WorldWideScience

Sample records for wide age-ranged population

  1. 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

    2011-05-01

    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 2, the happy-sad task featured photographs, and pictures for both measures were gray scale. All age groups made more errors and took longer to respond to the happy-sad versus the day-night versions. Unlike the day-night task, the happy-sad task did not suffer from ceiling effects, even in adults. The happy-sad task provides a methodological advance for measuring executive function across a wide age range.

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

    OpenAIRE

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

    2017-01-01

    Introduction 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 tha...

  3. 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

  4. Plant Mating Systems Often Vary Widely Among Populations

    Directory of Open Access Journals (Sweden)

    Michael R. Whitehead

    2018-04-01

    Full Text Available Most flowering plants are hermaphroditic, yet the proportion of seeds fertilized by self and outcross pollen varies widely among species, ranging from predominant self-fertilization to exclusive outcrossing. A population's rate of outcrossing has important evolutionary outcomes as it influences genetic structure, effective population size, and offspring fitness. Because most mating system studies have quantified outcrossing rates for just one or two populations, past reviews of mating system diversity have not been able to characterize the extent of variation among populations. Here we present a new database of more than 30 years of mating system studies that report outcrossing rates for three or more populations per species. This survey, which includes 741 populations from 105 species, illustrates substantial and prevalent among-population variation in the mating system. Intermediate outcrossing rates (mixed mating are common; 63% of species had at least one mixed mating population. The variance among populations and within species was not significantly correlated with pollination mode or phylogeny. Our review underscores the need for studies exploring variation in the relative influence of ecological and genetic factors on the mating system, and how this varies among populations. We conclude that estimates of outcrossing rates from single populations are often highly unreliable indicators of the mating system of an entire species.

  5. Area-wide population suppression of codling moth

    International Nuclear Information System (INIS)

    Calkins, C.O.; Knight, A.L.; Richardson, G.; Bloem, K.A.

    2000-01-01

    The area-wide pest population control concept began with E.F. Knipling (1979) in the 1970s. Control of a pest population on individual fields does little to control the overall pest population because only a portion of the population is being affected. Expanding control tactics beyond individual farms tends to suppress the population on a wider scale and frequently results in suppression of the population for more than one year. The Agriculture Research Service (ARS) believes that this concept has not been addressed with the focus and support that it deserves. The ARS Administration made a conscious decision in 1994 to create a series of area-wide programmes funded out of ARS-based funds that had previously been used for pilot tests. These programmes involve a coordinated effort among ARS and university scientists, growers, and fieldmen for agriculture supply centres and fruit packing houses. The first area-wide programme supported by ARS was the codling moth (CM), Cydia pomonella L. (Lepidoptera: Tortricidae) suppression programme. The codling moth is the key pest of pome fruit throughout the western United States (Beers et al. 1993). About half of the insecticides applied on these crops are directed toward this pest. A non-insecticidal control technique, mating disruption (MD), is available to replace the organophosphates. Removal of the hard pesticides directed against this pest would do the most to allow natural enemies to survive and reproduce in the orchards, which in turn would have the effect of reducing secondary pests. Elimination of the pesticides would also remove much of the health risks to workers and would minimise buildup of pesticide resistance. The objectives of the Codling Moth Area-wide Program are to enhance the efficacy of the non-pesticide approach, to demonstrate that mating disruption will work if conducted properly, to develop biological technology to lower costs of control that complement mating disruption, to implement effective

  6. Formation of the wide asynchronous binary asteroid population

    International Nuclear Information System (INIS)

    Jacobson, Seth A.; Scheeres, Daniel J.; McMahon, Jay

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Bacterial charity work leads to population-wide resistance.

    Science.gov (United States)

    Lee, Henry H; Molla, Michael N; Cantor, Charles R; Collins, James J

    2010-09-02

    Bacteria show remarkable adaptability in the face of antibiotic therapeutics. Resistance alleles in drug target-specific sites and general stress responses have been identified in individual end-point isolates. Less is known, however, about the population dynamics during the development of antibiotic-resistant strains. Here we follow a continuous culture of Escherichia coli facing increasing levels of antibiotic and show that the vast majority of isolates are less resistant than the population as a whole. We find that the few highly resistant mutants improve the survival of the population's less resistant constituents, in part by producing indole, a signalling molecule generated by actively growing, unstressed cells. We show, through transcriptional profiling, that indole serves to turn on drug efflux pumps and oxidative-stress protective mechanisms. The indole production comes at a fitness cost to the highly resistant isolates, and whole-genome sequencing reveals that this bacterial altruism is made possible by drug-resistance mutations unrelated to indole production. This work establishes a population-based resistance mechanism constituting a form of kin selection whereby a small number of resistant mutants can, at some cost to themselves, provide protection to other, more vulnerable, cells, enhancing the survival capacity of the overall population in stressful environments.

  9. THE SUBSTELLAR POPULATION OF {sigma} ORIONIS: A DEEP WIDE SURVEY

    Energy Technology Data Exchange (ETDEWEB)

    Bejar, V. J. S.; Rebolo, R. [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain); Zapatero Osorio, M. R.; Martin, E. L. [Centro de Astrobiologia (INTA-CSIC), Crta. Ajalvir km 4, E-28850 Torrejon de Ardoz, Madrid (Spain); Caballero, J. A.; Barrado, D. [Centro de Astrobiologia (INTA-CSIC), ESAC campus, P.O. Box 78, E-28691 Villanueva de la Canada, Madrid (Spain); Mundt, R.; Bailer-Jones, C. A. L., E-mail: vbejar@iac.es, E-mail: mosorio@cab.inta-csic.es, E-mail: ege@cab.inta-csic.es, E-mail: rrl@iac.es, E-mail: caballero@cab.inta-csic.es, E-mail: barrado@cab.inta-csic.es, E-mail: mundt@mpia.de, E-mail: calj@mpia.de [Max-Planck-Institut fuer Astronomie, Koenigstuhl 17, D-69117 Heidelberg (Germany)

    2011-12-10

    We present a deep I, Z photometric survey covering a total area of 1.12 deg{sup 2} of the {sigma} Orionis cluster and reaching completeness magnitudes of I = 22 and Z = 21.5 mag. From I, I - Z color-magnitude diagrams we have selected 153 candidates that fit the previously known sequence of the cluster. They have magnitudes in the range I = 16-23 mag, which corresponds to a mass interval from 0.1 down to 0.008 M{sub Sun} at the most probable age of {sigma} Orionis (2-4 Myr). Using J-band photometry, we find that 124 of the 151 candidates within the completeness of the optical survey (82%) follow the previously known infrared photometric sequence of the cluster and are probably members. We have studied the spatial distribution of the very low mass stars and brown dwarf population of the cluster and found that there are objects located at distances greater than 30 arcmin to the north and west of {sigma} Orionis that probably belong to different populations of the Orion's Belt. For the 102 bona fide {sigma} Orionis cluster member candidates, we find that the radial surface density can be represented by a decreasing exponential function ({sigma}={sigma}{sub 0}e{sup -r/r{sub 0}}) with a central density of {sigma}{sub 0} = 0.23 {+-} 0.03 objects arcmin{sup -2} and a characteristic radius of r{sub 0} = 9.5 {+-} 0.7 arcmin. From a statistical comparison with Monte Carlo simulations, we conclude that the spatial distribution of the objects located at the same distance from the center of the cluster is compatible with a Poissonian distribution and, hence, that very low mass stars and brown dwarfs are not mainly forming aggregations or sub-clustering. Using near-infrared JHK-band data from Two Micron All Sky Survey and UKIRT Deep Infrared Sky Survey and mid-infrared data from Infrared Array Camera/Spitzer, we find that about 5%-9% of the brown dwarf candidates in the {sigma} Orionis cluster have K-band excesses and 30% {+-} 7% of them show mid-infrared excesses at

  10. 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

    -wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass...... these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role...... in protecting plant breeders’ rights....

  11. Thorium, uranium and plutonium in human tissues of world-wide general population

    International Nuclear Information System (INIS)

    Singh, N.P.

    1990-01-01

    The results on the concentrations of thorium, uranium and plutonium in human tissues of world-wide general populations are summarized. The majority of thorium and uranium are accumulated in the skeleton, whereas, plutonium is divided between two major organs: the liver and skeleton. However, there is a wide variation in the fractions of plutonium in the liver and the skeleton of the different populations. (author) 44 refs.; 15 figs

  12. 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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

    Directory of Open Access Journals (Sweden)

    Karima Fadhlaoui-Zid

    Full Text Available The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

  16. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

    Science.gov (United States)

    Fadhlaoui-Zid, Karima; Haber, Marc; Martínez-Cruz, Begoña; Zalloua, Pierre; Benammar Elgaaied, Amel; Comas, David

    2013-01-01

    The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

  17. Weqaya: A Population-Wide Cardiovascular Screening Program in Abu Dhabi, United Arab Emirates

    Science.gov (United States)

    Harrison, Oliver; Al Siksek, Zaid

    2012-01-01

    Objectives. We sought to determine cardiovascular risk factor prevalence rates among adults in Abu Dhabi, United Arab Emirates. Methods. We used self-reported indicators, anthropometric measures, and blood tests to screen 50 138 adults aged 18 years or older taking part in a population-wide cardiovascular screening program. Results. Participants’ mean age was 36.82 years (SD = 14.3); 43% were men. Risk factor prevalence rates were as follows: obesity, 35%; overweight, 32%; central obesity, 55%; diabetes, 18%; prediabetes, 27%; dyslipidemia, 44%; and hypertension, 23.1%. In addition, 26% of men were smokers, compared with 0.8% of women. Age-standardized diabetes and prediabetes rates were 25% and 30%, respectively, and age-standardized rates of obesity and overweight were 41% and 34%. Conclusions. This population-wide cardiovascular screening program demonstrated a high cardiovascular burden for our small sample in Abu Dhabi. The data form a baseline against which interventions can be implemented and progress monitored as part of the population-wide Abu Dhabi Cardiovascular Disease Program. PMID:21940918

  18. Making the Paradigm Shift from Siloed Population Health Management to an Enterprise-Wide Approach.

    Science.gov (United States)

    Matthews, Marc R; Miller, Claudia; Stroebel, Robert J; Bunkers, Kari S

    2017-08-01

    Health systems across the United States have started their journeys toward population health management and the future of accountable care. Models of population health management include patient-centered medical homes and private sector accountable care organizations (ACOs). Other models include public sector efforts, such as Physician Group Practice Transition Demonstrations, Medicare Health Care Quality Demonstration Programs, Beacon Communities, Medicare Shared Savings Program, and Pioneer ACOs. As a result, health care organizations often have pockets of population health initiatives that lack an enterprise-wide strategy. The next steps are to build on these efforts, leverage the learnings from these experiences, and incorporate the initiatives into an overarching framework and a road map for the future. This paper describes the current challenge many organizations face to implement an enterprise solution, describes how to transition from existing siloed initiatives, and shares a case study of how Mayo Clinic launched its Mayo Model of Community Care.

  19. 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.

  20. Genome-wide association study of susceptibility loci for breast cancer in Sardinian population.

    Science.gov (United States)

    Palomba, Grazia; Loi, Angela; Porcu, Eleonora; Cossu, Antonio; Zara, Ilenia; Budroni, Mario; Dei, Mariano; Lai, Sandra; Mulas, Antonella; Olmeo, Nina; Ionta, Maria Teresa; Atzori, Francesco; Cuccuru, Gianmauro; Pitzalis, Maristella; Zoledziewska, Magdalena; Olla, Nazario; Lovicu, Mario; Pisano, Marina; Abecasis, Gonçalo R; Uda, Manuela; Tanda, Francesco; Michailidou, Kyriaki; Easton, Douglas F; Chanock, Stephen J; Hoover, Robert N; Hunter, David J; Schlessinger, David; Sanna, Serena; Crisponi, Laura; Palmieri, Giuseppe

    2015-05-10

    Despite progress in identifying genes associated with breast cancer, many more risk loci exist. Genome-wide association analyses in genetically-homogeneous populations, such as that of Sardinia (Italy), could represent an additional approach to detect low penetrance alleles. We performed a genome-wide association study comparing 1431 Sardinian patients with non-familial, BRCA1/2-mutation-negative breast cancer to 2171 healthy Sardinian blood donors. DNA was genotyped using GeneChip Human Mapping 500 K Arrays or Genome-Wide Human SNP Arrays 6.0. To increase genomic coverage, genotypes of additional SNPs were imputed using data from HapMap Phase II. After quality control filtering of genotype data, 1367 cases (9 men) and 1658 controls (1156 men) were analyzed on a total of 2,067,645 SNPs. Overall, 33 genomic regions (67 candidate SNPs) were associated with breast cancer risk at the p <  0(-6) level. Twenty of these regions contained defined genes, including one already associated with breast cancer risk: TOX3. With a lower threshold for preliminary significance to p < 10(-5), we identified 11 additional SNPs in FGFR2, a well-established breast cancer-associated gene. Ten candidate SNPs were selected, excluding those already associated with breast cancer, for technical validation as well as replication in 1668 samples from the same population. Only SNP rs345299, located in intron 1 of VAV3, remained suggestively associated (p-value, 1.16 x 10(-5)), but it did not associate with breast cancer risk in pooled data from two large, mixed-population cohorts. This study indicated the role of TOX3 and FGFR2 as breast cancer susceptibility genes in BRCA1/2-wild-type breast cancer patients from Sardinian population.

  1. Genome-wide association study of susceptibility loci for breast cancer in Sardinian population

    International Nuclear Information System (INIS)

    Palomba, Grazia; Loi, Angela; Porcu, Eleonora; Cossu, Antonio; Zara, Ilenia

    2015-01-01

    Despite progress in identifying genes associated with breast cancer, many more risk loci exist. Genome-wide association analyses in genetically-homogeneous populations, such as that of Sardinia (Italy), could represent an additional approach to detect low penetrance alleles. We performed a genome-wide association study comparing 1431 Sardinian patients with non-familial, BRCA1/2-mutation-negative breast cancer to 2171 healthy Sardinian blood donors. DNA was genotyped using GeneChip Human Mapping 500 K Arrays or Genome-Wide Human SNP Arrays 6.0. To increase genomic coverage, genotypes of additional SNPs were imputed using data from HapMap Phase II. After quality control filtering of genotype data, 1367 cases (9 men) and 1658 controls (1156 men) were analyzed on a total of 2,067,645 SNPs. Overall, 33 genomic regions (67 candidate SNPs) were associated with breast cancer risk at the p < 10 −6 level. Twenty of these regions contained defined genes, including one already associated with breast cancer risk: TOX3. With a lower threshold for preliminary significance to p < 10 −5 , we identified 11 additional SNPs in FGFR2, a well-established breast cancer-associated gene. Ten candidate SNPs were selected, excluding those already associated with breast cancer, for technical validation as well as replication in 1668 samples from the same population. Only SNP rs345299, located in intron 1 of VAV3, remained suggestively associated (p-value, 1.16x10 −5 ), but it did not associate with breast cancer risk in pooled data from two large, mixed-population cohorts. This study indicated the role of TOX3 and FGFR2 as breast cancer susceptibility genes in BRCA1/2-wild-type breast cancer patients from Sardinian population. The online version of this article (doi:10.1186/s12885-015-1392-9) contains supplementary material, which is available to authorized users

  2. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  3. Considerations for a Human Rights Impact Assessment of a Population Wide Treatment for HIV Prevention Intervention.

    Science.gov (United States)

    Hanefeld, Johanna; Bond, Virginia; Seeley, Janet; Lees, Shelley; Desmond, Nicola

    2015-12-01

    Increasing attention is being paid to the potential of anti-retroviral treatment (ART) for HIV prevention. The possibility of eliminating HIV from a population through a universal test and treat intervention, where all people within a population are tested for HIV and all positive people immediately initiated on ART, as part of a wider prevention intervention, was first proposed in 2009. Several clinical trials testing this idea are now in inception phase. An intervention which relies on universally testing the entire population for HIV will pose challenges to human rights, including obtaining genuine consent to testing and treatment. It also requires a context in which people can live free from fear of stigma, discrimination and violence, and can access services they require. These challenges are distinct from the field of medical ethics which has traditionally governed clinical trials and focuses primarily on patient researcher relationship. This paper sets out the potential impact of a population wide treatment as prevention intervention on human rights. It identifies five human right principles of particular relevance: participation, accountability, the right to health, non-discrimination and equality, and consent and confidentiality. The paper proposes that explicit attention to human rights can strengthen a treatment as prevention intervention, contribute to mediating likely health systems challenges and offer insights on how to reach all sections of the population. © 2013 John Wiley & Sons Ltd.

  4. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    Science.gov (United States)

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier

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

    NARCIS (Netherlands)

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

    2017-01-01

    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 (FST) in multi-ethnic (admixed) populations; (ii) evaluate the statistical power and effect size estimates;

  6. Determinants of Generic vs. Brand Drug Choice: Evidence from Population-wide Danish Data

    DEFF Research Database (Denmark)

    Skipper, Niels; Vejlin, Rune Majlund

    driven. We use population-wide Danish register data including all prescriptions for seven blockbuster drugs from 1998-2008. At the outset, descriptive statistics suggest large variation in drug choice over doctors. Nonetheless, using a two-way fixed effects model we find that the primary determinants...... 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. Reducing the age range of tsunami deposits by 14C dating of rip-up clasts

    Science.gov (United States)

    Ishizawa, Takashi; Goto, Kazuhisa; Yokoyama, Yusuke; Miyairi, Yosuke; Sawada, Chikako; Takada, Keita

    2018-02-01

    Erosion by tsunami waves represents an important issue when determining the age of a tsunami deposit, because the age is usually estimated using dating of sediments above and below the deposit. Dating of material within the tsunami deposit, if suitable material is obtainable, can be used to further constrain its age. Eroded sediments are sometimes incorporated within the tsunami deposits as rip-up clasts, which might therefore be used as minimum age dating material. However, the single calibrated 14C age often shows a wide age range because of fluctuations in the calibration curve. Therefore, it remains uncertain whether rip-up clast measurements are useful to constrain the depositional age of tsunami deposits, or not. In this study, we carried out high-resolution 14C dating of tsunami deposits, including rip-up clasts of peat, in Rikuzentakata, northeastern Japan, where numerous rip-up clasts were observed within a tsunami deposit. Sediments above and below the tsunami deposit and a 5 cm large rip-up clast were dated sequentially. Comparison of these dating results with the calibration curve revealed that the clast was inverted. Its age was better constrained based on the stratigraphic order, and we infer that the clast corresponds to approximately 100 years of sedimentation. The oldest age of the clast was consistent with the age of the peat immediately below the tsunami deposit, suggesting that surface sediments probably formed the rip-up clast at the time of the tsunami. Thus, the dating of the rip-up clast was useful to further constrain the depositional age of the tsunami deposit, as we narrowed the tsunami deposit age range by approximately 100 years. Results show that ignoring tsunami-related erosion might lead to overestimation of the tsunami deposit age. For this reason, an appropriate dating site, which is less affected by minor tsunami-related erosion with regards to the paleo-topography, should be explored. We therefore propose a more effective

  8. Preliminary genome-wide association study of bipolar disorder in the Japanese population.

    Science.gov (United States)

    Hattori, Eiji; Toyota, Tomoko; Ishitsuka, Yuichi; Iwayama, Yoshimi; Yamada, Kazuo; Ujike, Hiroshi; Morita, Yukitaka; Kodama, Masafumi; Nakata, Kenji; Minabe, Yoshio; Nakamura, Kazuhiko; Iwata, Yasuhide; Takei, Nori; Mori, Norio; Naitoh, Hiroshi; Yamanouchi, Yoshio; Iwata, Nakao; Ozaki, Norio; Kato, Tadafumi; Nishikawa, Toru; Kashiwa, Atsushi; Suzuki, Mika; Shioe, Kunihiko; Shinohara, Manabu; Hirano, Masami; Nanko, Shinichiro; Akahane, Akihisa; Ueno, Mikako; Kaneko, Naoshi; Watanabe, Yuichiro; Someya, Toshiyuki; Hashimoto, Kenji; Iyo, Masaomi; Itokawa, Masanari; Arai, Makoto; Nankai, Masahiro; Inada, Toshiya; Yoshida, Sumiko; Kunugi, Hiroshi; Nakamura, Michiko; Iijima, Yoshimi; Okazaki, Yuji; Higuchi, Teruhiko; Yoshikawa, Takeo

    2009-12-05

    Recent progress in genotyping technology and the development of public databases has enabled large-scale genome-wide association tests with diseases. We performed a two-stage genome-wide association study (GWAS) of bipolar disorder (BD) in Japanese cohorts. First we used Affymetrix 100K GeneChip arrays in the analysis of 107 cases with bipolar I disorder and 107 controls, and selected markers that were nominally significant (P < 0.01) in at least one of the three models (1,577 markers in total). In the follow-up stage, we analyzed these markers using an Illumina platform (1,526 markers; 51 markers were not designable for the platform) and an independent sample set, which consisted of 395 cases (bipolar I + II) and 409 controls. We also assessed the population stratification of current samples using principal components analysis. After the two-stage analysis, 89 markers remained nominally significant (allelic P < 0.05) with the same allele being consistently over-represented in both the first and the follow-up stages. However, none of these were significant after correction for multiple-testing by false discovery rates. Sample stratification was virtually negligible. Collectively, this is the first GWAS of BD in the Japanese population. But given the small sample size and the limited genomic coverage, these results should be taken as preliminary. 2009 Wiley-Liss, Inc.

  9. Decoherence in yeast cell populations and its implications for genome-wide expression noise.

    Science.gov (United States)

    Briones, M R S; Bosco, F

    2009-01-20

    Gene expression "noise" is commonly defined as the stochastic variation of gene expression levels in different cells of the same population under identical growth conditions. Here, we tested whether this "noise" is amplified with time, as a consequence of decoherence in global gene expression profiles (genome-wide microarrays) of synchronized cells. The stochastic component of transcription causes fluctuations that tend to be amplified as time progresses, leading to a decay of correlations of expression profiles, in perfect analogy with elementary relaxation processes. Measuring decoherence, defined here as a decay in the auto-correlation function of yeast genome-wide expression profiles, we found a slowdown in the decay of correlations, opposite to what would be expected if, as in mixing systems, correlations decay exponentially as the equilibrium state is reached. Our results indicate that the populational variation in gene expression (noise) is a consequence of temporal decoherence, in which the slow decay of correlations is a signature of strong interdependence of the transcription dynamics of different genes.

  10. Population-wide distributions of neural activity during perceptual decision-making

    Science.gov (United States)

    Machens, Christian

    2018-01-01

    Cortical activity involves large populations of neurons, even when it is limited to functionally coherent areas. Electrophysiological recordings, on the other hand, involve comparatively small neural ensembles, even when modern-day techniques are used. Here we review results which have started to fill the gap between these two scales of inquiry, by shedding light on the statistical distributions of activity in large populations of cells. We put our main focus on data recorded in awake animals that perform simple decision-making tasks and consider statistical distributions of activity throughout cortex, across sensory, associative, and motor areas. We transversally review the complexity of these distributions, from distributions of firing rates and metrics of spike-train structure, through distributions of tuning to stimuli or actions and of choice signals, and finally the dynamical evolution of neural population activity and the distributions of (pairwise) neural interactions. This approach reveals shared patterns of statistical organization across cortex, including: (i) long-tailed distributions of activity, where quasi-silence seems to be the rule for a majority of neurons; that are barely distinguishable between spontaneous and active states; (ii) distributions of tuning parameters for sensory (and motor) variables, which show an extensive extrapolation and fragmentation of their representations in the periphery; and (iii) population-wide dynamics that reveal rotations of internal representations over time, whose traces can be found both in stimulus-driven and internally generated activity. We discuss how these insights are leading us away from the notion of discrete classes of cells, and are acting as powerful constraints on theories and models of cortical organization and population coding. PMID:23123501

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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.

  13. Population-Wide Impact of Non-Hip Non-Vertebral Fractures on Mortality.

    Science.gov (United States)

    Tran, Thach; Bliuc, Dana; van Geel, Tineke; Adachi, Jonathan D; Berger, Claudie; van den Bergh, Joop; Eisman, John A; Geusens, Piet; Goltzman, David; Hanley, David A; Josse, Robert G; Kaiser, Stephanie M; Kovacs, Christopher S; Langsetmo, Lisa; Prior, Jerilynn C; Nguyen, Tuan V; Center, Jacqueline R

    2017-09-01

    Data on long-term consequences of non-hip non-vertebral (NHNV) fractures, accounting for approximately two-thirds of all fragility fractures, are scanty. Our study aimed to quantify the population-wide impact of NHNV fractures on mortality. The national population-based prospective cohort study (Canadian Multicentre Osteoporosis Study) included 5526 community dwelling women and 2163 men aged 50 years or older followed from July 1995 to September 2013. Population impact number was used to quantify the average number of people for whom one death would be attributable to fracture and case impact number to quantify the number of deaths out of which one would be attributable to a fracture. There were 1370 fragility fractures followed by 296 deaths in women (mortality rate: 3.49; 95% CI, 3.11 to 3.91), and 302 fractures with 92 deaths in men (5.05; 95% CI, 4.12 to 6.20). NHNV fractures accounted for three-quarters of fractures. In women, the population-wide impact of NHNV fractures on mortality was greater than that of hip and vertebral fractures because of the greater number of NHNV fractures. Out of 800 women, one death was estimated to be attributable to a NHNV fracture, compared with one death in 2000 women attributable to hip or vertebral fracture. Similarly, out of 15 deaths in women, one was estimated to be attributable to a NHNV fracture, compared with one in over 40 deaths for hip or vertebral fracture. The impact of forearm fractures (ie, one death in 2400 women and one out of 42 deaths in women attributable to forearm fracture) was similar to that of hip, vertebral, or rib fractures. Similar, albeit not significant, results were noted for men. The study highlights the important contribution of NHNV fractures on mortality because many NHNV fracture types, except for the most distal fractures, have serious adverse consequences that affect a significant proportion of the population. © 2017 American Society for Bone and Mineral Research. © 2017 American Society

  14. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Kangmei Chen

    Full Text Available BACKGROUND: Genome-wide association studies (GWAS have identified three loci (rs17401966 in KIF1B, rs7574865 in STAT4, rs9275319 in HLA-DQ as being associated with hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC in a Chinese population, two loci (rs2596542 in MICA, rs9275572 located between HLA-DQA and HLA-DQB with hepatitis C virus-related HCC (HCV-related HCC in a Japanese population. In the present study, we sought to determine whether these SNPs are predictive for HBV-related HCC development in other Chinese population as well. METHOD AND FINDINGS: We genotyped 4 SNPs, rs2596542, rs9275572, rs17401966, rs7574865, in 506 HBV-related HCC patients and 772 chronic hepatitis B (CHB patients in Han Chinese by TaqMan methods. Odds ratio(ORand 95% confidence interval (CI were calculated by logistic regression. In our case-control study, significant association between rs9275572 and HCC were observed (P = 0.02, OR = 0.73, 95% CI = 0.56-0.95. In the further haplotype analysis between rs2596542 at 6p21.33 and rs9275572 at 6p21.3, G-A showed a protective effect on HBV-related HCC occurrence (P<0.001, OR = 0.66, 95% CI = 0.52-0.84. CONCLUSION: These findings provided convincing evidence that rs9275572 significantly associated with HBV-related HCC.

  15. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci in a Chinese population.

    Science.gov (United States)

    Chen, Kangmei; Shi, Weimei; Xin, Zhenhui; Wang, Huifen; Zhu, Xilin; Wu, Xiaopan; Li, Zhuo; Li, Hui; Liu, Ying

    2013-01-01

    Genome-wide association studies (GWAS) have identified three loci (rs17401966 in KIF1B, rs7574865 in STAT4, rs9275319 in HLA-DQ) as being associated with hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC) in a Chinese population, two loci (rs2596542 in MICA, rs9275572 located between HLA-DQA and HLA-DQB) with hepatitis C virus-related HCC (HCV-related HCC) in a Japanese population. In the present study, we sought to determine whether these SNPs are predictive for HBV-related HCC development in other Chinese population as well. We genotyped 4 SNPs, rs2596542, rs9275572, rs17401966, rs7574865, in 506 HBV-related HCC patients and 772 chronic hepatitis B (CHB) patients in Han Chinese by TaqMan methods. Odds ratio(OR)and 95% confidence interval (CI) were calculated by logistic regression. In our case-control study, significant association between rs9275572 and HCC were observed (P = 0.02, OR = 0.73, 95% CI = 0.56-0.95). In the further haplotype analysis between rs2596542 at 6p21.33 and rs9275572 at 6p21.3, G-A showed a protective effect on HBV-related HCC occurrence (P<0.001, OR = 0.66, 95% CI = 0.52-0.84). These findings provided convincing evidence that rs9275572 significantly associated with HBV-related HCC.

  16. 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.

  17. Assessing genome-wide copy number variation in the Han Chinese population.

    Science.gov (United States)

    Lu, Jianqi; Lou, Haiyi; Fu, Ruiqing; Lu, Dongsheng; Zhang, Feng; Wu, Zhendong; Zhang, Xi; Li, Changhua; Fang, Baijun; Pu, Fangfang; Wei, Jingning; Wei, Qian; Zhang, Chao; Wang, Xiaoji; Lu, Yan; Yan, Shi; Yang, Yajun; Jin, Li; Xu, Shuhua

    2017-10-01

    Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. To build a representative CNV map for the Han Chinese population. We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data. We detected CNVs by using 4.2M NimbleGen comparative genomic hybridisation array and whole-genome deep sequencing of 51 samples to optimise the filtering conditions in CNV discovery. A comprehensive Han Chinese CNV map was built based on a set of high-quality variants (positive predictive value >0.8, with sizes ranging from 369 bp to 4.16 Mb and a median of 5907 bp). The map consists of 4012 CNV regions (CNVRs), and more than half are novel to the 30 East Asian CNV Project and the 1000 Genomes Project Phase 3. We further identified 81 CNVRs specific to regional groups, which was indicative of the subpopulation structure within the Han Chinese population. Our data are complementary to public data sources, and the CNV map may facilitate in the identification of pathogenic CNVs and further biomedical research studies involving the Han Chinese population. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. 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

  19. A Population Study of Wide-Separation Brown Dwarf Companions to Main Sequence Stars

    Science.gov (United States)

    Smith, Jeffrey J.

    2005-01-01

    Increased interest in infrared astronomy has opened the frontier to study cooler objects that shed significant light on the formation of planetary systems. Brown dwarf research provides a wealth of information useful for sorting through a myriad of proposed formation theories. Our study combines observational data from 2MASS with rigorous computer simulations to estimate the true population of long-range (greater than 1000 AU) brown dwarf companions in the solar neighborhood (less than 25 pc from Earth). Expanding on Gizis et al. (2001), we have found the margin of error in previous estimates to be significantly underestimated after we included orbit eccentricity, longitude of pericenter, angle of inclination, field star density, and primary and secondary luminosities as parameters influencing the companion systems in observational studies. We apply our simulation results to current L- and T-dwarf catalogs to provide updated estimates on the frequency of wide-separation brown dwarf companions to main sequence stars.

  20. Genome-Wide Association Study for Autism Spectrum Disorder in Taiwanese Han Population.

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    Po-Hsiu Kuo

    Full Text Available Autism spectrum disorder (ASD is a neurodevelopmental disorder with strong genetic components. Several recent genome-wide association (GWA studies in Caucasian samples have reported a number of gene regions and loci correlated with the risk of ASD--albeit with very little consensus across studies.A two-stage GWA study was employed to identify common genetic variants for ASD in the Taiwanese Han population. The discovery stage included 315 patients with ASD and 1,115 healthy controls, using the Affymetrix SNP array 6.0 platform for genotyping. Several gene regions were then selected for fine-mapping and top markers were examined in extended samples. Single marker, haplotype, gene-based, and pathway analyses were conducted for associations.Seven SNPs had p-values ranging from 3.4~9.9*10-6, but none reached the genome-wide significant level. Five of them were mapped to three known genes (OR2M4, STYK1, and MNT with significant empirical gene-based p-values in OR2M4 (p = 3.4*10(-5 and MNT (p = 0.0008. Results of the fine-mapping study showed single-marker associations in the GLIS1 (rs12082358 and rs12080993 and NAALADL2 (rs3914502 and rs2222447 genes, and gene-based associations for the OR2M3-OR2T5 (olfactory receptor genes, p = 0.02, and GLIPR1/KRR1 gene regions (p = 0.015. Pathway analyses revealed important pathways for ASD, such as olfactory and G protein-coupled receptors signaling pathways.We reported Taiwanese Han specific susceptibility genes and variants for ASD. However, further replication in other Asian populations is warranted to validate our findings. Investigation in the biological functions of our reported genetic variants might also allow for better understanding on the underlying pathogenesis of autism.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. Genome-wide population-based association study of extremely overweight young adults--the GOYA study

    DEFF Research Database (Denmark)

    Paternoster, Lavinia; Evans, David M; Nohr, Ellen Aagaard

    2011-01-01

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

  4. Population-Wide Genetic Risk Prediction of Complex Diseases: A Pilot Feasibility Study in Macau Population for Precision Public Healthcare Planning

    OpenAIRE

    Tsui, Nancy B. Y.; Cheng, Gregory; Chung, Teresa; Lam, Christopher W. K.; Yee, Anita; Chung, Peter K. C.; Kwan, Tsz-Ki; Ko, Elaine; He, Daihai; Wong, Wing-Tak; Lau, Johnson Y. N.; Lau, Lok Ting; Fok, Manson

    2018-01-01

    The genetic bases of many common diseases have been identified through genome-wide association studies in the past decade. However, the application of this approach on public healthcare planning has not been well established. Using Macau with population of around 650,000 as a basis, we conducted a pilot study to evaluate the feasibility of population genomic research and its potential on public health decisions. By performing genome-wide SNP genotyping of over a thousand Macau individuals, we...

  5. 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

  6. Community-wide intervention and population-level physical activity: a 5-year cluster randomized trial

    Science.gov (United States)

    Kamada, Masamitsu; Kitayuguchi, Jun; Abe, Takafumi; Taguri, Masataka; Inoue, Shigeru; Ishikawa, Yoshiki; Bauman, Adrian; Lee, I-Min; Miyachi, Motohiko; Kawachi, Ichiro

    2018-01-01

    Abstract Background Evidence from a limited number of short-term trials indicates the difficulty in achieving population-level improvements in physical activity (PA) through community-wide interventions (CWIs). We sought to evaluate the effectiveness of a 5-year CWI for promoting PA in middle-aged and older adults using a cluster randomized design. Methods We randomized 12 communities in Unnan, Japan, to either intervention (9) or control (3). Additionally, intervention communities were randomly allocated to three subgroups by different PA types promoted. Randomly sampled residents aged 40–79 years responded to the baseline survey (n = 4414; 74%) and were followed at 1, 3 and 5 years (78–83% response rate). The intervention was a 5-year CWI using social marketing to promote PA. The primary outcome was a change in recommended levels of PA. Results Compared with control communities, adults achieving recommended levels of PA increased in intervention communities [adjusted change difference = 4.6 percentage points (95% confidence interval: 0.4, 8.8)]. The intervention was effective for promoting all types of recommended PAs, i.e. aerobic (walking, 6.4%), flexibility (6.1%) and muscle-strengthening activities (5.7%). However, a bundled approach, which attempted to promote all forms of PAs above simultaneously, was not effective (1.3–3.4%, P ≥ 0.138). Linear dose–response relationships between the CWI awareness and changes in PA were observed (P ≤ 0.02). Pain intensity decreased in shoulder (intervention and control) and lower back (intervention only) but there was little change difference in all musculoskeletal pain outcomes between the groups. Conclusions The 5-year CWI using the focused social marketing strategy increased the population-level of PA. PMID:29228255

  7. Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population

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    Alencar Xavier

    2018-02-01

    Full Text Available Genetic improvement toward optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs. In this study, the genetic basis of soybean grain yield responsiveness to environmental factors was examined in a large soybean nested association population. For this, a genome-wide association to performance stability estimates generated from a Finlay-Wilkinson analysis and the inclusion of the interaction between marker genotypes and environmental factors was implemented. Genomic footprints were investigated by analysis and meta-analysis using a recently published multiparent model. Results indicated that specific soybean genomic regions were associated with stability, and that multiplicative interactions were present between environments and genetic background. Seven genomic regions in six chromosomes were identified as being associated with genotype-by-environment interactions. This study provides insight into genomic assisted breeding aimed at achieving a more stable agronomic performance of soybean, and documented opportunities to exploit genomic regions that were specifically associated with interactions involving environments and subpopulations.

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

    Directory of Open Access Journals (Sweden)

    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.

  9. 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

  10. Genome-Wide Association Study of Psychosis Proneness in the Finnish Population.

    Science.gov (United States)

    Ortega-Alonso, Alfredo; Ekelund, Jesper; Sarin, Antti-Pekka; Miettunen, Jouko; Veijola, Juha; Järvelin, Marjo-Riitta; Hennah, William

    2017-10-21

    The current study examined quantitative measures of psychosis proneness in a nonpsychotic population, in order to elucidate their underlying genetic architecture and to observe if there is any commonality to that already detected in the studies of individuals with overt psychotic conditions, such as schizophrenia and bipolar disorder. Heritability, univariate and multivariate genome-wide association (GWAs) tests, including a series of comprehensive gene-based association analyses, were developed in 4269 nonpsychotic persons participating in the Northern Finland Birth Cohort 1966 study with information on the following psychometric measures: Hypomanic Personality, Perceptual Aberration, Physical and Social Anhedonia (also known as Chapman's Schizotypia scales), and Schizoidia scale. Genome-wide genetic data was available for ~9.84 million SNPs. Heritability estimates ranged from 16% to 27%. Phenotypic, genetic and environmental correlations ranged from 0.04-0.43, 0.25-0.73, and 0.12-0.43, respectively. Univariate GWAs tests revealed an intronic SNP (rs12449097) at the TMC7 gene (16p12.3) that significantly associated (P = 3.485 × 10-8) with the hypomanic scale. Bivariate GWAs tests including the hypomanic and physical anhedonia scales suggested a further borderline significant SNP (rs188320715; P-value = 5.261 × 10-8, ~572 kb downstream the ARID1B gene at 6q25.3). Gene-based tests highlighted 20 additional genes of which 5 had previously been associated to schizophrenia and/or bipolar disorder: CSMD1, CCDC141, SLC1A2, CACNA1C, and SNAP25. Altogether the findings explained from 3.7% to 14.1% of the corresponding trait heritability. In conclusion, this study provides preliminary genomic evidence suggesting that qualitatively similar biological factors may underlie different psychosis proneness measures, some of which could further predispose to schizophrenia and bipolar disorder. © The Author 2017. Published by Oxford University Press on behalf of the Maryland

  11. Genome-wide association study with the risk of schizophrenia in a Korean population.

    Science.gov (United States)

    Kim, Lyoung Hyo; Park, Byung Lae; Cheong, Hyun Sub; Namgoong, Suhg; Kim, Ji On; Kim, Jeong-Hyun; Shin, Joong-Gon; Park, Chul Soo; Kim, Bong-Jo; Kim, Jae Won; Choi, Ihn-Geun; Hwang, Jaeuk; Shin, Hyoung Doo; Woo, Sung-Il

    2016-03-01

    Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies. © 2015 Wiley Periodicals, Inc.

  12. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    Science.gov (United States)

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytica...

  13. 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

    2017-01-01

    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. PMID:28589034

  14. 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

  15. 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

  16. 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

    The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic...... 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...... in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin...

  17. 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.

  18. 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 ...

  19. 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

  20. 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.

  1. 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.

  2. 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

    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...... 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...

  3. 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

    .Results: The Illumina BovineSNP50 BeadChip was used to identify single nucleotide polymorphisms (SNPs) that are associated with body conformation traits. A least absolute shrinkage and selection operator (LASSO) was applied to detect multiple SNPs simultaneously for 29 body conformation traits with 1,314 Chinese...... Holstein cattle and 52,166 SNPs. Totally, 59 genome-wide significant SNPs associated with 26 conformation traits were detected by genome-wide association analysis; five SNPs were within previously reported QTL regions (Animal Quantitative Trait Loci (QTL) database) and 11 were very close to the reported...... SNPs. Twenty-two SNPs were located within annotated gene regions, while the remainder were 0.6-826 kb away from known genes. Some of the genes had clear biological functions related to conformation traits. By combining information about the previously reported QTL regions and the biological functions...

  4. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

    NARCIS (Netherlands)

    Onzima, R.B.; Upadhyay, M.R.; Mukiibi, R.; Kanis, E.; Groenen, M.A.M.; Crooijmans, R.P.M.A.

    2018-01-01

    Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential

  5. Genome-wide detection and characterization of positive selection in human populations.

    Science.gov (United States)

    Sabeti, Pardis C; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H; McCarroll, Steven A; Gaudet, Rachelle; Schaffner, Stephen F; Lander, Eric S; Frazer, Kelly A; Ballinger, Dennis G; Cox, David R; Hinds, David A; Stuve, Laura L; Gibbs, Richard A; Belmont, John W; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M; Pasternak, Shiran; Wheeler, David A; Willis, Thomas D; Yu, Fuli; Yang, Huanming; Zeng, Changqing; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhao, Hui; Zhou, Jun; Gabriel, Stacey B; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Onofrio, Robert C; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Ziaugra, Liuda; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M Y; Tsui, Stephen K W; Xue, Hong; Wong, J Tze-Fei; Galver, Luana M; Fan, Jian-Bing; Gunderson, Kevin; Murray, Sarah S; Oliphant, Arnold R; Chee, Mark S; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean-François; Phillips, Michael S; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J; Kwok, Pui-Yan; Cai, Dongmei; Koboldt, Daniel C; Miller, Raymond D; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap-Chee; Mak, William; Song, You Qiang; Tam, Paul K H; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, Tatsuhiko; Deloukas, Panos; Bird, Christine P; Delgado, Marcos; Dermitzakis, Emmanouil T; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara E; Whittaker, Pamela; Bentley, David R; Daly, Mark J; de Bakker, Paul I W; Barrett, Jeff; Chretien, Yves R; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Price, Alkes; Purcell, Shaun; Richter, Daniel J; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F; Sham, Pak C; Varilly, Patrick; Altshuler, David; Stein, Lincoln D; Krishnan, Lalitha; Smith, Albert Vernon; Tello-Ruiz, Marcela K; Thorisson, Gudmundur A; Chakravarti, Aravinda; Chen, Peter E; Cutler, David J; Kashuk, Carl S; Lin, Shin; Abecasis, Gonçalo R; Guan, Weihua; Li, Yun; Munro, Heather M; Qin, Zhaohui Steve; Thomas, Daryl J; McVean, Gilean; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R; Clarke, Geraldine; Evans, David M; Morris, Andrew P; Weir, Bruce S; Tsunoda, Tatsuhiko; Johnson, Todd A; Mullikin, James C; Sherry, Stephen T; Feolo, Michael; Skol, Andrew; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R; Suda, Eiko; Rotimi, Charles N; Adebamowo, Clement A; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A; Nkwodimmah, Chibuzor; Royal, Charmaine D M; Leppert, Mark F; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F; Knoppers, Bartha M; Foster, Morris W; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A; Belmont, John W; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M; Wheeler, David A; Yakub, Imtaz; Gabriel, Stacey B; Onofrio, Robert C; Richter, Daniel J; Ziaugra, Liuda; Birren, Bruce W; Daly, Mark J; Altshuler, David; Wilson, Richard K; Fulton, Lucinda L; Rogers, Jane; Burton, John; Carter, Nigel P; Clee, Christopher M; Griffiths, Mark; Jones, Matthew C; McLay, Kirsten; Plumb, Robert W; Ross, Mark T; Sims, Sarah K; Willey, David L; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L; Brooks, Lisa D; McEwen, Jean E; Guyer, Mark S; Wang, Vivian Ota; Peterson, Jane L; Shi, Michael; Spiegel, Jack; Sung, Lawrence M; Zacharia, Lynn F; Collins, Francis S; Kennedy, Karen; Jamieson, Ruth; Stewart, John

    2007-10-18

    With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

  6. Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

    Czech Academy of Sciences Publication Activity Database

    Safran, R. J.; Scordato, E. S. C.; Wilkins, M. R.; Hubbard, J. K.; Jenkins, B. R.; Albrecht, Tomáš; Flaxman, S. M.; Karaardic, H.; Vortman, Y.; Lotem, A.; Nosil, P.; Pap, P.; Shen, S.; Chan, S.-F.; Parchman, T. L.; Kane, N. C.

    2016-01-01

    Roč. 25, č. 16 (2016), s. 3865-3883 ISSN 0962-1083 R&D Projects: GA MŠk(CZ) LH14045 Institutional support: RVO:68081766 Keywords : climate variability * climate variability * genotyping by sequencing * population genetics * reproductive isolation * speciation Subject RIV: EG - Zoology Impact factor: 6.086, year: 2016

  7. Dense reconstruction of brain-wide neuronal population close to the ground truth

    OpenAIRE

    Li, Yun; Zhou, Hang; Li, Shiwei; Li, Jing; Su, Lei; Li, Anan; Feng, Xiong; Li, Ning; Han, Jiacheng; Kang, Hongtao; Chen, Yijun; Fang, Wenqian; Liu, Yidong; Lin, Huimin; Jin, Sen

    2017-01-01

    Neuron is the basic structure and functional unit of the brain, its projection and connections with other neurons provide a basic physical infrastructure for neural signal storage, allocation, processing, and integration. Recent technique progresses allow for labeling and imaging specific neuronal populations at single axonal level across a whole mouse brain. However, digital reconstruction of these neuron individuals needs months of human labor or sometimes is even an impossible task. Here w...

  8. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa

    OpenAIRE

    Fadhlaoui-Zid, Karima; Haber, Marc, 1980-; Martínez Cruz, Begoña; Zalloua, Pierre A; Elgaaied, Amel Benammar; Comas, David, 1969-

    2013-01-01

    The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete descr...

  9. 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 subsequent validation analyses (23,399 T2D cases and 31,722 controls) identify 7 new loci with genome-wide significance (P2, rs7107784 near MIR4686 and rs67839313 near INAFM2....... Of these, the association of 4 loci with T2D is replicated in multi-ethnic populations other than Japanese (up to 65,936 T2Ds and 158,030 controls, P

  10. 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.

  11. 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

  12. 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.

  13. Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant.

    Science.gov (United States)

    Rabeling, Christian; Gonzales, Omar; Schultz, Ted R; Bacci, Maurício; Garcia, Marcos V B; Verhaagh, Manfred; Ishak, Heather D; Mueller, Ulrich G

    2011-07-26

    Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species Mycocepurus smithii was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless, M. smithii is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that M. smithii actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in M. smithii. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that M. smithii is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that M. smithii evolved 0.5-1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.

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

    Science.gov (United States)

    de Oliveira, Thais C; Rodrigues, Priscila T; Menezes, Maria José; Gonçalves-Lopes, Raquel M; Bastos, Melissa S; Lima, Nathália F; Barbosa, Susana; Gerber, Alexandra L; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U

    2017-07-01

    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 diverse sites

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

    Science.gov (United States)

    de Oliveira, Thais C.; Rodrigues, Priscila T.; Menezes, Maria José; Gonçalves-Lopes, Raquel M.; Bastos, Melissa S.; Lima, Nathália F.; Barbosa, Susana; Gerber, Alexandra L.; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R.

    2017-01-01

    Background 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. Methods 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). Principal findings/Conclusions 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

  16. 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.

  17. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.

    Science.gov (United States)

    Jinam, Timothy; Nishida, Nao; Hirai, Momoki; Kawamura, Shoji; Oota, Hiroki; Umetsu, Kazuo; Kimura, Ryosuke; Ohashi, Jun; Tajima, Atsushi; Yamamoto, Toshimichi; Tanabe, Hideyuki; Mano, Shuhei; Suto, Yumiko; Kaname, Tadashi; Naritomi, Kenji; Yanagi, Kumiko; Niikawa, Norio; Omoto, Keiichi; Tokunaga, Katsushi; Saitou, Naruya

    2012-12-01

    The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

  18. 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.

  19. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

    Science.gov (United States)

    Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

    2018-02-01

    Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  20. Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selection.

    Science.gov (United States)

    Parejo, M; Wragg, D; Henriques, D; Vignal, A; Neuditschko, M

    2017-12-01

    Human-mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole-genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp., which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated-selection arising from different applied breeding practices in the two managed populations. © 2017 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  1. 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

  2. Spatial and temporal country-wide survey of temephos resistance in Brazilian populations of Aedes aegypti

    Directory of Open Access Journals (Sweden)

    Mateus Chediak

    2016-01-01

    Full Text Available The organophosphate temephos has been the main insecticide used against larvae of the dengue and yellow fever mosquito (Aedes aegypti in Brazil since the mid-1980s. Reports of resistance date back to 1995; however, no systematic reports of widespread temephos resistance have occurred to date. As resistance investigation is paramount for strategic decision-making by health officials, our objective here was to investigate the spatial and temporal spread of temephos resistance in Ae. aegypti in Brazil for the last 12 years using discriminating temephos concentrations and the bioassay protocols of the World Health Organization. The mortality results obtained were subjected to spatial analysis for distance interpolation using semi-variance models to generate maps that depict the spread of temephos resistance in Brazil since 1999. The problem has been expanding. Since 2002-2003, approximately half the country has exhibited mosquito populations resistant to temephos. The frequency of temephos resistance and, likely, control failures, which start when the insecticide mortality level drops below 80%, has increased even further since 2004. Few parts of Brazil are able to achieve the target 80% efficacy threshold by 2010/2011, resulting in a significant risk of control failure by temephos in most of the country. The widespread resistance to temephos in Brazilian Ae. aegypti populations greatly compromise effective mosquito control efforts using this insecticide and indicates the urgent need to identify alternative insecticides aided by the preventive elimination of potential mosquito breeding sites.

  3. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    Science.gov (United States)

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of 100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations. © 2016 Stichting International Foundation for Animal Genetics.

  4. Male breast cancer: a nation-wide population-based comparison with female breast cancer.

    Science.gov (United States)

    Lautrup, Marianne D; Thorup, Signe S; Jensen, Vibeke; Bokmand, Susanne; Haugaard, Karen; Hoejris, Inger; Jylling, Anne-Marie B; Joernsgaard, Hjoerdis; Lelkaitis, Giedrius; Oldenburg, Mette H; Qvamme, Gro M; Soee, Katrine; Christiansen, Peer

    2018-05-01

    Describe prognostic parameters of Danish male breast cancer patients (MBCP) diagnosed from 1980-2009. Determine all-cause mortality compared to the general male population and analyze survival/mortality compared with Danish female breast cancer patients (FBCP) in the same period. The MBCP cohort was defined from three national registers. Data was extracted from medical journals. Data for FBCP is from the DBCG database. Overall survival (OS) was quantified by Kaplan-Meier estimates. Standardized mortality ratios (SMRs) were calculated based on mortality rate among patients relative to the mortality rate in the general population. The association between SMR and risk factors were analyzed in univariate and multivariable Poisson regression models. Separate models for each gender were used for the analyses. We found a marked difference in OS for the two genders. For the total population of MBCP, 5- and 10-year survivals were 55.1% and 31.7%, respectively. For FBCP, the corresponding figures were 76.8% and 59.3%. Median age at diagnosis for FBCP was 61 years and 70 years for MBCP. By applying SMR, the difference in mortality between genders equalized and showed pronounced age-dependency. For males <40 years, SMR was 9.43 and for females 19.56 compared to SMR for males 80 + years (0.95) and females 80 + years (0.89). During the period 1980-2009, the risk of dying gradually decreased for FBCP (p < .0001). The risk 1980-1984 was 35% higher than 2005-2009 (RR 1.35). Although the risk of dying for MBCP was also lowest in 2005-2009, there was no clear tendency (p = .1439). The risk was highest in 1990-1994 (RR =2.48). We found better OS for FBCP than for MBCP. But SMR showed similar mortality rate for the two genders, except for very young FBCP, who had higher SMR. Furthermore, significantly improved survival over time for FBCP was observed, with no clear tendency for MBCP.

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

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    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.

  6. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia.

    Science.gov (United States)

    Metspalu, Mait; Romero, Irene Gallego; Yunusbayev, Bayazit; Chaubey, Gyaneshwer; Mallick, Chandana Basu; Hudjashov, Georgi; Nelis, Mari; Mägi, Reedik; Metspalu, Ene; Remm, Maido; Pitchappan, Ramasamy; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Kivisild, Toomas

    2011-12-09

    South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  7. Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population

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    Tae-Joon Park

    2015-01-01

    Full Text Available Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.

  8. 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.

  9. Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population

    Directory of Open Access Journals (Sweden)

    Chan Juliana CN

    2010-02-01

    Full Text Available Abstract Background Shared genetic factors may contribute to the phenotypic clustering of different components of the metabolic syndrome (MES. This study aims to identify genetic loci that contribute to individual or multiple factors related to MES. Results We studied 478 normoglycemic subjects ascertained through 163 families participating in the Hong Kong Family Diabetes Study. Factor analysis on 15 MES-related traits yielded 6 factors including adiposity factor (body mass index, waist and hip circumferences, insulin factor (fasting insulin and insulin AUC during OGTT, glucose factor (fasting glucose and glucose AUC during OGTT, TC-LDLC factor (total cholesterol and LDL-cholesterol, blood pressure factor (systolic and diastolic blood pressure and TG-HDLC factor (triglycerides and HDL-cholesterol. Genome-wide linkage analyses were performed on these factors using variance component approach. Suggestive evidence for linkage (LOD = 1.24 - 2.46 were observed for adiposity factor (chromosome 1 at 187 cM, chromosome 9 at 34 cM and chromosome 17 at 10 cM, insulin factor (chromosome 2 at 128 cM, chromosome 5 at 21 cM and chromosome 12 at 7 cM, glucose factor (chromosome 7 at 155 cM, TC-LDLC factor (chromosome 7 at 151 cM and chromosome 13 at 15 cM and TG-HDLC factor (chromosome 7 at 155 cM. Conclusions In summary, our findings suggest the presence of susceptibility loci that influence either single (chromosomes 1, 2, 5, 9, 12, 13 and 17 or multiple factors (chromosome 7 for MES in Hong Kong Chinese without diabetes.

  10. Joint genome-wide association study for milk fatty acid traits in Chinese and Danish Holstein populations

    DEFF Research Database (Denmark)

    Li, Xiujin; Buitenhuis, Albert Johannes; Lund, Mogens Sandø

    2015-01-01

    is highly consistent between the Chinese and Danish Holstein populations, such that a joint genome-wide association study (GWAS) can be performed. In this study, a joint GWAS was performed for 16 milk FA traits based on data of 784 Chinese and 371 Danish Holstein cows genotyped by a high-density bovine...... different effects in the 2 populations. Ten FA were influenced by a quantitative trait loci (QTL) region including DGAT1. Both C14:1 and the C14 index were influenced by a QTL region including SCD1 in the combined population. Other QTL regions also showed significant associations with the studied FA....... A large region (14.9–24.9 Mbp) in BTA26 significantly influenced C14:1 and the C14 index in both populations, mostly likely due to the SNP in SCD1. A QTL region (69.97–73.69 Mbp) on BTA9 showed a significantly different effect on C18:0 between the 2 populations. Detection of these important SNP...

  11. Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats.

    Science.gov (United States)

    Cañas, Rafael A; Feito, Isabel; Fuente-Maqueda, José Francisco; Ávila, Concepción; Majada, Juan; Cánovas, Francisco M

    2015-11-06

    Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.

  12. 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

    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......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...

  13. 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

  14. 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.

  15. Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers

    Directory of Open Access Journals (Sweden)

    Melka Melkaye G

    2012-03-01

    Full Text Available Abstract Background Studies of genetic diversity are essential in understanding the extent of differentiation between breeds, and in designing successful diversity conservation strategies. The objective of this study was to evaluate the level of genetic diversity within and between North American Brown Swiss (BS, n = 900, Jersey (JE, n = 2,922 and Holstein (HO, n = 3,535 cattle, using genotyped bulls. GENEPOP and FSTAT software were used to evaluate the level of genetic diversity within each breed and between each pair of the three breeds based on genome-wide SNP markers (n = 50,972. Results Hardy-Weinberg equilibrium (HWE exact test within breeds showed a significant deviation from equilibrium within each population (P st indicated that the combination of BS and HO in an ideally amalgamated population had higher genetic diversity than the other pairs of breeds. Conclusion Results suggest that the three bull populations have substantially different gene pools. BS and HO show the largest gene differentiation and jointly the highest total expected gene diversity compared to when JE is considered. If the loss of genetic diversity within breeds worsens in the future, the use of crossbreeding might be an option to recover genetic diversity, especially for the breeds with small population size.

  16. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

    Science.gov (United States)

    Zhan, Qimin; Hu, Zhibin; He, Zhonghu; Jia, Weihua; Zhou, Yifeng; Yu, Kai; Shu, Xiao-Ou; Yuan, Jian-Min; Zheng, Wei; Zhao, Xue-Ke; Gao, She-Gan; Yuan, Zhi-Qing; Zhou, Fu-You; Fan, Zong-Min; Cui, Ji-Li; Lin, Hong-Li; Han, Xue-Na; Li, Bei; Chen, Xi; Dawsey, Sanford M.; Liao, Linda; Lee, Maxwell P.; Ding, Ti; Qiao, You-Lin; Liu, Zhihua; Liu, Yu; Yu, Dianke; Chang, Jiang; Wei, Lixuan; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Han, Jing-Jing; Zhou, Sheng-Li; Zhang, Peng; Zhang, Dong-Yun; Yuan, Yuan; Huang, Ying; Liu, Chunling; Zhai, Kan; Qiao, Yan; Jin, Guangfu; Guo, Chuanhai; Fu, Jianhua; Miao, Xiaoping; Lu, Changdong; Yang, Haijun; Wang, Chaoyu; Wheeler, William A.; Gail, Mitchell; Yeager, Meredith; Yuenger, Jeff; Guo, Er-Tao; Li, Ai-Li; Zhang, Wei; Li, Xue-Min; Sun, Liang-Dan; Ma, Bao-Gen; Li, Yan; Tang, Sa; Peng, Xiu-Qing; Liu, Jing; Hutchinson, Amy; Jacobs, Kevin; Giffen, Carol; Burdette, Laurie; Fraumeni, Joseph F.; Shen, Hongbing; Ke, Yang; Zeng, Yixin; Wu, Tangchun; Kraft, Peter; Chung, Charles C.; Tucker, Margaret A.; Hou, Zhi-Chao; Liu, Ya-Li; Hu, Yan-Long; Liu, Yu; Wang, Li; Yuan, Guo; Chen, Li-Sha; Liu, Xiao; Ma, Teng; Meng, Hui; Sun, Li; Li, Xin-Min; Li, Xiu-Min; Ku, Jian-Wei; Zhou, Ying-Fa; Yang, Liu-Qin; Wang, Zhou; Li, Yin; Qige, Qirenwang; Yang, Wen-Jun; Lei, Guang-Yan; Chen, Long-Qi; Li, En-Min; Yuan, Ling; Yue, Wen-Bin; Wang, Ran; Wang, Lu-Wen; Fan, Xue-Ping; Zhu, Fang-Heng; Zhao, Wei-Xing; Mao, Yi-Min; Zhang, Mei; Xing, Guo-Lan; Li, Ji-Lin; Han, Min; Ren, Jing-Li; Liu, Bin; Ren, Shu-Wei; Kong, Qing-Peng; Li, Feng; Sheyhidin, Ilyar; Wei, Wu; Zhang, Yan-Rui; Feng, Chang-Wei; Wang, Jin; Yang, Yu-Hua; Hao, Hong-Zhang; Bao, Qi-De; Liu, Bao-Chi; Wu, Ai-Qun; Xie, Dong; Yang, Wan-Cai; Wang, Liang; Zhao, Xiao-Hang; Chen, Shu-Qing; Hong, Jun-Yan; Zhang, Xue-Jun; Freedman, Neal D; Goldstein, Alisa M.; Lin, Dongxin; Taylor, Philip R.; Wang, Li-Dong; Chanock, Stephen J.

    2014-01-01

    We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region. PMID:25129146

  17. 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

  18. 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.

  19. Retrospective Cohort Study of the Prevalence of Lumbosacral Transitional Vertebra in a Wide and Well-Represented Population

    Directory of Open Access Journals (Sweden)

    Demet Uçar

    2013-01-01

    Full Text Available Purpose. The aim of this study is to determine the prevalence of lumbosacral transitional vertebra (LSTV in a well-represented general population. Methods. For a retrospective cohort study, abdominal radiographs of adult subjects were queried with clear visibility of the vertebral body articulation of the last rib, all lumbar transverse processes, and complete sacral wings. Exclusion criteria included any radiologic evidence of previous lumbosacral surgery that would block our view. A total of 6200 abdominal films were reviewed, and 3607 were identified as being suitable for the measurement of the desired parameters. Results. A total of 3607 subjects were identified as eligible for the study, and 683 (18.9% were classified as positive for a lumbosacral transitional vertebra. The prevalence of sacralization and lumbarization was found as 17.2% and 1.7%, respectively. The average age at the time of the study was 39.5±15.2 years (18–86 years. Conclusions. As a result of different opinions, LSTV retains its controversial status. Our prevalence study of the general population will provide assistance for resolution of the controversy. Prevalence studies of the general population with a wide participation will shed light on comparative studies.

  20. 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.

  1. An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population

    DEFF Research Database (Denmark)

    Lu, Timothy Tehua; Lao, Oscar; Nothnagel, Michael

    2009-01-01

    of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable......Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix Gene......Chip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    Jacqui Webster

    2018-01-01

    Full Text Available 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.

  4. 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

    Background 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. Methods A population-wide survey of dermatology practices using simulated calls asking for the earliest appointment for a Non-Urgent, Urgent and Cosmetic service. Results 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 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. PMID:27632206

  5. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.

    Directory of Open Access Journals (Sweden)

    Caitlin Collins

    2018-02-01

    Full Text Available Genome-Wide Association Studies (GWAS in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

  6. A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive

    Science.gov (United States)

    Bergfelder-Drüing, Sarah; Grosse-Brinkhaus, Christine; Lind, Bianca; Erbe, Malena; Schellander, Karl; Simianer, Henner; Tholen, Ernst

    2015-01-01

    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. PMID:25781935

  7. 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.

  8. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

    Science.gov (United States)

    2014-01-01

    Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

  9. Plasticity in reproduction and growth among 52 range-wide populations of a Mediterranean conifer: adaptive responses to environmental stress.

    Science.gov (United States)

    Santos-Del-Blanco, L; Bonser, S P; Valladares, F; Chambel, M R; Climent, J

    2013-09-01

    A plastic response towards enhanced reproduction is expected in stressful environments, but it is assumed to trade off against vegetative growth and efficiency in the use of available resources deployed in reproduction [reproductive efficiency (RE)]. Evidence supporting this expectation is scarce for plants, particularly for long-lived species. Forest trees such as Mediterranean pines provide ideal models to study the adaptive value of allocation to reproduction vs. vegetative growth given their among-population differentiation for adaptive traits and their remarkable capacity to cope with dry and low-fertility environments. We studied 52 range-wide Pinus halepensis populations planted into two environmentally contrasting sites during their initial reproductive stage. We investigated the effect of site, population and their interaction on vegetative growth, threshold size for female reproduction, reproductive-vegetative size relationships and RE. We quantified correlations among traits and environmental variables to identify allocation trade-offs and ecotypic trends. Genetic variation for plasticity was high for vegetative growth, whereas it was nonsignificant for reproduction. Size-corrected reproduction was enhanced in the more stressful site supporting the expectation for adverse conditions to elicit plastic responses in reproductive allometry. However, RE was unrelated with early reproductive investment. Our results followed theoretical predictions and support that phenotypic plasticity for reproduction is adaptive under stressful environments. Considering expectations of increased drought in the Mediterranean, we hypothesize that phenotypic plasticity together with natural selection on reproductive traits will play a relevant role in the future adaptation of forest tree species. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  12. Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.

    Science.gov (United States)

    Zhang, Xiao; Zhang, Hua; Li, Lujiang; Lan, Hai; Ren, Zhiyong; Liu, Dan; Wu, Ling; Liu, Hailan; Jaqueth, Jennifer; Li, Bailin; Pan, Guangtang; Gao, Shibin

    2016-08-31

    Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs). With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5-3 Mb) than that in the entire panel (0.5-0.75 Mb) and the Tropical group (0.25-0.5 Mb). A large region at 30-120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines. For the panel covered most of widely used inbred lines in Southwest China, this work

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

    Directory of Open Access Journals (Sweden)

    Geeta Yadav

    Full Text Available 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 < 0.05. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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. 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.

  17. Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

    Science.gov (United States)

    Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

    2015-01-01

    The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the

  18. Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina as a Case Study.

    Directory of Open Access Journals (Sweden)

    María Vergara

    Full Text Available The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP. However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA sequencing (621 bp and microsatellite genotyping (23 polymorphic markers to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a spatial and non-spatial Bayesian individual-based clustering (IBC approaches (STRUCTURE, TESS, BAPS and GENELAND, and b multivariate methods [discriminant analysis of principal components (DAPC and spatial principal component analysis (sPCA]. Additionally, because isolation by distance (IBD is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence

  19. Pharmacokinetics and dose requirements of factor VIII over the age range 3-74 years

    DEFF Research Database (Denmark)

    Björkman, Sven; Folkesson, Anna; Jönsson, Siv

    2009-01-01

    in the sparse clinical data. Model-predicted doses (based on age and body weight) to maintain a recommended 0.01 U/mL trough level of FVIII with administration on alternate days started at around 60 U/kg in the small children, decreasing to 10 U/kg or less in middle age. However, "true" dose requirements......, as estimated from individual PK parameter data, showed a much greater variation. CONCLUSION: Appropriate dosing of FVIII for prophylactic treatment cannot be calculated only from body weight and/or age. However, plausible starting doses for most patients would be 1,000 U every other day. FVIII levels should...... can be calculated according to patient characteristics, and (3) to present dosing recommendations for initiating prophylactic treatment. METHODS: A population PK model was developed using data from four PK studies on patients aged 7-74 years. The model was tested on sparse FVIII data from 42...

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

    Science.gov (United States)

    Kim, Eui-Soo; Sonstegard, Tad S; da Silva, Marcos V G B; Gasbarre, Louis C; Van Tassell, Curtis P

    2015-01-01

    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.

  1. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    Directory of Open Access Journals (Sweden)

    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.

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

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    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.

  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. 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

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

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    K Michael Hambidge

    2017-07-01

    Full Text Available Abstract Background 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. Methods 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/m2 was calculated. Z-scores were determined using WHO reference data. Results 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. Conclusions 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

  7. 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.

  8. 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.

  9. Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia.

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    Maaike A de Jong

    Full Text Available This study investigates the genetic diversity, population structure and demographic history of the afrotropical butterfly Bicyclus anynana using mitochondrial DNA (mtDNA. Samples from six wild populations covering most of the species range from Uganda to South Africa were compared for the cytochrome c oxidase subunit gene (COI. Molecular diversity indices show overall high mtDNA diversity for the populations, but low nucleotide divergence between haplotypes. Our results indicate relatively little geographic population structure among the southern populations, especially given the extensive distributional range and an expectation of limited gene flow between populations. We implemented neutrality tests to assess signatures of recent historical demographic events. Tajima's D test and Fu's F(S test both suggested recent population growth for the populations. The results were only significant for the southernmost populations when applying Tajima's D, but Fu's F(S indicated significant deviations from neutrality for all populations except the one closest to the equator. Based on our own findings and those from pollen and vegetation studies, we hypothesize that the species range of B. anynana was reduced to equatorial refugia during the last glacial period, and that the species expanded southwards during the past 10.000 years. These results provide crucial background information for studies of phenotypic and molecular adaptation in wild populations of B. anynana.

  10. Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences.

    Science.gov (United States)

    Liu, Shenglin; Hansen, Michael M; Jacobsen, Magnus W

    2016-10-01

    We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations. © 2016 John Wiley & Sons Ltd.

  11. Differences in survival on chronic dialysis treatment between ethnic groups in Denmark: a population-wide, national cohort study.

    Science.gov (United States)

    van den Beukel, Tessa O; Hommel, Kristine; Kamper, Anne-Lise; Heaf, James G; Siegert, Carl E H; Honig, Adriaan; Jager, Kitty J; Dekker, Friedo W; Norredam, Marie

    2016-07-01

    In Western countries, black and Asian dialysis patients experience better survival compared with white patients. The aim of this study is to compare the survival of native Danish dialysis patients with that of dialysis patients originating from other countries and to explore the association between the duration of residence in Denmark before the start of dialysis and the mortality on dialysis. We performed a population-wide national cohort study of incident chronic dialysis patients in Denmark (≥18 years old) who started dialysis between 1995 and 2010. In total, 8459 patients were native Danes, 344 originated from other Western countries, 79 from North Africa or West Asia, 173 from South or South-East Asia and 54 from sub-Saharan Africa. Native Danes were more likely to die on dialysis compared with the other groups (crude incidence rates for mortality: 234, 166, 96, 110 and 53 per 1000 person-years, respectively). Native Danes had greater hazard ratios (HRs) for mortality compared with the other groups {HRs for mortality adjusted for sociodemographic and clinical characteristics: 1.32 [95% confidence interval (CI) 1.14-1.54]; 2.22 [95% CI 1.51-3.23]; 1.79 [95% CI 1.41-2.27]; 2.00 [95% CI 1.10-3.57], respectively}. Compared with native Danes, adjusted HRs for mortality for Western immigrants living in Denmark for ≤10 years, >10 to ≤20 years and >20 years were 0.44 (95% CI 0.27-0.71), 0.56 (95% CI 0.39-0.82) and 0.86 (95% CI 0.70-1.04), respectively. For non-Western immigrants, these HRs were 0.42 (95% CI 0.27-0.67), 0.52 (95% CI 0.33-0.80) and 0.48 (95% CI 0.35-0.66), respectively. Incident chronic dialysis patients in Denmark originating from countries other than Denmark have a better survival compared with native Danes. For Western immigrants, this survival benefit declines among those who have lived in Denmark longer. For non-Western immigrants, the survival benefit largely remains over time. © The Author 2015. Published by Oxford University Press on

  12. Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

    Science.gov (United States)

    Hybridization is known to occur between cultivated and wild populations of numerous plant species. This represents a major mechanism by which a wild population’s genetic structure and evolutionary dynamics could be altered. Studying crop-derived alleles in wild populations is also relevant to assess...

  13. 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…

  14. A genome-wide search for genes involved in type 2 diabetes in a recently genetically isolated population from the Netherlands

    NARCIS (Netherlands)

    Y.S. Aulchenko (Yurii); N. Vaessen (Norbert); P. Heutink (Peter); J. Pullen (Jan); P.J.L.M. Snijders (Pieter); A. Hofman (Albert); L.A. Sandkuijl (Lodewijk); J.J. Houwing-Duistermaat (Jeanine); S. Bennett (Simon); B.A. Oostra (Ben); C.M. van Duijn (Cornelia); M. Edwards (Mark)

    2003-01-01

    textabstractMultiple genes, interacting with the environment, contribute to the susceptibility to type 2 diabetes. We performed a genome-wide search to localize type 2 diabetes susceptibility genes in a recently genetically isolated population in the Netherlands. We identified 79 nuclear families

  15. Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

    NARCIS (Netherlands)

    Matthies, I.E.; Hintum, van T.J.L.; Weise, S.; Röder, M.S.

    2012-01-01

    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be

  16. Genome-wide candidate regions for selective sweeps revealed through massive parallel sequencing of DNA across ten turkey populations

    NARCIS (Netherlands)

    Aslam, M.L.; Bastiaansen, J.W.M.; Megens, H.J.W.C.; Crooijmans, R.P.M.A.; Blomberg, L.; Groenen, M.

    2014-01-01

    Background The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated species and associating these variation patterns with the evolution, domestication, and selective

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Silva, João P; Correia, Ricardo; Alonso, Hany; Martins, Ricardo C; D'Amico, Marcello; Delgado, Ana; Sampaio, Hugo; Godinho, Carlos; Moreira, Francisco

    2018-01-01

    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 . 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. 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 . 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.

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

    Directory of Open Access Journals (Sweden)

    Lorraine Scotson

    Full Text Available 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

  20. Replication of endometriosis-associated single-nucleotide polymorphisms from genome-wide association studies in a Caucasian population.

    Science.gov (United States)

    Sundqvist, J; Xu, H; Vodolazkaia, A; Fassbender, A; Kyama, C; Bokor, A; Gemzell-Danielsson, K; D'Hooghe, T M; Falconer, H

    2013-03-01

    Is it possible to replicate the previously identified genetic association of four single-nucleotide polymorphisms (SNPs), rs12700667, rs7798431, rs1250248 and rs7521902, with endometriosis in a Caucasian population? A borderline association was observed for rs1250248 and endometriosis (P = 0.049). However, we could not replicate the other previously identified endometriosis-associated SNPs (rs12700667, rs7798431 and rs7521902) in the same population. Endometriosis is considered a complex disease, influenced by several genetic and environmental factors, as well as interactions between them. Previous studies have found genetic associations with endometriosis for SNPs at the 7p15 and 2q35 loci in a Caucasian population. Allele frequencies of SNPs were investigated in patients with endometriosis and controls. Blood samples and peritoneal biopsies were taken from a Caucasian female population consisting of 1129 patients with endometriosis and 831 controls. DNA was extracted for genotyping. The study was performed at a University hospital and research laboratories. A weak association with endometriosis (all stages) was observed for rs1250248 (P = 0.049). No significant associations were observed for the SNPs rs12700667, rs7798431 and rs7521902. A non-significant trend towards the association of rs1250248 with moderate/severe endometriosis was observed (odds ratio 1.18, 95% confidence interval 0.97-1.44). The inability to confirm all previous findings may result from differences between populations and type II errors. Our result demonstrates the difficulty of identifying common genetic variants in complex diseases. This study was supported by grants from the Karolinska Institutet and Stockholm City County/Karolinska Institutet (ALF), Stockholm, Sweden, Swedish Medical Research Council (K2007-54X-14212-06-3, K2010-54X-14212-09-3), Stockholm, Sweden, Leuven University Research Council (Onderzoeksraad KU Leuven), the Leuven University Hospitals Clinical Research Foundation

  1. 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.

  2. Tobacco policy reform and population-wide antismoking activities in Australia: the impact on smoking during pregnancy.

    Science.gov (United States)

    Havard, Alys; Tran, Duong T; Kemp-Casey, Anna; Einarsdóttir, Kristjana; Preen, David B; Jorm, Louisa R

    2017-08-04

    This study examined the impact of antismoking activities targeting the general population and an advertising campaign targeting smoking during pregnancy on the prevalence of smoking during pregnancy in New South Wales (NSW), Australia. Monthly prevalence of smoking during pregnancy was calculated using linked health records for all pregnancies resulting in a birth (800 619) in NSW from 2003 to 2011. Segmented regression of interrupted time series data assessed the effects of the extension of the ban on smoking in enclosed public places to include licensed premises (evaluated in combination with the mandating of graphic warnings on cigarette packs), television advertisements targeting smoking in the general population, print and online magazine advertisements targeting smoking during pregnancy and increased tobacco tax. Analyses were conducted for all pregnancies, and for the population stratified by maternal age, parity and socioeconomic status. Further analyses adjusted for the effect of the Baby Bonus maternity payment. Prevalence of smoking during pregnancy decreased from 2003 to 2011 overall (0.39% per month), and for all strata examined. For pregnancies overall, none of the evaluated initiatives was associated with a change in the trend of smoking during pregnancy. Significant changes associated with increased tobacco tax and the extension of the smoking ban (in combination with graphic warnings) were found in some strata. The declining prevalence of smoking during pregnancy between 2003 and 2011, while encouraging, does not appear to be directly related to general population antismoking activities or a pregnancy-specific campaign undertaken in this period. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  3. Socioeconomic Heterogeneity in the Effect of Health Shocks on Earnings: Evidence from Population-Wide Data on Swedish Workers

    OpenAIRE

    Lundborg, Petter; Nilsson, Martin; Vikström, Johan

    2011-01-01

    In this paper, we estimate socioeconomic heterogeneity in the effect of unexpected health shocks on labor market outcomes, using register-based data on the entire population of Swedish workers. We effectively exploit a Difference-in-Difference-in-Differences design, in which we compare the change in labor earnings across treated and control groups with high and low education levels. If the anticipation effects are similar for individuals with high and low education, any difference in the esti...

  4. Range-wide population genetic structure of the European bitterling (Rhodeus amarus) based on microsatellite and mitochondrial DNA analysis

    Czech Academy of Sciences Publication Activity Database

    Bryja, Josef; Smith, C.; Konečný, Adam; Reichard, Martin

    2010-01-01

    Roč. 19, č. 21 (2010), s. 4708-4722 ISSN 0962-1083 R&D Projects: GA AV ČR KJB600930802; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519 Keywords : co-evolution * conservation * fish * intraspecific introduction * non-native populations Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.457, year: 2010

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

    Science.gov (United States)

    Haraldsdottir, Sigurdis; Rafnar, Thorunn; Frankel, Wendy L.; Einarsdottir, Sylvia; Sigurdsson, Asgeir; Hampel, Heather; Snaebjornsson, Petur; Masson, Gisli; Weng, Daniel; Arngrimsson, Reynir; Kehr, Birte; Yilmaz, Ahmet; Haraldsson, Stefan; Sulem, Patrick; Stefansson, Tryggvi; Shields, Peter G.; Sigurdsson, Fridbjorn; Bekaii-Saab, Tanios; Moller, Pall H.; Steinarsdottir, Margret; Alexiusdottir, Kristin; Hitchins, Megan; Pritchard, Colin C.; de la Chapelle, Albert; Jonasson, Jon G.; Goldberg, Richard M.; Stefansson, Kari

    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 of uncertain significance that are not associated with cancer risk. We find that founder mutations in MSH6 and PMS2 prevail in Iceland unlike most other populations. PMID:28466842

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

    Science.gov (United States)

    Haraldsdottir, Sigurdis; Rafnar, Thorunn; Frankel, Wendy L; Einarsdottir, Sylvia; Sigurdsson, Asgeir; Hampel, Heather; Snaebjornsson, Petur; Masson, Gisli; Weng, Daniel; Arngrimsson, Reynir; Kehr, Birte; Yilmaz, Ahmet; Haraldsson, Stefan; Sulem, Patrick; Stefansson, Tryggvi; Shields, Peter G; Sigurdsson, Fridbjorn; Bekaii-Saab, Tanios; Moller, Pall H; Steinarsdottir, Margret; Alexiusdottir, Kristin; Hitchins, Megan; Pritchard, Colin C; de la Chapelle, Albert; Jonasson, Jon G; Goldberg, Richard M; Stefansson, Kari

    2017-05-03

    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 of uncertain significance that are not associated with cancer risk. We find that founder mutations in MSH6 and PMS2 prevail in Iceland unlike most other populations.

  8. 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.

  9. 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.

  10. Effects of age, replicative lifespan and growth rate of human nucleus pulposus cells on selecting age range for cell-based biological therapies for degenerative disc diseases.

    Science.gov (United States)

    Lee, J S; Lee, S M; Jeong, S W; Sung, Y G; Lee, J H; Kim, K W

    2016-07-01

    Autologous disc cell implantation, growth factors and gene therapy appear to be promising therapies for disc regeneration. Unfortunately, the replicative lifespan and growth kinetics of human nucleus pulposus (NP) cells related to host age are unclear. We investigated the potential relations among age, replicative lifespan and growth rate of NP cells, and determined the age range that is suitable for cell-based biological therapies for degenerative disc diseases. We used NP tissues classified by decade into five age groups: 30s, 40s, 50s, 60s and 70s. The mean cumulative population doubling level (PDL) and population doubling rate (PDR) of NP cells were assessed by decade. We also investigated correlations between cumulative PDL and age, and between PDR and age. The mean cumulative PDL and PDR decreased significantly in patients in their 60s. The mean cumulative PDL and PDR in the younger groups (30s, 40s and 50s) were significantly higher than those in the older groups (60s and 70s). There also were significant negative correlations between cumulative PDL and age, and between PDR and age. We found that the replicative lifespan and growth rate of human NP cells decreased with age. The replicative potential of NP cells decreased significantly in patients 60 years old and older. Young individuals less than 60 years old may be suitable candidates for NP cell-based biological therapies for treating degenerative disc diseases.

  11. The burden of cancer in 25-29 year olds in New Zealand: a case for a wider adolescent and young adult age range?

    Science.gov (United States)

    Ballantine, Kirsten R; Utley, Victoria; Watson, Heidi; Sullivan, Michael J; Spearing, Ruth

    2018-01-19

    New Zealand currently defines the adolescent and young adult (AYA) group for cancer services as young people 12-24 years of age, while other countries favour a designation of 15-29 years. This study was undertaken to compare cancer incidence and survival among 25-29 year olds to New Zealand's younger AYA population and to assess survival for our 15-29 year population against international benchmarks. Diagnostic and demographic information for cancer registrations between 2000 and 2009 for 25-29 year olds was obtained from the New Zealand Cancer Registry. Incidence rates (IR) and five-year relative survival estimates were calculated according to AYA diagnostic group/sub-group, sex and prioritised ethnicity. 1,541 new primary malignant cancers were diagnosed (IR: 588 per million). Five-year relative survival was 85%, but was significantly lower for Māori and Pacific peoples (both 77%) compared to non-Māori/non-Pacific peoples (88%). In the overall 15-29 year AYA cohort, disease-specific outcomes for bone tumours (46%) and breast cancer (64%) were inferior to international standards. New Zealand 25 to 29 year olds are at twice the risk of developing cancer as those 15-24 years. Given that the survival disparities identified were remarkably consistent with those for younger AYA, consideration should be given widening New Zealand's AYA age range.

  12. 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

    DEFF Research Database (Denmark)

    Andersen, Vibeke; Ernst, Anja; Sventoraityte, Jurgita

    2011-01-01

    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 significance in the combined analyses of all the panels. Conclusions......Background: 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. Methods...

  13. 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),

  14. 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.

  15. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

    Directory of Open Access Journals (Sweden)

    Meghann K. Devlin-Durante

    2017-11-01

    Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  16. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

    Science.gov (United States)

    Devlin-Durante, Meghann K; Baums, Iliana B

    2017-01-01

    The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  17. Virus epidemics can lead to a population-wide spread of intragenomic parasites in a previously parasite-free asexual population.

    Science.gov (United States)

    Jalasvuori, Matti; Lehtonen, Jussi

    2014-03-01

    Sexual reproduction is problematic to explain due to its costs, most notably the twofold cost of sex. Yet, sex has been suggested to be favourable in the presence of proliferating intragenomic parasites given that sexual recombination provides a mechanism to confine the accumulation of deleterious mutations. Kraaijeveld et al. compared recently the accumulation of transposons in sexually and asexually reproducing lines of the same species, the parasitoid wasp Leptopilina clavipes. They discovered that within asexually reproducing wasps, the number of gypsy-like retrotransposons was increased fourfold, whereas other retrotransposons were not. Interestingly, gypsy-like retrotransposons are closely related to retroviruses. Endogenous retroviruses are retroviruses that have integrated to the germ line cells and are inherited thereafter vertically. They can also replicate within the genome similarly to retrotransposons as well as form virus particles and infect previously uninfected cells. This highlights the possibility that endogenous retroviruses could play a role in the evolution of sexual reproduction. Here, we show with an individual-based computational model that a virus epidemic within a previously parasite-free asexual population may establish a new intragenomic parasite to the population. Moreover and in contrast to other transposons, the possibility of endogenous viruses to maintain a virus epidemic and simultaneously provide resistance to individuals carrying active endogenous viruses selects for the presence of active intragenomic parasites in the population despite their deleterious effects. Our results suggest that the viral nature of certain intragenomic parasites should be taken into account when sex and its benefits are being considered. © 2014 John Wiley & Sons Ltd.

  18. [Preventing cardiovascular diseases through a screening modelling applicable to wide population groups: results from the first phase of the project].

    Science.gov (United States)

    Ferro, Antonio; Cinquetti, Sandro; Moro, Alessandro; Siddu, Andrea; Trimarchi, Antonino; Penon, Maria Gabriella; Pavan, Pierpaolo; Camillotto, Raffaella; Rossetto, Luca; Volpe, Valter; Zevrain, Simone; Brusaferro, Silvio

    2014-01-01

    evaluate, through active call, lifestyles of an asymptomatic population in order to identify hyperglycaemic subjects and/or high-blood pressure sufferers to dispatch to their GP to perform suitable checking, and subjects to invite to a cardiovascular disease prevention programme because of their lifestyles. between January 2009 and July 2012, all healthy residents in the Local Health Authority of Este (ULSS 17 Este) aged 45-59 years were invited to join a cardiovascular disease prevention programme. all participants were evaluated through an administered lifestyle questionnaire. Parameters such as blood pressure (BP), glycaemia, waist circumference and body mass index were collected and recorded. Participants also received counseling, informational materials on lifestyle and were invited to individual or group health promotion initiatives in relation to personal risk factors. among the invited, 55.5% (3,922/7,071) adhered. Women (58.8%) responded significantly better than men (51.9%) (p diseases.

  19. Radiation tumorigenesis in inbred laboratory animals and cancer risks in irradiated human populations. Two widely different problems

    International Nuclear Information System (INIS)

    Walinder, G.

    1978-01-01

    The mammal has efficient defence mechanisms against the development of tumours. These mechanisms are successively deteriorated by ionizing radiation when the dose increases beyond certain 'borderline levels'. Consequently, most animal strains demonstrate a bi-phasic dose-tumour relationship with a low-dose limb, the slope of which cannot be distinguished from zero, and a high-dose limb that increases with increasing doses. There are four or five exceptions to this 'rule' but in most of these cases the probable reasons for the deviations are known. Some human tumours as observed in epidemiological investigations do not demonstrate a similar clearly bi-phasic dose response. In all probability, this discrepancy does not reflect a higher susceptibility to radiation-induced tumours in man compared with other mammals. It is rather a consequence of a greater statistical variation in radiosensitivity in heterogeneous human populations than among inbred animals living standardized conditions. Accordingly, when maximum permissible dose levels are to be determined one should extrapolate from epidemiological data. Furthermore, these extrapolations should be linear if the data do not clearly deviate from a straight line, and if there are no scientific reasons to assume that a threshold exists. This formal method would not produce a biological description of what may happen in the low-dose area but rather an upper risk limit for the population studied. The real low-dose risk cannot be known. For the same pragmatic reason other radiological or non-radiological risks should be determined in the same manner, particularly when risks are to be compared. (author)

  20. 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

  1. 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

  2. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data.

    Science.gov (United States)

    Yew, Chee Wei; Hoque, Mohd Zahirul; Pugh-Kitingan, Jacqueline; Minsong, Alexander; Voo, Christopher Lok Yung; Ransangan, Julian; Lau, Sophia Tiek Ying; Wang, Xu; Saw, Woei Yuh; Ong, Rick Twee-Hee; Teo, Yik-Ying; Xu, Shuhua; Hoh, Boon-Peng; Phipps, Maude E; Kumar, S Vijay

    2018-07-01

    The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (F ST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent

  3. Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis.

    Directory of Open Access Journals (Sweden)

    Hong Zhu

    Full Text Available Rheumatoid arthritis (RA is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations.Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects. For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected 'highly verified' genes were measured by ELISA among our in-house RA cases and controls.A total of 221 RA-associated genes were newly identified by gene-based association study, including 71'overlapped', 76 'European-specific' and 74 'Asian-specific' genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 'overlapped' (ABCF1, FLOT1, HLA-F, IER3, TUBB, ZKSCAN4, BTN3A3, HSP90AB1, CUTA, BRD2, HLA-DMA, 5 'European-specific' (PHTF1, RPS18, BAK1, TNFRSF14, SUOX and 4 'Asian-specific' (RNASET2, HFE, BTN2A2, MAPK13 genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes FLOT1 (P value = 1.70E-02 and HLA-DMA (P value = 4.70E-02 in plasma were significantly different in our in-house samples.Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and detected a long list of overlapped or ethnic specific RA

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

    Science.gov (United States)

    Rommel, Alexander; Varnaccia, Gianni; Lahmann, Nils; Kottner, Jan; Kroll, Lars Eric

    2016-01-01

    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

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

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    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

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

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    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.

  7. Genome-Wide Association Study Reveals Four Loci for Lipid Ratios in the Korean Population and the Constitutional Subgroup.

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    Kim, Taehyeung; Park, Ah Yeon; Baek, Younghwa; Cha, Seongwon

    2017-01-01

    Circulating lipid ratios are considered predictors of cardiovascular risks and metabolic syndrome, which cause coronary heart diseases. One constitutional type of Korean medicine prone to weight accumulation, the Tae-Eum type, predisposes the consumers to metabolic syndrome, hypertension, diabetes mellitus, etc. Here, we aimed to identify genetic variants for lipid ratios using a genome-wide association study (GWAS) and followed replication analysis in Koreans and constitutional subgroups. GWASs in 5,292 individuals of the Korean Genome and Epidemiology Study and replication analyses in 2,567 subjects of the Korea medicine Data Center were performed to identify genetic variants associated with triglyceride (TG) to HDL cholesterol (HDLC), LDL cholesterol (LDLC) to HDLC, and non-HDLC to HDLC ratios. For subgroup analysis, a computer-based constitution analysis tool was used to categorize the constitutional types of the subjects. In the discovery stage, seven variants in four loci, three variants in three loci, and two variants in one locus were associated with the ratios of log-transformed TG:HDLC (log[TG]:HDLC), LDLC:HDLC, and non-HDLC:HDLC, respectively. The associations of the GWAS variants with lipid ratios were replicated in the validation stage: for the log[TG]:HDLC ratio, rs6589566 near APOA5 and rs4244457 and rs6586891 near LPL; for the LDLC:HDLC ratio, rs4420638 near APOC1 and rs17445774 near C2orf47; and for the non-HDLC:HDLC ratio, rs6589566 near APOA5. Five of these six variants are known to be associated with TG, LDLC, and/or HDLC, but rs17445774 was newly identified to be involved in lipid level changes in this study. Constitutional subgroup analysis revealed effects of variants associated with log[TG]:HDLC and non-HDLC:HDLC ratios in both the Tae-Eum and non-Tae-Eum types, whereas the effect of the LDLC:HDLC ratio-associated variants remained only in the Tae-Eum type. In conclusion, we identified three log[TG]:HDLC ratio-associated variants, two LDLC

  8. Genome-Wide Association Study Reveals Four Loci for Lipid Ratios in the Korean Population and the Constitutional Subgroup.

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    Taehyeung Kim

    Full Text Available Circulating lipid ratios are considered predictors of cardiovascular risks and metabolic syndrome, which cause coronary heart diseases. One constitutional type of Korean medicine prone to weight accumulation, the Tae-Eum type, predisposes the consumers to metabolic syndrome, hypertension, diabetes mellitus, etc. Here, we aimed to identify genetic variants for lipid ratios using a genome-wide association study (GWAS and followed replication analysis in Koreans and constitutional subgroups. GWASs in 5,292 individuals of the Korean Genome and Epidemiology Study and replication analyses in 2,567 subjects of the Korea medicine Data Center were performed to identify genetic variants associated with triglyceride (TG to HDL cholesterol (HDLC, LDL cholesterol (LDLC to HDLC, and non-HDLC to HDLC ratios. For subgroup analysis, a computer-based constitution analysis tool was used to categorize the constitutional types of the subjects. In the discovery stage, seven variants in four loci, three variants in three loci, and two variants in one locus were associated with the ratios of log-transformed TG:HDLC (log[TG]:HDLC, LDLC:HDLC, and non-HDLC:HDLC, respectively. The associations of the GWAS variants with lipid ratios were replicated in the validation stage: for the log[TG]:HDLC ratio, rs6589566 near APOA5 and rs4244457 and rs6586891 near LPL; for the LDLC:HDLC ratio, rs4420638 near APOC1 and rs17445774 near C2orf47; and for the non-HDLC:HDLC ratio, rs6589566 near APOA5. Five of these six variants are known to be associated with TG, LDLC, and/or HDLC, but rs17445774 was newly identified to be involved in lipid level changes in this study. Constitutional subgroup analysis revealed effects of variants associated with log[TG]:HDLC and non-HDLC:HDLC ratios in both the Tae-Eum and non-Tae-Eum types, whereas the effect of the LDLC:HDLC ratio-associated variants remained only in the Tae-Eum type. In conclusion, we identified three log[TG]:HDLC ratio

  9. Genome-wide association analysis and replication of coronary artery disease in South Korea suggests a causal variant common to diverse populations

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    Cho, Eun Young; Jang, Yangsoo; Shin, Eun Soon; Jang, Hye Yoon; Yoo, Yeon-Kyeong; Kim, Sook; Jang, Ji Hyun; Lee, Ji Yeon; Yun, Min Hye; Park, Min Young; Chae, Jey Sook; Lim, Jin Woo; Shin, Dong Jik; Park, Sungha; Lee, Jong Ho; Han, Bok Ghee; Rae, Kim Hyung; Cardon, Lon R; Morris, Andrew P; Lee, Jong Eun; Clarke, Geraldine M

    2010-01-01

    Background Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations. Methods The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490 032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population. Results The association previously observed on chromosome 9p21 was independently replicated (p=3.08e–07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population. Conclusion A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors. PMID:27325954

  10. 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.

  11. Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus.

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    Müller, Bárbara S F; Neves, Leandro G; de Almeida Filho, Janeo E; Resende, Márcio F R; Muñoz, Patricio R; Dos Santos, Paulo E T; Filho, Estefano Paludzyszyn; Kirst, Matias; Grattapaglia, Dario

    2017-07-11

    The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000-10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range historical linkage disequilibrium (LD) was likely captured for E. pellita. A GWAS identified only one significant association for volume growth in E. pellita, illustrating the fact that while genome-wide regression is able to account for large proportions of the heritability, very little or none of it is captured into significant associations using GWAS in breeding populations of the size evaluated in this study. This study provides further experimental data supporting positive prospects of using genome-wide data to

  12. 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.

  13. 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

  14. Southern montane populations did not contribute to the recolonization of West Siberian Plain by Siberian larch (Larix sibirica): a range-wide analysis of cytoplasmic markers.

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    Semerikov, Vladimir L; Semerikova, Svetlana A; Polezhaeva, Maria A; Kosintsev, Pavel A; Lascoux, Martin

    2013-10-01

    While many species were confined to southern latitudes during the last glaciations, there has lately been mounting evidence that some of the most cold-tolerant species were actually able to survive close to the ice sheets. The contribution of these higher latitude outposts to the main recolonization thrust remains, however, untested. In the present study, we use the first range-wide survey of genetic diversity at cytoplasmic markers in Siberian larch (Larix sibirica; four mitochondrial (mt) DNA loci and five chloroplast (cp) DNA SSR loci) to (i) assess the relative contributions of southern and central areas to the current L. sibirica distribution range; and (ii) date the last major population expansion in both L. sibirica and adjacent Larix species. The geographic distribution of cpDNA variation was uninformative, but that of mitotypes clearly indicates that the southernmost populations, located in Mongolia and the Tien-Shan and Sayan Mountain ranges, had a very limited contribution to the current populations of the central and northern parts of the range. It also suggests that the contribution of the high latitude cryptic refugia was geographically limited and that most of the current West Siberian Plain larch populations likely originated in the foothills of the Sayan Mountains. Interestingly, the main population expansion detected through Approximate Bayesian Computation (ABC) in all four larch species investigated here pre-dates the LGM, with a mode in a range of 220,000-1,340,000 years BP. Hence, L. sibirica, like other major conifer species of the boreal forest, was strongly affected by climatic events pre-dating the Last Glacial Maximum. © 2013 John Wiley & Sons Ltd.

  15. Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

    Science.gov (United States)

    Garcia, Martín N.; Acuña, Cintia; Borralho, Nuno M. G.; Grattapaglia, Dario; Marcucci Poltri, Susana N.

    2013-01-01

    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

  16. Genome-Wide Association Study Identifies Two Novel Loci with Sex-Specific Effects for Type 2 Diabetes Mellitus and Glycemic Traits in a Korean Population

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    Min Jin Go

    2014-10-01

    Full Text Available BackgroundUntil recently, genome-wide association study (GWAS-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population.MethodsWe performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842. The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500. A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively.ResultsA combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356 loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of β-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study.ConclusionOur study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population.

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

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    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

  18. 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

  19. 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

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    Jonaitis Laimas

    2011-10-01

    Full Text Available Abstract Background 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. Methods 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. Results 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

  20. 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.

  1. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci of STAT4 and HLA-DQ in a Korean population.

    Science.gov (United States)

    Kim, Lyoung Hyo; Cheong, Hyun Sub; Namgoong, Suhg; Kim, Ji On; Kim, Jeong-Hyun; Park, Byung Lae; Cho, Sung Won; Park, Neung Hwa; Cheong, Jae Youn; Koh, InSong; Shin, Hyoung Doo; Kim, Yoon-Jun

    2015-07-01

    A recent genome-wide association study (GWAS) for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) identified two loci (rs7574865 in STAT4 and rs9275319 in HLA-DQ) in a Chinese population. We attempted to replicate the associations between the two SNP loci and the risk of HCC in a Korean population. The rs7574865 in STAT4 and rs9275319 in HLA-DQ were genotyped in a total of 3838 Korean subjects composed of 287 HBV-related hepatocellular carcinoma patients, 671 chronic hepatitis B virus (CHB) patients, and 2880 population controls using TaqMan genotyping assay. Gene expression was measured by microarray. A logistic regression analysis revealed that rs7574865 in STAT4 and rs9275319 in HLA-DQ were associated with the risk of CHB (OR = 1.25, P = 0.0002 and OR = 1.57, P= 1.44 × 10(-10), respectively). However, these loci were no association with the risk of HBV-related HCC among CHB patients. In the gene expression analyses, although no significant differences in mRNA expression of nearby genes according to genotypes were detected, a significantly decreased mRNA expression in HCC subjects was observed in STAT4, HLA-DQA1, and HLA-DQB1. Although the genetic effects of two HCC susceptibility loci were not replicated, the two loci were found to exert susceptibility effects on the risk of CHB in a Korean population. In addition, the decreased mRNA expression of STAT4, HLA-DQA1, and HLA-DQB1 in HCC tissue might provide a clue to understanding their role in the progression to HCC. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population.

    Science.gov (United States)

    Johnston, Susan E; McEwan, John C; Pickering, Natalie K; Kijas, James W; Beraldi, Dario; Pilkington, Jill G; Pemberton, Josephine M; Slate, Jon

    2011-06-01

    Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ∼36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation. © 2011 Blackwell Publishing Ltd.

  3. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  4. Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling.

    Science.gov (United States)

    Castagné, Raphaële; Boulangé, Claire Laurence; Karaman, Ibrahim; Campanella, Gianluca; Santos Ferreira, Diana L; Kaluarachchi, Manuja R; Lehne, Benjamin; Moayyeri, Alireza; Lewis, Matthew R; Spagou, Konstantina; Dona, Anthony C; Evangelos, Vangelis; Tracy, Russell; Greenland, Philip; Lindon, John C; Herrington, David; Ebbels, Timothy M D; Elliott, Paul; Tzoulaki, Ioanna; Chadeau-Hyam, Marc

    2017-10-06

    1 H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1 H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies.

  5. 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; Oskarsson, Sven; Littvay, Levente; Dawes, Christopher T; Verhulst, Brad; McDermott, Rose; Nørgaard, Asbjørn Sonne; Klofstad, Casey A; Christensen, Kaare; Johannesson, Magnus; Magnusson, Patrik K E; Eaves, Lindon J; Martin, Nicholas G

    2014-05-01

    Almost 40 years ago, evidence from large studies of adult twins and their relatives suggested that between 30 and 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.

  6. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Genome-wide association studies and epistasis analyses of candidate genes related to age at menarche and age at natural menopause in a Korean population.

    Science.gov (United States)

    Pyun, Jung-A; Kim, Sunshin; Cho, Nam H; Koh, InSong; Lee, Jong-Young; Shin, Chol; Kwack, KyuBum

    2014-05-01

    The aim of this study was to identify polymorphisms and gene-gene interactions that are significantly associated with age at menarche and age at menopause in a Korean population. A total of 3,452 and 1,827 women participated in studies of age at menarche and age at natural menopause, respectively. Linear regression analyses adjusted for residence area were used to perform genome-wide association studies (GWAS), candidate gene association studies, and interactions between the candidate genes for age at menarche and age at natural menopause. In GWAS, four single nucleotide polymorphisms (SNPs; rs7528241, rs1324329, rs11597068, and rs6495785) were strongly associated with age at natural menopause (lowest P = 9.66 × 10). However, GWAS of age at menarche did not reveal any strong associations. In candidate gene association studies, SNPs with P menopause, there was a significant interaction between intronic SNPs on ADAM metallopeptidase with thrombospondin type I motif 9 (ADAMTS9) and SMAD family member 3 (SMAD3) genes (P = 9.52 × 10). For age at menarche, there were three significant interactions between three intronic SNPs on follicle-stimulating hormone receptor (FSHR) gene and one SNP located at the 3' flanking region of insulin-like growth factor 2 receptor (IGF2R) gene (lowest P = 1.95 × 10). Novel SNPs and synergistic interactions between candidate genes are significantly associated with age at menarche and age at natural menopause in a Korean population.

  9. High Prevalence of Hepatitis B Virus Infection in the Age Range of 20-39 Years Old Individuals in Lome

    OpenAIRE

    Kolou, Malewe; Katawa, Gnatoulma; Salou, Mounerou; Gozo-Akakpo, Komlan Selom; Dossim, Sika; Kwarteng, Alexander; Prince-David, Mireille

    2017-01-01

    Background: Hepatitis B is a liver infection caused by the hepatitis B virus (HBV). It affects all women and men irrespective of age. Although sub-Saharan Africa is an area of high prevalence of this disease, data on the prevalence of acute and chronic HBV infections in this region remain to be widely documented. Objective: This study aimed to investigate the prevalence of HBV in relation to age in Centre Hospitalier Universitaire Campus (CHU-C), one of the two teaching hospitals of Lome, Tog...

  10. Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population.

    Science.gov (United States)

    Chung, Ren-Hua; Chiu, Yen-Feng; Hung, Yi-Jen; Lee, Wen-Jane; Wu, Kwan-Dun; Chen, Hui-Ling; Lin, Ming-Wei; Chen, Yii-Der I; Quertermous, Thomas; Hsiung, Chao A

    2017-08-08

    Fasting glucose and fasting insulin are glycemic traits closely related to diabetes, and understanding the role of genetic factors in these traits can help reveal the etiology of type 2 diabetes. Although single nucleotide polymorphisms (SNPs) in several candidate genes have been found to be associated with fasting glucose and fasting insulin, copy number variations (CNVs), which have been reported to be associated with several complex traits, have not been reported for association with these two traits. We aimed to identify CNVs associated with fasting glucose and fasting insulin. We conducted a genome-wide CNV association analysis for fasting plasma glucose (FPG) and fasting plasma insulin (FPI) using a family-based genome-wide association study sample from a Han Chinese population in Taiwan. A family-based CNV association test was developed in this study to identify common CNVs (i.e., CNVs with frequencies ≥ 5%), and a generalized estimating equation approach was used to test the associations between the traits and counts of global rare CNVs (i.e., CNVs with frequencies <5%). We found a significant genome-wide association for common deletions with a frequency of 5.2% in the Scm-like with four mbt domains 1 (SFMBT1) gene with FPG (association p-value = 2×10 -4 and an adjusted p-value = 0.0478 for multiple testing). No significant association was observed between global rare CNVs and FPG or FPI. The deletions in 20 individuals with DNA samples available were successfully validated using PCR-based amplification. The association of the deletions in SFMBT1 with FPG was further evaluated using an independent population-based replication sample obtained from the Taiwan Biobank. An association p-value of 0.065, which was close to the significance level of 0.05, for FPG was obtained by testing 9 individuals with CNVs in the SFMBT1 gene region and 11,692 individuals with normal copies in the replication cohort. Previous studies have found that SNPs in SFMBT1 are

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

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    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.

  12. 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.

  13. Seroprevalence of Trypanosoma cruzi Infection in Students at the Seven-Fourteen Age Range, Londrina, PR, Brazil, in 1995

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    Bonametti Ana Maria

    1998-01-01

    Full Text Available Seropositivity for Chagas disease was evaluated in 834 children aged between 7 and 14 from the Municipal Teaching System in the district of Londrina, State of Paraná. A seroprevalence rate of 0.1% was found through the use of an indirect immunofluorescent test and an enzyme-linked immunosorbent assay. This low rate of seroprevalence provides evidence that the vectorial transmission of Chagas disease has been eliminated in Londrina. The main reason for the elimination of vectorial transmission of Trypanosoma cruzi infection, as evaluated by serological tests, may be a remarkable change in the economic structure of the northern region of Paraná in the 1960's. At that time coffee production was almost completely replaced by soy beans, wheat and grazing in the rural areas. This change deeply affected the rural ecology and caused an exodus of the population from rural to urban areas as well as a decrease in the total number of the population of that region. The measures introduced for controlling the disease through the Program of Chagas Disease Control established by the Fundação Nacional de Saúde of the Brazilian Ministry of Health, certainly, had a positive impact on the reduction of American trypanosomiasis prevalence in the area under study. However, it does not seem that this was the most relevant factor responsible for the elimination of vectorial transmission of Chagas disease in Londrina.

  14. Preexisting CD4+ T-cell immunity in human population to avian influenza H7N9 virus: whole proteome-wide immunoinformatics analyses.

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    Venkata R Duvvuri

    Full Text Available In 2013, a novel avian influenza H7N9 virus was identified in human in China. The antigenically distinct H7N9 surface glycoproteins raised concerns about lack of cross-protective neutralizing antibodies. Epitope-specific preexisting T-cell immunity was one of the protective mechanisms in pandemic 2009 H1N1 even in the absence of cross-protective antibodies. Hence, the assessment of preexisting CD4+ T-cell immunity to conserved epitopes shared between H7N9 and human influenza A viruses (IAV is critical. A comparative whole proteome-wide immunoinformatics analysis was performed to predict the CD4+ T-cell epitopes that are commonly conserved within the proteome of H7N9 in reference to IAV subtypes (H1N1, H2N2, and H3N2. The CD4+ T-cell epitopes that are commonly conserved (∼ 556 were further screened against the Immune Epitope Database (IEDB to validate their immunogenic potential. This analysis revealed that 45.5% (253 of 556 epitopes are experimentally proven to induce CD4+ T-cell memory responses. In addition, we also found that 23.3% of CD4+ T-cell epitopes have ≥ 90% of sequence homology with experimentally defined CD8+ T-cell epitopes. We also conducted the population coverage analysis across different ethnicities using commonly conserved CD4+ T-cell epitopes and corresponding HLA-DRB1 alleles. Interestingly, the indigenous populations from Canada, United States, Mexico and Australia exhibited low coverage (28.65% to 45.62% when compared with other ethnicities (57.77% to 94.84%. In summary, the present analysis demonstrate an evidence on the likely presence of preexisting T-cell immunity in human population and also shed light to understand the potential risk of H7N9 virus among indigenous populations, given their high susceptibility during previous pandemic influenza events. This information is crucial for public health policy, in targeting priority groups for immunization programs.

  15. 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.

  16. If you see one, have you seen them all?: Community-wide effects of insecticide cross-resistance in zooplankton populations near and far from agriculture.

    Science.gov (United States)

    Bendis, Randall J; Relyea, Rick A

    2016-08-01

    The worldwide use of pesticides has led to increases in agricultural yields by reducing crop losses. However, increased pesticide use has resulted in pesticide-resistant pest species and recent studies have discovered pesticide-resistance in non-target species living close to farms. Such increased tolerance not only affects the species, but can alter the entire food web. Given that some species can evolve not only resistance to a single pesticide, but also cross-resistance to other pesticides that share the same mode of action, one would predict that cross-resistance to pesticides would also have effects on the entire community and affect community stability. To address this hypothesis, we conducted an outdoor mesocosm experiment comprised of 200 identical aquatic communities with phytoplankton, periphyton, and leopard frog (Lithobates pipiens) tadpoles. To these communities, we added one of four Daphnia pulex populations that we previously discovered were either resistant or sensitive to the insecticide of chlorpyrifos as a result of living close to or far from agriculture, respectively. We then exposed the communities to either no insecticide or three different concentrations of AChE-inhibiting insecticides (chlorpyrifos, malathion or carbaryl) or sodium channel-inhibiting insecticides (permethrin or cypermethrin). We discovered that communities containing sensitive Daphnia pulex experienced phytoplankton blooms and subsequent cascades through all trophic groups including amphibians at moderate to high concentrations of all five insecticides. However, communities containing resistant D. pulex were buffered from these effects at low to moderate concentrations of all AChE-inhibiting insecticides, but were not buffered against the pyrethroid insecticides. These data suggest that a simple change in the population-level resistance of zooplankton to a single insecticide can have widespread consequences for community stability and that the effects can be extrapolated

  17. Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus.

    Science.gov (United States)

    Schmidt, Thomas L; Rašić, Gordana; Zhang, Dongjing; Zheng, Xiaoying; Xi, Zhiyong; Hoffmann, Ary A

    2017-10-01

    Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Aedes albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.

  18. 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

  19. Genome-Wide Search for Quantitative Trait Loci Controlling Important Plant and Flower Traits in Petunia Using an Interspecific Recombinant Inbred Population of Petunia axillaris and Petunia exserta.

    Science.gov (United States)

    Cao, Zhe; Guo, Yufang; Yang, Qian; He, Yanhong; Fetouh, Mohammed; Warner, Ryan M; Deng, Zhanao

    2018-05-15

    A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F 7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia. Copyright © 2018, G3: Genes, Genomes, Genetics.

  20. 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...

  1. 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

    NARCIS (Netherlands)

    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.; Stukovsky, Karen D. Hinckley; Crapo, James D.; Beaty, Terri H.; Hokanson, John E.; Silverman, Edwin K.; Dupuis, Josee; O'Connor, George T.; Boezen, Hendrika; Rich, Stephen S.; Barr, R. Graham

    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

  2. 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

    BACKGROUND: Chronic inflammatory bowel disease (IBD) negatively affects the patient's health-related quality of life (HRQoL). Only a few population-based studies have compared the HRQoL of patients with the background population. The aim of this study was to evaluate the HRQoL in a European cohor...

  3. 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.

  4. Genome-wide association for plant height and flowering time across 15 tropical maize populations under managed drought stress and well-watered conditions in sub-Saharan Africa

    Science.gov (United States)

    Genotyping breeding materials is now relatively inexpensive but phenotyping costs have remained the same. One method to increase gene mapping power is to use genome-wide genetic markers to combine existing phenotype data for multiple populations into a unified analysis. We combined data from 15 bipa...

  5. Range-Wide Genetic Analysis of Little Brown Bat (Myotis lucifugus Populations: Estimating the Risk of Spread of White-Nose Syndrome.

    Directory of Open Access Journals (Sweden)

    Maarten J Vonhof

    Full Text Available The little brown bat (Myotis lucifugus is one of the most widespread bat species in North America and is experiencing severe population declines because of an emerging fungal disease, white-nose syndrome (WNS. To manage and conserve this species effectively it is important to understand patterns of gene flow and population connectivity to identify possible barriers to disease transmission. However, little is known about the population genetic structure of little brown bats, and to date, no studies have investigated population structure across their entire range. We examined mitochondrial DNA and nuclear microsatellites in 637 little brown bats (including all currently recognized subspecific lineages from 29 locations across North America, to assess levels of genetic variation and population differentiation across the range of the species, including areas affected by WNS and those currently unaffected. We identified considerable spatial variation in patterns of female dispersal and significant genetic variation between populations in eastern versus western portions of the range. Overall levels of nuclear genetic differentiation were low, and there is no evidence for any major barriers to gene flow across their range. However, patterns of mtDNA differentiation are highly variable, with high ΦST values between most sample pairs (including between all western samples, between western and eastern samples, and between some eastern samples, while low mitochondrial differentiation was observed within two groups of samples found in central and eastern regions of North America. Furthermore, the Alaskan population was highly differentiated from all others, and western populations were characterized by isolation by distance while eastern populations were not. These data raise the possibility that the current patterns of spread of WNS observed in eastern North America may not apply to the entire range and that there may be broad-scale spatial variation in

  6. 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.

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

    Science.gov (United States)

    Huppertz-Hauss, Gert; Høivik, Marte Lie; Langholz, Ebbe; Odes, Selwyn; Småstuen, Milada; Stockbrugger, Reinhold; Hoff, Geir; Moum, Bjørn; Bernklev, Tomm

    2015-02-01

    Chronic inflammatory bowel disease (IBD) negatively affects the patient's health-related quality of life (HRQoL). Only a few population-based studies have compared the HRQoL of patients with the background population. The aim of this study was to evaluate the HRQoL in a European cohort of patients with ulcerative colitis and Crohn's disease 10 years after diagnosis (European Collaborative study group of Inflammatory Bowel Disease) compared with the national background population in each country and to assess possible country-specific differences. Patients with IBD from 7 European 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's effect size index. Seven hundred sixty-nine patients were eligible for the study. We registered statistically significant and clinically relevant decreases in the short form health survey-36 dimensional scores in patients with symptoms at the time of follow-up and for patients reporting sick leave during the previous year or having received disablement pension. In the Netherlands and Norway, there was a moderate difference between the patients with IBD and the background population for the general health dimension. Overall, the HRQoL was not reduced in the IBD cohort compared with the background populations. However, in addition to older age and female gender, current symptoms at follow-up, disablement pension, and sick leave during the previous year were significantly associated with a reduced HRQoL in patients with IBD.

  8. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes.

    Science.gov (United States)

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

    2017-03-21

    It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous). Randomness of genotypes was accounted for by deriving the joint probability mass function of marker genotypes conditional on allelic frequencies and pedigree information. As a consequence, these models incorporated kinship and genotypic information that not only permitted to account for heterogeneity of allelic frequencies, but also to include individuals with missing genotypes at some or all loci without the need for previous imputation. This was possible because the non-observed fraction of the design matrix was treated as an unknown model parameter. For each model, a simpler version ignoring population structure, but still accounting for randomness of genotypes was proposed. Implementation of these models and computation of some criteria for model comparison were illustrated using two simulated datasets. Theoretical and computational issues along with possible applications, extensions and refinements were discussed. Some features of the models developed in this study make them promising for genome-wide prediction, the use of information contained in the probability distribution of genotypes is perhaps the most appealing. Further studies to assess the performance of the models proposed here and also to compare them with conventional models used in genome-wide prediction are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. 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...

  10. Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

    OpenAIRE

    Zheng, Xiaoying; Hoffmann, Ary; Xi, Zhiyong; Zhang, Dongjing; Rasic, Gordana; Schmidt, Thomas

    2017-01-01

    Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found ...

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

    OpenAIRE

    Liang, Jingjing; Le, Thu H.; Edwards, Digna R. Velez; Tayo, Bamidele O.; Gaulton, Kyle J.; Smith, Jennifer A.; Lu, Yingchang; Jensen, Richard A.; Chen, Guanjie; Yanek, Lisa R.; Schwander, Karen; Tajuddin, Salman M.; Sofer, Tamar; Kim, Wonji; Kayima, James

    2017-01-01

    © 2017 Public Library of Science. All Rights Reserved. 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 genom...

  12. A Genome-Wide Association Meta-Analysis of Attention-Deficit/Hyperactivity Disorder Symptoms in Population-Based Paediatric Cohorts

    OpenAIRE

    Middeldorp, Christel M.; Hammerschlag, Anke R.; Ouwens, Klaasjan G.; Groen-Blokhuis, Maria M.; St. Pourcain, Beate; Greven, Corina U.; Pappa, Irene; Tiesler, Carla M.T.; Ang, Wei; Nolte, Ilja M.; Vilor-Tejedor, Natalia; Bacelis, Jonas; Ebejer, Jane L.; Zhao, Huiying; Davies, Gareth E.

    2016-01-01

    ObjectiveTo elucidate the influence of common genetic variants on childhood attention-deficit/hyperactivity disorder (ADHD) symptoms, to identify genetic variants that explain its high heritability, and to investigate the genetic overlap of ADHD symptom scores with ADHD diagnosis.MethodWithin the EArly Genetics and Lifecourse Epidemiology (EAGLE) consortium, genome-wide single nucleotide polymorphisms (SNPs) and ADHD symptom scores were available for 17,666 children (< 13 years) from nine ...

  13. Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape.

    Science.gov (United States)

    Pilliod, David S; Arkle, Robert S; Robertson, Jeanne M; Murphy, Melanie A; Funk, W Chris

    2015-09-01

    Amphibian species persisting in isolated streams and wetlands in desert environments can be susceptible to low connectivity, genetic isolation, and climate changes. We evaluated the past (1900-1930), recent (1981-2010), and future (2071-2100) climate suitability of the arid Great Basin (USA) for the Columbia spotted frog (Rana luteiventris) and assessed whether changes in surface water may affect connectivity for remaining populations. We developed a predictive model of current climate suitability and used it to predict the historic and future distribution of suitable climates. We then modeled changes in surface water availability at each time period. Finally, we quantified connectivity among existing populations on the basis of hydrology and correlated it with interpopulation genetic distance. We found that the area of the Great Basin with suitable climate conditions has declined by approximately 49% over the last century and will likely continue to decline under future climate scenarios. Climate conditions at currently occupied locations have been relatively stable over the last century, which may explain persistence at these sites. However, future climates at these currently occupied locations are predicted to become warmer throughout the year and drier during the frog's activity period (May - September). Fall and winter precipitation may increase, but as rain instead of snow. Earlier runoff and lower summer base flows may reduce connectivity between neighboring populations, which is already limited. Many of these changes could have negative effects on remaining populations over the next 50-80 years, but milder winters, longer growing seasons, and wetter falls might positively affect survival and dispersal. Collectively, however, seasonal shifts in temperature, precipitation, and stream flow patterns could reduce habitat suitability and connectivity for frogs and possibly other aquatic species inhabiting streams in this arid region.

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

    OpenAIRE

    Pinto, M. Alice; Henriques, Dora; Chavez-Galarza, Julio; Kryger, Per; Garnery, Lionel; Zee, Romée van der; Dahle, Bjørn; Soland-Reckeweg, Gabriele; De la Rúa, Pilar; Dall’ Olio, Raffaele; Carreck, Norman L.; Johnston, J. Spencer

    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 f...

  15. 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...

  16. Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape

    Science.gov (United States)

    Pilliod, David S.; Arkle, Robert S.; Robertson, Jeanne M; Murphy, Melanie; Funk, W. Chris

    2015-01-01

    Amphibian species persisting in isolated streams and wetlands in desert environments can be susceptible to low connectivity, genetic isolation, and climate changes. We evaluated the past (1900–1930), recent (1981–2010), and future (2071–2100) climate suitability of the arid Great Basin (USA) for the Columbia spotted frog (Rana luteiventris) and assessed whether changes in surface water may affect connectivity for remaining populations. We developed a predictive model of current climate suitability and used it to predict the historic and future distribution of suitable climates. We then modeled changes in surface water availability at each time period. Finally, we quantified connectivity among existing populations on the basis of hydrology and correlated it with interpopulation genetic distance. We found that the area of the Great Basin with suitable climate conditions has declined by approximately 49% over the last century and will likely continue to decline under future climate scenarios. Climate conditions at currently occupied locations have been relatively stable over the last century, which may explain persistence at these sites. However, future climates at these currently occupied locations are predicted to become warmer throughout the year and drier during the frog's activity period (May – September). Fall and winter precipitation may increase, but as rain instead of snow. Earlier runoff and lower summer base flows may reduce connectivity between neighboring populations, which is already limited. Many of these changes could have negative effects on remaining populations over the next 50–80 years, but milder winters, longer growing seasons, and wetter falls might positively affect survival and dispersal. Collectively, however, seasonal shifts in temperature, precipitation, and stream flow patterns could reduce habitat suitability and connectivity for frogs and possibly other aquatic species inhabiting streams in this arid region.

  17. Genome-Wide Supported Risk Variants in MIR137, CACNA1C, CSMD1, DRD2, and GRM3 Contribute to Schizophrenia Susceptibility in Pakistani Population.

    Science.gov (United States)

    Fatima, Ambrin; Farooq, Muhammad; Abdullah, Uzma; Tariq, Muhammad; Mustafa, Tanveer; Iqbal, Muhammad; Tommerup, Niels; Mahmood Baig, Shahid

    2017-09-01

    Schizophrenia is a chronic neuropsychiatric disease afflicting around 1.1% of the population worldwide. Recently, MIR137 , CACNA1C , CSMD1 , DRD2 , and GRM3 have been reported as the most robustly emerging candidates involved in the etiology of schizophrenia. In this case control study, we performed an association analysis of rs1625579 ( MIR137 ), rs1006737, rs4765905 ( CACNA1C ), rs10503253 ( CSMD1 ), rs1076560 ( DRD2 ), rs12704290, rs6465084, and rs148754219 ( GRM3 ) in Pakistani population. Schizophrenia was diagnosed on the basis of the Diagnostic and Statistical Manual of Mental Disorders 4th ed (DSM-IV). Detailed clinical information, family history of all patients and healthy controls were collected. RFLP based case control association study was performed in a Pakistani cohort of 508 schizophrenia patients and 300 healthy control subjects. Alleles and genotype frequencies were calculated using SPSS. A significant difference in the genotype and allele frequencies for rs4765905, rs1076560 and rs6465084 were found between the patients and controls (p=0.000). This study provides substantial evidence supporting the role of CACNA1C , GRM3 and DRD2 as schizophrenia susceptibility genes in Pakistani population.

  18. 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 F4, and the Normative Aging Study. Environ Health Perspect 124:983-990; http://dx.doi.org/10.1289/ehp.1509966.

  19. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

    Science.gov (United States)

    Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

    2018-06-01

    We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

  20. 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

  1. 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

    We conducted a genome-wide association study of type 2 diabetes (T2D) using 459,359 SNPs in a Japanese population with a three-stage study design (stage 1, 4,470 cases and 3,071 controls; stage 2, 2,886 cases and 3,087 controls; stage 3, 3,622 cases and 2,356 controls). We identified new associat...

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

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    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.

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

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    Ma, Kaifeng; Sun, Lidan; Cheng, Tangren; Pan, Huitang; Wang, Jia; Zhang, Qixiang

    2018-01-01

    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.

  4. The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle.

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    Spinks, Phillip Q; Thomson, Robert C; Shaffer, H Bradley

    2014-05-01

    As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle (Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller-scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management. © 2014 John Wiley & Sons Ltd.

  5. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.

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    Wanling Yang

    2010-02-01

    Full Text Available Systemic lupus erythematosus is a complex and potentially fatal autoimmune disease, characterized by autoantibody production and multi-organ damage. By a genome-wide association study (320 patients and 1,500 controls and subsequent replication altogether involving a total of 3,300 Asian SLE patients from Hong Kong, Mainland China, and Thailand, as well as 4,200 ethnically and geographically matched controls, genetic variants in ETS1 and WDFY4 were found to be associated with SLE (ETS1: rs1128334, P = 2.33x10(-11, OR = 1.29; WDFY4: rs7097397, P = 8.15x10(-12, OR = 1.30. ETS1 encodes for a transcription factor known to be involved in a wide range of immune functions, including Th17 cell development and terminal differentiation of B lymphocytes. SNP rs1128334 is located in the 3'-UTR of ETS1, and allelic expression analysis from peripheral blood mononuclear cells showed significantly lower expression level from the risk allele. WDFY4 is a conserved protein with unknown function, but is predominantly expressed in primary and secondary immune tissues, and rs7097397 in WDFY4 changes an arginine residue to glutamine (R1816Q in this protein. Our study also confirmed association of the HLA locus, STAT4, TNFSF4, BLK, BANK1, IRF5, and TNFAIP3 with SLE in Asians. These new genetic findings may help us to gain a better understanding of the disease and the functions of the genes involved.

  6. Effects of Find Thirty every day(R): cross-sectional findings from a Western Australian population-wide mass media campaign, 2008-2010.

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    Leavy, Justine E; Rosenberg, Michael; Bauman, Adrian E; Bull, Fiona C; Giles-Corti, Billie; Shilton, Trevor; Maitland, Clover; Barnes, Rosanne

    2013-08-01

    Internationally, over the last four decades large-scale mass media campaigns have been delivered to promote physical activity and its associated health benefits. In 2002-2005, the first Western Australian statewide adult physical activity campaign Find Thirty. It's Not a Big Exercise was launched. In 2007, a new iteration of the campaign was proposed with new objectives, executions, and tag line Find Thirty every day(®). This article reports on the population-level effects of the Find Thirty every day (®) campaign from 2008 to 2010, with a focus on changes in awareness, intention, and physical activity. Evaluation of the campaign involved pre- and posttest serial cross-sectional surveys. Baseline data were collected in May 2008, and subsequent surveys in 2009 and 2010. Samples sizes were as follows: baseline (n = 972), first follow-up (n = 938), and second follow-up (n = 937). Data were derived from self-reported responses to a random-sample computer-assisted telephone interview. Total awareness increased from 30.4% at baseline to 48.5% at second follow-up. Total awareness was higher in women and low socioeconomic status adults. Intention was 21.0%, double that reported at baseline. There were positive significant changes from baseline to first follow-up across all four categories: walking, moderate, vigorous, and total physical activity. There also were positive significant changes for self-reported walking from baseline to second follow-up. Find Thirty every day (®) resulted in an increase in awareness, intention, walking, vigorous intensity, and total level of physical activity in priority target groups. Campaign effects should be further examined by subgroups to identify the most receptive population segments.

  7. Anemia and Iron Status Among Different Body Size Phenotypes in Chinese Adult Population: a Nation-Wide, Health and Nutrition Survey.

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    Li, Jiang; Xiao, Cheng; Yang, Hui; Zhou, Yun; Wang, Rui; Cao, Yongtong

    2017-12-09

    Previous studies have shown that there is a controversial relationship between iron homeostasis and obesity. This study aims to explore the relationship of anemia and iron status with different body size phenotypes in adult Chinese population. Using information on iron status-related parameters and lifestyle data from 8462 participants of the 2009 wave of China Health and Nutrition Survey (2009 CHNS), we performed multivariable logistic regression analyses to estimate the odds ratios (ORs) for the risk of anemia and iron parameters according to different body size phenotypes. Participants with higher body mass index (BMI) had a lower anemia prevalence with significant trends in both metabolic status groups (P different metabolic status groups and in different body size phenotypes, respectively. The ORs for higher ferritin and transferrin increased across different body size phenotypes in both genders, and for sTfR/log ferritin index decreased (P < 0.01 for trend). This association was still statistically significant after adjustment for multiple confounders. We found an inverse association of BMI levels with the prevalence of anemia and strong association of serum ferritin and transferrin with higher risk of obesity or overweight in both metabolic status groups.

  8. Philippines -- country wide water development projects and funds needed. Water crisis in Manila coincide with parliamentarians seminar on water resources and population.

    Science.gov (United States)

    1997-01-01

    The Philippines' Clean Water Act was developed to protect the country's remaining water resources by institutionalizing mechanisms to monitor, regulate, and control human and industrial activities which contribute to the ongoing environmental degradation of marine and freshwater resources. Approximately 70 participants attended the Philippine Parliamentarians' Conference on Water Resources, Population and Development held December 3-4, 1997, at the Sulo Hotel in Quezon City. Participants included the legislative staff of the members of the House of Representatives and the Senate, Committee Secretaries of the House and Senate, and government and nongovernmental organization officials. Following the opening programs, panel discussions were held on the role of nongovernmental organizations as legitimate monitors of governments' activities; the need to evaluate water sector assessment methods, water policy and strategy, and water legislation standards; and waste water treatment and sewerage systems used in households and industries. The following issues were raised during the conference's open forum: the need to implement new methods in water resource management; the handling of water for both economic and social purposes; the need to implement guidelines, policies, and pricing mechanisms on bottled water; regulating the construction of recreational facilities such as golf courses; and transferring watershed rehabilitation from the Department of Environment and Natural Resources to local water districts. A declaration was prepared and signed by the participants at the close of the conference.

  9. [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].

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    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.

  10. Increased risks of tic disorders in children with epilepsy: A nation-wide population-based case-control study in Taiwan.

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    Weng, Wen-Chin; Huang, Hui-Ling; Wong, Lee Chin; Jong, Yuh-Jyh; Yin, Yun-Ju; Chen, Hong-An; Lee, Wang-Tso; Ho, Shinn-Ying

    2016-01-01

    Both epilepsy and tic disorders may share common mechanisms with the involvement of abnormal cortical-basal ganglion circuit connection and dopaminergic dysfunction. However, the association between epilepsy and tic disorders has never been studied. This study investigated the risks of developing tic disorders among children with epilepsy using databases of a universal health insurance system in Taiwan. The data analyzed in this study were retrieved from the National Health Insurance Research Database in Taiwan. The study cohort included children with epilepsy between 2001 and 2007 (n=2629) and a three-fold age- and gender-matched controls (n=7887). All subjects were followed up for 3 years from the date of cohort entry to identify their admissions due to tic disorders (ICD-9-CM codes 307.2, 307.20-307.23). Cox hazard regression analysis was performed to estimate the effect of epilepsy on the occurrence of tics. The epilepsy cohort had a higher prevalence of tics (1.7% vs. 0.2%), and a 8.70-fold increased risk of developing a tic disorder compared with the controls (adjusted hazard ratio (AHR) 8.70, 95% confidence interval (CI) 4.26-16.37, ptic disorder (AHR 1.90, 95% CI=1.04-3.46, ptic disorders. This nationwide population-based cohort study, for the first time, demonstrated that there is a significantly increased risk for tic disorders among children with epilepsy. We also found males, attention deficit disorder and the use of multiple AEDs to be independent risk factors of tic disorders. Closely evaluating possible tic disorders would be crucial for improving the outcome and life quality in children with epilepsy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Prevalence and correlates of night eating in the German general population.

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    Martina de Zwaan

    Full Text Available Recently, night eating syndrome (NES was included into the DSM-5 as an example of "Other Specified Feeding and Eating Disorders." The study provides insight into the population prevalence of NES using a large representative German population sample (n = 2,460 with a wide age range (14-85 years. The prevalence of NES was 1.1% using a cut-off on the Night Eating Questionnaire (NEQ of 25. A positive screening for NES was positively associated with depression and anxiety, eating disorder psychopathology, and body weight.

  12. A dynamic urban air pollution population exposure assessment study using model and population density data derived by mobile phone traffic

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    Gariazzo, Claudio; Pelliccioni, Armando; Bolignano, Andrea

    2016-04-01

    A dynamic city-wide air pollution exposure assessment study has been carried out for the urban population of Rome, Italy, by using time resolved population distribution maps, derived by mobile phone traffic data, and modelled air pollutants (NO2, O3 and PM2.5) concentrations obtained by an integrated air dispersion modelling system. More than a million of persons were tracked during two months (March and April 2015) for their position within the city and its surroundings areas, with a time resolution of 15 min and mapped over an irregular grid system with a minimum resolution of 0.26 × 0.34 Km2. In addition, demographics information (as gender and age ranges) were available in a separated dataset not connected with the total population one. Such BigData were matched in time and space with air pollution model results and then used to produce hourly and daily resolved cumulative population exposures during the studied period. A significant mobility of population was identified with higher population densities in downtown areas during daytime increasing of up to 1000 people/Km2 with respect to nigh-time one, likely produced by commuters, tourists and working age population. Strong variability (up to ±50% for NO2) of population exposures were detected as an effect of both mobility and time/spatial changing in pollutants concentrations. A comparison with the correspondent stationary approach based on National Census data, allows detecting the inability of latter in estimating the actual variability of population exposure. Significant underestimations of the amount of population exposed to daily PM2.5 WHO guideline was identified for the Census approach. Very small differences (up to a few μg/m3) on exposure were detected for gender and age ranges population classes.

  13. High participation rate among 25 721 patients with broad age range in a hospital-based research project involving whole-genome sequencing - the Lausanne Institutional Biobank.

    Science.gov (United States)

    Bochud, Murielle; Currat, Christine; Chapatte, Laurence; Roth, Cindy; Mooser, Vincent

    2017-10-24

    We aimed to evaluate the interest of adult inpatients and selected outpatients in engaging in a large, real-life, hospital-based, genomic medicine research project and in receiving clinically actionable incidental findings. Within the framework of the cross-sectional Institutional Biobank of Lausanne, Switzerland, a total of 25721 patients of the CHUV University Hospital were systematically invited to grant researchers access to their biomedical data and to donate blood for future analyses, including whole-genome sequencing. Multivariable logistic regression analysis was used to identify personal factors, including age, gender, religion, ethnicity, citizenship, education level and mode of admission, associated with willingness to participate in this genomic research project and with interest in receiving clinically actionable incidental findings. The overall participation rate was 79% (20343/25721). Participation rate declined progressively with age, averaging 83%, 75%, 67% and 62% in patients aged rate, but not with higher willingness to receive incidental findings within the population who had agreed to participate. A large proportion of adult patients, even among the elderly, are willing to actively participate and receive incidental findings in this systematic hospital-based precision and genomic medicine research program with broad consent.

  14. Stakeholder discussion to reduce population-wide sodium intake and decrease sodium in the food supply: a conference report from the American Heart Association Sodium Conference 2013 Planning Group.

    Science.gov (United States)

    Antman, Elliott M; Appel, Lawrence J; Balentine, Douglas; Johnson, Rachel K; Steffen, Lyn M; Miller, Emily Ann; Pappas, Antigoni; Stitzel, Kimberly F; Vafiadis, Dorothea K; Whitsel, Laurie

    2014-06-24

    A 2-day interactive forum was convened to discuss the current status and future implications of reducing sodium in the food supply and to identify opportunities for stakeholder collaboration. Participants included 128 stakeholders engaged in food research and development, food manufacturing and retail, restaurant and food service operations, regulatory and legislative activities, public health initiatives, healthcare, academia and scientific research, and data monitoring and surveillance. Presentation topics included scientific evidence for sodium reduction and public health policy recommendations; consumer sodium intakes, attitudes, and behaviors; food technologies and solutions for sodium reduction and sensory implications; experiences of the food and dining industries; and translation and implementation of sodium intake recommendations. Facilitated breakout sessions were conducted to allow for sharing of current practices, insights, and expertise. A well-established body of scientific research shows that there is a strong relationship between excess sodium intake and high blood pressure and other adverse health outcomes. With Americans getting >75% of their sodium from processed and restaurant food, this evidence creates mounting pressure for less sodium in the food supply. The reduction of sodium in the food supply is a complex issue that involves multiple stakeholders. The success of new technological approaches for reducing sodium will depend on product availability, health effects (both intended and unintended), research and development investments, quality and taste of reformulated foods, supply chain management, operational modifications, consumer acceptance, and cost. The conference facilitated an exchange of ideas and set the stage for potential collaboration opportunities among stakeholders with mutual interest in reducing sodium in the food supply and in Americans' diets. Population-wide sodium reduction remains a critically important component of

  15. 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

  16. A 10-Year Experience of Therapeutic Drug Monitoring (TDM) of Linezolid in a Hospital-wide Population of Patients Receiving Conventional Dosing: Is there Enough Evidence for Suggesting TDM in the Majority of Patients?

    Science.gov (United States)

    Pea, Federico; Cojutti, Pier Giorgio; Baraldo, Massimo

    2017-10-01

    A retrospective study was conducted to assess our 10-year experience of therapeutic drug monitoring (TDM) of linezolid in a large patient population to establish whether conventional dosing may result in adequate drug exposure in the majority of patients. Patients included in this study underwent TDM of linezolid trough concentration (C min ) during treatment with conventional doses of 600 mg every 12 hr in the period between January 2007 and June 2016. The desired range of C min was set between 2 and 7 mg/L (underexposure, C min   7 mg/L). Multivariate logistic regression analysis investigated variables potentially correlated with linezolid C min . One thousand and forty-nine patients had 2484 linezolid C min assessed during treatment with conventional doses. Median (IQR) linezolid C min was 5.08 mg/L (2.78-8.52 mg/L). Linezolid C min was within the desired range in 50.8% of cases (1262/2484). Overexposure (n = 821; 33%) occurred much more frequently than underexposure (n = 401; 16.2%) and was severe (>20 mg/L) in 3.9% of cases (98/2484). Linezolid overexposure was significantly associated with CrCL C -G estimates ≤40 mL/min. (OR 1.463; 95% CI 1.124-1.904, p = 0.005). Linezolid underexposure was significantly associated with CrCL C -G estimates >100 mL/min. (OR 3.046; 95% CI 2.234-4.152, p Linezolid C min was not correlated linearly with CrCL C -G (R 2  = 0.061). Variability in renal function explained only partially the very wide interindividual linezolid C min variability. Our study suggests that TDM could represent a valuable approach in optimizing linezolid exposure in the majority of patients. © 2017 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

  17. A preliminary study of the mini-mental state examination in a Spanish child population.

    Science.gov (United States)

    Rubial-Alvarez, Sandra; Machado, María-Clara; Sintas, Elena; de Sola, Susana; Böhm, Peter; Peña-Casanova, Jordi

    2007-11-01

    The Mini-Mental State Examination is one of the most widely used screening tests for the adult population in daily neurologic practice. The aim of this study was to describe and to analyze the results of the Mini-Mental State Examination administered to Spanish children and to assess the relationship between Mini-Mental State Examination scores and the child's mental age/intelligence quotient. The study population included 181 children whose ages ranged between 4 and 12 years. The neuropsychologic battery consisted of the Mini-Mental State Examination and Kaufman Brief Intelligence Test. Percentiles were obtained for the Mini-Mental State Examination total score according to age ranges. Performance gradually increased from 4 to 10 years of age when a plateau in the total Mini-Mental State Examination score was reached. At the age of 6 years, results exceeded 24 on average. Pairwise mean comparisons showed statistically significant differences between the age groups (P Mini-Mental State Examination score correlated significantly with the child's chronologic (r = 0.80, P mental (r = 0.76, P Mini-Mental State Examination in a Spanish child population as well as a first step for the assessment of the usefulness of this instrument as a cognitive screening tool for children's development.

  18. Genome-Wide Association Studies of a Broad Spectrum of Antisocial Behavior.

    Science.gov (United States)

    Tielbeek, Jorim J; Johansson, Ada; Polderman, Tinca J C; Rautiainen, Marja-Riitta; Jansen, Philip; Taylor, Michelle; Tong, Xiaoran; Lu, Qing; Burt, Alexandra S; Tiemeier, Henning; Viding, Essi; Plomin, Robert; Martin, Nicholas G; Heath, Andrew C; Madden, Pamela A F; Montgomery, Grant; Beaver, Kevin M; Waldman, Irwin; Gelernter, Joel; Kranzler, Henry R; Farrer, Lindsay A; Perry, John R B; Munafò, Marcus; LoParo, Devon; Paunio, Tiina; Tiihonen, Jari; Mous, Sabine E; Pappa, Irene; de Leeuw, Christiaan; Watanabe, Kyoko; Hammerschlag, Anke R; Salvatore, Jessica E; Aliev, Fazil; Bigdeli, Tim B; Dick, Danielle; Faraone, Stephen V; Popma, Arne; Medland, Sarah E; Posthuma, Danielle

    2017-12-01

    Antisocial behavior (ASB) places a large burden on perpetrators, survivors, and society. Twin studies indicate that half of the variation in this trait is genetic. Specific causal genetic variants have, however, not been identified. To estimate the single-nucleotide polymorphism-based heritability of ASB; to identify novel genetic risk variants, genes, or biological pathways; to test for pleiotropic associations with other psychiatric traits; and to reevaluate the candidate gene era data through the Broad Antisocial Behavior Consortium. Genome-wide association data from 5 large population-based cohorts and 3 target samples with genome-wide genotype and ASB data were used for meta-analysis from March 1, 2014, to May 1, 2016. All data sets used quantitative phenotypes, except for the Finnish Crime Study, which applied a case-control design (370 patients and 5850 control individuals). This study adopted relatively broad inclusion criteria to achieve a quantitative measure of ASB derived from multiple measures, maximizing the sample size over different age ranges. The discovery samples comprised 16 400 individuals, whereas the target samples consisted of 9381 individuals (all individuals were of European descent), including child and adult samples (mean age range, 6.7-56.1 years). Three promising loci with sex-discordant associations were found (8535 female individuals, chromosome 1: rs2764450, chromosome 11: rs11215217; 7772 male individuals, chromosome X, rs41456347). Polygenic risk score analyses showed prognostication of antisocial phenotypes in an independent Finnish Crime Study (2536 male individuals and 3684 female individuals) and shared genetic origin with conduct problems in a population-based sample (394 male individuals and 431 female individuals) but not with conduct disorder in a substance-dependent sample (950 male individuals and 1386 female individuals) (R2 = 0.0017 in the most optimal model, P = 0.03). Significant inverse genetic correlation

  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

    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; Sanna, Serena; van der Most, Peter J; Van Vliet-Ostaptchouk, Jana V.; Alizadeh, Behrooz Z; Hartman, Catharina A; Swertz, Morris; Oldehinkel, Albertine J; Snieder, Harold; Wolffenbuttel, Bruce H R

    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

  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

    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 E.H.; 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

  1. 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, Dorte; Salo, Perttu; Tanaka, Toshiko; van Iperen, Erik P. A.; Abecasis, Goncalo; Afaq, Saima; Alizadeh, Behrooz Z.; Bertoni, Alain G.; Bonnefond, Amelie; Bottcher, 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; Muller, Gabriele; Muller-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; Tonjes, Anke; Wareham, Nicholas J.; Willemsen, Gonneke; Wilsgaard, Tom; Hingorani, Aroon D.; Egan, Josephine; Ferrucci, Luigi; Hovingh, G. Kees; Jula, Antti; Kivimaki, Mika; Kumari, Meena; Njolstad, Inger; Palmer, Colin N. A.; Serrano Rios, Manuel; Stumvoll, Michael; Watkins, Hugh; Aung, Tin; Bluher, 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.; Korner, Antje; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lin, Xu; Liu, Yongmei; Loos, Ruth J. F.; Magnusson, Patrik K. E.; Marz, 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, Josee; Morris, Andrew P.; Tai, E.-Shyong; Selvin, Elizabeth; Rotter, Jerome I.; Langenberg, Claudia; Barroso, Ines; 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

  2. 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

  3. Just how wide should 'wide reading' be?

    Science.gov (United States)

    Lipscomb, Martin

    2015-10-01

    Educationalists introduce students to literature search strategies that, with rare exceptions, focus chiefly on the location of primary research reports and systematic reviews of those reports. These sources are, however, unlikely to adequately address the normative and/or metaphysical questions that nurses frequently and legitimately interest themselves in. To meet these interests, non-research texts exploring normative and/or metaphysical topics might and perhaps should, in some situations, be deemed suitable search targets. This seems plausible and, moreover, students are encouraged to 'read widely'. Yet accepting this proposition creates significant difficulties. Specifically, if non-research scholarly sources and artistic or literary (humanities) products dealing with normative/metaphysical issues were included in what are, at present, scientifically orientated searches, it is difficult to draw boundaries around what--if anything--is to be excluded. Engaging with this issue highlights problems with qualitative scholarship's designation as 'evidence'. Thus, absurdly, if qualitative scholarship's findings are labelled evidence because they generate practice-relevant understanding/insight, then any literary or artistic artefact (e.g. a throwaway lifestyle magazine) that generates kindred understandings/insights is presumably also evidence? This conclusion is rejected and it is instead proposed that while artistic, literary, and qualitative inquiries can provide practitioners with powerful and stimulating non-evidential understanding, these sources are not evidence as commonly conceived. © 2015 John Wiley & Sons Ltd.

  4. 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.

  5. 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

  6. 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

  7. Wide angle isotope separator

    International Nuclear Information System (INIS)

    Kantrowitz, A.

    1976-01-01

    A method and apparatus is described for particle separation. The method uses a wide angle radially expanding vapor of a particle mixture. In particular, selective ionization of one isotope type in the particle mixture is produced in a multichamber separator and the ionized isotope type is accelerated out of the path of the vapor expansion for separate collection

  8. Are regional variations in activity of dispatcher-assisted cardiopulmonary resuscitation associated with out-of-hospital cardiac arrests outcomes? A nation-wide population-based cohort study.

    Science.gov (United States)

    Nishi, Taiki; Kamikura, Takahisa; Funada, Akira; Myojo, Yasuhiro; Ishida, Tetsuya; Inaba, Hideo

    2016-01-01

    Dispatcher-assisted cardiopulmonary resuscitation (DA-CPR) impacts the rates of bystander CPR (BCPR) and survival after out-of-hospital cardiac arrests (OHCAs). This study aimed to elucidate whether regional variations in indexes for BCPR and emergency medical service (EMS) may be associated with OHCA outcomes. We conducted a population-based observational study involving 157,093 bystander-witnessed, resuscitation-attempted OHCAs without physician involvement between 2007 and 2011. For each index of BCPR and EMS, we classified the 47 prefectures into the following three groups: advanced, intermediate, and developing regions. Nominal logit analysis followed by multivariable logistic regression including OHCA backgrounds was employed to examine the association between neurologically favourable 1-month survival, and regional classifications based on BCPR- and EMS-related indexes. Logit analysis including all regional classifications revealed that the number of BLS training course participants per population or bystander's own performance of BCPR without DA-CPR was not associated with the survival. Multivariable logistic regression including the OHCA backgrounds known to be associated with survival (BCPR provision, arrest aetiology, initial rhythm, patient age, time intervals of witness-to-call and call-to-arrival at patient), the following regional classifications based on DA-CPR but not on EMS were associated with survival: sensitivity of DA-CPR [adjusted odds ratio (95% confidence intervals) for advanced region; those for intermediate region, with developing region as reference, 1.277 (1.131-1.441); 1.162 (1.058-1.277)]; the proportion of bystanders to follow DA-CPR [1.749 (1.554-1.967); 1.280 (1.188-1.380)]. Good outcomes of bystander-witnessed OHCAs correlate with regions having higher sensitivity of DA-CPR and larger proportion of bystanders to follow DA-CPR. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. Comparison of the Multiattribute Utility Instruments EQ-5D and SF-6D in a Europe-Wide Population-Based Cohort of Patients with Inflammatory Bowel Disease 10 Years after Diagnosis.

    Science.gov (United States)

    Huppertz-Hauss, Gert; Aas, Eline; Lie Høivik, Marte; Langholz, Ebbe; Odes, Selwyn; Småstuen, Milada; Stockbrugger, Reinhold; Hoff, Geir; Moum, Bjørn; Bernklev, Tomm

    2016-01-01

    Background. The treatment of chronic inflammatory bowel disease (IBD) is costly, and limited resources call for analyses of the cost effectiveness of therapeutic interventions. The present study evaluated the equivalency of the Short Form 6D (SF-6D) and the Euro QoL (EQ-5D), two preference-based HRQoL instruments that are broadly used in cost-effectiveness analyses, in an unselected IBD patient population. Methods. IBD patients from seven European countries were invited to a follow-up visit ten years after their initial diagnosis. Clinical and demographic data were assessed, and the Short Form 36 (SF-36) was employed. Utility scores were obtained by calculating the SF-6D index values from the SF-36 data for comparison with the scores obtained with the EQ-5D questionnaire. Results. The SF-6D and EQ-5D provided good sensitivities for detecting disease activity-dependent utility differences. However, the single-measure intraclass correlation coefficient was 0.58, and the Bland-Altman plot indicated numerous values beyond the limits of agreement. Conclusions. There was poor agreement between the measures retrieved from the EQ-5D and the SF-6D utility instruments. Although both instruments may provide good sensitivity for the detection of disease activity-dependent utility differences, the instruments cannot be used interchangeably. Cost-utility analyses performed with only one utility instrument must be interpreted with caution.

  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. Comparison of the Multiattribute Utility Instruments EQ-5D and SF-6D in a Europe-Wide Population-Based Cohort of Patients with Inflammatory Bowel Disease 10 Years after Diagnosis

    Directory of Open Access Journals (Sweden)

    Gert Huppertz-Hauss

    2016-01-01

    Full Text Available Background. The treatment of chronic inflammatory bowel disease (IBD is costly, and limited resources call for analyses of the cost effectiveness of therapeutic interventions. The present study evaluated the equivalency of the Short Form 6D (SF-6D and the Euro QoL (EQ-5D, two preference-based HRQoL instruments that are broadly used in cost-effectiveness analyses, in an unselected IBD patient population. Methods. IBD patients from seven European countries were invited to a follow-up visit ten years after their initial diagnosis. Clinical and demographic data were assessed, and the Short Form 36 (SF-36 was employed. Utility scores were obtained by calculating the SF-6D index values from the SF-36 data for comparison with the scores obtained with the EQ-5D questionnaire. Results. The SF-6D and EQ-5D provided good sensitivities for detecting disease activity-dependent utility differences. However, the single-measure intraclass correlation coefficient was 0.58, and the Bland-Altman plot indicated numerous values beyond the limits of agreement. Conclusions. There was poor agreement between the measures retrieved from the EQ-5D and the SF-6D utility instruments. Although both instruments may provide good sensitivity for the detection of disease activity-dependent utility differences, the instruments cannot be used interchangeably. Cost-utility analyses performed with only one utility instrument must be interpreted with caution.

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

    Science.gov (United States)

    Miao, Yuanxin; Soudy, Fathia; Xu, Zhong; Liao, Mingxing; Zhao, Shuhong; Li, Xinyun

    2017-01-01

    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.

  13. 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.

  14. 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....... It distinguishes two main groups of scholarly definitions, some careful and narrow, and some appearing to match loose media usage. However, it shows that even these scholarly definitions actually make important distinctions between jihadism and associated political and theological ideology. The article closes...

  15. With eyes wide open

    DEFF Research Database (Denmark)

    Frølunde, Lisbeth; Pedersen, Chistina Hee

    2013-01-01

    and that vulnerability and discomfort are often overlooked as transformative forces. The analysis draws on data from a classroom context in which university students tested methods for facilitating creative thinking in a course on data production and creativity. The data stem from a session on the method “Lego Serious...... in constructions of group identity when an external facilitator disrupts a context. We argue that the facilitation of creative methods calls for keeping our eyes wide open for tensions, for they are the mulch that improves the soil....

  16. Population crises and population cycles.

    Science.gov (United States)

    Russell, C; Russell, W M

    2000-01-01

    To prevent a population irretrievably depleting its resources, mammals have evolved a behavioural and physiological response to population crisis. When a mammalian population becomes dangerously dense, there is a reversal of behaviour. Co-operation and parental behaviour are replaced by competition, dominance and aggressive violence, leading to high mortality, especially of females and young, and a reduced population. The stress of overpopulation and the resulting violence impairs both the immune and the reproductive systems. Hence epidemics complete the crash of the population, and reproduction is slowed for three or four generations, giving the resources ample time to recover. In some mammal species, crisis and crisis response recur regularly, leading to cycles of population growth and relapse, oscillating about a fixed mean. Population crisis response and population cycles have been equally prominent in the history of human societies. But in man successive advances in food production have made possible growing populations, though with every such advance population soon outgrew resources again. Hence human cycles have been superimposed on a rising curve, producing a saw-tooth graph. Because advances in food production amounted to sudden disturbances in the relations between human populations and their environments, the crisis response in man has failed to avert famine and resource damage. In the large human societies evolved since the coming of settled agriculture and cities, the basic effects of violence, epidemics, famine and resource damage have been mediated by such specifically human disasters as inflation, unemployment, and political tyranny. An account of past crises, periods of relative relief from population pressure, and resulting cycles, is given for a number of regions: China, North Africa and Western Asia, the northern Mediterranean, and north-western Europe. The paper ends with an account of the present world-wide population crisis, and the solution

  17. World wide spatial capital.

    Science.gov (United States)

    Sen, Rijurekha; Quercia, Daniele

    2018-01-01

    In its most basic form, the spatial capital of a neighborhood entails that most aspects of daily life are located close at hand. Urban planning researchers have widely recognized its importance, not least because it can be transformed in other forms of capital such as economical capital (e.g., house prices, retail sales) and social capital (e.g., neighborhood cohesion). Researchers have already studied spatial capital from official city data. Their work led to important planning decisions, yet it also relied on data that is costly to create and update, and produced metrics that are difficult to compare across cities. By contrast, we propose to measure spatial capital in cheap and standardized ways around the world. Hence the name of our project "World Wide Spatial Capital". Our measures are cheap as they rely on the most basic information about a city that is currently available on the Web (i.e., which amenities are available and where). They are also standardized because they can be applied in any city in the five continents (as opposed to previous metrics that were mainly applied in USA and UK). We show that, upon these metrics, one could produce insights at the core of the urban planning discipline: which areas would benefit the most from urban interventions; how to inform planning depending on whether a city's activity is mono- or poly-centric; how different cities fare against each other; and how spatial capital correlates with other urban characteristics such as mobility patterns and road network structure.

  18. Weaving a wide net.

    Science.gov (United States)

    Garber, Linda

    2002-10-01

    SUMMARY Any single approach tostudents' heterosexism and homophobia, however well conceived and executed, is most successful when supported by an integrated campus approach to the problem. Taking as a model the multifaceted efforts at California State University, Fresno-a large public institution located in what can be considered the state's Bible Belt-this essay discusses the strengths and logistics of a campus-wide program to address homophobia and alleviate LGBTQ students' feelings of alienation from the institution and their oppression in society. The efforts of CSUF take place at a number of different levels-classroom, academic department, student services, faculty networking-and can be considered a successful work in progress.

  19. World wide spatial capital.

    Directory of Open Access Journals (Sweden)

    Rijurekha Sen

    Full Text Available In its most basic form, the spatial capital of a neighborhood entails that most aspects of daily life are located close at hand. Urban planning researchers have widely recognized its importance, not least because it can be transformed in other forms of capital such as economical capital (e.g., house prices, retail sales and social capital (e.g., neighborhood cohesion. Researchers have already studied spatial capital from official city data. Their work led to important planning decisions, yet it also relied on data that is costly to create and update, and produced metrics that are difficult to compare across cities. By contrast, we propose to measure spatial capital in cheap and standardized ways around the world. Hence the name of our project "World Wide Spatial Capital". Our measures are cheap as they rely on the most basic information about a city that is currently available on the Web (i.e., which amenities are available and where. They are also standardized because they can be applied in any city in the five continents (as opposed to previous metrics that were mainly applied in USA and UK. We show that, upon these metrics, one could produce insights at the core of the urban planning discipline: which areas would benefit the most from urban interventions; how to inform planning depending on whether a city's activity is mono- or poly-centric; how different cities fare against each other; and how spatial capital correlates with other urban characteristics such as mobility patterns and road network structure.

  20. Wide area monitoring study

    International Nuclear Information System (INIS)

    Wogman, N.A.; Holdren, G.R. Jr.

    1999-01-01

    Environmental sampling can be used to complement the safeguarding of nuclear material, especially in the detection of undeclared nuclear activities. Routine monitoring of nuclear installations has provided valuable information about the fate of key signature materials within different environmental settings. The approach collates information regarding the generation of individual radiochemical signatures within different nuclear processes, the potential for release of these signatures to the environment and, the chemical form and mobility of the signatures in environmental media along which the material could migrate. Meteorological, geological and hydrological information is used to determine where to sample, what to sample, and how often to sample to provide the greatest likelihood for detection. Multiple strategies can be used to implement wide area monitoring for safeguards purposes. The most complex, and expensive of these, involves establishing extensive networks of fixed location sampling sites. The sites would be operated continuously, and would be instrumented with automated sampling, analysis, and communication equipment to relay information regarding potential anomalies to control centers in near-real time. Alternative strategies can be used to supplement fixed location monitoring equipment, especially in regions that cannot support (financially or logistically) the fixed stations. Through combinations of these various strategies, using a variety of environmental media to monitor a region, we believe that a competent network, one with a quantifiable probability for detecting undeclared nuclear activities, can be designed. While this approach cannot and should not replace other inspection and monitoring activities, it can potentially contribute valuable information to an international safeguards system. (author)

  1. Wide Awake Hand Surgery.

    Science.gov (United States)

    Lied, Line; Borchgrevink, Grethe E; Finsen, Vilhjalmur

    2017-09-01

    "Wide awake hand surgery", where surgery is performed in local anaesthesia with adrenaline, without sedation or a tourniquet, has become widespread in some countries. It has a number of potential advantages and we wished to evaluate it among our patients. All 122 patients treated by this method during one year were evaluated by the surgeons and the patients on a numerical scale from 0 (best/least) to 10 (worst/most). Theatre time was compared to that recorded for a year when regional or general anaesthesia had been used. The patients' mean score for the general care they had received was 0.1 (SD 0.6), for pain during lidocaine injection 2.4 (SD 2.2), for pain during surgery 0.9 (SD 1.5), and for other discomfort during surgery 0.5 (SD 1.4). Eight reported that they would want general anaesthesia if they were to be operated again. The surgeons' mean evaluation of bleeding during surgery was 1.6 (SD 1.8), oedema during surgery 0.4 (SD 1.1), general disadvantages with the method 1.0 (SD 1.6) and general advantages 6.5 (SD 4.3). The estimation of advantages was 9.9 (DS 0.5) for tendon suture. 28 patients needed intra-operative additional anaesthesia. The proportion was lower among trained hand surgeons and fell significantly during the study period. Non-surgical theatre time was 46 (SD 15) minutes during the study period and 55 (SD 22) minutes during the regional/general period (p theatre.

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

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

    gain experience that will benefit other countries in the region looking to implement programs to reduce dietary salt intake. Project duration: February 2012 to February 2016. Funding: CA$284,190. Lead Researchers: Adriana Blanco-Metzler. (ablanco@inciensa.sa.cr), Institute for Research and. Education on Nutrition and ...

  3. 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

  4. UNUSUALLY WIDE BINARIES: ARE THEY WIDE OR UNUSUAL?

    International Nuclear Information System (INIS)

    Kraus, Adam L.; Hillenbrand, Lynne A.

    2009-01-01

    We describe an astrometric and spectroscopic campaign to confirm the youth and association of a complete sample of candidate wide companions in Taurus and Upper Sco. Our survey found 15 new binary systems (three in Taurus and 12 in Upper Sco) with separations of 3''-30'' (500-5000 AU) among all of the known members with masses of 2.5-0.012 M sun . The total sample of 49 wide systems in these two regions conforms to only some expectations from field multiplicity surveys. Higher mass stars have a higher frequency of wide binary companions, and there is a marked paucity of wide binary systems near the substellar regime. However, the separation distribution appears to be log-flat, rather than declining as in the field, and the mass ratio distribution is more biased toward similar-mass companions than the initial mass function or the field G-dwarf distribution. The maximum separation also shows no evidence of a limit at ∼ sun . We attribute this result to the post-natal dynamical sculpting that occurs for most field systems; our binary systems will escape to the field intact, but most field stars are formed in denser clusters and undergo significant dynamical evolution. In summary, only wide binary systems with total masses ∼ sun appear to be 'unusually wide'.

  5. Effect of geographical and ethnic variation on Dysphonia Severity Index: a study of Indian population.

    Science.gov (United States)

    Jayakumar, T; Savithri, S R

    2012-01-01

    Dysphonia Severity Index (DSI) is a widely used multiparametric approach to objectively quantify the voice quality. Few research groups have investigated the test-retest, interobserver variability, and influence of age and gender. They have also verified the application of DSI in various voice rehabilitation conditions. However, all these studies have been conducted on European population. There is a possibility of variation in the basic parameters of DSI across geographical and ethnic groups. Hence, the present study evaluated DSI in Indian population. One hundred twenty voluntary participants (60 males, 60 females) who had G(0) on the Grade, Roughness, Breathiness, Aesthenia, Strain (GRBAS) scale participated in the study (age range of 18-25 years, M=21.8, standard deviation=2.7). Maximum phonation time (MPT), frequency intensity, and jitter measurements were made using CSL 4500 (Kay Elemetrics, Pine Brook, NJ). Results showed noticeable difference between Indian and European population on MPT, Highest frequency (F(0)-High), and DSI values. Significant gender difference was also observed on MPT and F(0)-High. Test-retest reliability showed >95% for all the parameters. The MPT decrement lead to a reduction in the overall DSI value in both the genders. These results of the study caution voice professionals to reinvestigate and establish their own norms for their geographical and ethnic groups. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  6. Tinnitus: an epidemiologic study in Iranian population.

    Directory of Open Access Journals (Sweden)

    Maryam Jalessi

    2013-12-01

    Full Text Available A wide range of population, 4% to 30%, suffers from tinnitus that is defined as perception of sound without apparent acoustic stimulus. We conducted the present study to determine the prevalence of tinnitus in Iranian population; Tehran province. This cross-sectional study was conducted from January 2009 to December 2009, recruiting 3207 individuals (age range, 7-98 who were residing in Tehran province, Iran. Participants were asked to fill two questionnaires; the validated Persian version of Tinnitus Questionnaire (TQ and another one that was specifically designed for this study. Prevalence of tinnitus and its association factors were evaluated. 3207 participants enrolled into our study comprising 1429 (44.7% male and 1765 (55.3% female with mean age of 55.01±17.85. Of total of 3207 participants, 146 (4.6% had tinnitus consisting of 80 male (54.8% and 66 (45.2% female participants. It showed a rising trend with increasing age that was especially significant after the sixth decade of life (P=0.001. The analysis showed mean TQ global score of 35.96±25.52 that was significantly different between male and female participants (P=0.051 and had no significant correlation with increasing age (Spearman's r=0.1, P=0.10. The tinnitus intensity was moderate to very severe in 95 (56.1% of the participants. Its severity level was not significantly different between men and women (P=0.09. Tinnitus intensity had no significant association with increasing age (Spearman's r=0.1, P=0.31. Patients with higher TQ global score had higher tinnitus intensities (P=0.001. The annoyance level was significantly different between men and women (P=0.04 and its impact on the participants daily routine functions were significantly higher in men (P=0.003. Given the results of the study, demonstrating that prevalence of tinnitus in Iranian population (Tehran province was lower than the other countries and had a direct correlation with increasing age only after the sixth

  7. 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.

  8. World-wide environmental problems

    International Nuclear Information System (INIS)

    Wohlers, H.C.

    1975-01-01

    Man and the physical and natural resources necessary to support him in a civilized society are on a collision course. It is simple to say that man cannot continue to grow in number at an ever-increasing rate without a destructive effect upon the environment. Positive scientific proof for this impending calamity is not now available, yet many indications--sometimes physical and sometimes natural--point toward major world-wide environmental troubles in the near future. A number of environmental problems are described, particularly as they relate to the total world system. A computer model simulating future world-wide environmental trends from 1900 to 2100 A.D. is evaluated and suggested as a major tool for data-gathering purposes to determine the extent of world-wide environmental problems. It is suggested that scientists take an active role in the study of the environment, particularly in relation to man's future on earth

  9. Wide gap semiconductor microwave devices

    International Nuclear Information System (INIS)

    Buniatyan, V V; Aroutiounian, V M

    2007-01-01

    A review of properties of wide gap semiconductor materials such as diamond, diamond-like carbon films, SiC, GaP, GaN and AlGaN/GaN that are relevant to electronic, optoelectronic and microwave applications is presented. We discuss the latest situation and perspectives based on experimental and theoretical results obtained for wide gap semiconductor devices. Parameters are taken from the literature and from some of our theoretical works. The correspondence between theoretical results and parameters of devices is critically analysed. (review article)

  10. World Wide Web Homepage Design.

    Science.gov (United States)

    Tillman, Michael L.

    This paper examines hypermedia design and draws conclusions about how educational research and theory applies to various aspects of World Wide Web (WWW) homepage design. "Hypermedia" is defined as any collection of information which may be textual, graphical, visual, or auditory in nature and which may be accessed via a nonlinear route.…

  11. The World Wide Web Revisited

    Science.gov (United States)

    Owston, Ron

    2007-01-01

    Nearly a decade ago the author wrote in one of the first widely-cited academic articles, Educational Researcher, about the educational role of the web. He argued that educators must be able to demonstrate that the web (1) can increase access to learning, (2) must not result in higher costs for learning, and (3) can lead to improved learning. These…

  12. 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.

  13. Wide range neutron flux monitor

    International Nuclear Information System (INIS)

    Endo, Yorimasa; Fukushima, Toshiki.

    1983-01-01

    Purpose: To provide a wide range neutron-flux monitor adapted such that the flux monitoring function and alarming function can automatically by shifted from pulse counting system to cambel method system. Constitution: A wide range neutron-flux monitor comprises (la) pulse counting system and (lb) cambel-method system for inputting detection signals from neutron detectors and separating them into signals for the pulse measuring system and the cambel measuring system, (2) overlap detection and calculation circuit for detecting the existence of the overlap of two output signals from the (la) and (lb) systems, and (3) trip circuit for judging the abnormal state of neutron detectors upon input of the detection signals. (Seki, T.)

  14. NCenter wide band neutrino beam

    International Nuclear Information System (INIS)

    Stutte, L.G.

    1985-01-01

    This memo describes the physical properties of the currently operating N-Center wide band neutrino beam---commonly called the triplet train, following a past tradition of a triplet lens configuration. In reality, in order to gain a larger momentum acceptance and to minimize the angular divergence of the beam, a quadruplet beam (4 lenses) employing point-to-parallel optics at a central momentum of 300 GeV was built. 6 refs., 13 figs., 1 tab

  15. Wide range neutron detection system

    International Nuclear Information System (INIS)

    Todt, W.H. Sr.

    1978-01-01

    A neutron detection system for reactor control is described which is operable over a wide range of neutron flux levels. The system includes a fission type ionization chamber neutron detector, means for gamma and alpha signal compensation, and means for operating the neutron detector in the pulse counting mode for low neutron flux levels, and in the direct current mode for high neutron flux levels

  16. 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.

  17. 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.

  18. World wide developments in shortwall and wide web mining techniques

    Energy Technology Data Exchange (ETDEWEB)

    Pollard, T

    1975-11-01

    The paper describes the progress to date with continuous pillar extraction, and how the typical longwall powered support has been modified to be both strong enough and stable enough to provide roof support for very wide webs. It also describes the operating systems which have been specially designed. The next stages of development are discussed, particularly the provision of continuous conveyor haulage in place of the present-day shuttle car. The author suggests that marrying American coal-getting technology and British roof support technology might increase productivity.

  19. 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

  20. Wide-range voltage modulation

    International Nuclear Information System (INIS)

    Rust, K.R.; Wilson, J.M.

    1992-06-01

    The Superconducting Super Collider's Medium Energy Booster Abort (MEBA) kicker modulator will supply a current pulse to the abort magnets which deflect the proton beam from the MEB ring into a designated beam stop. The abort kicker will be used extensively during testing of the Low Energy Booster (LEB) and the MEB rings. When the Collider is in full operation, the MEBA kicker modulator will abort the MEB beam in the event of a malfunction during the filling process. The modulator must generate a 14-μs wide pulse with a rise time of less than 1 μs, including the delay and jitter times. It must also be able to deliver a current pulse to the magnet proportional to the beam energy at any time during ramp-up of the accelerator. Tracking the beam energy, which increases from 12 GeV at injection to 200 GeV at extraction, requires the modulator to operate over a wide range of voltages (4 kV to 80 kV). A vacuum spark gap and a thyratron have been chosen for test and evaluation as candidate switches for the abort modulator. Modulator design, switching time delay, jitter and pre-fire data are presented

  1. Bayes-Based Fault Discrimination in Wide Area Backup Protection

    Directory of Open Access Journals (Sweden)

    WANG, Z.

    2012-02-01

    Full Text Available Multivariate statistical analysis is an effective tool to finish the fault location for electric power system. In Bayesian discriminant analysis as a subbranch, by the research of several populations, one can calculate the conditional probability that some samples belong to these populations, and compare the corresponding probability. The sample will be classified as population with maximum probability. In this paper, based on Bayesian discriminant analysis principle, a great number of simulation examples have confirmed that the results of Bayesian fault discriminant in wide area backup protection are accurate and reliable.

  2. Improving the wide resonance approximation

    International Nuclear Information System (INIS)

    Aboustta, Mohamed A.; Martinez, Aquilino S.

    1999-01-01

    A resonance is considered wide if its practical width, in energy, exceeds the average energy loss per collision, E(1-α A )/2, of the absorbing material. When the mass number, A, is taken infinite, the scattering produces only a change in the direction of motion of the neutron and not in its energy. Based on this assumption, the integral in the slowing-down equation describing the contribution of the resonant absorber is evaluated by taking its limit when α A →1. This work questions the necessity to take such a limit and shows that it is still possible to obtain a simple and more accurate expression for the integral without taking such limit

  3. Improving the wide resonance approximation

    Energy Technology Data Exchange (ETDEWEB)

    Aboustta, Mohamed A.; Martinez, Aquilino S

    1999-03-01

    A resonance is considered wide if its practical width, in energy, exceeds the average energy loss per collision, E(1-{alpha}{sub A})/2, of the absorbing material. When the mass number, A, is taken infinite, the scattering produces only a change in the direction of motion of the neutron and not in its energy. Based on this assumption, the integral in the slowing-down equation describing the contribution of the resonant absorber is evaluated by taking its limit when {alpha}{sub A}{yields}1. This work questions the necessity to take such a limit and shows that it is still possible to obtain a simple and more accurate expression for the integral without taking such limit.

  4. Enterprise wide transparent information access

    International Nuclear Information System (INIS)

    Brown, J.

    1995-05-01

    The information management needs of the Department of Energy (DOE) represents a fertile domain for the development of highly sophisticated yet intuitive enterprise-wide computing solutions. These solutions must support business operations, research agendas, technology development efforts, decision support, and other application areas with a user base ranging from technical staff to the highest levels of management. One area of primary interest is in the Environmental Restoration and Waste Management Branch of DOE. In this arena, the issue of tracking and managing nuclear waste related to the long legacy of prior defense production and research programs is one of high visibility and great concern. The Tank Waste Information Network System (TWINS) application has been created by the Pacific Northwest Laboratory (PNL) for the DOE to assist in managing and accessing the information related to this mission. The TWINS solution addresses many of the technical issues faced by other efforts to provide integrated information access to a wide variety of stakeholders. TWINS provides secure transparent access to distributed heterogeneous multimedia information sources from around the DOE complex. The users interact with the information through a consistent user interface that presents the desired data in a common format regardless of the structure of the source information. The solutions developed by the TWINS project represent an integration of several technologies and products that can be applied to other mission areas within DOE and other government agencies. These solutions are now being applied to public and private sector problem domains as well. The successful integration and inter-operation of both commercial and custom modules into a flexible and extensible information architecture will help ensure that new problems facing DOE and other clients can be addressed more rapidly in the future by re-use of existing tools and techniques proven viable through the TWINS efforts

  5. 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…

  6. Understanding Population.

    Science.gov (United States)

    Mothner, Ira

    Activities and concerns of Ford Foundation supported population research and training centers are described in this report. The centers are concerned with population growth, consequences of growth for human welfare, forces that determine family planning, interrelations among population variables, economics of contraceptive distribution, and…

  7. Juvenile Resilience and Adult Longevity Explain Residual Populations of the Andean Wax Palm Ceroxylon quindiuense after Deforestation

    Science.gov (United States)

    Sanín, María José; Anthelme, Fabien; Pintaud, Jean-Christophe; Galeano, Gloria; Bernal, Rodrigo

    2013-01-01

    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 m2 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. PMID:24194823

  8. 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.

  9. 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.

  10. Wide Field Radio Transient Surveys

    Science.gov (United States)

    Bower, Geoffrey

    2011-04-01

    The time domain of the radio wavelength sky has been only sparsely explored. Nevertheless, serendipitous discovery and results from limited surveys indicate that there is much to be found on timescales from nanoseconds to years and at wavelengths from meters to millimeters. These observations have revealed unexpected phenomena such as rotating radio transients and coherent pulses from brown dwarfs. Additionally, archival studies have revealed an unknown class of radio transients without radio, optical, or high-energy hosts. The new generation of centimeter-wave radio telescopes such as the Allen Telescope Array (ATA) will exploit wide fields of view and flexible digital signal processing to systematically explore radio transient parameter space, as well as lay the scientific and technical foundation for the Square Kilometer Array. Known unknowns that will be the target of future transient surveys include orphan gamma-ray burst afterglows, radio supernovae, tidally-disrupted stars, flare stars, and magnetars. While probing the variable sky, these surveys will also provide unprecedented information on the static radio sky. I will present results from three large ATA surveys (the Fly's Eye survey, the ATA Twenty CM Survey (ATATS), and the Pi GHz Survey (PiGSS)) and several small ATA transient searches. Finally, I will discuss the landscape and opportunities for future instruments at centimeter wavelengths.

  11. 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.

  12. 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.

  13. Community wide interventions for increasing physical activity.

    Science.gov (United States)

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

    2011-04-13

    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 Specialised Register, 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, SPORTDiscus, 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.ca; the International Union for Health Promotion and Education; the NIHR Coordinating Centre for Health Technology (NCCHTA) and NICE and SIGN guidelines. Reference lists of all relevant systematic reviews, guidelines and primary studies were followed up. We contacted experts in the field from the National Obesity Observatory Oxford, Oxford University; Queensland Health, Queensland University of Technology, the University of Central Queensland; the University of Tennessee and Washington University; and handsearched six relevant journals. The searches were last updated to the end of November 2009 and were not restricted by language or publication status. Cluster randomised controlled trials, randomised controlled trials (RCT), quasi-experimental designs which used a control population for comparison, interrupted time-series (ITS) studies, and prospective controlled cohort studies (PCCS) 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

  14. Imaginary populations

    OpenAIRE

    Martínez-Abraín, Alejandro

    2010-01-01

    A few years ago, Camus & Lima (2002) wrote an essay to stimulate ecologists to think about how we define and use a fundamental concept in ecology: the population. They concluded, concurring with Berryman (2002), that a population is "a group of individuals of the same species that live together in an area of sufficient size to permit normal dispersal and/or migration behaviour and in which population changes are largely the results of birth and death processes". They pointed out that ecologis...

  15. Population growth changes targets for immunization.

    Science.gov (United States)

    Tuljapurkar, S; John, A M

    1995-01-01

    The faster the rate of population growth in developing countries, the less likely it is that current protocols for immunization against measles, rubella, and mumps will eradicate these childhood diseases. Standard protocols (timing, percentage of children to be immunized) do not take into account the rapid rates of population growth in developing countries (3.0% per year on average in sub-Saharan Africa and 2.0% in the rest of Africa, in Latin America, and in Asia, excluding China). Most public health planning models in this area were created based on static infant populations. The World Health Organization advises vaccinating at least 85% of children aged 6 to 9 months, a 3-month immunization window during which maternal antibodies are low (so the vaccination takes) and herd immunity is high (the probability that a child will encounter the disease is low because most children have been immunized). In practice, the immunization window in developing countries is 1 year or more. More susceptible children are present than assumed by the models. A larger number of susceptible babies are added each year during rapid population growth. As the age range for immunization widens, a higher percentage of children must be vaccinated to eradicate disease (chart). The proportion of each birth cohort that must be immunized rises as the population growth rate increases. At zero population growth, 94% must be vaccinated; at population growth rates greater than 3%, 98% must be vaccinated.

  16. Age-related changes in abdominal fat distribution in Japanese adults in the general population.

    Science.gov (United States)

    Sugihara, Masako; Oka, Rie; Sakurai, Masaru; Nakamura, Koshi; Moriuchi, Tadashi; Miyamoto, Susumu; Takeda, Yoshiyu; Yagi, Kunimasa; Yamagishi, Masakazu

    2011-01-01

    Early studies have indicated that body fat shifts from peripheral stores to central stores with aging. The objective of this study was to investigate age-related changes in abdominal fat distribution of Japanese men and women of the general population over a wide range of body mass indices (BMI). A total of 2,220 non-diabetic, apparently healthy Japanese adults (1,240 men and 980 women; age range 40-69 years) were included in the study sample. All subjects underwent a CT scan at the level of the umbilicus, and the areas of visceral adipose tissue (AT) and subcutaneous AT were quantified. When the subjects were stratified by BMI into 18.5-23.0 kg/m(2), 23.0-27.5 kg/m(2), and 27.5 kg/m(2) or higher, visceral AT was positively correlated with age in all of the BMI strata in both genders (pabdominal fat distribution, women retained the subcutaneous-dominant type of fat distribution up to 70 years.

  17. 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…

  18. Natural background radiation exposures world-wide

    International Nuclear Information System (INIS)

    Bennett, B.G.

    1993-01-01

    The average radiation dose to the world's population from natural radiation sources has been assessed by UNSCEAR to be 2.4 mSv per year. The components of this exposure, methods of evaluation and, in particular, the variations in the natural background levels are presented in this paper. Exposures to cosmic radiation range from 0.26 mSv per year at sea level to 20 times more at an altitude of 6000 m. Exposures to cosmogenic radionuclides ( 3 H, 14 C) are relatively insignificant and little variable. The terrestrial radionuclides 40 K, 238 U, and 232 Th and the decay products of the latter two constitute the remainder of the natural radiation exposure. Wide variations in exposure occur for these components, particularly for radon and its decay products, which can accumulate to relatively high levels indoors. Unusually high exposures to uranium and thorium series radionuclides characterize the high natural background areas which occur in several localized regions in the world. Extreme values in natural radiation exposures have been estimated to range up to 100 times the average values. (author). 15 refs, 3 tabs

  19. 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

  20. 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.

  1. 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.

  2. Imaginary populations

    Directory of Open Access Journals (Sweden)

    A. Martínez–Abraín

    2010-01-01

    Full Text Available A few years ago, Camus & Lima (2002 wrote an essay to stimulate ecologists to think about how we define and use a fundamental concept in ecology: the population. They concluded, concurring with Berryman (2002, that a population is "a group of individuals of the same species that live together in an area of sufficient size to permit normal dispersal and/or migration behaviour and in which population changes are largely the results of birth and death processes". They pointed out that ecologists often forget "to acknowledge that many study units are neither natural nor even units in terms of constituting a population system", and hence claimed that we "require much more accuracy than in past decades in order to be more effective to characterize populations and predict their behaviour". They stated that this is especially necessary "in disciplines such as conservation biology or resource pest management, to avoid reaching wrong conclusions or making inappropriate decisions". As a population ecologist and conservation biologist I totally agree with these authors and, like them, I be¬lieve that greater precision and care is needed in the use and definition of ecological terms. The point I wish to stress here is that we ecologists tend to forget that when we use statistical tools to infer results from our sample to a population we work with what statisticians term "imaginary", "hypothetical" or "potential" popula¬tions. As Zar (1999 states, if our sample data consist of 40 measurements of growth rate in guinea pigs "the population about which conclusions might be drawn is the growth rates of all the guinea pigs that conceivably might have been administered the same food supplement under identical conditions". Such a population does not really exist, and hence it is considered a hypothetical or imaginary population. Compare that definition with the population concept that would be in our minds when performing such measurements. We would probably

  3. Population policy.

    Science.gov (United States)

    1987-03-01

    Participants in the Seminar on Population Policies for Top-level Policy Makers and Program Managers, meeting in Thailand during January 1987, examined the challenges now facing them regarding the implementation of fertility regulation programs in their respective countries -- Bangladesh, China, India, Indonesia, Malaysia, Nepal, Pakistan, the Philippines, the Republic of Korea, and Thailand. This Seminar was organized to coincide with the completion of an Economic and Social Commission for Asia and the Pacific (ESCAP) study investigating the impact and efficiency of family planning programs in the region. Country studies were reviewed at the Seminar along with policy issues about the status of women, incentive and disincentive programs, and socioeconomic factors affecting fertility. In Bangladesh the government recognizes population growth as its top priority problem related to the socioeconomic development of the country and is working to promote a reorientation strategy from the previous clinic-oriented to a multidimensional family welfare program. China's family planning program seeks to postpone marraige, space the births of children between 3-5 years, and promote the 1-child family. Its goal is to reduce the rate of natural increase from 12/1000 in 1978 to 5/1000 by 1985 and 0 by 2000. India's 7th Five-Year-Plan (1986-90) calls for establishing a 2-child family norm by 2000. In Indonesia the government's population policy includes reducing the rate of population growth, achieving a redistribution of the population, adjusting economic factors, and creating prosperous families. The government of Indonesia reversed its policy to reduce the population growth rate in 1984 and announced its goal of achieving a population of 70 million by 2100 in order to support mass consumption industries. It has created an income tax deduction system favoring large families and maternity benefits for women who have up to 5 children as incentives. Nepal's official policy is to

  4. 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.

  5. Directional Wide-Angle Range Finder (DWARF)

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation, the Directional Wide-Angle Range Finder (DWARF) is the creation of a laser range-finder with a wide field-of-view (FOV) and a directional...

  6. 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.

  7. Population catastrophe.

    Science.gov (United States)

    Ankomah, B

    1990-07-01

    UNFPA estimates predict that Africa's population will be 1.5 billion by 2025. In the next 10 years the growth rate will be 3%, the highest for any region in human history. Nigeria is expected to have 301 million people in 35 years, making it the 3rd largest country behind India and China. Currently the economies of African countries can not provide enough jobs or food for the current population. What is going to happen in 35 years when the population will almost double? In 1950 Africa only made up 9% of the world population, but by 2025 it will be 18.4% of a global population of 8.4 billion. Currently half of Africa's population is under 15. This means that there is still time to affect change. There is time to convince this generation not to behave like their parents. A 2 child limit per family is an absolute limit if any progress is to be made that will actually have an effect. Many have suggested that the young people should go back to the land instead of living in poverty in the city. However, currently the land distribution is 0.4 hectares/rural person. This figure is going to drop to 0.29/rural person. Migration is simply not the solution. Many rural farmers want to have enough children to ensure that their land is inherited and stays in the family. The same goal can be achieved, with less children. According to the UNFPA 77% of married women who do not want to have more children do not use contraceptives. Only 14% of African women use contraceptives, so that by age 20 50% of African women have had 1 birth. The only way to seriously cut down the birth rate is to get the men of Africa involved in contraceptive use.

  8. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

    DEFF Research Database (Denmark)

    Bulik-Sullivan, Brendan K.; Loh, Po-Ru; Finucane, Hilary K.

    2015-01-01

    Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from...

  9. 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

  10. Nigerian population

    African Journals Online (AJOL)

    Transverse thoracic diameter in frontal chest radiographs of an adult. Nigerian population. *E. N. Obikili and I. J. Okoye. Department of Radiation Medicine. University of Nigeria Teaching Hospital,. Enugu, Nigeria. Email: enobikili @ yahoo. com. Summary. Background: Normal standards for thoracic dimensions that are ...

  11. Populations games

    Czech Academy of Sciences Publication Activity Database

    Křivan, Vlastimil

    2015-01-01

    Roč. 2, č. 1 (2015), s. 14-19 ISSN 2367-5233. [Featuring International Conferences Biomath 2015. Blagoevgrad, 14.06.2015-19.06.2015] R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : populations dynamics

  12. Introduction to the world wide web.

    Science.gov (United States)

    Downes, P K

    2007-05-12

    The World Wide Web used to be nicknamed the 'World Wide Wait'. Now, thanks to high speed broadband connections, browsing the web has become a much more enjoyable and productive activity. Computers need to know where web pages are stored on the Internet, in just the same way as we need to know where someone lives in order to post them a letter. This section explains how the World Wide Web works and how web pages can be viewed using a web browser.

  13. Population success.

    Science.gov (United States)

    1982-01-01

    "The commitment to population programs is now widespread," says Rafael Salas, Executive Director of the UNFPA, in its report "State of World Population." About 80% of the total population of the developing world live in countries which consider their fertility levels too high and would like them reduced. An important impetus came from the World Conference of 1974. The Plan of Action from the conference projected population growth rates in developing countries of 2.0% by 1985. Today it looks as though this projection will be realized. While in 1969, for example, only 26 developing countries had programs aimed at lowering or maintaining fertility levels, by 1980 there were 59. The International Population Conference, recently announced by the UN for 1984, will, it is hoped, help sustain that momentum. Cuba is the country which has shown the greatest decline in birth rate so far. The birth rate fell 47% between 1965-1970 and 1975-1980. Next came China with a 34% decline in the same period. After these came a group of countries--each with populations of over 10 million--with declines of between 15 and 25%: Chile, Colombia, India, Indonesia, the Republic of Korea, Malaysia and Thailand. Though birth rates have been dropping significantly the decline in mortality rates over recent years has been less than was hoped for. The 1974 conference set 74 years as the target for the world's average expectation of life, to be reached by the year 2000. But the UN now predicts that the developing countries will have only reached 63 or 64 years by then. High infant and child mortality rates, particularly in Africa, are among the major causes. The report identifies the status of women as an important determinant of family size. Evidence from the UNFPA-sponsored World Fertility Survey shows that in general the fertility of women decreases as their income increases. It also indicates that women who have been educated and who work outside the home are likely to have smaller families

  14. 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.

  15. 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.

  16. Matrix population models from 20 studies of perennial plant populations

    Science.gov (United States)

    Ellis, Martha M.; Williams, Jennifer L.; Lesica, Peter; Bell, Timothy J.; Bierzychudek, Paulette; Bowles, Marlin; Crone, Elizabeth E.; Doak, Daniel F.; Ehrlen, Johan; Ellis-Adam, Albertine; McEachern, Kathryn; Ganesan, Rengaian; Latham, Penelope; Luijten, Sheila; Kaye, Thomas N.; Knight, Tiffany M.; Menges, Eric S.; Morris, William F.; den Nijs, Hans; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Shelly, J. Stephen; Stanley, Amanda; Thorpe, Andrea; Tamara, Ticktin; Valverde, Teresa; Weekley, Carl W.

    2012-01-01

    Demographic transition matrices are one of the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the 'Testing Matrix Models' working group through the National Center for Ecological Analysis and Synthesis (NCEAS). In sum, these data represent 82 populations with >460 total population-years of data. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics.

  17. 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…

  18. World-Wide Web: The Information Universe.

    Science.gov (United States)

    Berners-Lee, Tim; And Others

    1992-01-01

    Describes the World-Wide Web (W3) project, which is designed to create a global information universe using techniques of hypertext, information retrieval, and wide area networking. Discussion covers the W3 data model, W3 architecture, the document naming scheme, protocols, document formats, comparison with other systems, experience with the W3…

  19. Reduction operator for wide-SIMDs reconsidered

    NARCIS (Netherlands)

    Waeijen, L.J.W.; She, D.; Corporaal, H.; He, Y.

    2014-01-01

    It has been shown that wide Single Instruction Multiple Data architectures (wide-SIMDs) can achieve high energy efficiency, especially in domains such as image and vision processing. In these and various other application domains, reduction is a frequently encountered operation, where multiple input

  20. 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…

  1. 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

  2. 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

  3. Transcriptome-wide patterns of divergence during allopatric evolution.

    Science.gov (United States)

    Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

    2016-04-01

    Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level. © 2016 John Wiley & Sons Ltd.

  4. 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.

  5. Probabilistic population aging

    Science.gov (United States)

    2017-01-01

    We merge two methodologies, prospective measures of population aging and probabilistic population forecasts. We compare the speed of change and variability in forecasts of the old age dependency ratio and the prospective old age dependency ratio as well as the same comparison for the median age and the prospective median age. While conventional measures of population aging are computed on the basis of the number of years people have already lived, prospective measures are computed also taking account of the expected number of years they have left to live. Those remaining life expectancies change over time and differ from place to place. We compare the probabilistic distributions of the conventional and prospective measures using examples from China, Germany, Iran, and the United States. The changes over time and the variability of the prospective indicators are smaller than those that are observed in the conventional ones. A wide variety of new results emerge from the combination of methodologies. For example, for Germany, Iran, and the United States the likelihood that the prospective median age of the population in 2098 will be lower than it is today is close to 100 percent. PMID:28636675

  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. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci

    NARCIS (Netherlands)

    Keurentjes, Joost J.B.; Fu, Jingyuan; Terpstra, Inez R.; Garcia, Juan M.; Ackerveken, Guido van den; Snoek, L. Basten; Peeters, Anton J.M.; Vreugdenhil, Dick; Koornneef, Maarten; Jansen, Ritsert C.

    2007-01-01

    Accessions of a plant species can show considerable genetic differences that are analyzed effectively by using recombinant inbred line (RIL) populations. Here we describe the results of genome-wide expression variation analysis in an RIL population of Arabidopsis thaliana. For many genes, variation

  8. Epidemiology of Endometriosis in France: A Large, Nation-Wide Study Based on Hospital Discharge Data

    Directory of Open Access Journals (Sweden)

    Peter von Theobald

    2016-01-01

    Full Text Available We aimed to assess the prevalence of hospitalization for endometriosis in the general population in France and in each French region and to describe temporal trends, rehospitalization rates, and prevalence of the different types of endometriosis. The analyses were carried out on French hospital discharge data and covered the period 2008–2012 and a population of 14,239,197 women of childbearing age. In this population, the prevalence of hospitalization for endometriosis was 0.9%, ranging from 0.4% to 1.6% between regions. Endometriosis affected 1.5% of hospitalized women of childbearing age, ranging from 1.0% to 2.4% between regions. The number of patients hospitalized for endometriosis significantly increased over the study period (p<0.01. Of these, 4.2% were rehospitalized at least once at one year: ranging from 2.7% to 6.3% between regions. The cumulative rehospitalization rate at 3 years was 6.9%. The types of endometriosis according to the procedures performed were as follows: ovarian (40–50%, peritoneal (20–30%, intestinal (10–20%, and ureteral or bladder (<10%, with significant differences between regions. This is the first detailed epidemiological study of endometriosis in France. Further studies are needed to assess the reasons for the increasing prevalence of endometriosis and for the significant differences in regional prevalence of this disease.

  9. Bacteriophage populations

    International Nuclear Information System (INIS)

    Klieve, A.V.; Gilbert, R.A.

    2005-01-01

    Bacteriophages are ubiquitous to the rumen ecosystem; they have a role in nitrogen metabolism through bacterial lysis in the rumen, they may help to regulate bacterial population densities, be an agent for genetic exchange and be of use in biocontrol of bacterial populations through phage therapy. In Chapter 2.1, classical methodologies to enable the isolation, enumeration, storage and morphological characterization of phages were presented. In addition to these classic procedures, molecular biological techniques have resulted in a range of methodologies to investigate the type, topology and size of phage nucleic acids, to fingerprint individual phage strains and to create a profile of ruminal phage populations. Different phage families possess all the currently identified combinations of double-stranded or single-stranded RNA or DNA and may also possess unusual bases such as 5-hydroxymethylcytosine (found in T-even phage) or 5- hydroxymethyluracil and uracil in place of thymidine. In all morphological groups of phage except the filamentous phages, the nucleic acid is contained within a head or polyhedral structure, predominantly composed of protein. Filamentous phages have their nucleic acid contained inside the helical filament, occupying much of its length. Many of the procedures used with phage nucleic acids and double-stranded (ds) DNA, in particular, are not specific to ruminal phages but are the same as in other areas where nucleic acids are investigated and are covered elsewhere in the literature and this chapter. Most applications with rumen phages are similar to those reported for phages of non-ruminal bacteria and are covered in general texts such as Maniatis et al. In this chapter, we will concentrate on aspects of methodology as they relate to ruminal phages

  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. 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.

  12. 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...... to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome...

  13. Pest management strategies: Area-wide and conventional

    International Nuclear Information System (INIS)

    Lindquist, D.A.

    2000-01-01

    Conventional Insect Control The usual approach to insect control is to treat the commodity only after a damaging population of insects has developed. In other words, the producer, home owner or casual gardener fights a defensive battle. He reacts to an insect attack. When he sees the enemy or the damage caused by the enemy, he loads up his sprayer with an insecticide and mounts a counter attack. Most insect control procedures are applied by an individual producer on his own relatively small production area. This conventional insect control approach encourages the producer to make his own decisions about whether or not any insect control is to be used, which insect control method or product to use, when to use it, how to use it, who applies it, etc. Advice to producers on insect control is usually available from government extension personnel, private insect control consultants or representatives of companies that sell insecticides or other insect control materials or methods. The conventional procedure results in great variability in the efficacy of insect control because each producer makes his own decisions. The objective of conventional insect control is to protect the commodity. This is usually accomplished by treating the commodity, be it cows or corn or rice in a warehouse. Conventional insect control requires virtually no planning to achieve results. The 'programme' is short-term, frequently measured in days until the next insecticide application is needed. It is reactive (defensive). Area-wide Insect Control Area-wide insect control is applied against an important insect pest over a relatively large area involving many individual producers of the same or similar crops. The 'area' is a combination of geography and the range of hosts of the target insect pest. The term 'area' in 'area-wide' refers to the area where the target insect population survives. The area is not limited to production of the major crop(s) to be protected. It is very likely that a large

  14. World-wide termination of nuclear energy application

    International Nuclear Information System (INIS)

    Quirin, W.

    1991-01-01

    It is easy to require the widely discussed termination of nuclear energy application, but it is hardly possible to realise it, unless one is prepared to accept enormous economic and ecological problems. The article investigates, whether the other energy carriers or energy saving methods, respectively, would be in a position to replace the nuclear energy. Thereby the aspects of securing the supply and its economy are of considerable importance. The author describes furthermore the effects of terminating nuclear energy on the growing world population and the economy of trading countries. Ecological problems that may also be aggravated are dealt with, too. (orig.) [de

  15. 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...

  16. Nasa-wide Standard Administrative Systems

    Science.gov (United States)

    Schneck, P.

    1984-01-01

    Factors to be considered in developing agency-wide standard administrative systems for NASA include uniformity of hardware and software; centralization vs. decentralization; risk exposure; and models for software development.

  17. Genomic selection: genome-wide prediction in plant improvement.

    Science.gov (United States)

    Desta, Zeratsion Abera; Ortiz, Rodomiro

    2014-09-01

    Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. 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.

  19. 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.

  20. 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.

  1. 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/...

  2. Genome-Wide Mutagenesis in Borrelia burgdorferi.

    Science.gov (United States)

    Lin, Tao; Gao, Lihui

    2018-01-01

    population of mutants with different tags, after recovered from different tissues of infected mice and ticks, mutants from output pool and input pool are detected using high-throughput, semi-quantitative Luminex ® FLEXMAP™ or next-generation sequencing (Tn-seq) technologies. Thus far, we have created a high-density, sequence-defined transposon library of over 6600 STM mutants for the efficient genome-wide investigation of genes and gene products required for wild-type pathogenesis, host-pathogen interactions, in vitro growth, in vivo survival, physiology, morphology, chemotaxis, motility, structure, metabolism, gene regulation, plasmid maintenance and replication, etc. The insertion sites of 4480 transposon mutants have been determined. About 800 predicted protein-encoding genes in the genome were disrupted in the STM transposon library. The infectivity and some functions of 800 mutants in 500 genes have been determined. Analysis of these transposon mutants has yielded valuable information regarding the genes and gene products important in the pathogenesis and biology of B. burgdorferi and its tick vectors.

  3. Not-so-simple stellar populations in the intermediate-age Large Magellanic Cloud star clusters NGC 1831 and NGC 1868

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chengyuan; De Grijs, Richard [Kavli Institute for Astronomy and Astrophysics and Department of Astronomy, Peking University, Yi He Yuan Lu 5, Hai Dian District, Beijing 100871 (China); Deng, Licai, E-mail: joshuali@pku.edu.cn, E-mail: grijs@pku.edu.cn [Key Laboratory for Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, 20A Datun Road, Chaoyang District, Beijing 100012 (China)

    2014-04-01

    Using a combination of high-resolution Hubble Space Telescope/Wide-Field and Planetary Camera-2 observations, we explore the physical properties of the stellar populations in two intermediate-age star clusters, NGC 1831 and NGC 1868, in the Large Magellanic Cloud based on their color-magnitude diagrams. We show that both clusters exhibit extended main-sequence turn offs. To explain the observations, we consider variations in helium abundance, binarity, age dispersions, and the fast rotation of the clusters' member stars. The observed narrow main sequence excludes significant variations in helium abundance in both clusters. We first establish the clusters' main-sequence binary fractions using the bulk of the clusters' main-sequence stellar populations ≳ 1 mag below their turn-offs. The extent of the turn-off regions in color-magnitude space, corrected for the effects of binarity, implies that age spreads of order 300 Myr may be inferred for both clusters if the stellar distributions in color-magnitude space were entirely due to the presence of multiple populations characterized by an age range. Invoking rapid rotation of the population of cluster members characterized by a single age also allows us to match the observed data in detail. However, when taking into account the extent of the red clump in color-magnitude space, we encounter an apparent conflict for NGC 1831 between the age dispersion derived from that based on the extent of the main-sequence turn off and that implied by the compact red clump. We therefore conclude that, for this cluster, variations in stellar rotation rate are preferred over an age dispersion. For NGC 1868, both models perform equally well.

  4. Corn rootworm area-wide management across the United States

    International Nuclear Information System (INIS)

    Chandler, Laurence D.; Coppedge, James R.; Richard Edwards, C.; Tollefson, Jon J.; Wilde, Gerald E.

    2000-01-01

    The western corn rootworm, Diabrotica virgifera virgifera LeConte, northern corn rootworm, D. barberi Smith and Lawrence, and Mexican corn rootworm, D. virgifera zeae Krysan and Smith are among the most economically and environmentally important pests of United States maize (Zea mays L.) production systems (Metcalf 1986). Annually, 8 to 10 million hectares of maize are treated with soil applied insecticides to protect the crop from larval feeding damage. Crop rotation, however, is also widely used to minimise the need for soil insecticide applications. Insecticides for adult rootworm management are also frequently used. Numerous problems are currently associated with corn rootworm management approaches. Soil insecticides are normally used to protect maize roots from larval feeding damage. However, they are ineffective in controlling the management of corn rootworm populations (Gray et al. 1992, Sutter et al. 1991). It is not uncommon for large numbers of rootworms to develop within treated fields. Thus, when maize is grown in the same field year after year (continuous cropping), soil insecticide applications must be used to protect the plant. These applications are generally made without knowledge (prophylactic) of the rootworm population levels within the field due to the difficulty of sampling for immature life stages. Western corn rootworm resistance to chlorinated hydrocarbon insecticides has been extensively documented (Ball and Weekman 1962). Recently, two distinct populations of western corn rootworms in Nebraska were found to be resistant to carbaryl and methyl parathion which are commonly used for adult control (Meinke et al. 1998). Although the occurrence of resistance has not spread outside of these areas, the potential for increased tolerance of western corn rootworm populations to carbamate and organophosphate insecticides across the region does exist. In response to many of the management problems discussed above, scientists with the USDA Agricultural

  5. 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 ...

  6. 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

  7. 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

  8. Australia: Population.

    Science.gov (United States)

    The Australian Bureau of Census and Statistics reported on 27 August 1979 that Australia's total population was 14,376,400 at the end of the first quarter of 1979. Net immigration gain during the same period was 12,700. Natural increase was 32,100--births were 57,100 and deaths were 25,000. In January 1979, Australia introduced a new immigration scheme to improve methods of selecting immigrants. Points are awarded on the basis of personal qualities and employability; an applicant must score 60 out of 100. This scheme supersedes the earlier system under which immigrants were selected on the family reunion criterion and employability. Migrants from Britain and Ireland made up the bulk of the new comers, but their proportion has dropped from 50% in the mid-1960s to 30% in early 1979. In contrast, Asian immigrants have risen from 2% to 22% over the same period. Asian immigration began in the mid-1960s with the relaxation of the "White Australia" policy which barred non-European migrants, and increased when the ban was abolished by Prime Minister Gough Whitlam in 1973.

  9. Wide dynamic range beam profile monitor

    International Nuclear Information System (INIS)

    Lee, D.M.; Brown, D.; Hardekopf, R.; Bilskie, J.R.; van Dyck, O.B.V.

    1985-01-01

    An economical harp multiplexer system has been developed to achieve a wide dynamic range. The harp system incorporates a pneumatically actuated harp detector with ceramic boards and carbon wires; a high-sensitivity multiplexer packaged in a double-wide NIM module; and flat, shielded ribbon cable consisting of individual twisted pairs. The system multiplexes 30 wires in each of the x and y planes simultaneously and operates with or without computer control. The system has operated in beams of 100 nA to 1 mA, 1- to 120-Hz repetition rate, with a signal-to-noise ratio of greater than 10/1

  10. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

    Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

  11. 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.…

  12. 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...... Excellence certificate program is a product of a co-creation process....

  13. Review The Ooty Wide Field Array

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. DOI 10.1007/s12036-017-9430-4. Review. The Ooty Wide Field ... salient features of the upgrade, as well as its main science drivers. There are three ..... tecture for low frequency arrays, Ph.D. thesis, Jawaharalal.

  14. 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.

  15. Wide Band to ''Double Band'' upgrade

    International Nuclear Information System (INIS)

    Kasper, P.; Currier, R.; Garbincius, P.; Butler, J.

    1988-06-01

    The Wide Band beam currently uses electrons obtained from secondary photon conversions to produce the photon beam incident on the experimental targets. By transporting the positrons produced in these conversions as well as the electrons it is possible to almost double the number of photons delivered to the experiments per primary beam proton. 11 figs

  16. WorldWide Web: Hypertext from CERN.

    Science.gov (United States)

    Nickerson, Gord

    1992-01-01

    Discussion of software tools for accessing information on the Internet focuses on the WorldWideWeb (WWW) system, which was developed at the European Particle Physics Laboratory (CERN) in Switzerland to build a worldwide network of hypertext links using available networking technology. Its potential for use with multimedia documents is also…

  17. Wide-band segmented power distribution networks

    NARCIS (Netherlands)

    Tereshchenko, O.V.; Buesink, Frederik Johannes Karel; Leferink, Frank Bernardus Johannes

    2013-01-01

    This paper discusses a novel design of Power Distribution Network (PDN). By physical structuring of the power plane into repetitive symmetrical and asymmetrical segments of varying size, suppression of the propagation of unwanted noise throughout the PDN over a wide frequency range is achieved.

  18. 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...

  19. Utilization of the world wide web

    International Nuclear Information System (INIS)

    Mohr, P.; Mallard, G.; Ralchenko, U.; Schultz, D.

    1998-01-01

    Two aspects of utilization of the World Wide Web are examined: (i) the communication of technical data through web cites that provide repositories of atomic and molecular data accessible through searchable databases; and (ii) the communication about issues of mutual concern among data producers, data compilers and evaluators, and data users. copyright 1998 American Institute of Physics

  20. News Resources on the World Wide Web.

    Science.gov (United States)

    Notess, Greg R.

    1996-01-01

    Describes up-to-date news sources that are presently available on the Internet and World Wide Web. Highlights include electronic newspapers; AP (Associated Press) sources and Reuters; sports news; stock market information; New York Times; multimedia capabilities, including CNN Interactive; and local and regional news. (LRW)

  1. Telepresence Robots in the Wide Wild World

    NARCIS (Netherlands)

    Bruijnes, Merijn; van Delden, Robby; Vroon, Jered Hendrik

    2017-01-01

    Mobile remote presence systems (MRPs) are the logical next step in telepresence, but what are the ethical, social, legal, and technical implications of such systems going into the wide wild world? We explored these potential issues by immersing ourselves in a range of possible applications by

  2. Lensless imaging for wide field of view

    Science.gov (United States)

    Nagahara, Hajime; Yagi, Yasushi

    2015-02-01

    It is desirable to engineer a small camera with a wide field of view (FOV) because of current developments in the field of wearable cameras and computing products, such as action cameras and Google Glass. However, typical approaches for achieving wide FOV, such as attaching a fisheye lens and convex mirrors, require a trade-off between optics size and the FOV. We propose camera optics that achieve a wide FOV, and are at the same time small and lightweight. The proposed optics are a completely lensless and catoptric design. They contain four mirrors, two for wide viewing, and two for focusing the image on the camera sensor. The proposed optics are simple and can be simply miniaturized, since we use only mirrors for the proposed optics and the optics are not susceptible to chromatic aberration. We have implemented the prototype optics of our lensless concept. We have attached the optics to commercial charge-coupled device/complementary metal oxide semiconductor cameras and conducted experiments to evaluate the feasibility of our proposed optics.

  3. 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…

  4. 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 Large...

  5. 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: https://www.ias.ac.in/article/fulltext/reso/002/02/0064-0074 ...

  6. 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.

  7. Wide-Screen Cinema and Stereophonic Sound.

    Science.gov (United States)

    Wysotsky, Michael Z.

    Developments in the techniques of wide screen cinema and stereophonic sound throughout the world are detailed in this book. Particular attention is paid to progress in the Soviet Union in these fields. Special emphasis is placed on the Soviet view of stereophonic sound as a vital adjunct in the search for enchanced realism as opposed to the…

  8. 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...

  9. How Large Asexual Populations Adapt

    Science.gov (United States)

    Desai, Michael

    2007-03-01

    We often think of beneficial mutations as being rare, and of adaptation as a sequence of selected substitutions: a beneficial mutation occurs, spreads through a population in a selective sweep, then later another beneficial mutation occurs, and so on. This simple picture is the basis for much of our intuition about adaptive evolution, and underlies a number of practical techniques for analyzing sequence data. Yet many large and mostly asexual populations -- including a wide variety of unicellular organisms and viruses -- live in a very different world. In these populations, beneficial mutations are common, and frequently interfere or cooperate with one another as they all attempt to sweep simultaneously. This radically changes the way these populations adapt: rather than an orderly sequence of selective sweeps, evolution is a constant swarm of competing and interfering mutations. I will describe some aspects of these dynamics, including why large asexual populations cannot evolve very quickly and the character of the diversity they maintain. I will explain how this changes our expectations of sequence data, how sex can help a population adapt, and the potential role of ``mutator'' phenotypes with abnormally high mutation rates. Finally, I will discuss comparisons of these predictions with evolution experiments in laboratory yeast populations.

  10. 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.

  11. Sex-dependent associations of genetic variants identified by GWAS with indices of adiposity and obesity risk in a Chinese children population.

    Science.gov (United States)

    Xi, Bo; Shen, Yue; Reilly, Kathleen Heather; Zhao, Xiaoyuan; Cheng, Hong; Hou, Dongqing; Wang, Xingyu; Mi, Jie

    2013-10-01

    Recent genome-wide association studies have identified a few single nucleotide polymorphisms (SNPs), which are associated with body mass index (BMI)/obesity. This study aimed to examine the identified associations among a population of Chinese children. Five SNPs (SEC16B rs10913469, SH2B1 rs4788102, PCSK1rs6235, KCTD15 rs29941, BAT2 rs2844479) were genotyped for a group of Chinese children (N = 2849, age range 6-18 years). A total of 1230 obese cases and 1619 controls with normal weight were identified based on the Chinese age- and sex-specific BMI references. Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated with indices of adiposity and obesity risk in girls and only SEC16B rs10913469 in children at puberty (p indicated that the genetic risk score (GRS) was associated with BMI, waist circumference and risk of obesity (defined by BMI) in girls, even after FDR adjustment for multiple testing. However, there was no statistical association of GRS with indices of adiposity and risk of obesity in children at puberty after multiple comparison correction. This study confirmed the synthetic effect of SNPs on the indices of adiposity and risk of obesity in Chinese girls, but failed to replicate the effect of five separate variants. We also did not found cumulative effect of SNPs in children at puberty. © 2012 John Wiley & Sons Ltd.

  12. Wide-Scale Adoption of Photovoltaic Energy

    DEFF Research Database (Denmark)

    Yang, Yongheng; Enjeti, Prasad; Blaabjerg, Frede

    2015-01-01

    Current grid standards largely require that low-power (e.g., several kilowatts) single-phase photovoltaic (PV) systems operate at unity power factor (PF) with maximum power point tracking (MPPT), and disconnect from the grid under grid faults by means of islanding detection. However, in the case...... of wide-scale penetration of single-phase PV systems in the distributed grid, disconnection under grid faults can contribute to 1) voltage flickers, 2) power outages, and 3) system instability. This article explores grid code modifications for a wide-scale adoption of PV systems in the distribution grid....... In addition, based on the fact that Italy and Japan have recently undertaken a major review of standards for PV power conversion systems connected to low-voltage networks, the importance of low voltage ride-through (LVRT) for single-phase PV power systems under grid faults is considered, along with three...

  13. Analytical approximations for wide and narrow resonances

    International Nuclear Information System (INIS)

    Suster, Luis Carlos; Martinez, Aquilino Senra; Silva, Fernando Carvalho da

    2005-01-01

    This paper aims at developing analytical expressions for the adjoint neutron spectrum in the resonance energy region, taking into account both narrow and wide resonance approximations, in order to reduce the numerical computations involved. These analytical expressions, besides reducing computing time, are very simple from a mathematical point of view. The results obtained with this analytical formulation were compared to a reference solution obtained with a numerical method previously developed to solve the neutron balance adjoint equations. Narrow and wide resonances of U 238 were treated and the analytical procedure gave satisfactory results as compared with the reference solution, for the resonance energy range. The adjoint neutron spectrum is useful to determine the neutron resonance absorption, so that multigroup adjoint cross sections used by the adjoint diffusion equation can be obtained. (author)

  14. Analytical approximations for wide and narrow resonances

    Energy Technology Data Exchange (ETDEWEB)

    Suster, Luis Carlos; Martinez, Aquilino Senra; Silva, Fernando Carvalho da [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Programa de Engenharia Nuclear]. E-mail: aquilino@lmp.ufrj.br

    2005-07-01

    This paper aims at developing analytical expressions for the adjoint neutron spectrum in the resonance energy region, taking into account both narrow and wide resonance approximations, in order to reduce the numerical computations involved. These analytical expressions, besides reducing computing time, are very simple from a mathematical point of view. The results obtained with this analytical formulation were compared to a reference solution obtained with a numerical method previously developed to solve the neutron balance adjoint equations. Narrow and wide resonances of U{sup 238} were treated and the analytical procedure gave satisfactory results as compared with the reference solution, for the resonance energy range. The adjoint neutron spectrum is useful to determine the neutron resonance absorption, so that multigroup adjoint cross sections used by the adjoint diffusion equation can be obtained. (author)

  15. Logarithmic circuit with wide dynamic range

    Science.gov (United States)

    Wiley, P. H.; Manus, E. A. (Inventor)

    1978-01-01

    A circuit deriving an output voltage that is proportional to the logarithm of a dc input voltage susceptible to wide variations in amplitude includes a constant current source which forward biases a diode so that the diode operates in the exponential portion of its voltage versus current characteristic, above its saturation current. The constant current source includes first and second, cascaded feedback, dc operational amplifiers connected in negative feedback circuit. An input terminal of the first amplifier is responsive to the input voltage. A circuit shunting the first amplifier output terminal includes a resistor in series with the diode. The voltage across the resistor is sensed at the input of the second dc operational feedback amplifier. The current flowing through the resistor is proportional to the input voltage over the wide range of variations in amplitude of the input voltage.

  16. 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...... aiming to promote and support PBL interests worldwide. This paper presents the UCPBL profile and plan of action. This includes a wide range of activities such as promoting research and development within the various PBL models and their implementation; Education and training in PBL through offering...

  17. 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.

  18. 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...

  19. Swell propagation across a wide continental shelf

    OpenAIRE

    Hendrickson, Eric J.

    1996-01-01

    The effects of wave refraction and damping on swell propagation across a wide continental shelf were examined with data from a transect of bottom pressure recorders extending from the beach to the shelf break near Duck, North Carolina. The observations generally show weak variations in swell energy across the shelf during benign conditions, in qualitative agreement with predictions of a spectral refraction model. Although the predicted ray trajectories are quite sensitive to the irregular she...

  20. PENYEBARAN INFORMASI MENGGUNAKAN WWW (WORLD WIDE WEB

    Directory of Open Access Journals (Sweden)

    Ika Atman Satya

    2011-12-01

    Full Text Available Media Informasi secara tradisional telah kita kenai dengan menggunakan koran, televisi, radio dan buku referensi. Media informasi tersebut untuk penyebarannya memerlukan penunjang agar informasi tersebut dapat disebarkan secara lutis. Selain penggunaan media tradisional tersebut penyebaran informasi dengan menggunakan jaringan komputer Internet juga berkembang. Salah satu cara penyebaran informasi dengan menggunakan aplikasi WWW (World Wide Web yang mempunyai kemampuan menggabungkan gambar, text dan suara secara interaktif. Pada tulisan ini akan dibahas tentang kemampuan, penggunaan dan pengembangan server WWW.

  1. Excessive current in wide superconducting films

    International Nuclear Information System (INIS)

    Volotskaya, V.G.; Sivakov, A.G.; Turutanov, O.G.

    1986-01-01

    The resistive state of a wide long film due to superconductivity destruction by current is studied. The voltage-independent excess current I 0 is observed on I-V curves at high transport currents. The two-dimensional image of the current-carrying sample obtained by laser scanning technique in this current range indicates that the whole film is in the resistive state. The current I 0 is measured as a function of magnetic field and SHF power

  2. Economics of area-wide pest control

    International Nuclear Information System (INIS)

    Mumford, J.D.

    2000-01-01

    Area-wide pest management is commonly practised throughout the world, probably much more so than is generally recognised (Lindquist 2000, Klassen 2000). Apart from highly publicised area-wide schemes such as the sterile insect technique (SIT) for fruit flies, pheromone disruption for cotton bollworms and classical biological control, there are many examples of actions such as concerted host plant eradication, enforced closed crop seasons, organised pesticide rotation for resistance management, coordination of resistant crop genotypes, etc., some going back several centuries, which should also be considered as area-wide practices. Each of these is faced with many of the economic issues generally associated with area-wide management which will be discussed below. In general, there are to be four major questions to answer in devising an area-wide pest management programme: 1) Should a particular pest be controlled locally or area-wide? 2) What is an appropriate area over which management should be attempted? 3) Within that area what form of control is most efficient? 4) What level of organisation should be used to get the job done? It should be noted that apart from clearly objective measures such as technical effectiveness (say, mortality) or cost efficiency (mortality per dollar), there are many subjective measures that come into the evaluation of area-wide control due to the element of risk (for example, in quarantine and eradication), the boundaries of externalities (for example, variable probabilities of pesticide drift under different conditions or target organism sensitivities) and time preferences for returns on capital investments (such as insect rearing facilities or research to develop pheromone technologies). As a result of these subjective components, it may sometimes be difficult to reach clearly agreed decisions based on objective economic analyses, even with a consensus on the data used. There are three general classes of economic problems in comparing

  3. A wide field X-ray camera

    International Nuclear Information System (INIS)

    Sims, M.; Turner, M.J.L.; Willingale, R.

    1980-01-01

    A wide field of view X-ray camera based on the Dicke or Coded Mask principle is described. It is shown that this type of instrument is more sensitive than a pin-hole camera, or than a scanning survey of a given region of sky for all wide field conditions. The design of a practical camera is discussed and the sensitivity and performance of the chosen design are evaluated by means of computer simulations. The Wiener Filter and Maximum Entropy methods of deconvolution are described and these methods are compared with each other and cross-correlation using data from the computer simulations. It is shown that the analytic expressions for sensitivity used by other workers are confirmed by the simulations, and that ghost images caused by incomplete coding can be substantially eliminated by the use of the Wiener Filter and the Maximum Entropy Method, with some penalty in computer time for the latter. The cyclic mask configuration is compared with the simple mask camera. It is shown that when the diffuse X-ray background dominates, the simple system is more sensitive and has the better angular resolution. When sources dominate the simple system is less sensitive. It is concluded that the simple coded mask camera is the best instrument for wide field imaging of the X-ray sky. (orig.)

  4. Proceedings of wide band gap semiconductors

    International Nuclear Information System (INIS)

    Moustakas, T.D.; Pankove, J.I.; Hamakawa, Y.

    1992-01-01

    This book contains the proceedings of wide band gap semiconductors. Wide band gap semiconductors are under intense study because of their potential applications in photonic devices in the visible and ultraviolet part of the electromagnetic spectrum, and devices for high temperature, high frequency and high power electronics. Additionally, due to their unique mechanical, thermal, optical, chemical, and electronic properties many wide band gap semiconductors are anticipated to find applications in thermoelectric, electrooptic, piezoelectric and acoustooptic devices as well as protective coatings, hard coatings and heat sinks. Material systems covered in this symposium include diamond, II-VI compounds, III-V nitrides, silicon carbide, boron compounds, amorphous and microcrystalline semiconductors, chalcopyrites, oxides and halides. The various papers addressed recent experimental and theoretical developments. They covered issues related to crystal growth (bulk and thin films), structure and microstructure, defects, doping, optoelectronic properties and device applications. A theoretical session was dedicated to identifying common themes in the heteroepitaxy and the role of defects in doping, compensation and phase stability of this unique class of materials. Important experimental milestones included the demonstrations of bright blue injection luminescence at room temperatures from junctions based on III-V nitrides and a similar result from multiple quantum wells in a ZnSe double heterojunction at liquid nitrogen temperatures

  5. Widely distributed SEP events and pseudostreamers

    Science.gov (United States)

    Panasenco, O.; Panasenco, A.; Velli, M.

    2017-12-01

    Our analysis of the pseudostreamer magnetic topology reveals new interesting implications for understanding SEP acceleration in CMEs. The possible reasons for the wide distribution of some SEP events can be the presence of pseudostreamers in the vicinity of the SEP source region which creates conditions for the existence of strong longitudinal spread of energetic particles as well as an anomalous longitudinal solar wind magnetic field component. We reconstructed the 3D magnetic configurations of pseudostreamers with a potential field source surface (PFSS) model, which uses as a lower boundary condition the magnetic field derived from an evolving surface-flux transport model. In order to estimate the possible magnetic connections between the spacecraft and the SEP source region, we used the Parker spiral, ENLIL and PFSS models. We found that in cases of the wide SEP distributions a specific configuration of magnetic field appears to exist at low solar latitudes all the way around the sun, we named this phenomenon a pseudostreamers belt. It appears that the presence of the well developed pseudostreamer or, rather multiple pseudostreamers, organized into the pseudostreamer belt can be considered as a very favorable condition for wide SEP events.

  6. Calibration device for wide range monitor

    International Nuclear Information System (INIS)

    Kodoku, Masaya; Sato, Toshifumi.

    1989-01-01

    The calibration device for a wide range monitor according to the present invention can continuously calibrate the entire counting regions of a wide range monitor. The wide range monitor detect the reactor power in the neutron source region by means of a pulse counting method and detects the reactor power in the intermediate region by means of a cambell method. A calibration signal outputting means is disposed for continuously outputting, as such calibration signals, pulse number varying signals in which the number of pulses per unit time varies depending on the reactor power in the neutron source region to be simulated and amplitude square means varying signal in which the mean square value of amplitude varies depending on the reactor power in the intermediate region to be simulated. By using both of the calibration signals, calibration can be conducted for the nuclear reactor power in the neutron source region and the intermediate region even if the calibration is made over two regions, further, calibration for the period present over the two region can be conducted easily as well. (I.S.)

  7. 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.

  8. 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)

  9. 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.

  10. Natural Selection in Large Populations

    Science.gov (United States)

    Desai, Michael

    2011-03-01

    I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.

  11. Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

    Science.gov (United States)

    Kuhn, Patricia C; Horimoto, Andréa R V Russo; Sanches, José Maurício; Vieira Filho, João Paulo B; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C; Moises, Regina S

    2012-01-01

    Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st) statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

  12. Susceptibility to Chronic Mucus Hypersecretion, a Genome Wide Association Study

    DEFF Research Database (Denmark)

    Dijkstra, Akkelies E; Smolonska, Joanna; van den Berge, Maarten

    2014-01-01

    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). RESULTS: 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 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...

  13. Brain-wide neuronal dynamics during motor adaptation in zebrafish.

    Science.gov (United States)

    Ahrens, Misha B; Li, Jennifer M; Orger, Michael B; Robson, Drew N; Schier, Alexander F; Engert, Florian; Portugues, Ruben

    2012-05-09

    A fundamental question in neuroscience is how entire neural circuits generate behaviour and adapt it to changes in sensory feedback. Here we use two-photon calcium imaging to record the activity of large populations of neurons at the cellular level, throughout the brain of larval zebrafish expressing a genetically encoded calcium sensor, while the paralysed animals interact fictively with a virtual environment and rapidly adapt their motor output to changes in visual feedback. We decompose the network dynamics involved in adaptive locomotion into four types of neuronal response properties, and provide anatomical maps of the corresponding sites. A subset of these signals occurred during behavioural adjustments and are candidates for the functional elements that drive motor learning. Lesions to the inferior olive indicate a specific functional role for olivocerebellar circuitry in adaptive locomotion. This study enables the analysis of brain-wide dynamics at single-cell resolution during behaviour.

  14. Lake-wide distribution of Dreissena in Lake Michigan, 1999

    Science.gov (United States)

    Fleischer, Guy W.; DeSorcie, Timothy J.; Holuszko, Jeffrey D.

    2001-01-01

    The Great Lakes Science Center has conducted lake-wide bottom trawl surveys of the fish community in Lake Michigan each fall since 1973. These systematic surveys are performed at depths of 9 to 110 m at each of seven index sites around Lake Michigan. Zebra mussel (Dreissena polymorpha) populations have expanded to all survey locations and at a level to sufficiently contribute to the bottom trawl catches. The quagga (Dreissena bugensis), recently reported in Lake Michigan, was likely in the catches though not recognized. Dreissena spp. biomass ranged from about 0.6 to 15 kg/ha at the various sites in 1999. Dreissenid mussels were found at depths of 9 to 82 m, with their peak biomass at 27 to 46 m. The colonization of these exotic mussels has ecological implications as well as potential ramifications on the ability to sample fish consistently and effectively with bottom trawls in Lake Michigan.

  15. Type 1 diabetes genome-wide association studies

    DEFF Research Database (Denmark)

    Pociot, Flemming

    2017-01-01

    Genetic studies have identified >60 loci associated with the risk of developing type 1 diabetes (T1D). The vast majority of these are identified by genome-wide association studies (GWAS) using large case-control cohorts of European ancestry. More than 80% of the heritability of T1D can be explained...... by GWAS data in this population group. However, with few exceptions, their individual contribution to T1D risk is low and understanding their function in disease biology remains a huge challenge. GWAS on its own does not inform us in detail on disease mechanisms, but the combination of GWAS data...... with other omics-data is beginning to advance our understanding of T1D etiology and pathogenesis. Current knowledge supports the notion that genetic variation in both pancreatic β cells and in immune cells is central in mediating T1D risk. Advances, perspectives and limitations of GWAS are discussed...

  16. Genome-wide patterns of nucleotide polymorphism in domesticated rice

    DEFF Research Database (Denmark)

    Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan D

    2007-01-01

    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...

  17. THE SPITZER DEEP, WIDE-FIELD SURVEY

    International Nuclear Information System (INIS)

    Ashby, M. L. N.; Brodwin, M.; Stern, D.; Griffith, R.; Eisenhardt, P.; Gorjian, V.; Kozlowski, S.; Kochanek, C. S.; Bock, J. J.; Borys, C.; Brand, K.; Grogin, N. A.; Brown, M. J. I.; Cool, R.; Cooray, A.; Croft, S.; Dey, A.; Eisenstein, D.; Gonzalez, A. H.; Ivison, R. J.

    2009-01-01

    The Spitzer Deep, Wide-Field Survey (SDWFS) is a four-epoch infrared survey of 10 deg. 2 in the Booetes field of the NOAO Deep Wide-Field Survey using the IRAC instrument on the Spitzer Space Telescope. SDWFS, a Spitzer Cycle 4 Legacy project, occupies a unique position in the area-depth survey space defined by other Spitzer surveys. The four epochs that make up SDWFS permit-for the first time-the selection of infrared-variable and high proper motion objects over a wide field on timescales of years. Because of its large survey volume, SDWFS is sensitive to galaxies out to z ∼ 3 with relatively little impact from cosmic variance for all but the richest systems. The SDWFS data sets will thus be especially useful for characterizing galaxy evolution beyond z ∼ 1.5. This paper explains the SDWFS observing strategy and data processing, presents the SDWFS mosaics and source catalogs, and discusses some early scientific findings. The publicly released, full-depth catalogs contain 6.78, 5.23, 1.20, and 0.96 x 10 5 distinct sources detected to the average 5σ, 4''-diameter, aperture-corrected limits of 19.77, 18.83, 16.50, and 15.82 Vega mag at 3.6, 4.5, 5.8, and 8.0 μm, respectively. The SDWFS number counts and color-color distribution are consistent with other, earlier Spitzer surveys. At the 6 minute integration time of the SDWFS IRAC imaging, >50% of isolated Faint Images of the Radio Sky at Twenty cm radio sources and >80% of on-axis XBooetes sources are detected out to 8.0 μm. Finally, we present the four highest proper motion IRAC-selected sources identified from the multi-epoch imaging, two of which are likely field brown dwarfs of mid-T spectral class.

  18. 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.

  19. Pickering Nuclear site wide groundwater monitoring system

    International Nuclear Information System (INIS)

    DeWilde, J.; Chin-Cheong, D.; Lledo, C.; Wootton, R.; Belanger, D.; Hansen, K.

    2001-01-01

    Ontario Power Generation Inc. (OPG) is continuing its efforts to understand the chemical and physical characteristics of the groundwater flow systems beneath the Pickering Nuclear Generating Station (PNGS). To this end, OPG constructed a site-wide Groundwater Monitoring System (GMS) at the PNGS to provide support to other ongoing environmental investigations and to provide a means to monitor current and future groundwater environmental issues. This paper will present the results of this work, including the development of a state-of-the-art data management system for storage and retrieval of environmental data for the site, which has applications for other power generation facilities. (author)

  20. Wide Strip Casting Technology of Magnesium Alloys

    Science.gov (United States)

    Park, W.-J.; Kim, J. J.; Kim, I. J.; Choo, D.

    Extensive investigations relating to the production of high performance and low cost magnesium sheet by strip casting have been performed for the application to automotive parts and electronic devices. Research on magnesium sheet production technology started in 2004 by Research Institute of Industrial Science and Technology (RIST) with support of Pohang Iron and Steel Company (POSCO). POSCO has completed the world's first plant to manufacture magnesium coil. Another big project in order to develop wide strip casting technology for the automotive applications of magnesium sheets was started in succession.

  1. 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.

  2. 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.

  3. Suicidal Decapitation by Hanging-A Population-based Study.

    Science.gov (United States)

    Byard, Roger W; Gilbert, John D

    2018-05-01

    A prospective study was undertaken at Forensic Science SA over a 15-year period from July 2002 to June 2017 for all cases of adult (>18 years) suicidal hangings with decapitation. A total of 1446 cases of suicidal hangings were identified from a general population of approximately 1.5 million (1206 males-age range 18-97 years, average 42.6; and 240 females-age range 18-96 years, average 40.1). Only three cases of decapitation were found, all from long-drop hangings; these consisted of three males (ages 32-55 years; average 45 years). Spinal transections had occurred between the first and second, second and third, and third and fourth cervical vertebrae, respectively. In this study, the number of suicidal hangings with decapitation represented only 0.2% of the total number of hangings. These events are therefore extremely rare, most likely due to most suicidal hangings occurring from relatively low levels in a domestic environment. © 2017 American Academy of Forensic Sciences.

  4. FGWAS: Functional genome wide association analysis.

    Science.gov (United States)

    Huang, Chao; Thompson, Paul; Wang, Yalin; Yu, Yang; Zhang, Jingwen; Kong, Dehan; Colen, Rivka R; Knickmeyer, Rebecca C; Zhu, Hongtu

    2017-10-01

    Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes. FGWAS consists of three components: a multivariate varying coefficient model, a global sure independence screening procedure, and a test procedure. Compared with the standard multivariate regression model, the multivariate varying coefficient model explicitly models the functional features of functional phenotypes through the integration of smooth coefficient functions and functional principal component analysis. Statistically, compared with existing methods for genome-wide association studies (GWAS), FGWAS can substantially boost the detection power for discovering important genetic variants influencing brain structure and function. Simulation studies show that FGWAS outperforms existing GWAS methods for searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. We have successfully applied FGWAS to large-scale analysis of data from the Alzheimer's Disease Neuroimaging Initiative for 708 subjects, 30,000 vertices on the left and right hippocampal surfaces, and 501,584 SNPs. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Review of stellarator research world wide

    International Nuclear Information System (INIS)

    Shonet, J.L.

    1987-01-01

    The world-wide effort in stellarators has evolved considerably during the past few years. Stellarator facilities are located in the Australia, Federal Republic of Germany, Japan, the Soviet Union, Spain, the United Kingdom and the United States. Dimensions of stellarators range from less than 20 centimeters in major radius to more than 2 meters, and magnetic field values between 0.2 Tesla to more than 3.0 Tesla. Stellarators are made in a variety of magnetic configurations with wide ranges of toroidal aspect ratios and methods of generating the stellarator magnetic surfaces. In particular, continuous helical coils, twisted modular coils, or twisted vacuum chambers all provide different means to generate nested toroidal magnetic surfaces without the need for currents flowing in the plasma. The goal of present day experiments is to accumulate a physics data base. This is being done by increasing electron and ion temperatures with non-ohmic heating, by transport and scaling studies considering neoclassical scaling, global scaling, effects of electric fields, the bootstrap current and magnetic islands. Higher betas are being attempted by designing suitable magnetic configurations, pellet injection and/or minimizing transport losses. Plasma-wall interactions and particle control are being examined by divertor, pumped-limiter and carbonization experiments

  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. Assessing Predictive Properties of Genome-Wide Selection in Soybeans

    Directory of Open Access Journals (Sweden)

    Alencar Xavier

    2016-08-01

    Full Text Available 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.

  8. 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.

  9. 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...

  10. 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...

  11. Analysis of area-wide management of insect pests based on sampling

    Science.gov (United States)

    David W. Onstad; Mark S. Sisterson

    2011-01-01

    The control of invasive species greatly depends on area-wide pest management (AWPM) in heterogeneous landscapes. Decisions about when and where to treat a population with pesticide are based on sampling pest abundance. One of the challenges of AWPM is sampling large areas with limited funds to cover the cost of sampling. Additionally, AWPM programs are often confronted...

  12. Genome-wide meta-analysis identifies new susceptibility loci for migraine

    NARCIS (Netherlands)

    Anttila, Verneri; Winsvold, Bendik S.; Gormley, Padhraig; Kurth, Tobias; Bettella, Francesco; McMahon, George; Kallela, Mikko; Malik, Rainer; de Vries, Boukje; Terwindt, Gisela; Medland, Sarah E.; Todt, Unda; McArdle, Wendy L.; Quaye, Lydia; Koiranen, Markku; Ikram, M. Arfan; Lehtimaki, Terho; Stam, Anine H.; Ligthart, Lannie; Wedenoja, Juho; Dunham, Ian; Neale, Benjamin M.; Palta, Priit; Hamalainen, Eija; Schuerks, Markus; Rose, Lynda M.; Buring, Julie E.; Ridker, Paul M.; Steinberg, Stacy; Stefansson, Hreinn; Jakobsson, Finnbogi; Lawlor, Debbie A.; Evans, David M.; Ring, Susan M.; Farkkila, Markus; Artto, Ville; Kaunisto, Mari A.; Freilinger, Tobias; Schoenen, Jean; Frants, Rune R.; Pelzer, Nadine; Weller, Claudia M.; Zielman, Ronald; Heath, Andrew C.; Madden, Pamela A. F.; Montgomery, Grant W.; Martin, Nicholas G.; Borck, Guntram; Goebel, Hartmut; Heinze, Axel

    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) and

  13. Genome-wide meta-analysis identifies new susceptibility loci for migraine

    NARCIS (Netherlands)

    Anttila, V.; Winsvold, B.S.; Gormley, P.; Kurth, T.; Bettella, F.; McMahon, G.; Kallela, M.; Malik, R.; de Vries, B.; Terwindt, G.; Medland, S.E.; Todt, U.; McArdle, W.L.; Quaye, L.; Koiranen, M.; Ikram, M.A.; Lehtimäki, T.; Stam, A.H.; Ligthart, R.S.L.; Wedenoja, J.; Dunham, I.; Neale, B. M.; Palta, P.; Hamalainen, E.; Schürks, M.; Rose, L.M.; Buring, J.E.; Ridker, P.M.; Steinberg, S.; Stefansson, H.; Jakobsson, F.; Lawlor, D.A.; Evans, D.M.; Ring, S.M.; Färkkilä, M.; Artto, V.; Kaunisto, M.A.; Freilinger, T.; Schoenen, J.; Frants, R.R.; Pelzer, N.; Weller, C.M.; Zielman, R.; Heath, A.C.; Madden, P.A.F.; Montgomery, G.W.; Martin, N.G.; Borck, G.; Göbel, H.; Heinze, A.; Heinze-Kuhn, K.; Williams, F.M.; Hartikainen, A.-L.; Pouta, A.; van den Ende, J..; Uitterlinden, A.G.; Hofman, A.; Amin, N.; Hottenga, J.J.; Vink, J.M.; Heikkilä, K.; Alexander, M.; Muller-Myhsok, B.; Schreiber, S; Meitinger, T.; Wichmann, H. E.; Aromaa, A.; Eriksson, J.G.; Traynor, B.J.; Trabzuni, D.; Rossin, E.; Lage, K.; Jacobs, S.B.; Gibbs, J.R.; Birney, E.; Kaprio, J.; Penninx, B.W.J.H.; Boomsma, D.I.; van Duijn, C.M.; Raitakari, O.; Jarvelin, M.-R.; Zwart, J.A.; Cherkas, L.; Strachan, D.P.; Kubisch, C.; Ferrari, M.D.; van den Maagdenberg, A.M.J.M.; Dichgans, M.; Wessman, M.; Smith, G.D.; Stefansson, K.; Daly, M.J.; Nyholt, DR; Chasman, D.I.; Palotie, A.

    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) and

  14. Genome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility

    NARCIS (Netherlands)

    Yin, Xianyong; Low, Hui Qi; Wang, Ling; Li, Yonghong; Ellinghaus, Eva; Han, Jiali; Estivill, Xavier; Sun, Liangdan; Zuo, Xianbo; Shen, Changbing; Zhu, Caihong; Zhang, Anping; Sanchez, Fabio; Padyukov, Leonid; Catanese, Joseph J; Krueger, Gerald G; Duffin, Kristina Callis; Mucha, Sören; Weichenthal, Michael; Weidinger, Stephan; Lieb, Wolfgang; Foo, Jia Nee; Li, Yi; Sim, Karseng; Liany, Herty; Irwan, Ishak; Teo, Yikying; Theng, Colin T S; Gupta, Rashmi; Bowcock, Anne; De Jager, Philip L; Qureshi, Abrar A; de Bakker, Paul I W; Seielstad, Mark; Liao, Wilson; Ståhle, Mona; Franke, Andre; Zhang, Xuejun; Liu, Jianjun

    2015-01-01

    Psoriasis is a common inflammatory skin disease with complex genetics and different degrees of prevalence across ethnic populations. Here we present the largest trans-ethnic genome-wide meta-analysis (GWMA) of psoriasis in 15,369 cases and 19,517 controls of Caucasian and Chinese ancestries. We

  15. Software engineering the mixed model for genome-wide association studies on large samples

    Science.gov (United States)

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...

  16. 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.; Lehtimäki, T.; Lumley, T.; Marciante, K.; Pérusse, L.; Psaty, B.M.; Robbins, J.; Tranah, G.; Vink, J.M.; Wilk, J.B.; Stafford, J.M.; Bellis, M.; Biffar, R.; Bouchard, C.; Cade, B.; Curhan, G.C.; Eriksson, J.G.; Ewert, R.; Ferrucci, L.; Fülöp, T.; Gehrman, P.R.; Goodloe, R.; Harris, T.B.; Heath, A.C.; Hernandez, D.; Hofman, A.; Hottenga, J.J.; Hunter, D.J.; Jensen, M.K.; Johnson, A.D.; Kähönen, 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.; Widén, E.; Willemsen, G.; Young, T.; Zhang, X.; Liu, Y.; Blanger, 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.; Räikkönen, 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

  17. [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.

  18. Genome-wide Analysis of Gene Regulation

    DEFF Research Database (Denmark)

    Chen, Yun

    to protein: through epigenetic modifications, transcription regulators or post-transcriptional controls. The following papers concern several layers of gene regulation with questions answered by different HTS approaches. Genome-wide screening of epigenetic changes by ChIP-seq allowed us to study both spatial...... and temporal alterations of histone modifications (Papers I and II). Coupling the data with machine learning approaches, we established a prediction framework to assess the most informative histone marks as well as their most influential nucleosome positions in predicting the promoter usages. (Papers I...... they regulated or if the sites had global elevated usage rates by multiple TFs. Using RNA-seq, 5’end-seq in combination with depletion of 5’exonuclease as well as nonsensemediated decay (NMD) factors, we systematically analyzed NMD substrates as well as their degradation intermediates in human cells (Paper V...

  19. 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...

  20. 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.

  1. Wide Angle Michelson Doppler Imaging Interferometer (WAMDII)

    Science.gov (United States)

    Roberts, B.

    1986-01-01

    The wide angle Michelson Doppler imaging interferometer (WAMDII) is a specialized type of optical Michelson interferometer working at sufficiently long path difference to measure Doppler shifts and to infer Doppler line widths of naturally occurring upper atmospheric Gaussian line emissions. The instrument is intended to measure vertical profiles of atmospheric winds and temperatures within the altitude range of 85 km to 300 km. The WAMDII consists of a Michelson interferometer followed by a camera lens and an 85 x 106 charge coupled device photodiode array. Narrow band filters in a filter wheel are used to isolate individual line emissions and the lens forms an image of the emitting region on the charge coupled device array.

  2. Noonan syndrome in diverse populations.

    Science.gov (United States)

    Kruszka, Paul; Porras, Antonio R; Addissie, Yonit A; Moresco, Angélica; Medrano, Sofia; Mok, Gary T K; Leung, Gordon K C; Tekendo-Ngongang, Cedrik; Uwineza, Annette; Thong, Meow-Keong; Muthukumarasamy, Premala; Honey, Engela; Ekure, Ekanem N; Sokunbi, Ogochukwu J; Kalu, Nnenna; Jones, Kelly L; Kaplan, Julie D; Abdul-Rahman, Omar A; Vincent, Lisa M; Love, Amber; Belhassan, Khadija; Ouldim, Karim; El Bouchikhi, Ihssane; Shukla, Anju; Girisha, Katta M; Patil, Siddaramappa J; Sirisena, Nirmala D; Dissanayake, Vajira H W; Paththinige, C Sampath; Mishra, Rupesh; Klein-Zighelboim, Eva; Gallardo Jugo, Bertha E; Chávez Pastor, Miguel; Abarca-Barriga, Hugo H; Skinner, Steven A; Prijoles, Eloise J; Badoe, Eben; Gill, Ashleigh D; Shotelersuk, Vorasuk; Smpokou, Patroula; Kisling, Monisha S; Ferreira, Carlos R; Mutesa, Leon; Megarbane, Andre; Kline, Antonie D; Kimball, Amy; Okello, Emmy; Lwabi, Peter; Aliku, Twalib; Tenywa, Emmanuel; Boonchooduang, Nonglak; Tanpaiboon, Pranoot; Richieri-Costa, Antonio; Wonkam, Ambroise; Chung, Brian H Y; Stevenson, Roger E; Summar, Marshall; Mandal, Kausik; Phadke, Shubha R; Obregon, María G; Linguraru, Marius G; Muenke, Maximilian

    2017-09-01

    Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world. © 2017 Wiley Periodicals, Inc.

  3. 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.

  4. bayesPop: Probabilistic Population Projections

    Science.gov (United States)

    Ševčíková, Hana; Raftery, Adrian E.

    2016-01-01

    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. PMID:28077933

  5. 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.

  6. Population control II: The population establishment today.

    Science.gov (United States)

    Hartmann, B

    1997-01-01

    Although population assistance represents a relatively small share of official development assistance, it influences many other aspects of development planning. The organizations that comprise the population establishment have a common purpose--the reduction of population growth in the Third World--but they are not homogeneous and sometimes have conflicting goals and strategies. National governments, multilateral agencies, nongovernmental organizations, foundations, academic centers, and pressure groups all contribute to creating and sustaining what has become a virtual population control industry. Through scholarships, travel grants, awards, and favorable publicity, Third World elites have been encouraged to join the population establishment. The World Bank, the U.S. Agency for International Development, and the U.N. Fund for Population Activities have pursued explicit strategies for pressuring Third World governments to design and implement population policies, most recently in Africa.

  7. Collecting behavioural data using the world wide web: considerations for researchers.

    Science.gov (United States)

    Rhodes, S D; Bowie, D A; Hergenrather, K C

    2003-01-01

    To identify and describe advantages, challenges, and ethical considerations of web based behavioural data collection. This discussion is based on the authors' experiences in survey development and study design, respondent recruitment, and internet research, and on the experiences of others as found in the literature. The advantages of using the world wide web to collect behavioural data include rapid access to numerous potential respondents and previously hidden populations, respondent openness and full participation, opportunities for student research, and reduced research costs. Challenges identified include issues related to sampling and sample representativeness, competition for the attention of respondents, and potential limitations resulting from the much cited "digital divide", literacy, and disability. Ethical considerations include anonymity and privacy, providing and substantiating informed consent, and potential risks of malfeasance. Computer mediated communications, including electronic mail, the world wide web, and interactive programs will play an ever increasing part in the future of behavioural science research. Justifiable concerns regarding the use of the world wide web in research exist, but as access to, and use of, the internet becomes more widely and representatively distributed globally, the world wide web will become more applicable. In fact, the world wide web may be the only research tool able to reach some previously hidden population subgroups. Furthermore, many of the criticisms of online data collection are common to other survey research methodologies.

  8. Selection signatures in worldwide sheep populations.

    OpenAIRE

    Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon; Drögemüller, Cord; The International Sheep Genomics Consortium, ISGC

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep popula...

  9. Selection Signatures in Worldwide Sheep Populations

    OpenAIRE

    Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; Cristobal, Magali San; Boitard, Simon

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep popula...

  10. Systemic sclerosis: a world wide global analysis.

    Science.gov (United States)

    Coral-Alvarado, Paola; Pardo, Aryce L; Castaño-Rodriguez, Natalia; Rojas-Villarraga, Adriana; Anaya, Juan-Manuel

    2009-07-01

    The objective of this study was to analyze epidemiological tendencies of systemic sclerosis (SSc) around the world in order to identify possible local variations in the presentation and occurrence of the disease. A systematic review of the literature was performed through electronic databases using the keywords "Systemic Sclerosis" and "Clinical Characteristics." Out of a total of 167 articles, 41 were included in the analysis. Significant differences in the mean age at the time of diagnosis, subsets of SSc, clinical characteristics, and presence of antibodies were found between different regions of the word. Because variations in both additive and nonadditive genetic factors and the environmental variance are specific to the investigated population, ethnicity and geography are important characteristics to be considered in the study of SSc and other autoimmune diseases.

  11. Generalization of the Wide-Sense Markov Concept to a Widely Linear Processing

    International Nuclear Information System (INIS)

    Espinosa-Pulido, Juan Antonio; Navarro-Moreno, Jesús; Fernández-Alcalá, Rosa María; Ruiz-Molina, Juan Carlos; Oya-Lechuga, Antonia; Ruiz-Fuentes, Nuria

    2014-01-01

    In this paper we show that the classical definition and the associated characterizations of wide-sense Markov (WSM) signals are not valid for improper complex signals. For that, we propose an extension of the concept of WSM to a widely linear (WL) setting and the study of new characterizations. Specifically, we introduce a new class of signals, called widely linear Markov (WLM) signals, and we analyze some of their properties based either on second-order properties or on state-space models from a WL processing standpoint. The study is performed in both the forwards and backwards directions of time. Thus, we provide two forwards and backwards Markovian representations for WLM signals. Finally, different estimation recursive algorithms are obtained for these models

  12. Simulating Population Growth.

    Science.gov (United States)

    Byington, Scott

    1997-01-01

    Presents a strategy to help students grasp the important implications of population growth. Involves an interactive demonstration that allows students to experience exponential and logistic population growth followed by a discussion of the implications of population-growth principles. (JRH)

  13. 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.

  14. 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...

  15. 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.

  16. Metasurface Enabled Wide-Angle Fourier Lens.

    Science.gov (United States)

    Liu, Wenwei; Li, Zhancheng; Cheng, Hua; Tang, Chengchun; Li, Junjie; Zhang, Shuang; Chen, Shuqi; Tian, Jianguo

    2018-06-01

    Fourier optics, the principle of using Fourier transformation to understand the functionalities of optical elements, lies at the heart of modern optics, and it has been widely applied to optical information processing, imaging, holography, etc. While a simple thin lens is capable of resolving Fourier components of an arbitrary optical wavefront, its operation is limited to near normal light incidence, i.e., the paraxial approximation, which puts a severe constraint on the resolvable Fourier domain. As a result, high-order Fourier components are lost, resulting in extinction of high-resolution information of an image. Other high numerical aperture Fourier lenses usually suffer from the bulky size and costly designs. Here, a dielectric metasurface consisting of high-aspect-ratio silicon waveguide array is demonstrated experimentally, which is capable of performing 1D Fourier transform for a large incident angle range and a broad operating bandwidth. Thus, the device significantly expands the operational Fourier space, benefitting from the large numerical aperture and negligible angular dispersion at large incident angles. The Fourier metasurface will not only facilitate efficient manipulation of spatial spectrum of free-space optical wavefront, but also be readily integrated into micro-optical platforms due to its compact size. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. 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.

  18. 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

  19. Status of computed tomography dosimetry for wide cone beam scanners

    International Nuclear Information System (INIS)

    2011-01-01

    International standardization in dosimetry is essential for the successful exploitation of radiation technology. To provide such standardization in diagnostic radiology, the IAEA published Code of Practice entitled Dosimetry in Diagnostic Radiology: An International Code of Practice (IAEA Technical Reports Series No. 457; 2007), which recommends procedures for calibration and dosimetric measurement both in standards dosimetry laboratories, especially Secondary Standards Dosimetry Laboratories (SSDLs), and in clinical centres for radiology, as found in most hospitals. These standards address the main dosimetric methodologies needed in clinical diagnostic radiology, with the calibration of associated dosimetric equipment, including the measurement methodologies for computed tomography (CT). For some time now there has been a growing awareness that radiation dose originating from medical diagnostic procedures in radiology, is contributing an increasing proportion to the total population dose, with a large component coming from CT examinations. This is accompanied by rapid developments in CT technology, including the use of increasingly wide X ray scanning beams, which are presenting problems in dosimetry that currently cannot be adequately addressed by existing standards. This situation has received attention from a number of professional bodies, and institutions have proposed and are investigating new and adapted dosimetric models in order to find robust solutions to these problems that are critically affecting clinical application of CT dosimetry. In view of these concerns, and as a response to a recommendation from a coordinated research project that reviewed the implementation of IAEA Technical Reports Series No. 457, a meeting was held to review current dosimetric methodologies and to determine if a practical solution for dosimetry for wide X ray beam CT scanners was currently available. The meeting rapidly formed the view that there was an interim solution that

  20. 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.

  1. 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.

  2. Population and labour force growth and patterns in ASEAN countries.

    Science.gov (United States)

    Saw, S

    1988-01-01

    "The paper shows that the diverse labor dimensions prevailing in the ASEAN region can be attributed to changes in the structure of the society and economy in the course of recent economic development. It observes the considerable variety in the growth of the population and its effect on the labor force in the ASEAN region.... The paper details the similarity and diversity in the level and type of labor force participation rates. A common feature shared by ASEAN countries is a general pattern in the age-specific participation rate of men. In contrast, the women, aside from participating in the labor force at a much lower level than men at almost all ages, display diverse patterns of participation over the working age range. Lastly, the distribution of the labor force according to major industrial sectors in the six ASEAN countries is presented...." excerpt

  3. 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.

  4. 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.

  5. Seasonal variation of mood and behaviour in a healthy middle-aged population in Japan.

    Science.gov (United States)

    Okawa, M; Shirakawa, S; Uchiyama, M; Oguri, M; Kohsaka, M; Mishima, K; Sakamoto, K; Inoue, H; Kamei, K; Takahashi, K

    1996-10-01

    A population survey of seasonality in six representative cities in Japan was conducted using the Japanese version of the Seasonal Pattern Assessment Questionnaire (SPAQ). The questionnaires were given to 951 parents (male: female ratio 1:1 age range 34-59 years) of high-school students. Significant regional differences in seasonal variations of mood, length of sleep, and weight were observed; the proportion of individuals reporting high seasonality in the two northern cities was significantly higher than that in the other areas. These results provide evidence for a northern predominance in the prevalence of seasonal affective disorder in Japan.

  6. Context effects on processing widely deviant sounds in newborn infants

    Directory of Open Access Journals (Sweden)

    Gábor Péter Háden

    2013-09-01

    Full Text Available Detecting and orienting towards sounds carrying new information is a crucial feature of the human brain that supports adaptation to the environment. Rare, acoustically widely deviant sounds presented amongst frequent tones elicit large event related brain potentials (ERPs in neonates. Here we tested whether these discriminative ERP responses reflect only the activation of fresh afferent neuronal populations (i.e., neuronal circuits not affected by the tones or they also index the processing of contextual mismatch between the rare and the frequent sounds.In two separate experiments, we presented sleeping newborns with 150 different environmental sounds and the same number of white noise bursts. Both sounds served either as deviants in an oddball paradigm with the frequent standard stimulus a tone (Novel/Noise deviant, or as the standard stimulus with the tone as deviant (Novel/Noise standard, or they were delivered alone with the same timing as the deviants in the oddball condition (Novel/Noise alone.Whereas the ERP responses to noise–deviants elicited similar responses as the same sound presented alone, the responses elicited by environmental sounds in the corresponding conditions morphologically differed from each other. Thus whereas the ERP response to the noise sounds can be explained by the different refractory state of stimulus specific neuronal populations, the ERP response to environmental sounds indicated context sensitive processing. These results provide evidence for an innate tendency of context dependent auditory processing as well as a basis for the different developmental trajectories of processing acoustical deviance and contextual novelty.

  7. 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.

  8. Temporal fluctuation scaling in populations and communities

    Science.gov (United States)

    Michael Kalyuzhny; Yishai Schreiber; Rachel Chocron; Curtis H. Flather; David A. Kessler; Nadav M. Shnerb

    2014-01-01

    Taylor's law, one of the most widely accepted generalizations in ecology, states that the variance of a population abundance time series scales as a power law of its mean. Here we reexamine this law and the empirical evidence presented in support of it. Specifically, we show that the exponent generally depends on the length of the time series, and its value...

  9. Inferences from Genomic Models in Stratified Populations

    DEFF Research Database (Denmark)

    Janss, Luc; de los Campos, Gustavo; Sheehan, Nuala

    2012-01-01

    Unaccounted population stratification can lead to spurious associations in genome-wide association studies (GWAS) and in this context several methods have been proposed to deal with this problem. An alternative line of research uses whole-genome random regression (WGRR) models that fit all marker...

  10. 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

  11. Population Education Country Programmes.

    Science.gov (United States)

    Population Education in Asia and the Pacific Newsletter, 1983

    1983-01-01

    Describes population programs in Afghanistan (nonformal, population education literacy program), India (problems in planning/managing population education in higher education), Indonesia (training for secondary/out-of-school inspectors), and Pakistan (integration of population education into school curricula). Programs in China, Korea, Vietnam,…

  12. Why Population in 1974?

    Science.gov (United States)

    O'Connor, Marion

    1974-01-01

    Discusses the impact of world population growth leading to the establishment of the United Nations Fund for Population Activities and to the declaration of 1974 as World Population Year. Previews some of the parameters and interconnecting interests to be considered during this year of intensive population study. (JR)

  13. Human Population Problems

    Science.gov (United States)

    Emmel, Thomas C.; Sligh, Michael M.

    1970-01-01

    Asserts that overpopulation is the most pressing world problem. Topics discussed include population control in primitive societies, population growth and control in modern societies, methods of motivational population control, consequences of no population control, and mass famines during the 1970's in underdeveloped countries. Cities 33…

  14. Implementing a campus wide recycling program

    International Nuclear Information System (INIS)

    Alvarez, L.

    2002-01-01

    'Full text:' The University of Windsor is currently expanding its recycling program to include all buildings on campus, but faces two challenges: 1) uncertainty about the current waste composition and distribution on campus; and 2) uncertainty about the effectiveness of increased recycling. This project assesses the current waste composition and the attitudes of the students towards recycling, and evaluates the effectiveness of proposed recycling activities. At present, paper is the only material that is collected throughout the entire campus. Except for two buildings, all other potentially recyclable materials within buildings, such as metal, glass, and plastic beverage containers, are discarded. The main focus of this research is on beverage containers as they represent clearly identifiable materials, but other materials were examined as well. To quantify the waste, different buildings on campus were classified according to their function: academic,operational and administrative. The waste composition study indicated that approximately 33% of the campus waste which is landfilled is composed of potentially recyclable material. A survey was then conducted to gauge the campus population's views on recycling issues that could affect the design of a recycling program. Interestingly, 97% of the respondents indicated a high willingness to recycle, but were uncertain as to how and where to recycle on campus. The project is currently assessing potential diversion rates using new, clearly identifiable recycling receptacles placed within selected classrooms for all major materials. There is a significant tradeoff however because the cost for new receptacles is considerable: multiple materials containers are often placed in high pedestrian traffic locations (e.g., hallways) and not always in classrooms,of which there are often many. This project will evaluate the basic benefits and costs of implementing a more comprehensive recycling program, and recommend how other

  15. 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

  16. Hierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistory.

    Science.gov (United States)

    Lewis, Cecil M

    2010-02-01

    This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. 2009 Wiley-Liss, Inc.

  17. Pattern of Brain Weight in Three West African Populations

    Directory of Open Access Journals (Sweden)

    Clement Vhriterhire

    2010-08-01

    Full Text Available AIM: The usefulness of brain weight in facilitating proper identification of skeletal remains and in emphasizing a common origin of studied populations is far reaching. METHODS: This study involved 699 (male 361; female 338 volunteers whose age ranged 18 years and over. Respondents were selected along three ethnic groups including Urhobo (male 156; female 147, Ibo (male 141 female 145 and Edo (male 64; female 46 and it was ensured that population for the study was collected using a random stratified method. RESULTS: The brain weight was measured using standard techniques and the mean weight was observed to be 1318g±139.71g with maximum value of 1711.00g and minimum value of 958.42g. Gender had a significant effect on brain weight (p<0.05.Male and female values were significantly different (p<0.05. Mean male values were 1386.18g and mean female values were 1251.62g. Brain weight exhibited strong sexual dimorphism and was useful in differentiating inter and intra population groups. In spite of these observations, differences which enabled intracultural differentiation commonly occurred. CONCLUSION: Inevitably therefore, craniometric studies are most essential in the study of population dynamics especially with respect to quantitative variables. [TAF Prev Med Bull 2010; 9(4.000: 321-324

  18. Camera Trajectory fromWide Baseline Images

    Science.gov (United States)

    Havlena, M.; Torii, A.; Pajdla, T.

    2008-09-01

    angle θ of its corresponding rays w.r.t. the optical axis as θ = ar 1+br2 . After a successful calibration, we know the correspondence of the image points to the 3D optical rays in the coordinate system of the camera. The following steps aim at finding the transformation between the camera and the world coordinate systems, i.e. the pose of the camera in the 3D world, using 2D image matches. For computing 3D structure, we construct a set of tentative matches detecting different affine covariant feature regions including MSER, Harris Affine, and Hessian Affine in acquired images. These features are alternative to popular SIFT features and work comparably in our situation. Parameters of the detectors are chosen to limit the number of regions to 1-2 thousands per image. The detected regions are assigned local affine frames (LAF) and transformed into standard positions w.r.t. their LAFs. Discrete Cosine Descriptors are computed for each region in the standard position. Finally, mutual distances of all regions in one image and all regions in the other image are computed as the Euclidean distances of their descriptors and tentative matches are constructed by selecting the mutually closest pairs. Opposed to the methods using short baseline images, simpler image features which are not affine covariant cannot be used because the view point can change a lot between consecutive frames. Furthermore, feature matching has to be performed on the whole frame because no assumptions on the proximity of the consecutive projections can be made for wide baseline images. This is making the feature detection, description, and matching much more time-consuming than it is for short baseline images and limits the usage to low frame rate sequences when operating in real-time. Robust 3D structure can be computed by RANSAC which searches for the largest subset of the set of tentative matches which is, within a predefined threshold ", consistent with an epipolar geometry. We use ordered sampling as

  19. Wide Band and Wide Azimuth Beam Effect on High-resolution Synthetic Aperture Radar Radiometric Calibration

    Directory of Open Access Journals (Sweden)

    Hong Jun

    2015-06-01

    Full Text Available Passive corner reflectors and active transponders are often used as man-made reference targets in Synthetic Aperture Radar (SAR radiometric calibration, With the emergence of new radar systems and the increasing demand for greater accuracy, wide-band and wide-beam radars challenge the hypothesis that the Radar Cross Section (RCS of reference targets is constant. In this study, the FEKO electromagnetic simulation software is used to obtain the change curve of the target RCS as a function of frequency and aspect angle while incorporating high-resolution point-target SAR simulation, and quantitatively analyzing the effect of the modulation effect on SAR images. The simulation results suggest that the abovementioned factors affect the SAR calibration by more than 0.2 dB within a fractional bandwidth greater than 10% or azimuth beam width of more than 20°, which must be corrected in the data processing.

  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. Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

    Directory of Open Access Journals (Sweden)

    María Saura

    Full Text Available 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

  2. Gene flow analysis method, the D-statistic, is robust in a wide parameter space.

    Science.gov (United States)

    Zheng, Yichen; Janke, Axel

    2018-01-08

    We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, [Formula: see text] and [Formula: see text], to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background. The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.

  3. Complexity in a population of Artemia

    Energy Technology Data Exchange (ETDEWEB)

    Ali, A.A., E-mail: abduladem1@yahoo.co [Electrical Engineering Department, University of Basrah (Iraq); Fortuna, L., E-mail: lfortuna@diees.unict.i [DIEEI, Faculty of Engineering, University of Catania (Italy); Frasca, M., E-mail: mfrasca@diees.unict.i [DIEEI, Faculty of Engineering, University of Catania (Italy); Rashid, M.T., E-mail: mofid76@yahoo.co [Electrical Engineering Department, University of Basrah (Iraq); Xibilia, M.G., E-mail: mxibilia@ingegneria.unime.i [DiSIA, Faculty of Engineering, University of Messina (Italy)

    2011-04-15

    Highlights: Experiments on collective motion of populations of animals (Artemia salina). Design of low-cost experimental setup for complex systems. Control of collective motion of populations of Artemia. Models of collective motion of populations of Artemia. - Abstract: Artemia salina belongs to a genus of very primordial crustaceans, whose behavior is not widely investigated in literature. Their collective behavior is studied in this paper both experimentally and theoretically. Different experiments have been designed to control the direction of motion of an Artemia population by exploiting their sensitivity to light and to measure the response of the population to light at different wavelengths. Mathematical models have been also derived, explaining the mechanisms underlying Artemia flocking formation when a light spot is applied to the system. The results obtained allow to develop new strategies for distributed control of agents and to test them in a simple and low cost experimental setup.

  4. Complexity in a population of Artemia

    International Nuclear Information System (INIS)

    Ali, A.A.; Fortuna, L.; Frasca, M.; Rashid, M.T.; Xibilia, M.G.

    2011-01-01

    Highlights: → Experiments on collective motion of populations of animals (Artemia salina). → Design of low-cost experimental setup for complex systems. → Control of collective motion of populations of Artemia. → Models of collective motion of populations of Artemia. - Abstract: Artemia salina belongs to a genus of very primordial crustaceans, whose behavior is not widely investigated in literature. Their collective behavior is studied in this paper both experimentally and theoretically. Different experiments have been designed to control the direction of motion of an Artemia population by exploiting their sensitivity to light and to measure the response of the population to light at different wavelengths. Mathematical models have been also derived, explaining the mechanisms underlying Artemia flocking formation when a light spot is applied to the system. The results obtained allow to develop new strategies for distributed control of agents and to test them in a simple and low cost experimental setup.

  5. Inter-populations genetic and morphological diversity in three Silene ...

    African Journals Online (AJOL)

    enoho

    2012-03-30

    Mar 30, 2012 ... 2Biology Department, School of Basic Sciences, Science and Research Branch, Islamic Azad University (SRBIAU), ... other populations in both morphological and molecular features. ... species with world-wide distribution.

  6. 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/

  7. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.

    Science.gov (United States)

    Brynildsrud, Ola; Bohlin, Jon; Scheffer, Lonneke; Eldholm, Vegard

    2016-11-25

    Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .

  8. 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...

  9. Genome-Wide Specific Selection in Three Domestic Sheep Breeds.

    Directory of Open Access Journals (Sweden)

    Huihua Wang

    Full Text Available Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality and EDAR (associated with hair thickness were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9 were associated with pre-weaning gain in our previous genome-wide association study.Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

  10. Genome-Wide Specific Selection in Three Domestic Sheep Breeds.

    Science.gov (United States)

    Wang, Huihua; Zhang, Li; Cao, Jiaxve; Wu, Mingming; Ma, Xiaomeng; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Wei, Caihong; Du, Lixin

    2015-01-01

    Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

  11. Reconstructing Roma history from genome-wide data.

    Directory of Open Access Journals (Sweden)

    Priya Moorjani

    Full Text Available The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000-1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs. We estimate that the Roma harbor about 80% West Eurasian ancestry-derived from a combination of European and South Asian sources-and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe.

  12. 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.

  13. SLoWPoKES-II: 100,000 WIDE BINARIES IDENTIFIED IN SDSS WITHOUT PROPER MOTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Dhital, Saurav [Department of Physical Sciences, Embry-Riddle Aeronautical University, 600 South Clyde Morris Blvd., Daytona Beach, FL 32114 (United States); West, Andrew A.; Schluns, Kyle J.; Massey, Angela P. [Department of Astronomy, Boston University, 725 Commonwealth Avenue, Boston, MA 02215 (United States); Stassun, Keivan G., E-mail: dhitals@erau.edu [Department of Physics and Astronomy, Vanderbilt University, 6301 Stevenson Center, Nashville, TN, 37235 (United States)

    2015-08-15

    We present the Sloan Low-mass Wide Pairs of Kinematically Equivalent Stars (SLoWPoKES)-II catalog of low-mass visual binaries identified from the Sloan Digital Sky Survey (SDSS) by matching photometric distances. The candidate pairs are vetted by comparing the stellar information. The candidate pairs are vetted by comparing the stellar density at their respective Galactic positions to Monte Carlo realizations of a simulated Milky Way. In this way, we are able to identify large numbers of bona fide wide binaries without the need for proper motions. Here, 105,537 visual binaries with angular separations of ∼1–20″ were identified, each with a probability of chance alignment of ≤5%. This is the largest catalog of bona fide wide binaries to date, and it contains a diversity of systems—in mass, mass ratios, binary separations, metallicity, and evolutionary states—that should facilitate follow-up studies to characterize the properties of M dwarfs and white dwarfs. There is a subtle but definitive suggestion of multiple populations in the physical separation distribution, supporting earlier findings. We suggest that wide binaries are composed of multiple populations, most likely representing different formation modes. There are 141 M7 or later wide binary candidates, representing a seven-fold increase over the number currently known. These binaries are too wide to have been formed via the ejection mechanism. Finally, we found that 6% of spectroscopically confirmed M dwarfs are not included in the SDSS STAR catalog; they are misclassified as extended sources due to the presence of a nearby or partially resolved companion. The SLoWPoKES-II catalog is publicly available to the entire community on the World Wide Web via the Filtergraph data visualization portal.

  14. Night shift work at specific age ranges and chronic disease risk factors

    Science.gov (United States)

    Ramin, Cody; Devore, Elizabeth E; Wang, Weike; Pierre-Paul, Jeffrey; Wegrzyn, Lani R; Schernhammer, Eva S

    2014-01-01

    Objectives We examined the association of night shift work history and age when night shift work was performed with cancer and cardiovascular disease risk factors among 54 724 women in the Nurses' Health Study (NHS) II. Methods We calculated age-adjusted and socioeconomic status-adjusted means and percentages for cancer and cardiovascular risk factors in 2009 across categories of night shift work history. We used multivariable-adjusted logistic regression to estimate odds ratios (ORs) and 95% CIs for key risk factors among 54 724 participants (72% ever shift workers). We further examined these associations by age (20–25, 26–35, 36– 45 and 46+ years) at which shift work was performed. Results Ever night shift workers had increased odds of obesity (body mass index ≥30 kg/m2; OR=1.37, 95% CI 1.31 to 1.43); higher caffeine intake (≥131 mg/day; OR=1.16, 95% CI 1.12 to 1.22) and total calorie intake (≥1715 kcal/day; OR=1.09, 95% CI 1.04 to 1.13); current smoking (OR=1.30, 95% CI 1.19 to 1.42); and shorter sleep durations (≤7 h of sleep/day; OR=1.19, 95% CI 1.15 to 1.24) compared to never night shift workers. These estimates varied depending on age at which night work was performed, with a suggestion that night shift work before age 25 was associated with fewer risk factors compared to night shift work at older ages. Conclusions Our results indicate that night shift work may contribute to an adverse chronic disease risk profile, and that risk factors may vary depending on the age at which night shift work was performed. PMID:25261528

  15. Night shift work at specific age ranges and chronic disease risk factors.

    Science.gov (United States)

    Ramin, Cody; Devore, Elizabeth E; Wang, Weike; Pierre-Paul, Jeffrey; Wegrzyn, Lani R; Schernhammer, Eva S

    2015-02-01

    We examined the association of night shift work history and age when night shift work was performed with cancer and cardiovascular disease risk factors among 54 724 women in the Nurses' Health Study (NHS) II. We calculated age-adjusted and socioeconomic status-adjusted means and percentages for cancer and cardiovascular risk factors in 2009 across categories of night shift work history. We used multivariable-adjusted logistic regression to estimate odds ratios (ORs) and 95% CIs for key risk factors among 54 724 participants (72% ever shift workers). We further examined these associations by age (20-25, 26-35, 36-45 and 46+ years) at which shift work was performed. Ever night shift workers had increased odds of obesity (body mass index ≥30 kg/m(2); OR=1.37, 95% CI 1.31 to 1.43); higher caffeine intake (≥131 mg/day; OR=1.16, 95% CI 1.12 to 1.22) and total calorie intake (≥1715 kcal/day; OR=1.09, 95% CI 1.04 to 1.13); current smoking (OR=1.30, 95% CI 1.19 to 1.42); and shorter sleep durations (≤7 h of sleep/day; OR=1.19, 95% CI 1.15 to 1.24) compared to never night shift workers. These estimates varied depending on age at which night work was performed, with a suggestion that night shift work before age 25 was associated with fewer risk factors compared to night shift work at older ages. Our results indicate that night shift work may contribute to an adverse chronic disease risk profile, and that risk factors may vary depending on the age at which night shift work was performed. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

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

    African Journals Online (AJOL)

    2015-08-18

    Aug 18, 2015 ... is useful in cases of surgery, root canal treatment, apical ... by radiologists even in a panoramic radiograph. Even if identified ... or skeletal anomalies and between 10 and 70 years old were included in this study. Subjects with missing or incorrect images and individuals with cystic tumors in the MF region.

  17. Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

    Directory of Open Access Journals (Sweden)

    Kevin C. Deitz

    2016-09-01

    Full Text Available Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

  18. Pharmacogenetics in the Brazilian population

    Directory of Open Access Journals (Sweden)

    Guilherme eSuarez-Kurtz

    2010-10-01

    Full Text Available Brazil is the 5th largest country in the world and its present population, in excess of 190 million, is highly heterogeneous, as a result of centuries of admixture between Amerindians, Europeans and Sub-Saharan Africans. The estimated individual proportions of biogeographical ancestry vary widely and continuously among Brazilians, most individuals - irrespective of self-identification as White, Brown or Black, the major categories of the Brazilian Census race/color system - having significant degrees of European and African ancestry, while a sizeable number display also Amerindian ancestry. These features have important pharmacogenetic (PGx implications: first, extrapolation of PGx data from relatively well-defined ethnic groups is clearly not applicable to the majority of Brazilians; second, the frequency distribution of polymorphisms in pharmacogenes (e.g. CYP3A5, CYP2C9, GSTM1, ABCB1, GSTM3, VKORC, etc varies continuously among Brazilians and is not captured by race/color self-identification; third, the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of PGx studies in order to avoid spurious conclusions based on improper matching of study cohorts. The peculiarities of PGx in Brazilians are illustrated with data for different therapeutic groups, such as anticoagulants, HIV-protease inhibitors and nonsteroidal antinflammatory drugs, and the challenges and advantages created by population admixture for the study and implementation of PGx are discussed. PGx data for Amerindian groups and Brazilian-born, first generation Japanese are presented to illustrate the rich diversity of the Brazilian population. Finally, I introduce the reader to the Brazilian Pharmacogenetic Network or Refargen (www.refargen.org.br, a nationwide consortium of research groups, with the mission to provide leadership in PGx research and education in Brazil, with a population health impact.

  19. Population and population policy in Pakistan.

    Science.gov (United States)

    Mauldin, W P

    1963-02-01

    Pakistan is a divided country with different religious groups represented. Since independence in 1941, the Muslim population has increased more rapidly than the Hindu population, the West Pakistan population more rapidly and steadily than the East Pakistan population. In the late 1950s the Pakistan government initiated a family planning program. The program has trained medical and paramedical personnel in family planning, added family planning services to existing medical centers, planned for a National Research Institute of Family Planning, employed mobile units to reach outlying areas, conducted limited clinical studies on some contraceptives, and used mass media advertising. Only India and Japan are doing more with government-sponsored family planning. A weak organizational structure and an inadequate number of trained personnel are the main weakness of the program. It is too early to assess the success of the program. A 10-point reduction in annual birth rates will be considered successful.

  20. 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 Wide...... Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n¿=¿550 independent loci) were genotyped in a replication cohort and 122 SNPs (n¿=¿98 independent loci) were...... further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P...

  1. Glaucoma in Asian Populations

    Science.gov (United States)

    ... Involved News About Us Donate In This Section Glaucoma In Asian Populations email Send this article to ... lower than in their Asian counterparts. Normal Tension Glaucoma affects Japanese Japanese populations, however, have a substantially ...

  2. Contracting Data Analysis: Assessment of Government-Wide Trends

    Science.gov (United States)

    2017-03-01

    CONTRACTING DATA ANALYSIS Assessment of Government -wide Trends Report to Congressional Addressees March 2017...Office Highlights of GAO-17-244SP, a report to congressional addressees March 2017 CONTRACTING DATA ANALYSIS Assessment of Government -wide...Trends What GAO Found GAO’s analysis of government -wide contracting data found that while defense obligations to buy products and services

  3. Wide and ultra-wide bandgap oxides: where paradigm-shift photovoltaics meets transparent power electronics

    Science.gov (United States)

    Pérez-Tomás, Amador; Chikoidze, Ekaterine; Jennings, Michael R.; Russell, Stephen A. O.; Teherani, Ferechteh H.; Bove, Philippe;