared with the original report, we suggest that FCRS should be further clinical delineated according to the following leading anomalies: endocardial fibroelastosis, unusual facial appearance and mental retardation, in order to find more cases that allow a wider clinical description and the identification of the genetic defect(s).

  2. Golden Jubilee Photos: World Wide Web

    CERN Multimedia

    2004-01-01

    At the end of the 1980s, the Internet was already a valuable tool to scientists, allowing them to exchange e-mails and to access powerful computers remotely. A more simple means of sharing information was needed, however, and CERN, with its long tradition of informatics and networking, was the ideal place to find it. Moreover, hundreds of scientists from all over the world were starting to work together on preparations for the experiments at the Large Electron-Positron (LEP) collider. In 1989, Tim Berners-Lee (see photo), a young scientist working at CERN, drafted a proposal for an information-management system combining the internet, personal computers and computer-aided document consultation, known as hypertext. In 1990 he was joined by Robert Cailliau and the weaving of the World Wide Web began in earnest, even though only two CERN computers were allocated to the task at the time. The Web subsequently underwent a steady expansion to include the world's main particle physics institutes. The Web was not the...

  3. Monitoring city wide patterns of cycling safety.

    Science.gov (United States)

    Boss, Darren; Nelson, Trisalyn; Winters, Meghan

    2018-02-01

    Many cities are making significant financial investments in cycling infrastructure with the aim of making cycling safer for riders of all ages and abilities. Methods for evaluating cycling safety tend to summarize average change for a city or emphasize change on a single road segment. Few spatially explicit approaches are available to evaluate how patterns of safety change throughout a city due to cycling infrastructure investments or other changes. Our goal is to demonstrate a method for monitoring changes in the spatial-temporal distribution of cycling incidents across a city. Using cycling incident data provided by the Insurance Corporation of British Columbia, we first compare planar versus network constrained kernel density estimation for visualizing incident intensity across the street network of Vancouver, Canada. Second, we apply a change detection algorithm explicitly designed for detecting statistically significant change in kernel density estimates. The utility of network kernel density change detection is demonstrated through the comparison of cycling incident densities following the construction of two cycle tracks in the downtown core of Vancouver. The methods developed and demonstrated for this study provide city planners, transportation engineers and researchers a means of monitoring city-wide change in the intensity of cycling incidents following enhancements to cycling infrastructure or other significant changes to the transportation network. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies.

    Science.gov (United States)

    Hall, Molly A; Wallace, John; Lucas, Anastasia; Kim, Dokyoon; Basile, Anna O; Verma, Shefali S; McCarty, Cathy A; Brilliant, Murray H; Peissig, Peggy L; Kitchner, Terrie E; Verma, Anurag; Pendergrass, Sarah A; Dudek, Scott M; Moore, Jason H; Ritchie, Marylyn D

    2017-10-27

    Genome-wide, imputed, sequence, and structural data are now available for exceedingly large sample sizes. The needs for data management, handling population structure and related samples, and performing associations have largely been met. However, the infrastructure to support analyses involving complexity beyond genome-wide association studies is not standardized or centralized. We provide the PLatform for the Analysis, Translation, and Organization of large-scale data (PLATO), a software tool equipped to handle multi-omic data for hundreds of thousands of samples to explore complexity using genetic interactions, environment-wide association studies and gene-environment interactions, phenome-wide association studies, as well as copy number and rare variant analyses. Using the data from the Marshfield Personalized Medicine Research Project, a site in the electronic Medical Records and Genomics Network, we apply each feature of PLATO to type 2 diabetes and demonstrate how PLATO can be used to uncover the complex etiology of common traits.

  5. A Comparison Between Craniofacial Templates of Iranian and Western Populations

    Directory of Open Access Journals (Sweden)

    Tahereh Hosseinzadeh Nik

    2012-02-01

    Full Text Available Templates are very useful tools for diagnosis of malocclusions. A number of templates have been provided for some populations in previous years. Since craniofacial characteristics of different ethnic groups are not the same, each population needs its own norms. The aim of this study was to provide orthodontic craniofacial templates for 8-16 year old Iranian boys and compare dentoskeletal features between Iranian and western populations. 3330 boys with the age range of 8-16 years were examined in Tehran, and 107 cases were finally chosen for the study and their lateral cephalograms were traced. Since there is no universal, consensus about the selection of one specific point or line for cephalometric superimposition, both the sella nasion (SN and basion nasion (Ba-N lines were chosen for this purpose. Based on both SN and Ba-N lines, a template was prepared for each age. Simple linear regression analysis was used to evaluate the angles and the multivariant regression analysis for evaluation of landmark vectors. Posterior cranial base, maxillary and mandibular lengths, upper and lower anterior facial heights (N-ANS and ANS-Me and posterior facial height (S-Go are greater in Iranian population. But anterior cranial base, height and inclination of the incisors and molar height are similar in two populations.

  6. World Wide Web of Your Wide Web? Juridische aspecten van zoekmachine-personalisatie

    NARCIS (Netherlands)

    Oostveen, M.

    2012-01-01

    Het world wide web is een enorme bron van informatie. Iedere internetgebruiker maakt gebruik van zoekmachines om die informatie te kunnen vinden. Veel gebruikers weten echter niet dat zoekresultaten behorende bij een bepaalde zoekterm niet voor iedereen hetzelfde zijn. Dit personaliseren van

  7. bayesPop: Probabilistic Population Projections

    Directory of Open Access Journals (Sweden)

    Hana Ševčíková

    2016-12-01

    Full Text Available We describe bayesPop, an R package for producing probabilistic population projections for all countries. This uses probabilistic projections of total fertility and life expectancy generated by Bayesian hierarchical models. It produces a sample from the joint posterior predictive distribution of future age- and sex-specific population counts, fertility rates and mortality rates, as well as future numbers of births and deaths. It provides graphical ways of summarizing this information, including trajectory plots and various kinds of probabilistic population pyramids. An expression language is introduced which allows the user to produce the predictive distribution of a wide variety of derived population quantities, such as the median age or the old age dependency ratio. The package produces aggregated projections for sets of countries, such as UN regions or trading blocs. The methodology has been used by the United Nations to produce their most recent official population projections for all countries, published in the World Population Prospects.

  8. Genome-wide association and genomic selection in animal breeding.

    Science.gov (United States)

    Hayes, Ben; Goddard, Mike

    2010-11-01

    Results from genome-wide association studies in livestock, and humans, has lead to the conclusion that the effect of individual quantitative trait loci (QTL) on complex traits, such as yield, are likely to be small; therefore, a large number of QTL are necessary to explain genetic variation in these traits. Given this genetic architecture, gains from marker-assisted selection (MAS) programs using only a small number of DNA markers to trace a limited number of QTL is likely to be small. This has lead to the development of alternative technology for using the available dense single nucleotide polymorphism (SNP) information, called genomic selection. Genomic selection uses a genome-wide panel of dense markers so that all QTL are likely to be in linkage disequilibrium with at least one SNP. The genomic breeding values are predicted to be the sum of the effect of these SNPs across the entire genome. In dairy cattle breeding, the accuracy of genomic estimated breeding values (GEBV) that can be achieved and the fact that these are available early in life have lead to rapid adoption of the technology. Here, we discuss the design of experiments necessary to achieve accurate prediction of GEBV in future generations in terms of the number of markers necessary and the size of the reference population where marker effects are estimated. We also present a simple method for implementing genomic selection using a genomic relationship matrix. Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships.

  9. Continent-wide survey reveals massive decline in African savannah elephants

    Directory of Open Access Journals (Sweden)

    Michael J. Chase

    2016-08-01

    Full Text Available African elephants (Loxodonta africana are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC, the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat.

  10. Continent-wide survey reveals massive decline in African savannah elephants.

    Science.gov (United States)

    Chase, Michael J; Schlossberg, Scott; Griffin, Curtice R; Bouché, Philippe J C; Djene, Sintayehu W; Elkan, Paul W; Ferreira, Sam; Grossman, Falk; Kohi, Edward Mtarima; Landen, Kelly; Omondi, Patrick; Peltier, Alexis; Selier, S A Jeanetta; Sutcliffe, Robert

    2016-01-01

    African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants' downward trajectory by preventing poaching and protecting habitat.

  11. Genome wide application of DNA melting analysis.

    Science.gov (United States)

    Jost, Daniel; Everaers, Ralf

    2009-01-21

    Correspondences between functional and thermodynamic melting properties in a genome are being increasingly employed for ab initio gene finding and for the interpretation of the evolution of genomes. Here we present the first systematic genome wide comparison between biologically coding domains and thermodynamically stable regions. In particular, we develop statistical methods to estimate the reliability of the resulting predictions. Not surprisingly, we find that the success of the approach depends on the difference in GC content between the coding and the non-coding parts of the genome and on the percentage of coding base-pairs in the sequence. These prerequisites vary strongly between species, where we observe no systematic differences between eukaryotes and prokaryotes. We find a number of organisms in which the strong correlation of coding domains and thermodynamically stable regions allows us to identify putative exons or genes to complement existing approaches. In contrast to previous investigations along these lines we have not employed the Poland-Scheraga (PS) model of DNA melting but use the earlier Zimm-Bragg (ZB) model. The Ising-like form of the ZB model can be viewed as an approximation to the PS model, with averaged loop entropies included into the cooperative factor [Formula: see text]. This results in a speed-up by a factor of 20-100 compared to the Fixman-Freire algorithm for the solution of the PS model. We show that for genomic sequences the resulting systematic errors are negligible compared to the parameterization uncertainty of the models. We argue that for limited computing resources, available CPU power is better invested in broadening the statistical base for genomic investigations than in marginal improvements of the description of the physical melting behavior.

  12. Wide Bandgap Semiconductor Opportunities in Power Electronics

    Energy Technology Data Exchange (ETDEWEB)

    Das, Sujit [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Marlino, Laura D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Armstrong, Kristina O. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2018-01-01

    The report objective is to explore the Wide Bandgap (WBG) Power Electronics (PE) market, applications, and potential energy savings in order to identify key areas where further resources and investments of the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (DOE EERE) would have the most impact on U.S. competiveness. After considering the current market, several potential near-term application areas were identified as having significant market and energy savings potential with respect to clean energy applications: (1) data centers (uninterruptible power supplies and server power supplies); (2) renewable energy generation (photovoltaic-solar and wind); (3) motor drives (industrial, commercial and residential); (4) rail traction; and, (5) hybrid and electric vehicles (traction and charging). After the initial explorative analyses, it became clear that, SiC, not GaN, would be the principal WBG power device material for the chosen markets in the near future. Therefore, while GaN is discussed when appropriate, this report focuses on SiC devices, other WBG applications (e.g., solid-state transformers, combined heat and power, medical, and wireless power), the GaN market, and GaN specific applications (e.g., LiDAR, 5G) will be explored at a later date. In addition to the market, supply and value chain analyses addressed in Section 1 of this report, a SWOT (Strength, Weakness, Opportunity, Threat) analysis and potential energy savings analysis was conducted for each application area to identify the major potential WBG application area(s) with a U.S. competitiveness opportunity in the future.

  13. Wide Area Security Region Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Makarov, Yuri V.; Lu, Shuai; Guo, Xinxin; Gronquist, James; Du, Pengwei; Nguyen, Tony B.; Burns, J. W.

    2010-03-31

    This report develops innovative and efficient methodologies and practical procedures to determine the wide-area security region of a power system, which take into consideration all types of system constraints including thermal, voltage, voltage stability, transient and potentially oscillatory stability limits in the system. The approach expands the idea of transmission system nomograms to a multidimensional case, involving multiple system limits and parameters such as transmission path constraints, zonal generation or load, etc., considered concurrently. The security region boundary is represented using its piecewise approximation with the help of linear inequalities (so called hyperplanes) in a multi-dimensional space, consisting of system parameters that are critical for security analyses. The goal of this approximation is to find a minimum set of hyperplanes that describe the boundary with a given accuracy. Methodologies are also developed to use the security hyperplanes, pre-calculated offline, to determine system security margins in real-time system operations, to identify weak elements in the system, and to calculate key contributing factors and sensitivities to determine the best system controls in real time and to assist in developing remedial actions and transmission system enhancements offline . A prototype program that automates the simulation procedures used to build the set of security hyperplanes has also been developed. The program makes it convenient to update the set of security hyperplanes necessitated by changes in system configurations. A prototype operational tool that uses the security hyperplanes to assess security margins and to calculate optimal control directions in real time has been built to demonstrate the project success. Numerical simulations have been conducted using the full-size Western Electricity Coordinating Council (WECC) system model, and they clearly demonstrated the feasibility and the effectiveness of the developed

  14. Terpene synthases are widely distributed in bacteria

    Science.gov (United States)

    Yamada, Yuuki; Kuzuyama, Tomohisa; Komatsu, Mamoru; Shin-ya, Kazuo; Omura, Satoshi; Cane, David E.; Ikeda, Haruo

    2015-01-01

    Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes. PMID:25535391

  15. The Wide Field Imager instrument for Athena

    Science.gov (United States)

    Meidinger, Norbert; Barbera, Marco; Emberger, Valentin; Fürmetz, Maria; Manhart, Markus; Müller-Seidlitz, Johannes; Nandra, Kirpal; Plattner, Markus; Rau, Arne; Treberspurg, Wolfgang

    2017-08-01

    ESA's next large X-ray mission ATHENA is designed to address the Cosmic Vision science theme 'The Hot and Energetic Universe'. It will provide answers to the two key astrophysical questions how does ordinary matter assemble into the large-scale structures we see today and how do black holes grow and shape the Universe. The ATHENA spacecraft will be equipped with two focal plane cameras, a Wide Field Imager (WFI) and an X-ray Integral Field Unit (X-IFU). The WFI instrument is optimized for state-of-the-art resolution spectroscopy over a large field of view of 40 amin x 40 amin and high count rates up to and beyond 1 Crab source intensity. The cryogenic X-IFU camera is designed for high-spectral resolution imaging. Both cameras share alternately a mirror system based on silicon pore optics with a focal length of 12 m and large effective area of about 2 m2 at an energy of 1 keV. Although the mission is still in phase A, i.e. studying the feasibility and developing the necessary technology, the definition and development of the instrumentation made already significant progress. The herein described WFI focal plane camera covers the energy band from 0.2 keV to 15 keV with 450 μm thick fully depleted back-illuminated silicon active pixel sensors of DEPFET type. The spatial resolution will be provided by one million pixels, each with a size of 130 μm x 130 μm. The time resolution requirement for the WFI large detector array is 5 ms and for the WFI fast detector 80 μs. The large effective area of the mirror system will be completed by a high quantum efficiency above 90% for medium and higher energies. The status of the various WFI subsystems to achieve this performance will be described and recent changes will be explained here.

  16. Geomorphology and the World Wide Web

    Science.gov (United States)

    Shroder, John F.; Bishop, Michael P.; Olsenholler, Jeffrey; Craiger, J. Philip

    2002-10-01

    The Internet and the World Wide Web have brought many dimensions of new technology to education and research in geomorphology. As with other disciplines on the Web, Web-based geomorphology has become an eclectic mix of whatever material an individual deems worthy of presentation, and in many cases is without quality control. Nevertheless, new electronic media can facilitate education and research in geomorphology. For example, virtual field trips can be developed and accessed to reinforce concepts in class. Techniques for evaluating Internet references helps students to write traditional term papers, but professional presentations can also involve student papers that are published on the Web. Faculty can also address plagiarism issues by using search engines. Because of the lack of peer review of much of the content on the Web, care must be exercised in using it for reference searches. Today, however, refereed journals are going online and can be accessed through subscription or payment per article viewed. Library reference desks regularly use the Web for searches of refereed articles. Research on the Web ranges from communication between investigators, data acquisition, scientific visualization, or comprehensive searches of refereed sources, to interactive analyses of remote data sets. The Nanga Parbat and the Global Land Ice Measurements from Space (GLIMS) Projects are two examples of geomorphologic research that are achieving full potential through use of the Web. Teaching and research in geomorphology are undergoing a beneficial, but sometimes problematic, transition with the new technology. The learning curve is steep for some users but the view from the top is bright. Geomorphology can only prosper from the benefits offered by computer technologies.

  17. Genome-wide association study of antisocial personality disorder

    Science.gov (United States)

    Rautiainen, M-R; Paunio, T; Repo-Tiihonen, E; Virkkunen, M; Ollila, H M; Sulkava, S; Jolanki, O; Palotie, A; Tiihonen, J

    2016-01-01

    The pathophysiology of antisocial personality disorder (ASPD) remains unclear. Although the most consistent biological finding is reduced grey matter volume in the frontal cortex, about 50% of the total liability to developing ASPD has been attributed to genetic factors. The contributing genes remain largely unknown. Therefore, we sought to study the genetic background of ASPD. We conducted a genome-wide association study (GWAS) and a replication analysis of Finnish criminal offenders fulfilling DSM-IV criteria for ASPD (N=370, N=5850 for controls, GWAS; N=173, N=3766 for controls and replication sample). The GWAS resulted in suggestive associations of two clusters of single-nucleotide polymorphisms at 6p21.2 and at 6p21.32 at the human leukocyte antigen (HLA) region. Imputation of HLA alleles revealed an independent association with DRB1*01:01 (odds ratio (OR)=2.19 (1.53–3.14), P=1.9 × 10-5). Two polymorphisms at 6p21.2 LINC00951–LRFN2 gene region were replicated in a separate data set, and rs4714329 reached genome-wide significance (OR=1.59 (1.37–1.85), P=1.6 × 10−9) in the meta-analysis. The risk allele also associated with antisocial features in the general population conditioned for severe problems in childhood family (β=0.68, P=0.012). Functional analysis in brain tissue in open access GTEx and Braineac databases revealed eQTL associations of rs4714329 with LINC00951 and LRFN2 in cerebellum. In humans, LINC00951 and LRFN2 are both expressed in the brain, especially in the frontal cortex, which is intriguing considering the role of the frontal cortex in behavior and the neuroanatomical findings of reduced gray matter volume in ASPD. To our knowledge, this is the first study showing genome-wide significant and replicable findings on genetic variants associated with any personality disorder. PMID:27598967

  18. Demographic history of Oceania inferred from genome-wide data.

    Science.gov (United States)

    Wollstein, Andreas; Lao, Oscar; Becker, Christian; Brauer, Silke; Trent, Ronald J; Nürnberg, Peter; Stoneking, Mark; Kayser, Manfred

    2010-11-23

    The human history of Oceania comprises two extremes: the initial colonizations of Near Oceania, one of the oldest out-of-Africa migrations, and of Remote Oceania, the most recent expansion into unoccupied territories. Genetic studies, mostly using uniparentally inherited DNA, have shed some light on human origins in Oceania, particularly indicating that Polynesians are of mixed East Asian and Near Oceanian ancestry. Here, we use ∼1 million single nucleotide polymorphisms (SNPs) to investigate the demographic history of Oceania in a more detailed manner. We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians ∼27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (∼87%) and Near Oceanians (∼13%) occurred ∼3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (∼65%) and additional Near Oceanian (∼35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea. Despite the inherent ascertainment bias, genome-wide SNP data provide new insights into the genetic history of Oceana. Our approach to correct for ascertainment bias and obtain reliable inferences concerning demographic history should prove useful in other such studies. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. Susceptibility to chronic mucus hypersecretion, a genome wide association study.

    Directory of Open Access Journals (Sweden)

    Akkelies E Dijkstra

    Full Text Available Chronic mucus hypersecretion (CMH is associated with an increased frequency of respiratory infections, excess lung function decline, and increased hospitalisation and mortality rates in the general population. It is associated with smoking, but it is unknown why only a minority of smokers develops CMH. A plausible explanation for this phenomenon is a predisposing genetic constitution. Therefore, we performed a genome wide association (GWA study of CMH in Caucasian populations.GWA analysis was performed in the NELSON-study using the Illumina 610 array, followed by replication and meta-analysis in 11 additional cohorts. In total 2,704 subjects with, and 7,624 subjects without CMH were included, all current or former heavy smokers (≥20 pack-years. Additional studies were performed to test the functional relevance of the most significant single nucleotide polymorphism (SNP.A strong association with CMH, consistent across all cohorts, was observed with rs6577641 (p = 4.25×10(-6, OR = 1.17, located in intron 9 of the special AT-rich sequence-binding protein 1 locus (SATB1 on chromosome 3. The risk allele (G was associated with higher mRNA expression of SATB1 (4.3×10(-9 in lung tissue. Presence of CMH was associated with increased SATB1 mRNA expression in bronchial biopsies from COPD patients. SATB1 expression was induced during differentiation of primary human bronchial epithelial cells in culture.Our findings, that SNP rs6577641 is associated with CMH in multiple cohorts and is a cis-eQTL for SATB1, together with our additional observation that SATB1 expression increases during epithelial differentiation provide suggestive evidence that SATB1 is a gene that affects CMH.

  20. Human Chorioretinal Layer Thicknesses Measured in Macula-wide, High-Resolution Histologic Sections

    Science.gov (United States)

    Messinger, Jeffrey D.; Sloan, Kenneth R.; Mitra, Arnab; McGwin, Gerald; Spaide, Richard F.

    2011-01-01

    Purpose. To provide a comprehensive description of chorioretinal layer thicknesses in the normal human macula, including two-layer pairs that can produce a combined signal in some optical coherence tomography (OCT) devices (ganglion cell [GCL] and inner plexiform [IPL] layers and outer plexiform [OPL] and outer nuclear [ONL] layers). Methods. In 0.8-μm-thick, macula-wide sections through the foveola of 18 donors (age range, 40–92 years), 21 layers were measured at 25 locations by a trained observer and validated by a second observer. Tissue volume changes were assessed by comparing total retinal thickness in ex vivo OCT and in sections. Results. Median tissue shrinkage was 14.5% overall and 29% in the fovea. Histologic laminar boundaries resembled those in SD-OCT scans, but the shapes of the foveolar OPL and ONL differed. Histologic GCL, IPL, and OPLHenle were thickest at 0.8. to 1, 1.5, and 0.4 mm eccentricity, respectively. ONL was thickest in an inward bulge at the foveal center. At 1 mm eccentricity, GCL, INL, and OPLHenle represented 17.3% to 21.1%, 18.0% to 18.5%, and 14.2% to 16.6% of total retinal thickness, respectively. In donors ≥70 years of age, the RPE and choroid were 17.1% and 29.6% thinner and OPLHenle was 20.8% thicker than in donors macula were generated. Newer OCT systems can separate GCL from IPL and OPLHenle from ONL, with good agreement for the proportion of retinal thickness occupied by OPLHenle in OCT and histology. The thickening of OPLHenle in older eyes may reflect Müller cell hypertrophy associated with rod loss. PMID:21421869

  1. Components of adult class III malocclusion in an Iranian population

    Directory of Open Access Journals (Sweden)

    Roodabeh Koodaryan

    2009-03-01

    Full Text Available Background and aims. Class III malocclusions are considered complex and difficult orthodontic problems to diagnose and treat. The purpose of this study was to investigate the morphologic characteristics of the craniofacial complex of adults with Class III malocclusion in an Iranian population. Materials and methods. Lateral cephalometric radiographs of 50 patients with Class III malocclusion (20 males and 30 females; age range of 18-27 years were selected on the basis of molar relationship, concave profile and an overjet of ≤ 0 mm. The standard values of 19 soft tissue measurements were determined using McNamara, Burstone and Viazis methods. Results. Adults with Class III malocclusion exhibited distinct craniofacial morphologic characteristics manifested by a combination of retrusion of maxilla and protrusion of mandible. Conclusion. The most prevalent component was mandibular prognathism, normal maxilla and LAFH on the basis of the component analysis.

  2. Deployable Wide-Aperture Array Antennas

    Science.gov (United States)

    Fink, Patrick W.; Dobbins, Justin A.; Lin, Greg Y.; Chu, Andrew; Scully, Robert C.

    2005-01-01

    membrane, can also be used. Finally, wide bandwidth antennas or arrays can be formed in which the principal direction of radiation is in the plane of the membrane. For this embodiment, the set of elements on the membrane is arranged to form one or more traveling wave antennas. In this case, a nonconductive form of the perimeter springlike material is required to provide the deploying force.

  3. The wide field imager instrument for Athena

    Science.gov (United States)

    Meidinger, Norbert; Nandra, Kirpal; Plattner, Markus; Porro, Matteo; Rau, Arne; Santangelo, Andrea E.; Tenzer, Chris; Wilms, Jörn

    2014-07-01

    The "Hot and Energetic Universe" has been selected as the science theme for ESA's L2 mission, scheduled for launch in 2028. The proposed Athena X-ray observatory provides the necessary capabilities to achieve the ambitious goals of the science theme. The X-ray mirrors are based on silicon pore optics technology and will have a 12 m focal length. Two complementary camera systems are foreseen which can be moved in and out of the focal plane by an interchange mechanism. These instruments are the actively shielded micro-calorimeter spectrometer X-IFU and the Wide Field Imager (WFI). The WFI will combine an unprecedented survey power through its large field of view of 40 arcmin with a high countrate capability (approx. 1 Crab). It permits a state-of-the-art energy resolution in the energy band of 0.1 keV to 15 keV during the entire mission lifetime (e.g. FWHM serial analog output. The architecture of sensor and readout ASIC allows readout in full frame mode and window mode as well by addressing selectively arbitrary sub-areas of the sensor allowing time resolution in the order of 10 μs. The further detector electronics has mainly the following tasks: digitization, pre-processing and telemetry of event data as well as supply and control of the detector system. Although the sensor will already be equipped with an on-chip light blocking filter, a filter wheel is necessary to provide an additional external filter, an on-board calibration source, an open position for outgassing, and a closed position for protection of the sensor. The sensor concept provides high quantum efficiency over the entire energy band and we intend to keep the instrumental background as low as possible by designing a graded Z-shield around the sensor. All these properties make the WFI a very powerful survey instrument, significantly surpassing currently existing observatories and in addition allow high-time resolution of the brightest X-ray sources with low pile-up and high efficiency. This

  4. Developing Basic Space Science World-Wide

    Science.gov (United States)

    Wamsteker, W.; Albrecht, Rudolf; Haubold, Hans J.

    2004-03-01

    When the first United Nations/European Space Agency Workshop for Basic Space Science was planned to be held in Bangalore, India (1991) on the invitation of ISRO, few of those involved could expect that a unique forum was going to be created for scientific dialogue between scientists from developing and industrialized nations. As the format of the first workshop was on purpose left free with time for presentations, working sessions, and plenary discussions, the workshop was left to find its own dynamics. After a decade of UN/ESA Workshops, this book brings together the historical activities, the plans which have been developed over the past decade in the different nations, and the results which have materialized during this time in different developing nations. It aims to achieve for development agencies to be assisted in ways to find more effective tools for the application of development aid. The last section of the book contains a guide for teachers to introduce astrophysics into university physics courses. This will be of use to teachers in many nations. Everything described in this book is the result of a truly collective effort from all involved in all UN/ESA workshops. The mutual support from the participants has helped significantly to implement some of the accomplishments described in the book. Rather than organizing this book in a subject driven way, it is essentially organized according to the common economic regions of the world, as defined by the United Nations (Africa, Asia and the Pacific, Europe, Latin America and the Caribbean, Western Asia). This allows better recognition of the importance of a regional (and at times) global approach to basic space science for the developing nation's world wide. It highlights very specific scientific investigations which have been completed successfully in the various developing nations. The book supplements the published ten volumes of workshop proceedings containing scientific papers presented in the workshops

  5. Real Time Wide Area Radiation Surveillance System

    Science.gov (United States)

    Biafore, M.

    2012-04-01

    We present the REWARD project, financed within the FP7 programme, theme SEC-2011.1.5-1 (Development of detection capabilities of difficult to detect radioactive sources and nuclear materials - Capability Project). Within this project, we propose a novel mobile system for real time, wide area radiation surveillance. The system is based on the integration of new miniaturized solid-state radiation sensors: a CdZnTe detector for gamma radiation and a high efficiency neutron detector based on novel silicon technologies. The sensing unit will include a wireless communication interface to send the data remotely to a monitoring base station which also uses a GPS system to calculate the position of the tag. The system will also incorporate middleware and high level software to provide web-service interfaces for the exchange of information, and that will offer top level functionalities as management of users, mobile tags and environment data and alarms, database storage and management and a web-based graphical user interface. Effort will be spent to ensure that the software is modular and re-usable across as many architectural levels as possible. Finally, an expert system will continuously analyze the information from the radiation sensor and correlate it with historical data from the tag location in order to generate an alarm when an abnormal situation is detected. The system will be useful for many different scenarios, including such lost radioactive sources and radioactive contamination. It will be possible to deploy in emergency units and in general in any type of mobile or static equipment. The sensing units will be highly portable thanks to their low size and low energy consumption. The complete system will be scalable in terms of complexity and cost and will offer very high precision on both the measurement and the location of the radiation. The modularity and flexibility of the system will allow for a realistic introduction to the market. Authorities may start with a

  6. Structural dynamics and ecology of flatfish populations

    Science.gov (United States)

    Bailey, Kevin M.

    1997-11-01

    The concept of structure in populations of marine fishes is fundamental to how we manage and conduct research on these resources. The degree of population structure ranges widely among flatfishes. Although we know that large populations tend to be subdivided into local populations, based on morphological, meristic and reproductive characteristics, these data often conflict with evidence on genetic stock structure, due to the scale and organization of movement within the metapopulation. Movement of individuals between local subpopulations and colonization events on a macroecological scale are probably important to some flatfish populations. Dispersal of larvae is known to be a major factor affecting population mixing. Some flatfishes have planktonic stages of long duration and for these species there is often, but not always, little population structure; gene flow sometimes may be limited by oceanographic features, such as eddies and fronts. At the juvenile stage dispersal can result in colonization of under-utilized habitats; however, for flatfishes with strong habitat requirements, this type of event may be less likely when suitable habitats are fragmented. Complex population structure has major implications for management, e.g. lumping harvested populations with little gene flow can have detrimental local effects. Moreover, the issue of population structure and movement influences the interpretation of research data, where populations are generally treated as closed systems. There is currently a strong need for a multidisciplinary approach to study fish population dynamics and the structure of their populations. This research should involve molecular geneticists, population geneticists, animal behaviourists and ecologists. Migration mechanisms, colonization and extinction events, gene flow and density-dependent movements are subject areas of great importance to managing large harvested populations, but our understanding of them at ecological scales, at least for

  7. Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

    Science.gov (United States)

    Saura, María; Fernández, Almudena; Rodríguez, M Carmen; Toro, Miguel A; Barragán, Carmen; Fernández, Ana I; Villanueva, Beatriz

    2013-01-01

    Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative

  8. World Wide Web voted most wonderful wonder by web-wide world

    CERN Multimedia

    2007-01-01

    The results are in, and the winner is...the World Wide Web! An online survey conducted by the CNN news group ranks the World Wide Web-invented at CERN--as the most wonderful of the seven modern wonders of the world. (See Bulletin No. 49/2006.) There is currently no speculation about whether they would have had the same results had they distributed the survey by post. The World Wide Web won with a whopping 50 per cent of the votes (3,665 votes). The runner up was CERN again, with 16 per cent of voters (1130 votes) casting the ballot in favour of the CERN particle accelerator. Stepping into place behind CERN and CERN is 'None of the Above' with 8 per cent of the votes (611 votes), followed by the development of Dubai (7%), the bionic arm (7%), China's Three Gorges Damn (5%), The Channel Tunnel (4%), and France's Millau viaduct (3%). Thanks to everyone from CERN who voted. You can view the results on http://edition.cnn.com/SPECIALS/2006/modern.wonders/

  9. WIDE-FIELD WIDE-BAND INTERFEROMETRIC IMAGING: THE WB A-PROJECTION AND HYBRID ALGORITHMS

    Energy Technology Data Exchange (ETDEWEB)

    Bhatnagar, S.; Rau, U.; Golap, K., E-mail: sbhatnag@nrao.edu, E-mail: rurvashi@nrao.edu, E-mail: kgolap@nrao.edu [National Radio Astronomy Observatory, Socorro, NM 87801 (United States)

    2013-06-20

    Variations of the antenna primary beam (PB) pattern as a function of time, frequency, and polarization form one of the dominant direction-dependent effects at most radio frequency bands. These gains may also vary from antenna to antenna. The A-Projection algorithm, published earlier, accounts for the effects of the narrow-band antenna PB in full polarization. In this paper, we present the wide-band A-Projection algorithm (WB A-Projection) to include the effects of wide bandwidth in the A-term itself and show that the resulting algorithm simultaneously corrects for the time, frequency, and polarization dependence of the PB. We discuss the combination of the WB A-Projection and the multi-term multi-frequency synthesis (MT-MFS) algorithm for simultaneous mapping of the sky brightness distribution and the spectral index distribution across a wide field of view. We also discuss the use of the narrow-band A-Projection algorithm in hybrid imaging schemes that account for the frequency dependence of the PB in the image domain.

  10. A genome-wide association study of cognitive function in Chinese adult twins

    DEFF Research Database (Denmark)

    Xu, Chunsheng; Zhang, Dongfeng; Wu, Yili

    2017-01-01

    Multiple loci or genes have been identified using genome-wide association studies mainly in western countries but with inconsistent results. No similar studies have been conducted in the world's largest and rapidly aging Chinese population. The paper aimed to identify the specific genetic variants....... Gene-based analysis was performed on VEGAS2. The statistically significant genes were then subject to gene set enrichment analysis to further identify the specific biological pathways associated with cognitive function. No SNPs reached genome-wide significance although there were 13 SNPs of suggestive...

  11. Population dynamics of species-rich ecosystems: the mixture of matrix population models approach

    DEFF Research Database (Denmark)

    Mortier, Frédéric; Rossi, Vivien; Guillot, Gilles

    2013-01-01

    Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size...... species with similar population dynamics....... of the calibration data sets. However, the species classification is often disconnected from the matrix modelling and from the estimation of matrix parameters, thus bringing species groups that may not be optimal with respect to the predicted community dynamics. We proposed here a method that jointly classified...

  12. Why Does Population Aging Matter So Much for Asia? Population Aging, Economic Security and Economic Growth in Asia

    OpenAIRE

    Lee, Sang-Hyop; Mason, Andrew; Park, Donghyun

    2011-01-01

    Asia as a whole is experiencing a rapid demographic transition toward older population structures. Within this broader region-wide trend, there is considerable heterogeneity, with different countries at different stages of the demographic transition. In this paper, we document Asia’s population aging, describe the region’s old-age support systems, and draw out the regional socioeconomic implications of population aging and old-age support systems. Population aging gives rise to two fundamenta...

  13. Genome-Wide Association Studies of the Human Gut Microbiota.

    Directory of Open Access Journals (Sweden)

    Emily R Davenport

    Full Text Available The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both. These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%. For example, we identified an association between a taxon known to affect obesity (genus Akkermansia and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10-7. Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut.

  14. Genome-Wide Association Studies of the Human Gut Microbiota

    Science.gov (United States)

    Davenport, Emily R.; Cusanovich, Darren A.; Michelini, Katelyn; Barreiro, Luis B.; Ober, Carole; Gilad, Yoav

    2015-01-01

    The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both). These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%). For example, we identified an association between a taxon known to affect obesity (genus Akkermansia) and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL) mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10−7). Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut. PMID:26528553

  15. Reducing dimensionality for prediction of genome-wide breeding values