Wide variation in hospital and physician payment rates evidence of provider market power.

Science.gov (United States)

Ginsburg, Paul B

2010-11-01

Wide variation in private insurer payment rates to hospitals and physicians across and within local markets suggests that some providers, particularly hospitals, have significant market power to negotiate higher-than-competitive prices, according to a new study by the Center for Studying Health System Change (HSC). Looking across eight health care markets--Cleveland; Indianapolis; Los Angeles; Miami; Milwaukee; Richmond, Va.; San Francisco; and rural Wisconsin--average inpatient hospital payment rates of four large national insurers ranged from 147 percent of Medicare in Miami to 210 percent in San Francisco. In extreme cases, some hospitals command almost five times what Medicare pays for inpatient services and more than seven times what Medicare pays for outpatient care. Variation within markets was just as dramatic. For example, the hospital with prices at the 25th percentile of Los Angeles hospitals received 84 percent of Medicare rates for inpatient care, while the hospital with prices at the 75th percentile received 184 percent of Medicare rates. The highest-priced Los Angeles hospital with substantial inpatient claims volume received 418 percent of Medicare. While not as pronounced, significant variation in physician payment rates also exists across and within markets and by specialty. Few would characterize the variation in hospital and physician payment rates found in this study to be consistent with a highly competitive market. Purchasers and public policy makers can address provider market power, or the ability to negotiate higher-than-competitive prices, through two distinct approaches. One is to pursue market approaches to strengthen competitive forces, while the other is to constrain payment rates through regulation.

Genome-wide recombination dynamics are associated with phenotypic variation in maize.

Science.gov (United States)

Pan, Qingchun; Li, Lin; Yang, Xiaohong; Tong, Hao; Xu, Shutu; Li, Zhigang; Li, Weiya; Muehlbauer, Gary J; Li, Jiansheng; Yan, Jianbing

2016-05-01

Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Seasonal variation of radon concentrations in UK homes

International Nuclear Information System (INIS)

Miles, J C H; Howarth, C B; Hunter, N

2012-01-01

The patterns of seasonal variation of radon concentrations were measured in 91 homes in five regions of the UK over a period of two years. The results showed that there was no significant difference between the regions in the pattern or magnitude of seasonal variation in radon concentrations. The arithmetic mean variation was found to be close to that found previously in the UK national survey. Differences in the pattern between the two years of the study were not significant. Two-thirds of homes in the study followed the expected pattern of high radon in the winter and low radon in the summer. Most of the rest showed little seasonal variation, and a few showed a reversed seasonal pattern. The study does not provide any clear evidence for the recorded house characteristics having an effect on the seasonal variation in radon concentrations in UK homes, though the statistical power for determining such effects is limited in this study. The magnitude of the seasonal variation varied widely between homes. Analysis of the individual results from the homes showed that because of the wide variation in the amount of seasonal variation, applying seasonal correction factors to the results of three-month measurements can yield only relatively small improvements in the accuracy of estimates of annual mean concentrations.

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

Directory of Open Access Journals (Sweden)

Walker M Andrew

2006-09-01

Full Text Available Abstract Background The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. Results There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c, 54 (Dixon, 83 (Ann1 and 9 (Temecula-1. A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. Conclusion INDELs and strain specific genes

A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

Science.gov (United States)

Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Davey Smith, G; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

2016-08-01

Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

Genome-wide copy number variation (CNV) in patients with autoimmune Addison's disease

Science.gov (United States)

2011-01-01

Background Addison's disease (AD) is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV) could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352) and healthy controls (n = 353) by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28) and T cell maturation (ADAM3A). Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity. PMID:21851588

Genome-wide copy number variation (CNV in patients with autoimmune Addison's disease

Directory of Open Access Journals (Sweden)

Brønstad Ingeborg

2011-08-01

Full Text Available Abstract Background Addison's disease (AD is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352 and healthy controls (n = 353 by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28 and T cell maturation (ADAM3A. Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity.

Synchronized Pulsed dc - dc Converter as Maximum Power Position Tracker with Wide Load and Insolation Variation for Stand Alone PV System

International Nuclear Information System (INIS)

Hardik, P. Desai; Ranjan Maheshwari

2011-01-01

This paper investigates the interest focused on employing parallel connected dc-dc converter with high tracking effectiveness under wide variation in environmental conditions (Insolation) and wide load variation. dc-dc converter is an essential part of the stand alone PV system. Paper also presents an approach on how duty cycle for maximum power position (MPP) is adjusted by taking care of varying load conditions and without iterative steps. Synchronized PWM pulses are employed for the converter. High tracking efficiency is achieved with continuous input and inductor current. In this approach, the converter can he utilized in buck as well in boost mode. The PV system simulation was verified and experimental results were in agreement to the presented scheme. (authors)

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

A genome-wide association study of copy number variations with umbilical hernia in swine.

Science.gov (United States)

Long, Yi; Su, Ying; Ai, Huashui; Zhang, Zhiyan; Yang, Bin; Ruan, Guorong; Xiao, Shijun; Liao, Xinjun; Ren, Jun; Huang, Lusheng; Ding, Nengshui

2016-06-01

Umbilical hernia (UH) is one of the most common congenital defects in pigs, leading to considerable economic loss and serious animal welfare problems. To test whether copy number variations (CNVs) contribute to pig UH, we performed a case-control genome-wide CNV association study on 905 pigs from the Duroc, Landrace and Yorkshire breeds using the Porcine SNP60 BeadChip and penncnv algorithm. We first constructed a genomic map comprising 6193 CNVs that pertain to 737 CNV regions. Then, we identified eight CNVs significantly associated with the risk for UH in the three pig breeds. Six of seven significantly associated CNVs were validated using quantitative real-time PCR. Notably, a rare CNV (CNV14:13030843-13059455) encompassing the NUGGC gene was strongly associated with UH (permutation-corrected P = 0.0015) in Duroc pigs. This CNV occurred exclusively in seven Duroc UH-affected individuals. SNPs surrounding the CNV did not show association signals, indicating that rare CNVs may play an important role in complex pig diseases such as UH. The NUGGC gene has been implicated in human omphalocele and inguinal hernia. Our finding supports that CNVs, including the NUGGC CNV, contribute to the pathogenesis of pig UH. © 2016 Stichting International Foundation for Animal Genetics.

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

Science.gov (United States)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the

A wide-bandwidth and high-sensitivity robust microgyroscope

International Nuclear Information System (INIS)

Sahin, Korhan; Sahin, Emre; Akin, Tayfun; Alper, Said Emre

2009-01-01

This paper reports a microgyroscope design concept with the help of a 2 degrees of freedom (DoF) sense mode to achieve a wide bandwidth without sacrificing mechanical and electronic sensitivity and to obtain robust operation against variations under ambient conditions. The design concept is demonstrated with a tuning fork microgyroscope fabricated with an in-house silicon-on-glass micromachining process. When the fabricated gyroscope is operated with a relatively wide bandwidth of 1 kHz, measurements show a relatively high raw mechanical sensitivity of 131 µV (° s −1 ) −1 . The variation in the amplified mechanical sensitivity (scale factor) of the gyroscope is measured to be less than 0.38% for large ambient pressure variations such as from 40 to 500 mTorr. The bias instability and angle random walk of the gyroscope are measured to be 131° h −1 and 1.15° h −1/2 , respectively

Genome-wide variation in recombination rate in Eucalyptus.

Science.gov (United States)

Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

2016-08-09

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = -0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = -0.75). The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst

Modeling and control of LCL-filtered grid-tied inverters with wide inductance variation

DEFF Research Database (Denmark)

Xie, Chuan; Li, Kai; Zhang, Gang

2017-01-01

with the changing of the inductor current in one cycle of the grid, which challenges the system stability and power quality. In this paper, the current-dependent small-signal model of a three-phase LCL-filtered inverter is derived for designing the corresponding controller. Based on the developed small-signal model......Because of the low power losses and moderate cost, the magnetic powder cores are popular in producing the filtering inductors for the high efficient and cost-effective power converters. However, the soft magnetic property of the powder cores leads to the wide variation of inductance along......, a capacitor current feedback based active damping loop and a fractional order repetitive control based compound current control loop are designed to stabilize the system and enhance the control accuracy in steady-state, respectively. The controller design procedure is given in detail. Finally, all...

Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation.

Science.gov (United States)

Gao, Lexuan; Geng, Yupeng; Li, Bo; Chen, Jiakuan; Yang, Ji

2010-11-01

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylation-sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors. © 2010 Blackwell Publishing Ltd.

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

Background levels of methane in Mars’ atmosphere show strong seasonal variations

Science.gov (United States)

Webster, Christopher R.; Mahaffy, Paul R.; Atreya, Sushil K.; Moores, John E.; Flesch, Gregory J.; Malespin, Charles; McKay, Christopher P.; Martinez, German; Smith, Christina L.; Martin-Torres, Javier; Gomez-Elvira, Javier; Zorzano, Maria-Paz; Wong, Michael H.; Trainer, Melissa G.; Steele, Andrew; Archer, Doug; Sutter, Brad; Coll, Patrice J.; Freissinet, Caroline; Meslin, Pierre-Yves; Gough, Raina V.; House, Christopher H.; Pavlov, Alexander; Eigenbrode, Jennifer L.; Glavin, Daniel P.; Pearson, John C.; Keymeulen, Didier; Christensen, Lance E.; Schwenzer, Susanne P.; Navarro-Gonzalez, Rafael; Pla-García, Jorge; Rafkin, Scot C. R.; Vicente-Retortillo, Álvaro; Kahanpää, Henrik; Viudez-Moreiras, Daniel; Smith, Michael D.; Harri, Ari-Matti; Genzer, Maria; Hassler, Donald M.; Lemmon, Mark; Crisp, Joy; Sander, Stanley P.; Zurek, Richard W.; Vasavada, Ashwin R.

2018-06-01

Variable levels of methane in the martian atmosphere have eluded explanation partly because the measurements are not repeatable in time or location. We report in situ measurements at Gale crater made over a 5-year period by the Tunable Laser Spectrometer on the Curiosity rover. The background levels of methane have a mean value 0.41 ± 0.16 parts per billion by volume (ppbv) (95% confidence interval) and exhibit a strong, repeatable seasonal variation (0.24 to 0.65 ppbv). This variation is greater than that predicted from either ultraviolet degradation of impact-delivered organics on the surface or from the annual surface pressure cycle. The large seasonal variation in the background and occurrences of higher temporary spikes (~7 ppbv) are consistent with small localized sources of methane released from martian surface or subsurface reservoirs.

The role of copy number variation in susceptibility to amyotrophic lateral sclerosis: genome-wide association study and comparison with published loci.

Directory of Open Access Journals (Sweden)

Louise V Wain

2009-12-01

Full Text Available The genetic contribution to sporadic amyotrophic lateral sclerosis (ALS has not been fully elucidated. There are increasing efforts to characterise the role of copy number variants (CNVs in human diseases; two previous studies concluded that CNVs may influence risk of sporadic ALS, with multiple rare CNVs more important than common CNVs. A little-explored issue surrounding genome-wide CNV association studies is that of post-calling filtering and merging of raw CNV calls. We undertook simulations to define filter thresholds and considered optimal ways of merging overlapping CNV calls for association testing, taking into consideration possibly overlapping or nested, but distinct, CNVs and boundary estimation uncertainty.In this study we screened Illumina 300K SNP genotyping data from 730 ALS cases and 789 controls for copy number variation. Following quality control filters using thresholds defined by simulation, a total of 11321 CNV calls were made across 575 cases and 621 controls. Using region-based and gene-based association analyses, we identified several loci showing nominally significant association. However, the choice of criteria for combining calls for association testing has an impact on the ranking of the results by their significance. Several loci which were previously reported as being associated with ALS were identified here. However, of another 15 genes previously reported as exhibiting ALS-specific copy number variation, only four exhibited copy number variation in this study. Potentially interesting novel loci, including EEF1D, a translation elongation factor involved in the delivery of aminoacyl tRNAs to the ribosome (a process which has previously been implicated in genetic studies of spinal muscular atrophy were identified but must be treated with caution due to concerns surrounding genomic location and platform suitability.Interpretation of CNV association findings must take into account the effects of filtering and combining

A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

Directory of Open Access Journals (Sweden)

James W Kijas

Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing.

Science.gov (United States)

Yi, Guoqiang; Qu, Lujiang; Liu, Jianfeng; Yan, Yiyuan; Xu, Guiyun; Yang, Ning

2014-11-07

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

Genome-Wide Association Shows that Pigmentation Genes Play a Role in Skin Aging.

Science.gov (United States)

Law, Matthew H; Medland, Sarah E; Zhu, Gu; Yazar, Seyhan; Viñuela, Ana; Wallace, Leanne; Shekar, Sri Niranjan; Duffy, David L; Bataille, Veronique; Glass, Dan; Spector, Tim D; Wood, Diane; Gordon, Scott D; Barbour, Julie M; Henders, Anjali K; Hewitt, Alex W; Montgomery, Grant W; Sturm, Richard A; Mackey, David A; Green, Adèle C; Martin, Nicholas G; MacGregor, Stuart

2017-09-01

Loss of fine skin patterning is a sign of both aging and photoaging. Studies investigating the genetic contribution to skin patterning offer an opportunity to better understand a trait that influences both physical appearance and risk of keratinocyte skin cancer. We undertook a meta-analysis of genome-wide association studies of a measure of skin pattern (microtopography score) damage in 1,671 twin pairs and 1,745 singletons (N = 5,087) drawn from three independent cohorts. We identified that rs185146 near SLC45A2 is associated with a skin aging trait at genome-wide significance (P = 4.1 × 10 -9 ); to our knowledge this is previously unreported. We also confirm previously identified loci, rs12203592 near IRF4 (P = 8.8 × 10 -13 ) and rs4268748 near MC1R (P = 1.2 × 10 -15 ). At all three loci we highlight putative functionally relevant SNPs. There are a number of red hair/low pigmentation alleles of MC1R; we found that together these MC1R alleles explained 4.1% of variance in skin pattern damage. We also show that skin aging and reported experience of sunburns was proportional to the degree of penetrance for red hair of alleles of MC1R. Our work has uncovered genetic contributions to skin aging and confirmed previous findings, showing that pigmentation is a critical determinant of skin aging. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Studies on the Colour Variation in Larvae of Ephestia kuhniella (ZELLER)(Lepidoptera, Phycitidae) : 1. On the Inheritance of colour variation

OpenAIRE

Osamu, IMURA; Entomology Laboratory, National Food Research Institute

1980-01-01

The crossing experiment and the selection experiment were carried out at 25℃ and 67% r.h. to define genetic mechanisms of the colour variation in larvae of Ephestia kuhniella. The populations sampled from the Wild-type stock showed the wide range of continuous colour variation from white to deep pink in the 5th inster lavae. The results of the crossing experiment between white larval strain and red larval strain selected from the Wild-type stock suggested the larval colour variation was a qua...

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

Science.gov (United States)

Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

2015-06-01

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Geographic variation in lumbar diskectomy: a protocol for evaluation.

Science.gov (United States)

Barron, M; Kazandjian, V A

1992-03-01

In 1989 the Maryland Hospital Association (MHA) began developing a protocol related to lumbar diskectomy, a procedure with widely reported geographic variation in its use. The MHA's Laminectomy Advisory Committee drafted three criteria for performance of lumbar diskectomy and also developed a data-collection instrument with which the eight hospitals participating in a pilot study could abstract the necessary data from medical records. Both individual hospital and aggregate results showed wide variation in compliance with the criteria. These findings suggest research and development activities such as refinement of the data-collection instrument, use of the protocol for bench-marking, further investigation of clinical and other determinants of rate variation, and study of the effect of new diagnostic technology on utilization rates for this procedure.

Photographic Records Showing the Variations of the Virtual Height of Reflection as a Function of the Radio Frequency

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The standard (analog) ionosonde produces photographic records known as ionograms, which show the variations of the virtual height of reflection as a function of the...

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...

Calculus of variations

CERN Document Server

Elsgolc, L E; Stark, M

1961-01-01

Calculus of Variations aims to provide an understanding of the basic notions and standard methods of the calculus of variations, including the direct methods of solution of the variational problems. The wide variety of applications of variational methods to different fields of mechanics and technology has made it essential for engineers to learn the fundamentals of the calculus of variations. The book begins with a discussion of the method of variation in problems with fixed boundaries. Subsequent chapters cover variational problems with movable boundaries and some other problems; sufficiency

Inter-practice variation in diagnosing hypertension and diabetes mellitus: a cross-sectional study in general practice

NARCIS (Netherlands)

Nielen, M.M.J.; Schellevis, F.G.; Verheij, R.A.

2009-01-01

BACKGROUND: Previous studies of inter-practice variation of the prevalence of hypertension and diabetes mellitus showed wide variations between practices. However, in these studies inter-practice variation was calculated without controlling for clustering of patients within practices and without

Inter-practice variation in diagnosing hypertension and diabetes mellitus: a cross-sectional study in general practice.

NARCIS (Netherlands)

Nielen, M.M.J.; Schellevis, F.G.; Verheij, R.A.

2009-01-01

BACKGROUND: Previous studies of inter-practice variation of the prevalence of hypertension and diabetes mellitus showed wide variations between practices. However, in these studies inter-practice variation was calculated without controlling for clustering of patients within practices and without

Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops

Directory of Open Access Journals (Sweden)

Hongwei Wang

2017-06-01

Full Text Available Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.

The role of environment and core-margin effects on range-wide phenotypic variation in a montane grasshopper.

Science.gov (United States)

Noguerales, V; García-Navas, V; Cordero, P J; Ortego, J

2016-11-01

The integration of genetic information with ecological and phenotypic data constitutes an effective approach to gain insight into the mechanisms determining interpopulation variability and the evolutionary processes underlying local adaptation and incipient speciation. Here, we use the Pyrenean Morales grasshopper (Chorthippus saulcyi moralesi) as study system to (i) analyse the relative role of genetic drift and selection in range-wide patterns of phenotypic differentiation and (ii) identify the potential selective agents (environment, elevation) responsible for variation. We also test the hypothesis that (iii) the development of dispersal-related traits is associated with different parameters related to population persistence/turnover, including habitat suitability stability over the last 120 000 years, distance to the species distribution core and population genetic variability. Our results indicate that selection shaped phenotypic differentiation across all the studied morphological traits (body size, forewing length and shape). Subsequent analyses revealed that among-population differentiation in forewing length was significantly explained by a temperature gradient, suggesting an adaptive response to thermoregulation or flight performance under contrasting temperature regimes. We found support for our hypothesis predicting a positive association between the distance to the species distribution core and the development of dispersal-related morphology, which suggests an increased dispersal capability in populations located at range edges that, in turn, exhibit lower levels of genetic variability. Overall, our results indicate that range-wide patterns of phenotypic variation are partially explained by adaptation in response to local environmental conditions and differences in habitat persistence between core and peripheral populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary

Wide variation in cardiopulmonary resuscitation interruption intervals among commercially available automated external defibrillators may affect survival despite high defibrillation efficacy.

Science.gov (United States)

Snyder, David; Morgan, Carl

2004-09-01

Recent studies have associated interruptions of cardiopulmonary resuscitation imposed by automated external defibrillators (AEDs) with poor resuscitation outcome. In particular, the "hands-off" interval between precordial compressions and subsequent defibrillation shock has been implicated. We sought to determine the range of variation among current-generation AEDs with respect to this characteristic. Seven AEDs from six manufacturers were characterized via stopwatch and arrhythmia simulator with respect to the imposed hands-off interval. All AEDs were equipped with new batteries, and measurements were repeated five times for each AED. A wide variation in the hands-off interval between precordial compressions and shock delivery was observed, ranging from 5.2 to 28.4 secs, with only one AED achieving an interruption of <10 secs. Laboratory and clinical data suggest that this range of variation could be responsible for a more than two-fold variation in patient resuscitation success, an effect that far exceeds any defibrillation efficacy differences that may hypothetically exist. In addition to defibrillation waveform and dose, researchers should consider the hands-off cardiopulmonary resuscitation interruption interval between cardiopulmonary resuscitation and subsequent defibrillation shock to be an important covariate of outcome in resuscitation studies. Defibrillator design should minimize this interval to avoid potential adverse consequences on patient survival.

High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites.

Science.gov (United States)

Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

2008-06-01

Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied so far. Arid-adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate community. The only other species showing a similar absence of genetic structuring is the African buffalo (Syncerus caffer), but this taxon lacks the high levels of morphological variation present in the plains zebra.

Regenerant arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes

KAUST Repository

Jiang, Caifu

2011-07-28

Multicellular organisms can be regenerated from totipotent differentiated somatic cell or nuclear founders [1-3]. Organisms regenerated from clonally related isogenic founders might a priori have been expected to be phenotypically invariant. However, clonal regenerant animals display variant phenotypes caused by defective epigenetic reprogramming of gene expression [2], and clonal regenerant plants exhibit poorly understood heritable phenotypic ("somaclonal") variation [4-7]. Here we show that somaclonal variation in regenerant Arabidopsis lineages is associated with genome-wide elevation in DNA sequence mutation rate. We also show that regenerant mutations comprise a distinctive molecular spectrum of base substitutions, insertions, and deletions that probably results from decreased DNA repair fidelity. Finally, we show that while regenerant base substitutions are a likely major genetic cause of the somaclonal variation of regenerant Arabidopsis lineages, transposon movement is unlikely to contribute substantially to that variation. We conclude that the phenotypic variation of regenerant plants, unlike that of regenerant animals, is substantially due to DNA sequence mutation. 2011 Elsevier Ltd. All rights reserved.

Regenerant arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes

KAUST Repository

Jiang, Caifu; Mithani, Aziz; Gan, Xiangchao; Belfield, Eric J.; Klingler, John  P.; Zhu, Jian-Kang; Ragoussis, Jiannis; Mott, Richard; Harberd, Nicholas  P.

2011-01-01

Multicellular organisms can be regenerated from totipotent differentiated somatic cell or nuclear founders [1-3]. Organisms regenerated from clonally related isogenic founders might a priori have been expected to be phenotypically invariant. However, clonal regenerant animals display variant phenotypes caused by defective epigenetic reprogramming of gene expression [2], and clonal regenerant plants exhibit poorly understood heritable phenotypic ("somaclonal") variation [4-7]. Here we show that somaclonal variation in regenerant Arabidopsis lineages is associated with genome-wide elevation in DNA sequence mutation rate. We also show that regenerant mutations comprise a distinctive molecular spectrum of base substitutions, insertions, and deletions that probably results from decreased DNA repair fidelity. Finally, we show that while regenerant base substitutions are a likely major genetic cause of the somaclonal variation of regenerant Arabidopsis lineages, transposon movement is unlikely to contribute substantially to that variation. We conclude that the phenotypic variation of regenerant plants, unlike that of regenerant animals, is substantially due to DNA sequence mutation. 2011 Elsevier Ltd. All rights reserved.

Circadian pathway genetic variation and cancer risk: evidence from genome-wide association studies.

Science.gov (United States)

Mocellin, Simone; Tropea, Saveria; Benna, Clara; Rossi, Carlo Riccardo

2018-02-19

Dysfunction of the circadian clock and single polymorphisms of some circadian genes have been linked to cancer susceptibility, although data are scarce and findings inconsistent. We aimed to investigate the association between circadian pathway genetic variation and risk of developing common cancers based on the findings of genome-wide association studies (GWASs). Single nucleotide polymorphisms (SNPs) of 17 circadian genes reported by three GWAS meta-analyses dedicated to breast (Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) Consortium; cases, n = 15,748; controls, n = 18,084), prostate (Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE) Consortium; cases, n = 14,160; controls, n = 12,724) and lung carcinoma (Transdisciplinary Research In Cancer of the Lung (TRICL) Consortium; cases, n = 12,160; controls, n = 16,838) in patients of European ancestry were utilized to perform pathway analysis by means of the adaptive rank truncated product (ARTP) method. Data were also available for the following subgroups: estrogen receptor negative breast cancer, aggressive prostate cancer, squamous lung carcinoma and lung adenocarcinoma. We found a highly significant statistical association between circadian pathway genetic variation and the risk of breast (pathway P value = 1.9 × 10 -6 ; top gene RORA, gene P value = 0.0003), prostate (pathway P value = 4.1 × 10 -6 ; top gene ARNTL, gene P value = 0.0002) and lung cancer (pathway P value = 6.9 × 10 -7 ; top gene RORA, gene P value = 2.0 × 10 -6 ), as well as all their subgroups. Out of 17 genes investigated, 15 were found to be significantly associated with the risk of cancer: four genes were shared by all three malignancies (ARNTL, CLOCK, RORA and RORB), two by breast and lung cancer (CRY1 and CRY2) and three by prostate and lung cancer (NPAS2, NR1D1 and PER3), whereas four genes were specific for lung cancer

DNA methylation-based variation between human populations.

Science.gov (United States)

Kader, Farzeen; Ghai, Meenu

2017-02-01

Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

Charge Diffusion Variations in Pan-STARRS1 CCDs

Science.gov (United States)

Magnier, Eugene A.; Tonry, J. L.; Finkbeiner, D.; Schlafly, E.; Burgett, W. S.; Chambers, K. C.; Flewelling, H. A.; Hodapp, K. W.; Kaiser, N.; Kudritzki, R.-P.; Metcalfe, N.; Wainscoat, R. J.; Waters, C. Z.

2018-06-01

Thick back-illuminated deep-depletion CCDs have superior quantum efficiency over previous generations of thinned and traditional thick CCDs. As a result, they are being used for wide-field imaging cameras in several major projects. We use observations from the Pan-STARRS 3π survey to characterize the behavior of the deep-depletion devices used in the Pan-STARRS 1 Gigapixel Camera. We have identified systematic spatial variations in the photometric measurements and stellar profiles that are similar in pattern to the so-called “tree rings” identified in devices used by other wide-field cameras (e.g., DECam and Hypersuprime Camera). The tree-ring features identified in these other cameras result from lateral electric fields that displace the electrons as they are transported in the silicon to the pixel location. In contrast, we show that the photometric and morphological modifications observed in the GPC1 detectors are caused by variations in the vertical charge transportation rate and resulting charge diffusion variations.

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.

Varying couplings in the early universe: Correlated variations of α and G

International Nuclear Information System (INIS)

Martins, C. J. A. P.; Menegoni, Eloisa; Galli, Silvia; Mangano, Gianpiero; Melchiorri, Alessandro

2010-01-01

The cosmic microwave background anisotropies provide a unique opportunity to constrain simultaneous variations of the fine-structure constant α and Newton's gravitational constant G. Those correlated variations are possible in a wide class of theoretical models. In this brief paper we show that the current data, assuming that particle masses are constant, give no clear indication for such variations, but already prefer that any relative variations in α should be of the same sign of those of G for variations of ∼1%. We also show that a cosmic complementarity is present with big bang nucleosynthesis and that a combination of current CMB and big bang nucleosynthesis data strongly constraints simultaneous variations in α and G. We finally discuss the future bounds achievable by the Planck satellite mission.

Variation in genome-wide levels of meiotic recombination is established at the onset of prophase in mammalian males.

Directory of Open Access Journals (Sweden)

Brian Baier

2014-01-01

Full Text Available Segregation of chromosomes during the first meiotic division relies on crossovers established during prophase. Although crossovers are strictly regulated so that at least one occurs per chromosome, individual variation in crossover levels is not uncommon. In an analysis of different inbred strains of male mice, we identified among-strain variation in the number of foci for the crossover-associated protein MLH1. We report studies of strains with "low" (CAST/EiJ, "medium" (C3H/HeJ, and "high" (C57BL/6J genome-wide MLH1 values to define factors responsible for this variation. We utilized immunofluorescence to analyze the number and distribution of proteins that function at different stages in the recombination pathway: RAD51 and DMC1, strand invasion proteins acting shortly after double-strand break (DSB formation, MSH4, part of the complex stabilizing double Holliday junctions, and the Bloom helicase BLM, thought to have anti-crossover activity. For each protein, we identified strain-specific differences that mirrored the results for MLH1; i.e., CAST/EiJ mice had the lowest values, C3H/HeJ mice intermediate values, and C57BL/6J mice the highest values. This indicates that differences in the numbers of DSBs (as identified by RAD51 and DMC1 are translated into differences in the number of crossovers, suggesting that variation in crossover levels is established by the time of DSB formation. However, DSBs per se are unlikely to be the primary determinant, since allelic variation for the DSB-inducing locus Spo11 resulted in differences in the numbers of DSBs but not the number of MLH1 foci. Instead, chromatin conformation appears to be a more important contributor, since analysis of synaptonemal complex length and DNA loop size also identified consistent strain-specific differences; i.e., crossover frequency increased with synaptonemal complex length and was inversely related to chromatin loop size. This indicates a relationship between recombination

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

Science.gov (United States)

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Modelling basin-wide variations in Amazon forest photosynthesis

Science.gov (United States)

Mercado, Lina; Lloyd, Jon; Domingues, Tomas; Fyllas, Nikolaos; Patino, Sandra; Dolman, Han; Sitch, Stephen

2010-05-01

Given the importance of Amazon rainforest in the global carbon and hydrological cycles, there is a need to use parameterized and validated ecosystem gas exchange and vegetation models for this region in order to adequately simulate present and future carbon and water balances. Recent research has found major differences in above-ground net primary productivity (ANPP), above ground biomass and tree dynamics across Amazonia. West Amazonia is more dynamic, with younger trees, higher stem growth rates and lower biomass than central and eastern Amazon (Baker et al. 2004; Malhi et al. 2004; Phillips et al. 2004). A factor of three variation in above-ground net primary productivity has been estimated across Amazonia by Malhi et al. (2004). Different hypotheses have been proposed to explain the observed spatial variability in ANPP (Malhi et al. 2004). First, due to the proximity to the Andes, sites from western Amazonia tend to have richer soils than central and eastern Amazon and therefore soil fertility could possibly be highly related to the high wood productivity found in western sites. Second, if GPP does not vary across the Amazon basin then different patterns of carbon allocation to respiration could also explain the observed ANPP gradient. However since plant growth depends on the interaction between photosynthesis, transport of assimilates, plant respiration, water relations and mineral nutrition, variations in plant gross photosynthesis (GPP) could also explain the observed variations in ANPP. In this study we investigate whether Amazon GPP can explain variations of observed ANPP. We use a sun and shade canopy gas exchange model that has been calibrated and evaluated at five rainforest sites (Mercado et al. 2009) to simulate gross primary productivity of 50 sites across the Amazon basin during the period 1980-2001. Such simulation differs from the ones performed with global vegetation models (Cox et al. 1998; Sitch et al. 2003) where i) single plant functional

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.

Paediatric approaches to child maltreatment are subject to wide organisational variations across Europe.

Science.gov (United States)

Otterman, Gabriel; Jalsenius, Marie; Maguire, Sabine; Sarkadi, Anna; Janson, Staffan

2017-07-01

Little is known about the organisation of child maltreatment practice in Europe. We therefore explored medical child protection systems and training across Europe. An online survey was completed by physicians working in child maltreatment, identified through professional organisations in 28 member countries of the European Union, Iceland, Norway and Switzerland in 2012-2013. Respondents were questioned regarding management of suspected child maltreatment, mandatory reporting, professional training, patient referral and physician roles in multidisciplinary investigations. Responses underwent a narrative synthesis and descriptive enumerations. The survey was completed by 88 individuals, unevenly distributed in 22 of 31 countries. Physicians were mandated to report child maltreatment in 16 of 22 countries. All of 88 responding physicians described multidisciplinary involvement in the clinical and forensic management of suspected child maltreatment. Practitioners involved in physical examinations included general physicians, paediatricians, forensic medical examiners, gynaecologists and paediatric surgeons. Paediatricians were required to undergo child protection training according to 30 of 86 respondents in 14 of 22 countries. This survey demonstrates that there were wide variations in the organisation of child maltreatment paediatrics in Europe. The differing legislative frameworks and models of care are pertinent to consider when comparing epidemiology of maltreatment reported from across European countries. ©2017 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Genome-wide analysis of adolescent psychotic-like experiences shows genetic overlap with psychiatric disorders.

Science.gov (United States)

Pain, Oliver; Dudbridge, Frank; Cardno, Alastair G; Freeman, Daniel; Lu, Yi; Lundstrom, Sebastian; Lichtenstein, Paul; Ronald, Angelica

2018-03-31

This study aimed to test for overlap in genetic influences between psychotic-like experience traits shown by adolescents in the community, and clinically-recognized psychiatric disorders in adulthood, specifically schizophrenia, bipolar disorder, and major depression. The full spectra of psychotic-like experience domains, both in terms of their severity and type (positive, cognitive, and negative), were assessed using self- and parent-ratings in three European community samples aged 15-19 years (Final N incl. siblings = 6,297-10,098). A mega-genome-wide association study (mega-GWAS) for each psychotic-like experience domain was performed. Single nucleotide polymorphism (SNP)-heritability of each psychotic-like experience domain was estimated using genomic-relatedness-based restricted maximum-likelihood (GREML) and linkage disequilibrium- (LD-) score regression. Genetic overlap between specific psychotic-like experience domains and schizophrenia, bipolar disorder, and major depression was assessed using polygenic risk score (PRS) and LD-score regression. GREML returned SNP-heritability estimates of 3-9% for psychotic-like experience trait domains, with higher estimates for less skewed traits (Anhedonia, Cognitive Disorganization) than for more skewed traits (Paranoia and Hallucinations, Parent-rated Negative Symptoms). Mega-GWAS analysis identified one genome-wide significant association for Anhedonia within IDO2 but which did not replicate in an independent sample. PRS analysis revealed that the schizophrenia PRS significantly predicted all adolescent psychotic-like experience trait domains (Paranoia and Hallucinations only in non-zero scorers). The major depression PRS significantly predicted Anhedonia and Parent-rated Negative Symptoms in adolescence. Psychotic-like experiences during adolescence in the community show additive genetic effects and partly share genetic influences with clinically-recognized psychiatric disorders, specifically schizophrenia and

Genome-wide association study of clinical dimensions of schizophrenia

DEFF Research Database (Denmark)

Fanous, Ayman H; Zhou, Baiyu; Aggen, Steven H

2012-01-01

Multiple sources of evidence suggest that genetic factors influence variation in clinical features of schizophrenia. The authors present the first genome-wide association study (GWAS) of dimensional symptom scores among individuals with schizophrenia.......Multiple sources of evidence suggest that genetic factors influence variation in clinical features of schizophrenia. The authors present the first genome-wide association study (GWAS) of dimensional symptom scores among individuals with schizophrenia....

Epidemiology of hip fracture: Worldwide geographic variation

Directory of Open Access Journals (Sweden)

Dinesh K Dhanwal

2011-01-01

Full Text Available Osteoporosis is a major health problem, especially in elderly populations, and is associated with fragility fractures at the hip, spine, and wrist. Hip fracture contributes to both morbidity and mortality in the elderly. The demographics of world populations are set to change, with more elderly living in developing countries, and it has been estimated that by 2050 half of hip fractures will occur in Asia. This review conducted using the PubMed database describes the incidence of hip fracture in different regions of the world and discusses the possible causes of this wide geographic variation. The analysis of data from different studies show a wide geographic variation across the world, with higher hip fracture incidence reported from industrialized countries as compared to developing countries. The highest hip fracture rates are seen in North Europe and the US and lowest in Latin America and Africa. Asian countries such as Kuwait, Iran, China, and Hong Kong show intermediate hip fracture rates. There is also a north-south gradient seen in European studies, and more fractures are seen in the north of the US than in the south. The factors responsible of this variation are population demographics (with more elderly living in countries with higher incidence rates and the influence of ethnicity, latitude, and environmental factors. The understanding of this changing geographic variation will help policy makers to develop strategies to reduce the burden of hip fractures in developing countries such as India, which will face the brunt of this problem over the coming decades.

Black sea annual and inter-annual water mass variations from space

DEFF Research Database (Denmark)

Yildiz, H.; Andersen, Ole Baltazar; Simav, M.

2011-01-01

influenced by the leakage of hydrological signals from the surrounding land. After applying the corresponding correction, we found a good agreement with water mass variations derived from steric-corrected satellite altimetry observations. Both GRACE and altimetry show significant annual water mass variations......This study evaluates the performance of two widely used GRACE solutions (CNES/GRGS RL02 and CSR RL04) in deriving annual and inter-annual water mass variations in the Black Sea for the period 2003–2007. It is demonstrated that the GRACE derived water mass variations in the Black Sea are heavily...

Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors.

Science.gov (United States)

Schradin, Carsten

2013-05-19

Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation.

Variational and quasi-variational inequalities in mechanics

CERN Document Server

Kravchuk, Alexander S

2007-01-01

The essential aim of the present book is to consider a wide set of problems arising in the mathematical modelling of mechanical systems under unilateral constraints. In these investigations elastic and non-elastic deformations, friction and adhesion phenomena are taken into account. All the necessary mathematical tools are given: local boundary value problem formulations, construction of variational equations and inequalities, and the transition to minimization problems, existence and uniqueness theorems, and variational transformations (Friedrichs and Young-Fenchel-Moreau) to dual and saddle-point search problems. Important new results concern contact problems with friction. The Coulomb friction law and some others are considered, in which relative sliding velocities appear. The corresponding quasi-variational inequality is constructed, as well as the appropriate iterative method for its solution. Outlines of the variational approach to non-stationary and dissipative systems and to the construction of the go...

THE HUBBLE WIDE FIELD CAMERA 3 TEST OF SURFACES IN THE OUTER SOLAR SYSTEM: SPECTRAL VARIATION ON KUIPER BELT OBJECTS

International Nuclear Information System (INIS)

Fraser, Wesley C.; Brown, Michael E.; Glass, Florian

2015-01-01

Here, we present additional photometry of targets observed as part of the Hubble Wide Field Camera 3 (WFC3) Test of Surfaces in the Outer Solar System. Twelve targets were re-observed with the WFC3 in the optical and NIR wavebands designed to complement those used during the first visit. Additionally, all of the observations originally presented by Fraser and Brown were reanalyzed through the same updated photometry pipeline. A re-analysis of the optical and NIR color distribution reveals a bifurcated optical color distribution and only two identifiable spectral classes, each of which occupies a broad range of colors and has correlated optical and NIR colors, in agreement with our previous findings. We report the detection of significant spectral variations on five targets which cannot be attributed to photometry errors, cosmic rays, point-spread function or sensitivity variations, or other image artifacts capable of explaining the magnitude of the variation. The spectrally variable objects are found to have a broad range of dynamical classes and absolute magnitudes, exhibit a broad range of apparent magnitude variations, and are found in both compositional classes. The spectrally variable objects with sufficiently accurate colors for spectral classification maintain their membership, belonging to the same class at both epochs. 2005 TV189 exhibits a sufficiently broad difference in color at the two epochs that span the full range of colors of the neutral class. This strongly argues that the neutral class is one single class with a broad range of colors, rather than the combination of multiple overlapping classes

Genome Variation Map: a data repository of genome variations in BIG Data Center

OpenAIRE

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2017-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

Ensembl variation resources

Directory of Open Access Journals (Sweden)

Marin-Garcia Pablo

2010-05-01

Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity.

Directory of Open Access Journals (Sweden)

Vijee Mohan

Full Text Available Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS, carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1 involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima'D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.

Learning the solution sparsity of an ill-posed linear inverse problem with the Variational Garrote

DEFF Research Database (Denmark)

Andersen, Michael Riis; Hansen, Sofie Therese; Hansen, Lars Kai

2013-01-01

the Variational Garrote, we show, has a wide range of parameter values for which it at the same time provides low test error and high retrieval of the true feature locations. Furthermore, the new form of the prior and associated hyper-prior leads to a simple update rule in a Bayesian variational inference scheme...

Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake

NARCIS (Netherlands)

T. Tanaka (Toshiko); J.S. Ngwa; F.J.A. van Rooij (Frank); M.C. Zillikens (Carola); M.K. Wojczynski (Mary ); A.C. Frazier-Wood (Alexis); D.K. Houston (Denise); S. Kanoni (Stavroula); R.N. Lemaitre (Rozenn ); J. Luan; V. Mikkilä (Vera); F. Renström (Frida); E. Sonestedt (Emily); J.H. Zhao (Jing Hua); A.Y. Chu (Audrey); L. Qi (Lu); D.I. Chasman (Daniel); M.C. De Oliveira Otto (Marcia); E.J. Dhurandhar (Emily); M.F. Feitosa (Mary Furlan); I. Johansson (Ingegerd); K-T. Khaw (Kay-Tee); K. Lohman (Kurt); A. Manichaikul (Ani); N.M. McKeown (Nicola ); D. Mozaffarian (Dariush); A.B. Singleton (Andrew); K. Stirrups (Kathy); J. Viikari (Jorma); Z. Ye (Zheng); S. Bandinelli (Stefania); I.E. Barroso (Inês); P. Deloukas (Panagiotis); N.G. Forouhi (Nita); A. Hofman (Albert); Y. Liu (YongMei); L.-P. Lyytikäinen (Leo-Pekka); K.E. North (Kari); M. Dimitriou (Maria); G. Hallmans (Göran); M. Kähönen (Mika); C. Langenberg (Claudia); J.M. Ordovas (Jose); A.G. Uitterlinden (André); F.B. Hu (Frank); I.-P. Kalafati (Ioanna-Panagiota); O. Raitakari (Olli); O.H. Franco (Oscar); A. Johnson (Anthony); V. Emilsson (Valur); J.A. Schrack (Jennifer); R.D. Semba; D.S. Siscovick (David); D.K. Arnett (Donna); I.B. Borecki (Ingrid); P.W. Franks (Paul); S.B. Kritchevsky (Stephen); R.J.F. Loos (Ruth); M. Orho-Melander (Marju); J.I. Rotter (Jerome); N.J. Wareham (Nick); J.C.M. Witteman (Jacqueline); L. Ferrucci (Luigi); G.V. Dedoussis (George); L.A. Cupples (Adrienne); J.A. Nettleton (Jennifer )

2013-01-01

textabstractBackground: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake.

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.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations.

Science.gov (United States)

Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato ( Solanum lycopersicum ) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense , both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense . We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens ( Alternaria solani , Phytophthora infestans and a Fusarium sp .) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense , resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics

Directory of Open Access Journals (Sweden)

van Manen Daniëlle

2012-08-01

Full Text Available Abstract Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.

High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

DEFF Research Database (Denmark)

Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

2008-01-01

units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied...

Genome-wide recombination rate variation in a recombination map of cotton.

Science.gov (United States)

Shen, Chao; Li, Ximei; Zhang, Ruiting; Lin, Zhongxu

2017-01-01

Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species' genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.

Genetic variation in California oaks

Science.gov (United States)

Constance I. Millar; Diane L. Delany; Lawrence A. Riggs

1990-01-01

In forestry the importance of genetic variation for successful reproduction, survival and growth has been widely documented for commercial conifers; until recently, little genetic work has been done on the California oaks. Even before the nature of genetic variation was scientifically investigated, its importance was suspected in operational forestry. Many failures of...

Seismic noise level variation in South Korea

Science.gov (United States)

Sheen, D.; Shin, J.

2008-12-01

The variations of seismic background noise in South Korea have been investigated by means of power spectral analysis. The Korea Institute of Geoscience and Mineral Resources (KIGAM) and the Korea Meteorological Administation (KMA) have national wide seismic networks in South Korea, and, in the end of 2007, there are 30 broadband stations which have been operating for more than a year. In this study, we have estimated the power spectral density of seismic noise for 30 broadband stations from 2005 to 2007. Since we estimate PSDs from a large dataset of continuous waveform in this study, a robust PSD estimate of McNamara and Buland (2004) is used. In the frequency range 1-5 Hz, the diurnal variations of noise are observed at most of stations, which are especially larger at coastal stations and at insular than at inland. Some stations shows daily difference of diurnal variations, which represents that cultural activities contribute to the noise level of a station. The variation of number of triggered stations, however, shows that cultural noise has little influence on the detection capability of seismic network in South Korea. Seasonal variations are observed well in the range 0.1-0.5 Hz, while much less found in the frequency range 1-5 Hz. We observed that strong peaks in the range 0.1-0.5 Hz occur at the summer when Pacific typhoons are close to the Korean Peninsula.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

Directory of Open Access Journals (Sweden)

Remco Stam

2017-01-01

Full Text Available Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp. and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

Science.gov (United States)

Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved. PMID:28133579

A genome-wide association study demonstrates significant genetic variation for fracture risk in Thoroughbred racehorses

Science.gov (United States)

2014-01-01

Background Thoroughbred racehorses are subject to non-traumatic distal limb bone fractures that occur during racing and exercise. Susceptibility to fracture may be due to underlying disturbances in bone metabolism which have a genetic cause. Fracture risk has been shown to be heritable in several species but this study is the first genetic analysis of fracture risk in the horse. Results Fracture cases (n = 269) were horses that sustained catastrophic distal limb fractures while racing on UK racecourses, necessitating euthanasia. Control horses (n = 253) were over 4 years of age, were racing during the same time period as the cases, and had no history of fracture at the time the study was carried out. The horses sampled were bred for both flat and National Hunt (NH) jump racing. 43,417 SNPs were employed to perform a genome-wide association analysis and to estimate the proportion of genetic variance attributable to the SNPs on each chromosome using restricted maximum likelihood (REML). Significant genetic variation associated with fracture risk was found on chromosomes 9, 18, 22 and 31. Three SNPs on chromosome 18 (62.05 Mb – 62.15 Mb) and one SNP on chromosome 1 (14.17 Mb) reached genome-wide significance (p fracture than cases, p = 1 × 10-4), while a second haplotype increases fracture risk (cases at 3.39 times higher risk of fracture than controls, p = 0.042). Conclusions Fracture risk in the Thoroughbred horse is a complex condition with an underlying genetic basis. Multiple genomic regions contribute to susceptibility to fracture risk. This suggests there is the potential to develop SNP-based estimators for genetic risk of fracture in the Thoroughbred racehorse, using methods pioneered in livestock genetics such as genomic selection. This information would be useful to racehorse breeders and owners, enabling them to reduce the risk of injury in their horses. PMID:24559379

Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53 949)

Science.gov (United States)

Davies, G; Armstrong, N; Bis, J C; Bressler, J; Chouraki, V; Giddaluru, S; Hofer, E; Ibrahim-Verbaas, C A; Kirin, M; Lahti, J; van der Lee, S J; Le Hellard, S; Liu, T; Marioni, R E; Oldmeadow, C; Postmus, I; Smith, A V; Smith, J A; Thalamuthu, A; Thomson, R; Vitart, V; Wang, J; Yu, L; Zgaga, L; Zhao, W; Boxall, R; Harris, S E; Hill, W D; Liewald, D C; Luciano, M; Adams, H; Ames, D; Amin, N; Amouyel, P; Assareh, A A; Au, R; Becker, J T; Beiser, A; Berr, C; Bertram, L; Boerwinkle, E; Buckley, B M; Campbell, H; Corley, J; De Jager, P L; Dufouil, C; Eriksson, J G; Espeseth, T; Faul, J D; Ford, I; Scotland, Generation; Gottesman, R F; Griswold, M E; Gudnason, V; Harris, T B; Heiss, G; Hofman, A; Holliday, E G; Huffman, J; Kardia, S L R; Kochan, N; Knopman, D S; Kwok, J B; Lambert, J-C; Lee, T; Li, G; Li, S-C; Loitfelder, M; Lopez, O L; Lundervold, A J; Lundqvist, A; Mather, K A; Mirza, S S; Nyberg, L; Oostra, B A; Palotie, A; Papenberg, G; Pattie, A; Petrovic, K; Polasek, O; Psaty, B M; Redmond, P; Reppermund, S; Rotter, J I; Schmidt, H; Schuur, M; Schofield, P W; Scott, R J; Steen, V M; Stott, D J; van Swieten, J C; Taylor, K D; Trollor, J; Trompet, S; Uitterlinden, A G; Weinstein, G; Widen, E; Windham, B G; Jukema, J W; Wright, A F; Wright, M J; Yang, Q; Amieva, H; Attia, J R; Bennett, D A; Brodaty, H; de Craen, A J M; Hayward, C; Ikram, M A; Lindenberger, U; Nilsson, L-G; Porteous, D J; Räikkönen, K; Reinvang, I; Rudan, I; Sachdev, P S; Schmidt, R; Schofield, P R; Srikanth, V; Starr, J M; Turner, S T; Weir, D R; Wilson, J F; van Duijn, C; Launer, L; Fitzpatrick, A L; Seshadri, S; Mosley, T H; Deary, I J

2015-01-01

General cognitive function is substantially heritable across the human life course from adolescence to old age. We investigated the genetic contribution to variation in this important, health- and well-being-related trait in middle-aged and older adults. We conducted a meta-analysis of genome-wide association studies of 31 cohorts (N=53 949) in which the participants had undertaken multiple, diverse cognitive tests. A general cognitive function phenotype was tested for, and created in each cohort by principal component analysis. We report 13 genome-wide significant single-nucleotide polymorphism (SNP) associations in three genomic regions, 6q16.1, 14q12 and 19q13.32 (best SNP and closest gene, respectively: rs10457441, P=3.93 × 10−9, MIR2113; rs17522122, P=2.55 × 10−8, AKAP6; rs10119, P=5.67 × 10−9, APOE/TOMM40). We report one gene-based significant association with the HMGN1 gene located on chromosome 21 (P=1 × 10−6). These genes have previously been associated with neuropsychiatric phenotypes. Meta-analysis results are consistent with a polygenic model of inheritance. To estimate SNP-based heritability, the genome-wide complex trait analysis procedure was applied to two large cohorts, the Atherosclerosis Risk in Communities Study (N=6617) and the Health and Retirement Study (N=5976). The proportion of phenotypic variation accounted for by all genotyped common SNPs was 29% (s.e.=5%) and 28% (s.e.=7%), respectively. Using polygenic prediction analysis, ~1.2% of the variance in general cognitive function was predicted in the Generation Scotland cohort (N=5487; P=1.5 × 10−17). In hypothesis-driven tests, there was significant association between general cognitive function and four genes previously associated with Alzheimer's disease: TOMM40, APOE, ABCG1 and MEF2C. PMID:25644384

Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome.

Science.gov (United States)

Bassett, Anne S; Lowther, Chelsea; Merico, Daniele; Costain, Gregory; Chow, Eva W C; van Amelsvoort, Therese; McDonald-McGinn, Donna; Gur, Raquel E; Swillen, Ann; Van den Bree, Marianne; Murphy, Kieran; Gothelf, Doron; Bearden, Carrie E; Eliez, Stephan; Kates, Wendy; Philip, Nicole; Sashi, Vandana; Campbell, Linda; Vorstman, Jacob; Cubells, Joseph; Repetto, Gabriela M; Simon, Tony; Boot, Erik; Heung, Tracy; Evers, Rens; Vingerhoets, Claudia; van Duin, Esther; Zackai, Elaine; Vergaelen, Elfi; Devriendt, Koen; Vermeesch, Joris R; Owen, Michael; Murphy, Clodagh; Michaelovosky, Elena; Kushan, Leila; Schneider, Maude; Fremont, Wanda; Busa, Tiffany; Hooper, Stephen; McCabe, Kathryn; Duijff, Sasja; Isaev, Karin; Pellecchia, Giovanna; Wei, John; Gazzellone, Matthew J; Scherer, Stephen W; Emanuel, Beverly S; Guo, Tingwei; Morrow, Bernice E; Marshall, Christian R

2017-11-01

Chromosome 22q11.2 deletion syndrome (22q11.2DS) is associated with a more than 20-fold increased risk for developing schizophrenia. The aim of this study was to identify additional genetic factors (i.e., "second hits") that may contribute to schizophrenia expression. Through an international consortium, the authors obtained DNA samples from 329 psychiatrically phenotyped subjects with 22q11.2DS. Using a high-resolution microarray platform and established methods to assess copy number variation (CNV), the authors compared the genome-wide burden of rare autosomal CNV, outside of the 22q11.2 deletion region, between two groups: a schizophrenia group and those with no psychotic disorder at age ≥25 years. The authors assessed whether genes overlapped by rare CNVs were overrepresented in functional pathways relevant to schizophrenia. Rare CNVs overlapping one or more protein-coding genes revealed significant between-group differences. For rare exonic duplications, six of 19 gene sets tested were enriched in the schizophrenia group; genes associated with abnormal nervous system phenotypes remained significant in a stepwise logistic regression model and showed significant interactions with 22q11.2 deletion region genes in a connectivity analysis. For rare exonic deletions, the schizophrenia group had, on average, more genes overlapped. The additional rare CNVs implicated known (e.g., GRM7, 15q13.3, 16p12.2) and novel schizophrenia risk genes and loci. The results suggest that additional rare CNVs overlapping genes outside of the 22q11.2 deletion region contribute to schizophrenia risk in 22q11.2DS, supporting a multigenic hypothesis for schizophrenia. The findings have implications for understanding expression of psychotic illness and herald the importance of whole-genome sequencing to appreciate the overall genomic architecture of schizophrenia.

Host genetic variation impacts microbiome composition across human body sites.

Science.gov (United States)

Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G

2015-09-15

The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale. Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes. Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.

A plant-wide aqueous phase chemistry module describing pH variations and ion speciation/pairing in wastewater treatment process models.

Science.gov (United States)

Flores-Alsina, Xavier; Kazadi Mbamba, Christian; Solon, Kimberly; Vrecko, Darko; Tait, Stephan; Batstone, Damien J; Jeppsson, Ulf; Gernaey, Krist V

2015-11-15

There is a growing interest within the Wastewater Treatment Plant (WWTP) modelling community to correctly describe physico-chemical processes after many years of mainly focusing on biokinetics. Indeed, future modelling needs, such as a plant-wide phosphorus (P) description, require a major, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems. In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation/pairing is presented and interfaced with industry standard models. The module accounts for extensive consideration of non-ideality, including ion activities instead of molar concentrations and complex ion pairing. The general equilibria are formulated as a set of Differential Algebraic Equations (DAEs) instead of Ordinary Differential Equations (ODEs) in order to reduce the overall stiffness of the system, thereby enhancing simulation speed. Additionally, a multi-dimensional version of the Newton-Raphson algorithm is applied to handle the existing multiple algebraic inter-dependencies. The latter is reinforced with the Simulated Annealing method to increase the robustness of the solver making the system not so dependent of the initial conditions. Simulation results show pH predictions when describing Biological Nutrient Removal (BNR) by the activated sludge models (ASM) 1, 2d and 3 comparing the performance of a nitrogen removal (WWTP1) and a combined nitrogen and phosphorus removal (WWTP2) treatment plant configuration under different anaerobic/anoxic/aerobic conditions. The same framework is implemented in the Benchmark Simulation Model No. 2 (BSM2) version of the Anaerobic Digestion Model No. 1 (ADM1) (WWTP3) as well, predicting pH values at different cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated, by implementing the aqueous phase chemistry module in some

Latitudinal cogradient variation of development time and growth rate and a negative latitudinal body weight cline in a widely distributed cabbage beetle.

Directory of Open Access Journals (Sweden)

Jianjun Tang

Full Text Available The evolutionary and phenotypic responses to environmental gradients are often assumed to be the same, a phenomenon known as "cogradient variation". However, only a few insect species display cogradient variation in physiological traits along a latitudinal gradient. We found evidence for such a response in the examination of the life history traits of the cabbage beetle Colaphellus bowringi from 6 different geographical populations at 16, 19, 22, 24, 26 and 28°C. Our results showed that larval and pupal development times significantly decreased as rearing temperature increased, and that growth rates were positively correlated with temperature. Body weight tended to decrease with increasing temperature, consistent with the general pattern in ectothermic animals. Larval development time was positively correlated with latitude, whereas the growth rate decreased as latitude increased, showing an example of latitudinal cogradient variation. Body weight significantly decreased with increasing latitude in a stepwise manner, showing a negative latitudinal body weight cline. Females were significantly larger than males, consistent with the female biased sex dimorphism in insects. Body weight tended to decrease with increasing rearing temperature, whereas the differences in sexual size dimorphism (SSD tended to decrease with increasing body weight, which biased our results toward acceptance of Rensch's rule. We found that weight loss was an important regulator of SSD, and because male pupae lost significantly more weight at metamorphosis than female pupae, SSD was greater in adults than in pupae. Overall, our data provide a new example that a latitudinal cogradient variation in physiological traits is associated with a negative latitudinal body weight cline.

Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa

Science.gov (United States)

Huckins, L M; Hatzikotoulas, K; Southam, L; Thornton, L M; Steinberg, J; Aguilera-McKay, F; Treasure, J; Schmidt, U; Gunasinghe, C; Romero, A; Curtis, C; Rhodes, D; Moens, J; Kalsi, G; Dempster, D; Leung, R; Keohane, A; Burghardt, R; Ehrlich, S; Hebebrand, J; Hinney, A; Ludolph, A; Walton, E; Deloukas, P; Hofman, A; Palotie, A; Palta, P; van Rooij, F J A; Stirrups, K; Adan, R; Boni, C; Cone, R; Dedoussis, G; van Furth, E; Gonidakis, F; Gorwood, P; Hudson, J; Kaprio, J; Kas, M; Keski-Rahonen, A; Kiezebrink, K; Knudsen, G-P; Slof-Op 't Landt, M C T; Maj, M; Monteleone, A M; Monteleone, P; Raevuori, A H; Reichborn-Kjennerud, T; Tozzi, F; Tsitsika, A; van Elburg, A; Adan, R A H; Alfredsson, L; Ando, T; Andreassen, O A; Aschauer, H; Baker, J H; Barrett, J C; Bencko, V; Bergen, A W; Berrettini, W H; Birgegard, A; Boni, C; Boraska Perica, V; Brandt, H; Breen, G; Bulik, C M; Carlberg, L; Cassina, M; Cichon, S; Clementi, M; Cohen-Woods, S; Coleman, J; Cone, R D; Courtet, P; Crawford, S; Crow, S; Crowley, J; Danner, U N; Davis, O S P; de Zwaan, M; Dedoussis, G; Degortes, D; DeSocio, J E; Dick, D M; Dikeos, D; Dina, C; Ding, B; Dmitrzak-Weglarz, M; Docampo, E; Duncan, L; Egberts, K; Ehrlich, S; Escaramís, G; Esko, T; Espeseth, T; Estivill, X; Favaro, A; Fernández-Aranda, F; Fichter, M M; Finan, C; Fischer, K; Floyd, J A B; Foretova, L; Forzan, M; Franklin, C S; Gallinger, S; Gambaro, G; Gaspar, H A; Giegling, I; Gonidakis, F; Gorwood, P; Gratacos, M; Guillaume, S; Guo, Y; Hakonarson, H; Halmi, K A; Hatzikotoulas, K; Hauser, J; Hebebrand, J; Helder, S; Herms, S; Herpertz-Dahlmann, B; Herzog, W; Hilliard, C E; Hinney, A; Hübel, C; Huckins, L M; Hudson, J I; Huemer, J; Inoko, H; Janout, V; Jiménez-Murcia, S; Johnson, C; Julià, A; Juréus, A; Kalsi, G; Kaminska, D; Kaplan, A S; Kaprio, J; Karhunen, L; Karwautz, A; Kas, M J H; Kaye, W; Kennedy, J L; Keski-Rahkonen, A; Kiezebrink, K; Klareskog, L; Klump, K L; Knudsen, G P S; Koeleman, B P C; Koubek, D; La Via, M C; Landén, M; Le Hellard, S; Levitan, R D; Li, D; Lichtenstein, P; Lilenfeld, L; Lissowska, J; Lundervold, A; Magistretti, P; Maj, M; Mannik, K; Marsal, S; Martin, N; Mattingsdal, M; McDevitt, S; McGuffin, P; Merl, E; Metspalu, A; Meulenbelt, I; Micali, N; Mitchell, J; Mitchell, K; Monteleone, P; Monteleone, A M; Mortensen, P; Munn-Chernoff, M A; Navratilova, M; Nilsson, I; Norring, C; Ntalla, I; Ophoff, R A; O'Toole, J K; Palotie, A; Pante, J; Papezova, H; Pinto, D; Rabionet, R; Raevuori, A; Rajewski, A; Ramoz, N; Rayner, N W; Reichborn-Kjennerud, T; Ripatti, S; Roberts, M; Rotondo, A; Rujescu, D; Rybakowski, F; Santonastaso, P; Scherag, A; Scherer, S W; Schmidt, U; Schork, N J; Schosser, A; Slachtova, L; Sladek, R; Slagboom, P E; Slof-Op 't Landt, M C T; Slopien, A; Soranzo, N; Southam, L; Steen, V M; Strengman, E; Strober, M; Sullivan, P F; Szatkiewicz, J P; Szeszenia-Dabrowska, N; Tachmazidou, I; Tenconi, E; Thornton, L M; Tortorella, A; Tozzi, F; Treasure, J; Tsitsika, A; Tziouvas, K; van Elburg, A A; van Furth, E F; Wagner, G; Walton, E; Watson, H; Wichmann, H-E; Widen, E; Woodside, D B; Yanovski, J; Yao, S; Yilmaz, Z; Zeggini, E; Zerwas, S; Zipfel, S; Collier, D A; Sullivan, P F; Breen, G; Bulik, C M; Zeggini, E

2018-01-01

Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. To date, only one genome-wide significant locus associated with AN has been identified. We performed an exome-chip based genome-wide association studies (GWAS) in 2158 cases from nine populations of European origin and 15 485 ancestrally matched controls. Unlike previous studies, this GWAS also probed association in low-frequency and rare variants. Sixteen independent variants were taken forward for in silico and de novo replication (11 common and 5 rare). No findings reached genome-wide significance. Two notable common variants were identified: rs10791286, an intronic variant in OPCML (P=9.89 × 10−6), and rs7700147, an intergenic variant (P=2.93 × 10−5). No low-frequency variant associations were identified at genome-wide significance, although the study was well-powered to detect low-frequency variants with large effect sizes, suggesting that there may be no AN loci in this genomic search space with large effect sizes. PMID:29155802

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

Science.gov (United States)

Huang, Pu; Molina, Jeanmaire; Flowers, Jonathan M; Rubinstein, Samara; Jackson, Scott A; Purugganan, Michael D; Schaal, Barbara A

2012-09-01

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed. © 2012 Blackwell Publishing Ltd.

A plant wide aqueous phase chemistry model describing pH variations and ion speciation/pairing in wastewater treatment process models

DEFF Research Database (Denmark)

Flores-Alsina, X.; Mbamba, C. Kazadi; Solon, K.

cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated by implementing the aqueous phase chemistry module in some of the most frequently used WWTP process simulation models. Finally, it is shown how traditional wastewater modelling studies can......, require a major, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems (Ikumi et al., 2014). In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation...... of Ordinary Differential Equations (ODEs) in order to reduce the overall stiffness of the system, thereby enhancing simulation speed. Additionally, a multi-dimensional version of the Newton-Raphson algorithm is applied to handle the existing multiple algebraic inter-dependencies (Solon et al., 2015...

A plant-wide aqueous phase chemistry module describing pH variations and ion speciation/pairing in wastewater treatment process models

DEFF Research Database (Denmark)

Flores Alsina, Xavier; Kazadi Mbamba, Christian; Solon, Kimberly

2015-01-01

at different cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated, by implementing the aqueous phase chemistry module in some of the most frequently used WWTP process simulation models. Finally, it is shown how traditional wastewater modelling......, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems. In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation/pairing is presented and interfaced with industry......) in order to reduce the overall stiffness of the system, thereby enhancing simulation speed. Additionally, a multi-dimensional version of the Newton-Raphson algorithm is applied to handle the existing multiple algebraic inter-dependencies. The latter is reinforced with the Simulated Annealing method...

A survey of variational principles

International Nuclear Information System (INIS)

Lewins, J.D.

1993-01-01

In this article survey of variational principles has been given. Variational principles play a significant role in mathematical theory with emphasis on the physical aspects. There are two principals used i.e. to represent the equation of the system in a succinct way and to enable a particular computation in the system to be carried out with greater accuracy. The survey of variational principles has ranged widely from its starting point in the Lagrange multiplier to optimisation principles. In an age of digital computation, these classic methods can be adapted to improve such calculations. We emphasize particularly the advantage of basic finite element methods on variational principles. (A.B.)

Risk factors and between-hospital variation of caesarean section in Denmark

DEFF Research Database (Denmark)

Wehberg, Sonja; Guldberg, Rikke; Gradel, Kim Oren

2018-01-01

OBJECTIVES: The aim of this study was to estimate the effects of risk factors on elective and emergency caesarean section (CS) and to estimate the between-hospital variation of risk-adjusted CS proportions. DESIGN: Historical registry-based cohort study. SETTINGS AND PARTICIPANTS: The study......, for example, body mass index, parity, age and size of maternity unit and (2) risk-adjusted proportions of elective and emergency CS to evaluate between-hospital variation. RESULTS: The CS proportion was stable at 20%-21%, but showed wide variation between units, even in adjusted models. Large units performed...... CSs and one unit fewer CSs than expected. CONCLUSION: The main risk factors for elective CS were breech presentation and previous CS; for emergency CS they were breech presentation and cephalopelvic disproportion. The proportions of CS were stable during the study period. We found variation in risk...

Genome-wide detection of copy number variations among diverse horse breeds by array CGH.

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Wei Wang

Full Text Available Recent studies have found that copy number variations (CNVs are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs. The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO, genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.

Variation in the wood anatomical structure of Gmelina arborea (Verbenaceae) trees at different ecological conditions in Costa Rica

OpenAIRE

MOYA, Roger; FO, Mario Tomazello

2008-01-01

The tree Gmelina arborea has been widely introduced in Costa Rica for commercial purposes. This new conditions for melina cause variations on anatomy in secondary xylem of the trees growing in plantations. The objective of the present research was to determine the variation in the anatomy of xylem caused by the ecological conduction variation. Dimensions of fiber, axial parenchyma percentage of cross sections, parameters of vessels and the ray were measured. The results showed that some anato...

Wide variations in blood product transfusion practices among providers who care for patients with acute leukemia in the United States.

Science.gov (United States)

Pine, Alexander B; Lee, Eun-Ju; Sekeres, Mikkael; Steensma, David P; Zelterman, Daniel; Prebet, Thomas; DeZern, Amy; Komrokji, Rami; Litzow, Mark; Luger, Selina; Stone, Richard; Erba, Harry P; Garcia-Manero, Guillermo; Lee, Alfred I; Podoltsev, Nikolai A; Barbarotta, Lisa; Kasberg, Stephanie; Hendrickson, Jeanne E; Gore, Steven D; Zeidan, Amer M

2017-02-01

Transfusion of blood products is a key component of the supportive management in patients with acute leukemia (AL). However high-quality trial evidence and clinical outcome data to support specific transfusion goals for blood products for patients with AL remain limited leading to diverse transfusion practices. The primary objective of this study was to determine the spectrum of transfusion patterns in a variety of care settings among providers who treat AL patients. A 31-question survey queried providers caring for AL patients about the existence of institutional guidelines for transfusion of blood products, transfusion triggers for hemoglobin (Hb), platelets (PLTs), and fibrinogen in various settings including inpatient and outpatient and before procedures. We analyzed 130 responses and identified divergent transfusion Hb goals in hospitalized and ambulatory patients, fibrinogen goals for cryoprecipitate transfusions, and variation in practice for use of certain PLTs and red blood cell products. The least variable transfusion patterns were reported for PLT goals in thrombocytopenia and in the setting of invasive procedures such as bone marrow biopsy and lumbar punctures. This survey confirmed wide variations in blood product transfusion practices across several clinical scenarios in patients with AL. The findings emphasized the need for large prospective randomized trials to develop standardized evidence-based guidelines for blood product transfusions in patients with AL with the goal of limiting unnecessary transfusions without compromising outcomes. © 2016 AABB.

A genome-wide association study identifies protein quantitative trait loci (pQTLs.

Directory of Open Access Journals (Sweden)

David Melzer

2008-05-01

Full Text Available There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8x10(-57, CCL4L1 (p = 3.9x10(-21, IL18 (p = 6.8x10(-13, LPA (p = 4.4x10(-10, GGT1 (p = 1.5x10(-7, SHBG (p = 3.1x10(-7, CRP (p = 6.4x10(-6 and IL1RN (p = 7.3x10(-6 genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R, altered secretion rates of different sized proteins (LPA, variation in gene copy number (CCL4L1 and altered transcription (GGT1. We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha levels (p = 6.8x10(-40, but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis

Insights into Intraspecies Variation in Primate Prosocial Behavior: Capuchins (Cebus apella Fail to Show Prosociality on a Touchscreen Task

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Lindsey A. Drayton

2014-04-01

Full Text Available Over the past decade, many researchers have used food donation tasks to test whether nonhuman primates show human-like patterns of prosocial behavior in experimental settings. Although these tasks are elegant in their simplicity, performance within and across species is difficult to explain under a unified theoretical framework. Here, we attempt to better understand variation in prosociality by examining the circumstances that promote and hinder the expression of prosocial preferences. To this end, we tested whether capuchin monkeys (Cebus apella—a species that has previously demonstrated prosocial preferences—would behave prosocially using a novel touchscreen task. In contrast to previous studies, we found that capuchins as a group did not prosocially deliver food to a partner. Importantly however, data from control conditions revealed that subjects demonstrated limited understanding of the reward contingencies of the task. We also compared individuals’ performance in the current study with their performance in a previously published prosociality study. We conclude by discussing how continuing to explore intraspecies variation in performance on prosocial tasks may help inform debates regarding the existence of other-regarding preferences in nonhuman species.

Wide variation in absolute cardiovascular risk assessment in Aboriginal and Torres Strait Islander people with Type 2 diabetes

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Bhakti Ramesh Vasant

2016-03-01

Full Text Available Background: Absolute cardiovascular risk assessment (CVRA is based on the combined effects of multiple risk factors and can identify asymptomatic individuals at high risk of cardiovascular disease. Aboriginal and Torres Strait Islander people are disproportionately affected by cardiovascular disease and diabetes. Our study aimed to investigate variations in the use of absolute CVRA in patients with diabetes at Indigenous community healthcare centres, and to identify patient and health centre characteristics that may contribute to this variation. Methods: Audits of clinical records of 1,728 patients with a known diagnosis of diabetes across 121 health centres over the period 2012–2014 were conducted as part of a large-scale continuous quality improvement program. Multilevel regression modelling was used to quantify variation in recording of CVRA attributable to health centre and patient characteristics. Results: The proportion of eligible patients with documented CVRA was 33% (n=574/1,728. The majority (95% of assessments were conducted in the Northern Territory (NT. Multilevel regression analysis showed health centre characteristics accounted for 70% of the variation in assessments in the NT. Government-operated health centres had 18.8 times the odds (95% CI 7.7–46.2 of recording CVRA delivery compared with other health centres. Conclusion: Health centres in the NT delivered the majority of absolute CVRA to Indigenous patients with diabetes in our study. Health systems factors that may have facilitated provision of CVRA in the NT include decision support tools and a reporting process for CVRA delivery. Implementation of similar systems in other jurisdictions may help improve CVRA delivery. Early identification and treatment of high risk individuals through wider use of CVRA may help reduce the burden of cardiovascular disease in Indigenous Australians with diabetes.

Toward Meaningful Manufacturing Variation Data in Design - Feature Based Description of Variation in Manufacturing Processes

DEFF Research Database (Denmark)

Eifler, Tobias; Boorla, Srinivasa Murthy; Howard, Thomas J.

2016-01-01

The need to mitigate the effects of manufacturing variation already in design is nowadays commonly acknowledged and has led to a wide use of predictive modeling techniques, tolerancing approaches, etc. in industry. The trustworthiness of corresponding variation analyses is, however, not ensured...... by the availability of sophisticated methods and tools alone, but does evidently also depend on the accuracy of the input information used. As existing approaches for the description of manufacturing variation focus however, almost exclusively, on monitoring and controlling production processes, there is frequently...... a lack of objective variation data in design. As a result, variation analyses and tolerancing activities rely on numerous assumptions made to fill the gaps of missing or incomplete data. To overcome this hidden subjectivity, a schema for a consistent and standardised description of manufacturing...

A genome-wide association study of aging.

Science.gov (United States)

Walter, Stefan; Atzmon, Gil; Demerath, Ellen W; Garcia, Melissa E; Kaplan, Robert C; Kumari, Meena; Lunetta, Kathryn L; Milaneschi, Yuri; Tanaka, Toshiko; Tranah, Gregory J; Völker, Uwe; Yu, Lei; Arnold, Alice; Benjamin, Emelia J; Biffar, Reiner; Buchman, Aron S; Boerwinkle, Eric; Couper, David; De Jager, Philip L; Evans, Denis A; Harris, Tamara B; Hoffmann, Wolfgang; Hofman, Albert; Karasik, David; Kiel, Douglas P; Kocher, Thomas; Kuningas, Maris; Launer, Lenore J; Lohman, Kurt K; Lutsey, Pamela L; Mackenbach, Johan; Marciante, Kristin; Psaty, Bruce M; Reiman, Eric M; Rotter, Jerome I; Seshadri, Sudha; Shardell, Michelle D; Smith, Albert V; van Duijn, Cornelia; Walston, Jeremy; Zillikens, M Carola; Bandinelli, Stefania; Baumeister, Sebastian E; Bennett, David A; Ferrucci, Luigi; Gudnason, Vilmundur; Kivimaki, Mika; Liu, Yongmei; Murabito, Joanne M; Newman, Anne B; Tiemeier, Henning; Franceschini, Nora

2011-11-01

Human longevity and healthy aging show moderate heritability (20%-50%). We conducted a meta-analysis of genome-wide association studies from 9 studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium for 2 outcomes: (1) all-cause mortality, and (2) survival free of major disease or death. No single nucleotide polymorphism (SNP) was a genome-wide significant predictor of either outcome (p < 5 × 10(-8)). We found 14 independent SNPs that predicted risk of death, and 8 SNPs that predicted event-free survival (p < 10(-5)). These SNPs are in or near genes that are highly expressed in the brain (HECW2, HIP1, BIN2, GRIA1), genes involved in neural development and function (KCNQ4, LMO4, GRIA1, NETO1) and autophagy (ATG4C), and genes that are associated with risk of various diseases including cancer and Alzheimer's disease. In addition to considerable overlap between the traits, pathway and network analysis corroborated these findings. These findings indicate that variation in genes involved in neurological processes may be an important factor in regulating aging free of major disease and achieving longevity. Copyright © 2011 Elsevier Inc. All rights reserved.

Modeling response variation for radiometric calorimeters

International Nuclear Information System (INIS)

Mayer, R.L. II.

1986-01-01

Radiometric calorimeters are widely used in the DOE complex for accountability measurements of plutonium and tritium. Proper characterization of response variation for these instruments is, therefore, vital for accurate assessment of measurement control as well as for propagation of error calculations. This is not difficult for instruments used to measure items within a narrow range of power values; however, when a single instrument is used to measure items over a wide range of power values, improper estimates of uncertainty can result since traditional error models for radiometric calorimeters assume that uncertainty is not a function of sample power. This paper describes methods which can be used to accurately estimate random response variation for calorimeters used to measure items over a wide range of sample powers. The model is applicable to the two most common modes of calorimeter operation: heater replacement and servo control. 5 refs., 4 figs., 1 tab

Determinants of inter-specific variation in basal metabolic rate.

Science.gov (United States)

White, Craig R; Kearney, Michael R

2013-01-01

Basal metabolic rate (BMR) is the rate of metabolism of a resting, postabsorptive, non-reproductive, adult bird or mammal, measured during the inactive circadian phase at a thermoneutral temperature. BMR is one of the most widely measured physiological traits, and data are available for over 1,200 species. With data available for such a wide range of species, BMR is a benchmark measurement in ecological and evolutionary physiology, and is often used as a reference against which other levels of metabolism are compared. Implicit in such comparisons is the assumption that BMR is invariant for a given species and that it therefore represents a stable point of comparison. However, BMR shows substantial variation between individuals, populations and species. Investigation of the ultimate (evolutionary) explanations for these differences remains an active area of inquiry, and explanation of size-related trends remains a contentious area. Whereas explanations for the scaling of BMR are generally mechanistic and claim ties to the first principles of chemistry and physics, investigations of mass-independent variation typically take an evolutionary perspective and have demonstrated that BMR is ultimately linked with a range of extrinsic variables including diet, habitat temperature, and net primary productivity. Here we review explanations for size-related and mass-independent variation in the BMR of animals, and suggest ways that the various explanations can be evaluated and integrated.

From Genome-Wide Association Study to Phenome-Wide Association Study: New Paradigms in Obesity Research.

Science.gov (United States)

Zhang, Y-P; Zhang, Y-Y; Duan, D D

2016-01-01

Obesity is a condition in which excess body fat has accumulated over an extent that increases the risk of many chronic diseases. The current clinical classification of obesity is based on measurement of body mass index (BMI), waist-hip ratio, and body fat percentage. However, these measurements do not account for the wide individual variations in fat distribution, degree of fatness or health risks, and genetic variants identified in the genome-wide association studies (GWAS). In this review, we will address this important issue with the introduction of phenome, phenomics, and phenome-wide association study (PheWAS). We will discuss the new paradigm shift from GWAS to PheWAS in obesity research. In the era of precision medicine, phenomics and PheWAS provide the required approaches to better definition and classification of obesity according to the association of obese phenome with their unique molecular makeup, lifestyle, and environmental impact. Copyright © 2016 Elsevier Inc. All rights reserved.

Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Directory of Open Access Journals (Sweden)

Hongyang Wang

Full Text Available Copy number variations (CNVs refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

Variation in free jumping technique within and among horses with little experience in show jumping

NARCIS (Netherlands)

Santamaria, S.; Bobbert, M.F.; Back, W.; Barneveld, A.; van Weeren, P.R.

2004-01-01

Objective - To quantify variation in the jumping technique within and among young horses with little jumping experience, establish relationships between kinetic and kinematic variables, and identify a limited set of variables characteristic for detecting differences in jumping performance among

A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries).

Science.gov (United States)

Li, M-H; Tiirikka, T; Kantanen, J

2014-02-01

In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.

Isolation and identification of 4-a-rhamnosyloxy benzyl glucosinolate in Noccaea caerulescens showing intraspecific variation

NARCIS (Netherlands)

Graaf, de R.M.; Krosse, S.; Swolfs, A.E.M.; Brinke, te E.; Prill, N.; Leimu, R.; Galen, van P.M.; Wang, Y.; Aarts, M.G.M.; Dam, van N.M.

2015-01-01

Glucosinolates are secondary plant compounds typically found in members of the Brassicaceae and a few other plant families. Usually each plant species contains a specific subset of the ~130 different glucosinolates identified to date. However, intraspecific variation in glucosinolate profiles is

Variation of clinical expression in patients with Stargardt dystrophy and sequence variations in the ABCR gene.

Science.gov (United States)

Fishman, G A; Stone, E M; Grover, S; Derlacki, D J; Haines, H L; Hockey, R R

1999-04-01

To report the spectrum of ophthalmic findings in patients with Stargardt dystrophy or fundus flavimaculatus who have a specific sequence variation in the ABCR gene. Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from different pedigrees were identified with possible disease-causing sequence variations in the ABCR gene from a group of 66 patients who were screened for sequence variations in this gene. Patients underwent a routine ocular examination, including slitlamp biomicroscopy and a dilated fundus examination. Fluorescein angiography was performed on 22 patients, and electroretinographic measurements were obtained on 24 of 29 patients. Kinetic visual fields were measured with a Goldmann perimeter in 26 patients. Single-strand conformation polymorphism analysis and DNA sequencing were used to identify variations in coding sequences of the ABCR gene. Three clinical phenotypes were observed among these 29 patients. In phenotype I, 9 of 12 patients had a sequence change in exon 42 of the ABCR gene in which the amino acid glutamic acid was substituted for glycine (Gly1961Glu). In only 4 of these 9 patients was a second possible disease-causing mutation found on the other ABCR allele. In addition to an atrophic-appearing macular lesion, phenotype I was characterized by localized perifoveal yellowish white flecks, the absence of a dark choroid, and normal electroretinographic amplitudes. Phenotype II consisted of 10 patients who showed a dark choroid and more diffuse yellowish white flecks in the fundus. None exhibited the Gly1961Glu change. Phenotype III consisted of 7 patients who showed extensive atrophic-appearing changes of the retinal pigment epithelium. Electroretinographic cone and rod amplitudes were reduced. One patient showed the Gly1961Glu change. A wide variation in clinical phenotype can occur in patients with sequence changes in the ABCR gene. In individual patients, a certain phenotype seems to be associated with the presence of

Introduction to the calculus of variations

CERN Document Server

Sagan, Hans

1992-01-01

Excellent text provides basis for thorough understanding of the problems, methods and techniques of the calculus of variations and prepares readers for the study of modern optimal control theory. Treatment limited to extensive coverage of single integral problems in one and more unknown functions. Carefully chosen variational problems and over 400 exercises. ""Should find wide acceptance as a text and reference.""-American Mathematical Monthly. 1969 edition. Bibliography.

Impact of sampling resolution on estimation of community-wide daily illicit drug use

DEFF Research Database (Denmark)

Ramin, Pedram; Baz Lomba, J. A.; Reid, M.

It is a common approach to report daily community-wide drug consumption, based on single daily measurements of the influent from a treatment plant. This article suggests that neglecting diurnal variations of loads and flow can result in misestimating daily drug consumption.......It is a common approach to report daily community-wide drug consumption, based on single daily measurements of the influent from a treatment plant. This article suggests that neglecting diurnal variations of loads and flow can result in misestimating daily drug consumption....

Opinions among Danish knee surgeons about indications to perform total knee replacement showed considerable variation

DEFF Research Database (Denmark)

Troelsen, Anders; Schrøder, Henrik; Husted, Henrik

2012-01-01

During the past decade, the incidence of primary total knee replacement (TKA) surgery in Denmark has approximately doubled. This increase could be due to weakened indications to perform TKA surgery. We aimed to investigate variation in opinions about indications to perform TKA among Danish knee...

Genic intolerance to functional variation and the interpretation of personal genomes.

Directory of Open Access Journals (Sweden)

Slavé Petrovski

Full Text Available A central challenge in interpreting personal genomes is determining which mutations most likely influence disease. Although progress has been made in scoring the functional impact of individual mutations, the characteristics of the genes in which those mutations are found remain largely unexplored. For example, genes known to carry few common functional variants in healthy individuals may be judged more likely to cause certain kinds of disease than genes known to carry many such variants. Until now, however, it has not been possible to develop a quantitative assessment of how well genes tolerate functional genetic variation on a genome-wide scale. Here we describe an effort that uses sequence data from 6503 whole exome sequences made available by the NHLBI Exome Sequencing Project (ESP. Specifically, we develop an intolerance scoring system that assesses whether genes have relatively more or less functional genetic variation than expected based on the apparently neutral variation found in the gene. To illustrate the utility of this intolerance score, we show that genes responsible for Mendelian diseases are significantly more intolerant to functional genetic variation than genes that do not cause any known disease, but with striking variation in intolerance among genes causing different classes of genetic disease. We conclude by showing that use of an intolerance ranking system can aid in interpreting personal genomes and identifying pathogenic mutations.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

Science.gov (United States)

Schrider, Daniel R.; Hahn, Matthew W.; Begun, David J.

2016-01-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster. In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

NARCIS (Netherlands)

Postmus, Iris; Warren, Helen R.; Trompet, Stella; Arsenault, Benoit J.; Avery, Christy L.; Bis, Joshua C.; Chasman, Daniel I.; de Keyser, Catherine E.; Deshmukh, Harshal A.; Evans, Daniel S.; Feng, QiPing; Li, Xiaohui; Smit, Roelof A. J.; Smith, Albert V.; Sun, Fangui; Taylor, Kent D.; Arnold, Alice M.; Barnes, Michael R.; Barratt, Bryan J.; Betteridge, John; Boekholdt, S. Matthijs; Boerwinkle, Eric; Buckley, Brendan M.; Chen, Y.-D. Ida; de Craen, Anton J. M.; Cummings, Steven R.; Denny, Joshua C.; Dubé, Marie Pierre; Durrington, Paul N.; Eiriksdottir, Gudny; Ford, Ian; Guo, Xiuqing; Harris, Tamara B.; Heckbert, Susan R.; Hofman, Albert; Hovingh, G. Kees; Kastelein, John J. P.; Launer, Leonore J.; Liu, Ching-Ti; Liu, Yongmei; Lumley, Thomas; McKeigue, Paul M.; Munroe, Patricia B.; Neil, Andrew; Nickerson, Deborah A.; Nyberg, Fredrik; O'Brien, Eoin; O'Donnell, Christopher J.; Post, Wendy; Poulter, Neil; Vasan, Ramachandran S.; Rice, Kenneth; Rich, Stephen S.; Rivadeneira, Fernando; Sattar, Naveed; Sever, Peter; Shaw-Hawkins, Sue; Shields, Denis C.; Slagboom, P. Eline; Smith, Nicholas L.; Smith, Joshua D.; Sotoodehnia, Nona; Stanton, Alice; Stott, David J.; Stricker, Bruno H.; Stürmer, Til; Uitterlinden, André G.; Wei, Wei-Qi; Westendorp, Rudi G. J.; Whitsel, Eric A.; Wiggins, Kerri L.; Wilke, Russell A.; Ballantyne, Christie M.; Colhoun, Helen M.; Cupples, L. Adrienne; Franco, Oscar H.; Gudnason, Vilmundur; Hitman, Graham; Palmer, Colin N. A.; Psaty, Bruce M.; Ridker, Paul M.; Stafford, Jeanette M.; Stein, Charles M.; Tardif, Jean-Claude; Caulfield, Mark J.; Jukema, J. Wouter; Rotter, Jerome I.; Krauss, Ronald M.

2016-01-01

In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation. We performed a meta-analysis of genome-wide

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'.

Leishmania-specific surface antigens show sub-genus sequence variation and immune recognition.

Directory of Open Access Journals (Sweden)

Daniel P Depledge

2010-09-01

Full Text Available A family of hydrophilic acylated surface (HASP proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic and intracellular (amastigote stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia have lost HASP genes from their genomes.We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia species, L. (V. braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L. mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o HASPs are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family.These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are

Study on the wide-angle Michelson interferometer with large air gap.

Science.gov (United States)

Gao, Haiyang; Tang, Yuanhe; Hua, Dengxin; Liu, Hanchen

2011-10-10

A wide-angle Michelson interferometer with large air gap is proposed to effectively reduce the size of the glass arms and constraint on material. It provides a novel and practical instrument for ground based wind measurement of the upper atmosphere. The field widening conditions for the large air gap are calculated in theory. For the five spectral lines of 557.7 nm, 630.0 nm, 732.0 nm, 834.6 nm, and 865.7 nm, the optimal results under ideal condition are obtained with air gaps of 1.0 cm, 1.5 cm, and 2.0 cm, respectively. With the fixed optical path difference (OPD) of 7.495 cm, three pairs of glass arms are optimized. The pair with length of 1.5 cm for air gap, 5.765 cm for H-ZF12, and 2.956 cm for H-ZLaF54, has better effect of field widening than the other two pairs and its OPD variation is only within 0.30 wavelengths at incident angle of 3°. For developing a more practical wide-angle Michelson interferometer, the H-K9L glass with size of 4.445 cm is employed as the arm material of solid interferometer. The experiment for field of view of 3° is designed and the data processing and analysis for 60 images show the agreement between experimental results and theoretical simulation. The OPD variations are only within 0.27 wavelengths for image edge. The feasibility and practicality of the wide-angle Michelson interferometer with large air gap is proved by means of theory and experiment. © 2011 Optical Society of America

A genome-wide investigation of copy number variation in patients with sporadic brain arteriovenous malformation.

Directory of Open Access Journals (Sweden)

Nasrine Bendjilali

Full Text Available Brain arteriovenous malformations (BAVM are clusters of abnormal blood vessels, with shunting of blood from the arterial to venous circulation and a high risk of rupture and intracranial hemorrhage. Most BAVMs are sporadic, but also occur in patients with Hereditary Hemorrhagic Telangiectasia, a Mendelian disorder caused by mutations in genes in the transforming growth factor beta (TGFβ signaling pathway.To investigate whether copy number variations (CNVs contribute to risk of sporadic BAVM, we performed a genome-wide association study in 371 sporadic BAVM cases and 563 healthy controls, all Caucasian. Cases and controls were genotyped using the Affymetrix 6.0 array. CNVs were called using the PennCNV and Birdsuite algorithms and analyzed via segment-based and gene-based approaches. Common and rare CNVs were evaluated for association with BAVM.A CNV region on 1p36.13, containing the neuroblastoma breakpoint family, member 1 gene (NBPF1, was significantly enriched with duplications in BAVM cases compared to controls (P = 2.2×10(-9; NBPF1 was also significantly associated with BAVM in gene-based analysis using both PennCNV and Birdsuite. We experimentally validated the 1p36.13 duplication; however, the association did not replicate in an independent cohort of 184 sporadic BAVM cases and 182 controls (OR = 0.81, P = 0.8. Rare CNV analysis did not identify genes significantly associated with BAVM.We did not identify common CNVs associated with sporadic BAVM that replicated in an independent cohort. Replication in larger cohorts is required to elucidate the possible role of common or rare CNVs in BAVM pathogenesis.

Quantifying variation in speciation and extinction rates with clade data.

Science.gov (United States)

Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

2013-12-01

High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation

Science.gov (United States)

Malone, Molly

2012-01-01

Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

Factors influencing variation in dentist service rates.

Science.gov (United States)

Grembowski, D; Milgrom, P; Fiset, L

1990-01-01

In the previous article, we calculated dentist service rates for 200 general dentists based on a homogeneous, well-educated, upper-middle-class population of patients. Wide variations in the rates were detected. In this analysis, factors influencing variation in the rates were identified. Variation in rates for categories of dental services was explained by practice characteristics, patient exposure to fluoridated water supplies, and non-price competition in the dental market. Rates were greatest in large, busy practices in markets with high fees. Older practices consistently had lower rates across services. As a whole, these variables explained between 5 and 30 percent of the variation in the rates.

Copy Number Variations in Tilapia Genomes.

Science.gov (United States)

Li, Bi Jun; Li, Hong Lian; Meng, Zining; Zhang, Yong; Lin, Haoran; Yue, Gen Hua; Xia, Jun Hong

2017-02-01

Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2  > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.

Quantum Variational Calculus

OpenAIRE

Malinowska , Agnieszka B.; Torres , Delfim

2014-01-01

International audience; Introduces readers to the treatment of the calculus of variations with q-differences and Hahn difference operators Provides the reader with the first extended treatment of quantum variational calculus Shows how the techniques described can be applied to economic models as well as other mathematical systems This Brief puts together two subjects, quantum and variational calculi by considering variational problems involving Hahn quantum operators. The main advantage of it...

A survey of variational principles

International Nuclear Information System (INIS)

Lewins, J.D.

1993-01-01

The survey of variational principles has ranged widely from its starting point in the Lagrange multiplier to optimisation principles. In an age of digital computation, these classic methods can be adapted to improve such calculations. We emphasize particularly the advantage of basing finite element methods on variational principles, especially if, as maximum and minimum principles, these can provide bounds and hence estimates of accuracy. The non-symmetric (and hence stationary rather than extremum principles) are seen however to play a significant role in optimisation theory. (Orig./A.B.)

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Science.gov (United States)

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome Variation Map: a data repository of genome variations in BIG Data Center

Science.gov (United States)

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

Displacement and stress fields around rock fractures opened by irregular overpressure variations

Directory of Open Access Journals (Sweden)

Shigekazu eKusumoto

2014-05-01

Full Text Available Many rock fractures are entirely driven open by fluids such as ground water, geothermal water, gas, oil, and magma. These are a subset of extension fractures (mode I cracks; e.g., dikes, mineral veins and joints referred to as hydrofractures. Field measurements show that many hydrofractures have great variations in aperture. However, most analytical solutions for fracture displacement and stress fields assume the loading to be either constant or with a linear variation. While these solutions have been widely used, it is clear that a fracture hosted by heterogeneous and anisotropic rock is normally subject to loading that is neither constant nor with a linear variation. Here we present new general solutions for the displacement and stress fields around hydrofractures, modelled as two-dimensional elastic cracks, opened by irregular overpressure variations given by the Fourier cosine series. Each solution has two terms. The first term gives the displacement and stress fields due to the average overpressure acting inside the crack; it is given by the initial term of the Fourier coefficients expressing the overpressure variation. The second term gives the displacement and stress fields caused by the overpressure variation; it is given by general terms of the Fourier coefficients and solved through numerical integration. Our numerical examples show that the crack aperture variation closely reflects the overpressure variation. Also, that the general displacement and stress fields close to the crack follow the overpressure variation but tend to be more uniform far from the crack. The present solutions can be used to estimate the displacement and stress fields around any fluid-driven crack, that is, any hydrofracture, as well as its aperture, provided the variation in overpressure can be described by Fourier series. The solutions add to our understanding of local stresses, displacements, and fluid transport associated with hydrofractures in the crust.

Oligocene sea water temperatures offshore Wilkes Land (Antarctica) indicate warm and stable glacial-interglacial variation and show no 'late Oligocene warming'

Science.gov (United States)

Hartman, Julian; Bijl, Peter; Peterse, Francien; Schouten, Stefan; Salabarnada, Ariadna; Bohaty, Steven; Escutia, Carlota; Brinkhuis, Henk; Sangiorgi, Francesca

2017-04-01

At present, warming of the waters below the Antarctic ice shelves is a major contributor to the instability of the Antarctic cryosphere. In order to get insight into future melt behavior of the Antarctic ice sheet, it is important to look at past warm periods that can serve as an analogue for the future. The Oligocene ( 34-23 Ma) is a period within the range of CO2 concentrations predicted by the latest IPCC report for the coming century and is characterized by a very dynamic Antarctic ice sheet, as suggested by benthic δ18O records from ice-distal sites. We suspect that, like today, environmental changes in the Southern Ocean are in part responsible for this dynamicity. To gain more insight into this, we have reconstructed sea water temperatures (SWT) based on Thaumarchaeotal lipids (TEX86) for the Oligocene record obtained from the ice-proximal Site U1356 (Integrated Ocean Drilling Program), offshore Wilkes Land. Part of our record shows a strong coupling between the lithology and SWT, which we attribute to glacial-interglacial variation. Our data shows that both glacial and interglacial temperatures are relatively warm throughout the Oligocene: 14°C and 18°C respectively, which is consistent with previously published estimates based on UK'37 and clumped isotopes for the early Oligocene. Our SST records show only a minor decline between 30 and 24 Ma, and thus show no evidence for a 'late Oligocene warming' as was suggested based on benthic δ18O records from low latitudes. Instead, the discrepancy between our SST trend and the δ18O trend suggests that the late-Oligocene benthic δ18O decrease is likely related to a decline in ice volume. After 24 Ma, however, glacial-interglacial temperature variation appears to increase. In particular, some large temperature drops occur, one of which can be related to the Mi-1 event and a major expansion of the Antarctic ice sheet.

Gigwa-Genotype investigator for genome-wide analyses.

Science.gov (United States)

Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre

2016-06-06

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

SYSTEMATIC AND STOCHASTIC VARIATIONS IN PULSAR DISPERSION MEASURES

International Nuclear Information System (INIS)

Lam, M. T.; Cordes, J. M.; Chatterjee, S.; Jones, M. L.; McLaughlin, M. A.; Armstrong, J. W.

2016-01-01

We analyze deterministic and random temporal variations in the dispersion measure (DM) from the full three-dimensional velocities of pulsars with respect to the solar system, combined with electron-density variations over a wide range of length scales. Previous treatments have largely ignored pulsars’ changing distances while favoring interpretations involving changes in sky position from transverse motion. Linear trends in pulsar DMs observed over 5–10 year timescales may signify sizable DM gradients in the interstellar medium (ISM) sampled by the changing direction of the line of sight to the pulsar. We show that motions parallel to the line of sight can also account for linear trends, for the apparent excess of DM variance over that extrapolated from scintillation measurements, and for the apparent non-Kolmogorov scalings of DM structure functions inferred in some cases. Pulsar motions through atomic gas may produce bow-shock ionized gas that also contributes to DM variations. We discuss the possible causes of periodic or quasi-periodic changes in DM, including seasonal changes in the ionosphere, annual variations of the solar elongation angle, structure in the heliosphere and ISM boundary, and substructure in the ISM. We assess the solar cycle’s role on the amplitude of ionospheric and solar wind variations. Interstellar refraction can produce cyclic timing variations from the error in transforming arrival times to the solar system barycenter. We apply our methods to DM time series and DM gradient measurements in the literature and assess their consistency with a Kolmogorov medium. Finally, we discuss the implications of DM modeling in precision pulsar timing experiments

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...

Meta-analysis of genome-wide association studies for personality

NARCIS (Netherlands)

M.H.M. de Moor; P.T. Costa Jr; A. Terracciano; R.F. Krueger; E.J.C. de Geus (Eco); T. Toshiko; B.W.J.H. Penninx (Brenda); T. Esko; P.A.F. Madden (Pamela); J. Derringer; N. Amin (Najaf); G.A.H.M. Willemsen (Gonneke); J.J. Hottenga (Jouke Jan); M.A. Distel (Marijn); M. Uda (Manuela); S. Sanna (Serena); P. Spinhoven; C.A. Hartman; P.F. Sullivan (Patrick); A. Realo; J. Allik; A.C. Heath; M.L. Pergadia; P. Lin; R. Grucza; T. Nutile; M. Ciullo; D. Rujescu (Dan); I. Giegling (Ina); B. Konte; E. Widen (Elisabeth); D.L. Cousminer (Diana); J.G. Eriksson; A. Palotie; L. Peltonen; M. Luciano (Michelle); A. Tenesa (Albert); G. Davies; L.M. Lopez; N.K. Hansell (Narelle); S.E. Medland (Sarah Elizabeth); L. Ferrucci; D. Schlessinger; G.W. Montgomery; M.J. Wright (Margaret); Y.S. Aulchenko (Yurii); A.C.J.W. Janssens (Cécile); B.A. Oostra (Ben); A. Metspalu (Andres); I.J. Deary; K. Räikkönen (Katri); L.J. Bierut (Laura); N.G. Martin; C.M. van Duijn (Cornelia); D.I. Boomsma (Dorret); G.R. Abecasis (Gonçalo); A. Agrawal (Arpana)

2012-01-01

textabstractPersonality can be thought of as a set of characteristics that influence people's thoughts, feelings and behavior across a variety of settings. Variation in personality is predictive of many outcomes in life, including mental health. Here we report on a meta-analysis of genome-wide

A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB

Science.gov (United States)

Need, Anna C.; Attix, Deborah K.; McEvoy, Jill M.; Cirulli, Elizabeth T.; Linney, Kristen L.; Hunt, Priscilla; Ge, Dongliang; Heinzen, Erin L.; Maia, Jessica M.; Shianna, Kevin V.; Weale, Michael E.; Cherkas, Lynn F.; Clement, Gail; Spector, Tim D.; Gibson, Greg; Goldstein, David B.

2009-01-01

Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we performed a genome-wide association study involving 11 cognitive phenotypes from the Cambridge Neuropsychological Test Automated Battery. We showed these measures to be heritable by comparing the correlation in 100 monozygotic and 100 dizygotic twin pairs. The full battery was tested in ∼750 subjects, and for spatial and verbal recognition memory, we investigated a further 500 individuals to search for smaller genetic effects. We were unable to find any genome-wide significant associations with either SNPs or common copy number variants. Nor could we formally replicate any polymorphism that has been previously associated with cognition, although we found a weak signal of lower than expected P-values for variants in a set of 10 candidate genes. We additionally investigated SNPs in genomic loci that have been shown to harbor rare variants that associate with neuropsychiatric disorders, to see if they showed any suggestion of association when considered as a separate set. Only NRXN1 showed evidence of significant association with cognition. These results suggest that common genetic variation does not strongly influence cognition in healthy subjects and that cognitive measures do not represent a more tractable genetic trait than clinical endpoints such as schizophrenia. We discuss a possible role for rare variation in cognitive genomics. PMID:19734545

Variation in vertebral number and its morphological implication in Galaxias platei.

Science.gov (United States)

Barriga, J P; Milano, D; Cussac, V E

2013-11-01

Variation in the vertebral number of the puyen grande Galaxias platei was examined for specimens from 22 localities that span the entire distribution range of the species (from 40° to 55° S). The mean vertebral number (NMW ) increases towards high latitudes, i.e. Jordan's rule is applicable to this species. Owing to the wide geographic variation of the species, not only in latitude but also in altitude, the most explicative variable for NMW was mean winter air temperature, showing negative dependence. Morphological data suggest that the increment in vertebral number lies in the pre-pelvic region of the trunk and in the caudal region, but not in the segment between pelvic-fin insertion and the origin of the anal fin. As these alterations in body shape have important consequences for hydrodynamics and swimming performance, vertebral number variation in G. platei also holds implications for both individual and population fitness. © 2013 The Fisheries Society of the British Isles.

Four loci explain 83% of size variation in the horse.

Directory of Open Access Journals (Sweden)

Shokouh Makvandi-Nejad

Full Text Available Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many genetic variants with weak effects on size, we show that horses, like other domestic mammals, carry just a small number of size loci with alleles of large effect. Furthermore, three of our horse size loci contain the LCORL, HMGA2 and ZFAT genes that have previously been found to control human height. The LCORL/NCAPG locus is also implicated in cattle growth and HMGA2 is associated with dog size. Extreme size diversification is a hallmark of domestication. Our results in the horse, complemented by the prior work in cattle and dog, serve to pinpoint those very few genes that have played major roles in the rapid evolution of size during domestication.

Estimating System-wide Impacts of Smart Grid Demonstrations

Energy Technology Data Exchange (ETDEWEB)

Schneider, Kevin P.; Lightner, Eric M.; Fuller, Jason C.

2015-03-01

Quantifying the impact of a new technology on a single specific distribution feeder is relatively easy, but it does not provide insight into the complexities and variations of a system-wide deployment. It is the inability to extrapolate system-wide impacts that hinders the deployment of many promising new technologies. This paper presents a method of extrapolating technology impacts, either simulated or from a field demonstration, from a limited number of distribution feeders to a system-wide impact. The size of the system can vary from the service territory of a single utility, to a region, or to an entire country. The paper will include an example analysis using the United States Department of Energy (DOE) funded Smart Grid Investment Grant (SGIG) projects, extrapolating their benefits to a national level.

Genome - wide variation and demographic history of small cats with a focus on Felis species

Directory of Open Access Journals (Sweden)

Anubhab Khan

2017-10-01

Full Text Available Majority of the 38 known cat species are classified as small and they inhabit five of the seven continents. They survive in a vast range of habitats but still 12 out of the 18 threatened felids are small cats. However, there has not been enough progress in the field of small cat research as they generally get overshadowed by the charismatic big cats. Here we attempt to create a resource for small cat research especially of the genus Felis which has six species out of which two are classified as vulnerable by IUCN and at least one more is at risk. We collected tissue samples of four Felis chaus (Jungle cat from central India and used available whole genome sequences of nine individuals from four other Felis species, two individuals of Prionailurus bengalensis and an Otocolobus manul. These whole genome sequences were filtered and aligned with the already published domestic cat (Felis catus genome assembly. Felids are closely related species and reads from all species in our study aligned with the domestic cat genome with a rate of at least 93%. We estimated the existing genomic variation by calculating heterozygous SNP encounter rate. So far, it seems that all wild cats have more genetic variation than Felis catus species. This can be attributed to the inbreeding in these cats. Among the wild cats, Felis silvestris seems to have the highest level of genetic variation. To understand the reasons behind the distribution of genetic variation in small cats, we estimated the demographic histories of each of the species using PSMC. This method can only detect demographic changes more than 1000 generations ago. We observe that roughly all species share a parallel history in terms of population increase. The most interesting and important feature might be that all wild small cat population sizes increased exponentially around twenty thousand years ago as opposed to domestic cat and big cats which declined around this time. Another interesting feature of

Genome wide association study identifies KCNMA1 contributing to human obesity

DEFF Research Database (Denmark)

Jiao, Hong; Arner, Peter; Hoffstedt, Johan

2011-01-01

Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a minor fraction of the total genetic variation expected to be present in the population....... Thus many genetic variants controlling obesity remain to be identified. The aim of this study was to use GWA followed by multiple stepwise validations to identify additional genes associated with obesity....

Climatic and geographic predictors of life history variation in Eastern Massasauga (Sistrurus catenatus: A range-wide synthesis.

Directory of Open Access Journals (Sweden)

Eric T Hileman

Full Text Available Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size-fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions. To address Eastern Massasauga life history data gaps, we compiled data from 47 study sites representing 38 counties across the range. We used multimodel inference and general linear models with geographic coordinates and annual climate normals as explanatory variables to clarify patterns of variation in life history traits. We found strong evidence for geographic variation in six of nine life history variables. Adult female snout-vent length and neonate mass increased with increasing mean annual precipitation. Litter size decreased with increasing mean temperature, and the size-fecundity relationship and growth prior to first hibernation both increased with increasing latitude. The proportion of gravid females also increased with increasing latitude, but this relationship may be the result of geographically varying detection bias. Our results provide insights into ectotherm life history variation and fill critical data gaps, which will inform Eastern Massasauga conservation efforts by improving biological realism for models of population viability and climate change.

Genome-wide association study identifies five new schizophrenia loci

NARCIS (Netherlands)

Ripke, S.; Sanders, A. R.; Kendler, K. S.; Levinson, D. F.; Sklar, P.; Holmans, P. A.; Lin, D. Y.; Duan, J.; Ophoff, R. A.; Andreassen, O. A.; Scolnick, E.; Cichon, S.; St Clair, D.; Corvin, A.; Gurling, H.; Werge, T.; Rujescu, D.; Blackwood, D. H.; Pato, C. N.; Malhotra, A. K.; Purcell, S.; Dudbridge, F.; Neale, B. M.; Rossin, L.; Visscher, P. M.; Posthuma, D.; Ruderfer, D. M.; Fanous, A.; Stefansson, H.; Steinberg, S.; Mowry, B. J.; Golimbet, V.; de Hert, M.; Jonsson, E. G.; Bitter, I.; Pietilainen, O. P.; Collier, D. A.; Tosato, S.; Agartz, I.; Albus, M.; Alexander, M.; Amdur, R. L.; Amin, F.; Bass, N.; Bergen, S. E.; Black, D. W.; Borglum, A. D.; Brown, M. A.; Bruggeman, R.; Buccola, N. G.; Byerley, W. F.; Cahn, W.; Cantor, R. M.; Carr, V. J.; Catts, S. V.; Choudhury, K.; Cloninger, C. R.; Cormican, P.; Craddock, N.; Danoy, P. A.; Datta, S.; de Haan, L.; Demontis, D.; Dikeos, D.; Djurovic, S.; Donnely, P.; Donohoe, G.; Duong, L.; Dwyer, S.; Fink-Jensen, A.; Freedman, R.; Freimer, N. B.; Friedl, M.; Georgieva, L.; Giegling, I.; Gill, M.; Glenthoj, B.; Godard, S.; Hamshere, M.; Hansen, M.; Hartmann, A. M.; Henskens, F. A.; Hougaard, D. M.; Hultman, C. M.; Ingason, A.; Jablensky, A. V.; Jakobsen, K. D.; Jay, M.; Jurgens, G.; Kahn, R. S.; Keller, M. C.; Kenis, G.; Kenny, E.; Kim, Y.; Kirov, G. K.; Konnerth, H.; Konte, B.; Krabbendam, L.; Krasucki, R.; Lasseter, V. K.; Laurent, C.; Lawrence, J.; Lencz, T.; Lerer, F. B.; Liang, K. Y.; Lichtenstein, P.; Lieberman, J. A.; Linszen, D. H.; Lonnqvist, J.; Loughland, C. M.; Maclean, A. W.; Maher, B. S.; Maier, W.; Mallet, J.; Malloy, P.; Mattheisen, M.; Mattingsdal, M.; McGhee, K. A.; McGrath, J. J.; McIntosh, A.; McLean, D. E.; McQuillin, A.; Melle, I.; Michie, P. T.; Milanova, V.; Morris, D. W.; Mors, O.; Mortensen, P. B.; Moskvina, V.; Muglia, P.; Myin-Germeys, I.; Nertney, D. A.; Nestadt, G.; Nielsen, J.; Nikolov, I.; Nordentoft, M.; Norton, N.; Nothen, M. M.; O'Dushlaine, C. T.; Olincy, A.; Olsen, L.; O'Neill, F. A.; Orntoft, T. F.; Owen, M. J.; Pantelis, C.; Papadimitriou, G.; Pato, M. T.; Peltonen, L.; Petursson, H.; Pickard, B.; Pimm, J.; Pulver, A. E.; Puri, V.; Quested, D.; Quinn, E. M.; Rasmussen, H. B.; Rethelyi, J. M.; Ribble, R.; Rietschel, M.; Riley, B. P.; Ruggeri, M.; Schall, U.; Schulze, T. G.; Schwab, S. G.; Scott, R. J.; Shi, J.; Sigurdsson, E.; Silvermann, J. M.; Spencer, C. C.; Stefansson, K.; Strange, A.; Strengman, E.; Stroup, T. S.; Suvisaari, J.; Terenius, L.; Thirumalai, S.; Thygesen, J. H.; Timm, S.; Toncheva, D.; van den Oord, E.; van Os, J.; van Winkel, R.; Veldink, J.; Walsh, D.; Wang, A. G.; Wiersma, D.; Wildenauer, D. B.; Williams, H. J.; Williams, N. M.; Wormley, B.; Zammit, S.; Sullivan, P. F.; O'Donovan, M. C.; Daly, M. J.; Gejman, P. V.

2011-01-01

We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded

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...

Exhalation of Rn-222 from soil: some aspects of variations

International Nuclear Information System (INIS)

Raghavayya, M.; Khan, A.H.; Padmanabhan, N.; Srivastava, G.K.

1982-01-01

The exhalation of radon from soil and uranium mill tailings piles is discussed. This process is a complex phenomenon. The exhalation rate depends on such variables as radium content, moisture content and porosity of soil, variation of atmospheric pressure, humidity, temperature, wind speed, etc. In an attempt to eliminate variations introduced by geographical location the exhalation rate is estimated at a fixed location. Measurements were carried out almost daily over a one year period. Exhalation rate has shown a wide variation, from almost zero to plus 900 pCi/m 2 .min. Measurements are still being continued. It was seen that exhalation rate fell drastically soon after a heavy shower when the ground was soaking wet. Emanation was found to increase as the ground began to dry and fall again when the ground was bone dry. Radon exhalation rates were also measured at different locations on a uranium tailings pile. Here also wide variation was observed

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton.

Science.gov (United States)

Su, Junji; Li, Libei; Zhang, Chi; Wang, Caixiang; Gu, Lijiao; Wang, Hantao; Wei, Hengling; Liu, Qibao; Huang, Long; Yu, Shuxun

2018-06-01

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

Science.gov (United States)

Schrider, Daniel R; Hahn, Matthew W; Begun, David J

2016-05-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Natural variation in virulence of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes.

Science.gov (United States)

Valero-Jiménez, Claudio A; Debets, Alfons J M; van Kan, Jan A L; Schoustra, Sijmen E; Takken, Willem; Zwaan, Bas J; Koenraadt, Constantianus J M

2014-12-06

Insecticide resistance is greatly hampering current efforts to control malaria and therefore alternative methods are needed. Entomopathogenic fungi have been proposed as an alternative with a special focus on the cosmopolitan species Beauveria bassiana. However, few studies have analysed the effects of natural variation within fungal isolates on mosquito survival, and the implications and possible exploitation for malaria control. Laboratory bioassays were performed on adult female mosquitoes (Anopheles coluzzii) with spores from 29 isolates of B. bassiana, originating from different parts of the world. In addition, phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth rate were studied to explore their relationship with virulence. All tested isolates of B. bassiana killed An. coluzzii mosquitoes, and the rate at which this happened differed significantly among the isolates. The risk of mosquitoes dying was around ten times higher when they were exposed to the most virulent as compared to the least virulent isolate. There was significant variation among isolates in spore size, growth rate and sporulation, but none of these morphological characteristics were correlated, and thus predictive, for the ability of the fungal isolate to kill malaria mosquitoes. This study shows that there is a wide natural variation in virulence of isolates of B. bassiana, and that selecting an appropriate fungal isolate is highly relevant in killing and thus controlling malaria mosquitoes, particularly if used as part of an integrated vector management strategy. Also, the wide variation observed in virulence offers the opportunity to better understand the molecular and genetic mechanisms that drive this variation and thus to address the potential development of resistance against entomopathogenic fungi.

Radiation Induced Fault Analysis for Wide Temperature BiCMOS Circuits, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — State of the art Radiation Hardened by Design (RHBD) techniques do not account for wide temperature variations in BiCMOS process. Silicon-Germanium BiCMOS process...

Genome-wide association genetics of an adaptive trait in lodgepole pine.

Science.gov (United States)

Parchman, Thomas L; Gompert, Zachariah; Mudge, Joann; Schilkey, Faye D; Benkman, Craig W; Buerkle, C Alex

2012-06-01

Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographical variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is of interest owing to the wide-reaching ecological consequences of serotiny and also because of the repeated evolution of the trait across the genus. Here, we present and utilize an inexpensive and time-effective method for generating population genomic data. The method uses restriction enzymes and PCR amplification to generate a library of fragments that can be sequenced with a high level of multiplexing. We obtained data for more than 95,000 single nucleotide polymorphisms across 98 serotinous and nonserotinous lodgepole pines from three populations. We used a Bayesian generalized linear model (GLM) to test for an association between genotypic variation at these loci and serotiny. The probability of serotiny varied by genotype at 11 loci, and the association between genotype and serotiny at these loci was consistent in each of the three populations of pines. Genetic variation across these 11 loci explained 50% of the phenotypic variation in serotiny. Our results provide a first genome-wide association map of serotiny in pines and demonstrate an inexpensive and efficient method for generating population genomic data. © 2012 Blackwell Publishing Ltd.

Structure variations of carbonizing lignin

International Nuclear Information System (INIS)

Otani, C.; Polidoro, H.A.; Otani, S.; Craievich, A.F.

1984-01-01

The studied lignin is a by-product of the process of ethanol production from eucaliptus. It was heat-treated under inert atmosphere conditions at increasing temperatures from 300C up to 2400C. The structural variations were studied by wide-angle X-ray diffraction, small-angle X-ray scattering and infrared absorption spectroscopy. The bulk and 'real' density of the compacted materials have also been determined as functions of the final temperature. These experimental results enabled us to establish a mechanism of structure variation based on the formation of a turbostratic graphite-like and porous structure within the initially amorphous lignin matrix. (Author) [pt

Genome wide meta-analysis highlights the role of genetic variation in RARRES2 in the regulation of circulating serum chemerin.

Directory of Open Access Journals (Sweden)

Anke Tönjes

2014-12-01

Full Text Available Chemerin is an adipokine proposed to link obesity and chronic inflammation of adipose tissue. Genetic factors determining chemerin release from adipose tissue are yet unknown. We conducted a meta-analysis of genome-wide association studies (GWAS for serum chemerin in three independent cohorts from Europe: Sorbs and KORA from Germany and PPP-Botnia from Finland (total N = 2,791. In addition, we measured mRNA expression of genes within the associated loci in peripheral mononuclear cells by micro-arrays, and within adipose tissue by quantitative RT-PCR and performed mRNA expression quantitative trait and expression-chemerin association studies to functionally substantiate our loci. Heritability estimate of circulating chemerin levels was 16.2% in the Sorbs cohort. Thirty single nucleotide polymorphisms (SNPs at chromosome 7 within the retinoic acid receptor responder 2 (RARRES2/Leucine Rich Repeat Containing (LRRC61 locus reached genome-wide significance (p<5.0×10-8 in the meta-analysis (the strongest evidence for association at rs7806429 with p = 7.8×10-14, beta = -0.067, explained variance 2.0%. All other SNPs within the cluster were in linkage disequilibrium with rs7806429 (minimum r2 = 0.43 in the Sorbs cohort. The results of the subgroup analyses of males and females were consistent with the results found in the total cohort. No significant SNP-sex interaction was observed. rs7806429 was associated with mRNA expression of RARRES2 in visceral adipose tissue in women (p<0.05 after adjusting for age and body mass index. In conclusion, the present meta-GWAS combined with mRNA expression studies highlights the role of genetic variation in the RARRES2 locus in the regulation of circulating chemerin concentrations.

Effects of ionic strength and ion pairing on (plant-wide) modelling of anaerobic digestion

DEFF Research Database (Denmark)

Solon, Kimberly; Flores Alsina, Xavier; Mbamba, Christian Kazadi

2015-01-01

Plant-wide models of wastewater treatment (such as the Benchmark Simulation Model No. 2 or BSM2) are gaining popularity for use in holistic virtual studies of treatment plant control and operations. The objective of this study is to show the influence of ionic strength (as activity corrections....... The paper describes: 1) how the anaerobic digester performance is affected by physico-chemical corrections; 2) the effect on pH and the anaerobic digestion products (CO2, CH4 and H2); and, 3) how these variations are propagated from the sludge treatment to the water line. Results at high ionic strength...

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

Sources of variation in hair cortisol in wild and captive non-human primates.

Science.gov (United States)

Fourie, Nicolaas H; Brown, Janine L; Jolly, Clifford J; Phillips-Conroy, Jane E; Rogers, Jeffrey; Bernstein, Robin M

2016-04-01

Hair cortisol analysis is a potentially powerful tool for evaluating adrenal function and chronic stress. However, the technique has only recently been applied widely to studies of wildlife, including primates, and there are numerous practical and technical factors that should be considered to ensure good quality data and the validity of results and conclusions. Here we report on various intrinsic and extrinsic sources of variation in hair cortisol measurements in wild and captive primates. Hair samples from both wild and captive primates revealed that age and sex can affect hair cortisol concentrations; these effects need to be controlled for when making comparisons between individual animals or populations. Hair growth rates also showed considerable inter-specific variation among a number of primate species. We describe technical limitations of hair analyses and variation in cortisol concentrations as a function of asynchronous hair growth, anatomical site of collection, and the amount and numbers of hair/s used for cortisol extraction. We discuss these sources of variation and their implications for proper study design and interpretation of results. Published by Elsevier GmbH.

Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient.

Directory of Open Access Journals (Sweden)

Seifollah Poormohammad Kiani

Full Text Available As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness.

On the analysis of line profile variations: A statistical approach

International Nuclear Information System (INIS)

McCandliss, S.R.

1988-01-01

This study is concerned with the empirical characterization of the line profile variations (LPV), which occur in many of and Wolf-Rayet stars. The goal of the analysis is to gain insight into the physical mechanisms producing the variations. The analytic approach uses a statistical method to quantify the significance of the LPV and to identify those regions in the line profile which are undergoing statistically significant variations. Line positions and flux variations are then measured and subject to temporal and correlative analysis. Previous studies of LPV have for the most part been restricted to observations of a single line. Important information concerning the range and amplitude of the physical mechanisms involved can be obtained by simultaneously observing spectral features formed over a range of depths in the extended mass losing atmospheres of massive, luminous stars. Time series of a Wolf-Rayet and two of stars with nearly complete spectral coverage from 3940 angstrom to 6610 angstrom and with spectral resolution of R = 10,000 are analyzed here. These three stars exhibit a wide range of both spectral and temporal line profile variations. The HeII Pickering lines of HD 191765 show a monotonic increase in the peak rms variation amplitude with lines formed at progressively larger radii in the Wolf-Rayet star wind. Two times scales of variation have been identified in this star: a less than one day variation associated with small scale flickering in the peaks of the line profiles and a greater than one day variation associated with large scale asymmetric changes in the overall line profile shapes. However, no convincing period phenomena are evident at those periods which are well sampled in this time series

Genome-wide gene expression regulation as a function of genotype and age in C. elegans

NARCIS (Netherlands)

Viñuela Rodriguez, A.; Snoek, L.B.; Riksen, J.A.G.; Kammenga, J.E.

2010-01-01

Gene expression becomes more variable with age, and it is widely assumed that this is due to a decrease in expression regulation. But currently there is no understanding how gene expression regulatory patterns progress with age. Here we explored genome-wide gene expression variation and regulatory

Variation in radiographic protocols in paediatric interventional cardiology

International Nuclear Information System (INIS)

McFadden, S L; Hughes, C M; Winder, R J

2013-01-01

The aim of this work is to determine current radiographic protocols in paediatric interventional cardiology (IC) in the UK and Ireland. To do this we investigated which imaging parameters/protocols are commonly used in IC in different hospitals, to identify if a standard technique is used and illustrate any variation in practice. A questionnaire was sent to all hospitals in the UK and Ireland which perform paediatric IC to obtain information on techniques used in each clinical department and on the range of clinical examinations performed. Ethical and research governance approval was sought from the Office for Research Ethics Committees Northern Ireland and the individual trusts. A response rate of 79% was achieved, and a wide variation in technique was found between hospitals. The main differences in technique involved variations in the use of an anti-scatter grid and the use of additional filtration to the radiation beam, frame rates for digital acquisition and pre-programmed projections/paediatric specific programming in the equipment. We conclude that there is no standard protocol for carrying out paediatric IC in the UK or Ireland. Each hospital carries out the IC procedure according to its own local protocols resulting in a wide variation in radiation dose. (paper)

Variation in radiographic protocols in paediatric interventional cardiology.

Science.gov (United States)

McFadden, S L; Hughes, C M; Winder, R J

2013-06-01

The aim of this work is to determine current radiographic protocols in paediatric interventional cardiology (IC) in the UK and Ireland. To do this we investigated which imaging parameters/protocols are commonly used in IC in different hospitals, to identify if a standard technique is used and illustrate any variation in practice. A questionnaire was sent to all hospitals in the UK and Ireland which perform paediatric IC to obtain information on techniques used in each clinical department and on the range of clinical examinations performed. Ethical and research governance approval was sought from the Office for Research Ethics Committees Northern Ireland and the individual trusts. A response rate of 79% was achieved, and a wide variation in technique was found between hospitals. The main differences in technique involved variations in the use of an anti-scatter grid and the use of additional filtration to the radiation beam, frame rates for digital acquisition and pre-programmed projections/paediatric specific programming in the equipment. We conclude that there is no standard protocol for carrying out paediatric IC in the UK or Ireland. Each hospital carries out the IC procedure according to its own local protocols resulting in a wide variation in radiation dose.

Data analysis in the post-genome-wide association study era

Directory of Open Access Journals (Sweden)

Qiao-Ling Wang

2016-12-01

Full Text Available Since the first report of a genome-wide association study (GWAS on human age-related macular degeneration, GWAS has successfully been used to discover genetic variants for a variety of complex human diseases and/or traits, and thousands of associated loci have been identified. However, the underlying mechanisms for these loci remain largely unknown. To make these GWAS findings more useful, it is necessary to perform in-depth data mining. The data analysis in the post-GWAS era will include the following aspects: fine-mapping of susceptibility regions to identify susceptibility genes for elucidating the biological mechanism of action; joint analysis of susceptibility genes in different diseases; integration of GWAS, transcriptome, and epigenetic data to analyze expression and methylation quantitative trait loci at the whole-genome level, and find single-nucleotide polymorphisms that influence gene expression and DNA methylation; genome-wide association analysis of disease-related DNA copy number variations. Applying these strategies and methods will serve to strengthen GWAS data to enhance the utility and significance of GWAS in improving understanding of the genetics of complex diseases or traits and translate these findings for clinical applications. Keywords: Genome-wide association study, Data mining, Integrative data analysis, Polymorphism, Copy number variation

Genome-wide association study of serum selenium concentrations

DEFF Research Database (Denmark)

Gong, Jian; Hsu, Li; Harrison, Tabitha

2013-01-01

Selenium is an essential trace element and circulating selenium concentrations have been associated with a wide range of diseases. Candidate gene studies suggest that circulating selenium concentrations may be impacted by genetic variation; however, no study has comprehensively investigated...... this hypothesis. Therefore, we conducted a two-stage genome-wide association study to identify genetic variants associated with serum selenium concentrations in 1203 European descents from two cohorts: the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening and the Women’s Health Initiative (WHI). We...... tested association between 2,474,333 single nucleotide polymorphisms (SNPs) and serum selenium concentrations using linear regression models. In the first stage (PLCO) 41 SNPs clustered in 15 regions had p

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.

Science.gov (United States)

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O'Connor, Timothy D; Abecasis, Gonçalo R; Wojcik, Genevieve L; Gignoux, Christopher R; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E; Bustamante, Carlos; Beaty, Terri H; Mathias, Rasika A; Barnes, Kathleen C; Qin, Zhaohui S

2017-04-21

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense

Science.gov (United States)

Joseph, Bindu; Corwin, Jason A.; Kliebenstein, Daniel J.

2015-01-01

Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype. PMID:25569687

Genetic determination of human facial morphology: links between cleft-lips and normal variation.

Science.gov (United States)

Boehringer, Stefan; van der Lijn, Fedde; Liu, Fan; Günther, Manuel; Sinigerova, Stella; Nowak, Stefanie; Ludwig, Kerstin U; Herberz, Ruth; Klein, Stefan; Hofman, Albert; Uitterlinden, Andre G; Niessen, Wiro J; Breteler, Monique M B; van der Lugt, Aad; Würtz, Rolf P; Nöthen, Markus M; Horsthemke, Bernhard; Wieczorek, Dagmar; Mangold, Elisabeth; Kayser, Manfred

2011-11-01

Recent genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with non-syndromic cleft lip with or without cleft palate (NSCL/P), and other previous studies showed distinctly differing facial distance measurements when comparing unaffected relatives of NSCL/P patients with normal controls. Here, we test the hypothesis that genetic loci involved in NSCL/P also influence normal variation in facial morphology. We tested 11 SNPs from 10 genomic regions previously showing replicated evidence of association with NSCL/P for association with normal variation of nose width and bizygomatic distance in two cohorts from Germany (N=529) and the Netherlands (N=2497). The two most significant associations found were between nose width and SNP rs1258763 near the GREM1 gene in the German cohort (P=6 × 10(-4)), and between bizygomatic distance and SNP rs987525 at 8q24.21 near the CCDC26 gene (P=0.017) in the Dutch sample. A genetic prediction model explained 2% of phenotype variation in nose width in the German and 0.5% of bizygomatic distance variation in the Dutch cohort. Although preliminary, our data provide a first link between genetic loci involved in a pathological facial trait such as NSCL/P and variation of normal facial morphology. Moreover, we present a first approach for understanding the genetic basis of human facial appearance, a highly intriguing trait with implications on clinical practice, clinical genetics, forensic intelligence, social interactions and personal identity.

Diurnal variations in personal care products in seawater and mussels at three Mediterranean coastal sites.

Science.gov (United States)

Picot-Groz, Marina; Fenet, Hélène; Martinez Bueno, Maria Jesus; Rosain, David; Gomez, Elena

2018-03-01

The presence of personal care products (PCPs) in the marine environment is of major concern. PCPs, UV filters, and musks can enter the marine environment indirectly through wastewater or directly via recreational activities. We conducted this study to document patterns in the occurrence of seven PCPs at three coastal sites impacted by recreational activities during 1 day. The study focused on diurnal variations in these seven PCPs in seawater and indigenous mussels. In seawater, UV filters showed diurnal variations that mirrored variations in recreational activities at the sites. Ethylhexyl methoxycinnamate (EHMC) and octocrylene (OC) water concentrations increased from under the limit of quantification in the morning to 106 and 369 ng/L, respectively, when recreational activities were the highest. In mussels, diurnal variations in OC were observed, with the lowest concentrations recorded in the morning and then increasing throughout the day. As Mytilus spp. are widely used as sentinels in coastal pollution monitoring programs (mussel watch), our findings on diurnal variations could enhance sampling recommendations for recreational sites impacted by PCPs.

Epigenetic Variation in Monozygotic Twins: A Genome-Wide Analysis of DNA Methylation in Buccal Cells

NARCIS (Netherlands)

van Dongen, J.; Ehli, E.A.; Slieker, R.C.; Bartels, M.; Weber, Z.M.; Davies, G.E.; Slagboom, P.E.; Heijmans, B.T.; Boomsma, D.I.

2014-01-01

DNA methylation is one of the most extensively studied epigenetic marks in humans. Yet, it is largely unknown what causes variation in DNA methylation between individuals. The comparison of DNA methylation profiles of monozygotic (MZ) twins offers a unique experimental design to examine the extent

Induction of Genetic Variation with Recurrent Gamma Radiation in Centipedegrass (Eremochloa ophiuroides)

International Nuclear Information System (INIS)

Lim Keun- Bal; Rim Yong-Woo

1998-01-01

Centipedegrass (Eremochloa ophiuroides) is a popular lawn grass in the southeastern USA. It has a naturally light green color and grows well on a wide range of soil types. Studies show limited morphological variation present in centipedegrass germplasm. To obtain the high morphological variation, plants were established from the irradiated seed at 10 Kr, allowed to interpollinate and harvested bulk seed, and then irradiated again for the next cycles. Morphological characteristics were measured in the 5 genetic varition lines (TC201:cv. Common and non irradiated, TC202:4th cycles, TC241:6th cycles, TC306:8th cycles, and TC318:5th cycles) induced by recurrent gamma radiation. The ranges of variation of recurrently radiated centipedegrass lines TC202, TC241, and TC306 except TC318(TifBlair) for the stolons per plant, total stolon length per plant, longest stolon length, leaf length and width at top-most exposed internode were wider than those of non-irradiated line (TC201). Recurrent gamma radiation was very effective to enlarge the ranges of variation of morphological characteristics in reproductive organ like stolons of centipedegrass. The effect of quantity of gamma ray irradiation cycles on the means and ranges of variation in the morphological characteristics of centipedegrass was not regularly tended

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Science.gov (United States)

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available

Sex-stratified Genome-wide Association Studies Including 270000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

NARCIS (Netherlands)

Randall, J.C.; Winkler, T.W.; Kutalik, Z.; Berndt, S.I.; Jackson, A.U.; Monda, K.L.; Kilpeläinen, T.O.; Esko, T.; Mägi, R.; Li, S.; Workalemahu, T.; Feitosa, M.F.; Croteau-Chonka, D.C.; Day, F.R.; Fall, T.; Ferreira, T.; Gustafsson, S.; Locke, A.E.; Mathieson, I.; Scherag, A.; Vedantam, S.; Wood, A.R.; Liang, L.; Steinthorsdottir, V.; Thorleifsson, G.; Dermitzakis, E.T.; Dimas, A.S.; Karpe, F.; Min, J.L.; Nicholson, G.; Clegg, D.J.; Person, T.; Krohn, J.P.; Bauer, S.; Buechler, C.; Eisinger, K.; Bonnefond, A.; Froguel, P.; Hottenga, J.J.; Prokopenko, I.; Waite, L.L.; Harris, T.B.; Smith, A.V.; Shuldiner, A.R.; McArdle, W.L.; Caulfield, M.J.; Munroe, P.B.; Grönberg, H.; Chen, Y.D.; Li, G.; Beckmann, J.S.; Johnson, T.; Thorsteinsdottir, U.; Teder-Laving, M.; Khaw, K.T.; Wareham, N.J.; Zhao, J.H.; Amin, N.; Oostra, B.A.; Kraja, A.T.; Province, M.A.; Cupples, L.A.; Heard-Costa, N.L.; Kaprio, J.; Ripatti, S.; Surakka, I.; Collins, F.S.; Saramies, J.; Tuomilehto, J.; Jula, A.; Salomaa, V.; Erdmann, J.; Hengstenberg, C.; Loley, C.; Schunkert, H.; Lamina, C.; Wichmann, H.E.; Albrecht, E.; Gieger, C.; Hicks, A.A.; Johansson, A.; Pramstaller, P.P.; Kathiresan, S.; Speliotes, E.K.; Penninx, B.W.J.H.; Hartikainen, A.L.; Järvelin, M.R.; Gyllensten, U.; Boomsma, D.I.; Campbell, H.; Wilson, J.F.; Chanock, S.J.; Farrall, M.; Goel, A.; Medina-Gomez, C.; Rivadeneira, F.; Estrada, K.; Uitterlinden, A.G.; Hofman, A.; Zillikens, M.C.; den Heijer, M.; Kiemeney, L.A.; Maschio, A.; Hall, P.; Tyrer, J.; Teumer, A.; Völzke, H.; Kovacs, P.; Tönjes, A.; Mangino, M.; Spector, T.D.; Hayward, C.; Rudan, I.; Hall, A.S.; Samani, N.J.; Attwood, A.P.; Sambrook, J.G.; Hung, J.; Palmer, L.J.; Lokki, M.L.; Sinisalo, J.; Boucher, G.; Huikuri, H.V.; Lorentzon, M.; Ohlsson, C.; Eklund, N.; Eriksson, J.G.; Barlassina, C.; Rivolta, C.; Nolte, I.M.; Snieder, H.; van der Klauw, M.M.; van Vliet-Ostaptchouk, J.V.; Gejman, P.V.; Shi, J.; Jacobs, K.B.; Wang, Z.; Bakker, S.J.; Mateo Leach, I.; Navis, G.; van der Harst, P.; Martin, N.G.; Medland, S.E.; Montgomery, G.W.; Yang, J.; Chasman, D.I.; Ridker, P.M.; Rose, L.M.; Lehtimäki, T.; Raitakari, O.; Absher, D.; Iribarren, C.; Basart, H.; Hovingh, K.G.; Hyppönen, E.; Power, C.; Anderson, D.; Beilby, J.P.; Hui, J.; Jolley, J.; Sager, H.; Bornstein, S.R.; Schwarz, P.E.; Kristiansson, K.; Perola, M.; Lindström, J.; Swift, A.J.; Uusitupa, M.; Atalay, M.; Lakka, T.A.; Rauramaa, R.; Bolton, J.L.; Fowkes, G.; Fraser, R.M.; Price, J.F.; Fischer, K.; Krjuta Kov, K.; Metspalu, A.; Mihailov, E.; Langenberg, C.; Luan, J.; Ong, K.K.; Chines, P.S.; Keinanen-Kiukaanniemie, S.; Saaristo, T.E.; Edkins, S.; Franks, P.W.; Hallmans, G.; Shungin, D.; Morris, A.D.; Palmer, C.N.A.; Erbel, R.; Moebus, S.; Nöthen, M.M.; Pechlivanis, S.; Hveem, K.; Narisu, N.; Hamsten, A.; Humphries, S.E.; Strawbridge, R.J.; Tremoli, E.; Grallert, H.; Thorand, B.; Illig, T.; Koenig, W.; Müller-Nurasyid, M.; Peters, A.; Boehm, B.O.; Kleber, M.E.; März, W.; Winkelmann, B.R.; Kuusisto, J.; Laakso, M.; Arveiler, D.; Cesana, G.; Kuulasmaa, K.; Virtamo, J.; Yarnell, J.W.; Kuh, D; Wong, A.; Lind, L.; de Faire, U.; Gigante, B.; Magnusson, P.K.E.; Pedersen, N.L.; Dedoussis, G.; Dimitriou, M.; Kolovou, G.; Kanoni, S.; Stirrups, K.; Bonnycastle, L.L.; Njolstad, I.; Wilsgaard, T.; Ganna, A.; Rehnberg, E.; Hingorani, A.D.; Kivimaki, M.; Kumari, M.; Assimes, T.L.; Barroso, I.; Boehnke, M.; Borecki, I.B.; Deloukas, P.; Fox, C.S.; Frayling, T.M.; Groop, L.C.; Haritunians, T.; Hunter, D.; Ingelsson, E.; Kaplan, R.; Mohlke, K.L.; O'Connell, J.R.; Schlessinger, D.; Strachan, D.P.; Stefansson, K.; van Duijn, C.M.; Abecasis, G.R.; McCarthy, M.I.; Hirschhorn, J.N.; Qi, L.; Loos, R.J.; Lindgren, C.M.; North, K.E.; Heid, I.M.

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723

Somaclonal variation in rice

International Nuclear Information System (INIS)

Kucherenko, L.

1990-01-01

Full text: 32 varieties of Oryza sativa L. ssp. japonica were used as donors for callus induction from somatic tissues. In some cases, the callus was treated before regeneration with the chemical mutagen MNU. Some of the regenerated plants demonstrated heritable alterations, among them chlorophyll deficiencies, variation in plant height, awness, glume colouring and fertility. Along with these, a number of lines with agronomically valuable alterations concerning maturity time, panicle structure, plant productivity and grain quality were found. The spectrum of variability was very wide. Vivipary was noticed. Superdwarfs with plant height of about 15 cm were found. Plants with no visible distinctions could be variants too, for example, with increased protein content or disease resistance. The rate and the spectrum of the somaclonal variation were not influenced by the culture media but depended on the donor's genotype. On the basis of somaclonal variation a variety 'Bioryza' was developed. It is an early maturing (about 95-100 days), long grain variety, with grain yield up to 8 t/ha. (author)

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

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

NARCIS (Netherlands)

Lee, S.H.; Ripke, S.; Neale, B.; Faraone, S.V.; Purcell, S.M.; Perlis, R.H.; Mowry, B. J.; Thapar, A.; Goddard, M.E.; Witte, J.S.; Absher, D.; Agartz, I.; Akil, H.; Amin, F.; Andreassen, O.A.; Anjorin, A.; Anney, R.; Anttila, V.; Arking, D.E.; Asherson, P.; Azevedo, M.H.; Backlund, L.; Badner, J.A.; Bailey, A.J.; Banaschewski, T.; Barchas, J.D.; Barnes, M.R.; Barrett, T.B.; Bass, N.; Battaglia, A.; Bauer, M.; Bayés, M.; Bellivier, F.; Bergen, S.E.; Berrettini, W.; Betancur, C.; Bettecken, T.; Biederman, J; Binder, E.B.; Black, D.W.; Blackwood, D.H.; Bloss, C.S.; Boehnke, M.; Boomsma, D.I.; Breen, G.; Breuer, R.; Bruggeman, R.; Cormican, P.; Buccola, N.G.; Buitelaar, J.K.; Bunney, W.E.; Buxbaum, J.D.; Byerley, W. F.; Byrne, E.M.; Caesar, S.; Cahn, W.; Cantor, R.M.; Casas, M.; Chakravarti, A.; Chambert, K.; Choudhury, K.; Cichon, S.; Cloninger, C. R.; Collier, D.A.; Cook, E.H.; Coon, H.; Corman, B.; Corvin, A.; Coryell, W.H.; Craig, D.W.; Craig, I.W.; Crosbie, J.; Cuccaro, M.L.; Curtis, D.; Czamara, D.; Datta, S.; Dawson, G.; Day, R.; de Geus, E.J.C.; Degenhardt, F.; Djurovic, S.; Donohoe, G.; Doyle, A.E.; Duan, J.; Dudbridge, F.; Duketis, E.; Ebstein, R.P.; Edenberg, H.J.; Elia, J.; Ennis, S.; Etain, B.; Fanous, A.; Farmer, A.E.; Ferrier, I.N.; Flickinger, M.; Fombonne, E.; Foroud, T.; Frank, J.; Franke, B.; Fraser, C.; Freedman, R.; Freimer, N.B.; Freitag, C.; Friedl, M.; Frisén, L.; Gallagher, L.; Gejman, P.V.; Georgieva, L.; Gershon, E.S.; Geschwind, D.H.; Giegling, I.; Gill, M.; Gordon, S.D.; Gordon-Smith, K.; Green, E.K.; Greenwood, T.A.; Grice, D.E.; Gross, M.; Grozeva, D.; Guan, W.; Gurling, H.; de Haan, L.; Haines, J.L.; Hakonarson, H.; Hallmayer, J.; Hamilton, S.P.; Hamshere, M.L.; Hansen, T.F.; Hartmann, A.M.; Hautzinger, M.; Heath, A.C.; Henders, A.K.; Herms, S.; Hickie, I.B.; Hipolito, M.; Hoefels, S.; Holmans, P.A.; Holsboer, F.; Hoogendijk, W.J.G.; Hottenga, J.J.; Hultman, C. M.; Hus, V.; Ingason, A.; Ising, M.; Jamain, S.; Jones, E.G.; Jones, I.; Jones, L.; Tzeng, J.Y.; Kähler, A.K.; Kahn, R.S.; Kandaswamy, R.; Keller, M.C.; Kennedy, J.L.; Kenny, E.; Kent, L.; Kim, Y.; Kirov, G. K.; Klauck, S.M.; Klei, L.; Knowles, J.A.; Kohli, M.A.; Koller, D.L.; Konte, B.; Korszun, A.; Krabbendam, L.; Krasucki, R.; Kuntsi, J.; Kwan, P.; Landén, M.; Langstrom, N.; Lathrop, M.; Lawrence, J.; Lawson, W.B.; Leboyer, M.; Ledbetter, D.H.; Lee, P.H.; Lencz, T.; Lesch, K.P.; Levinson, D.F.; Lewis, C.M.; Li, J.; Lichtenstein, P.; Lieberman, J. A.; Lin, D.Y.; Linszen, D.H.; Liu, C.; Lohoff, F.W.; Loo, S.K.; Lord, C.; Lowe, J.K.; Lucae, S.; MacIntyre, D.J.; Madden, P.A.F.; Maestrini, E.; Magnusson, P.K.E.; Mahon, P.B.; Maier, W.; Malhotra, A.K.; Mane, S.M.; Martin, C.L.; Martin, N.G.; Mattheisen, M.; Matthews, K.; Mattingsdal, M.; McCarroll, S.A.; McGhee, K.A.; McGough, J.J.; McGrath, P.J.; McGuffin, P.; McInnis, M.G.; McIntosh, A.; McKinney, R.; McLean, A.W.; McMahon, F.J.; McMahon, W.M.; McQuillin, A.; Medeiros, H.; Medland, S.E.; Meier, S.; Melle, I.; Meng, F.; Meyer, J.; Middeldorp, C.M.; Middleton, L.; Milanova, V.; Miranda, A.; Monaco, A.P.; Montgomery, G.W.; Moran, J.L.; Moreno-De Luca, D.; Morken, G.; Morris, D.W.; Morrow, E.M.; Moskvina, V.; Muglia, P.; Mühleisen, T.W.; Muir, W.J.; Müller-Myhsok, B.; Murtha, M.; Myers, R.M.; Myin-Germeys, I.; Neale, M.C.; Nelson, S.F.; Nievergelt, C.M.; Nikolov, I.; Nimgaonkar, V.L.; Nolen, W.A.; Nöthen, M.M.; Nurnberger, J.I.; Nwulia, E.A.; Nyholt, DR; O'Dushlaine, C.; Oades, R.D.; Olincy, A.; Oliveira, G.; Olsen, L.; Ophoff, R.A.; Osby, U.; Owen, M.J.; Palotie, A.; Parr, J.R.; Paterson, A.D.; Pato, C.N.; Pato, M.T.; Penninx, B.W.J.H.; Pergadia, M.L.; Pericak-Vance, M.A.; Pickard, B.S.; Pimm, J.; Piven, J.; Posthuma, D.; Potash, J.B.; Poustka, F.; Propping, P.; Puri, V.; Quested, D.; Quinn, E.M.; Ramos-Quiroga, J.A.; Rasmussen, H.B.; Raychaudhuri, S.; Rehnström, K.; Reif, A.; Ribasés, M.; Rice, J.P.; Rietschel, M.; Roeder, K.; Roeyers, H.; Rossin, L.; Rothenberger, A.; Rouleau, G.; Ruderfer, D.; Rujescu, D.; Sanders, A.R.; Sanders, S.J.; Santangelo, S.; Sergeant, J.A.; Schachar, R.; Schalling, M.; Schatzberg, A.F.; Scheftner, W.A.; Schellenberg, G.D.; Scherer, S.W.; Schork, N.J.; Schulze, T.G.; Schumacher, J.; Schwarz, M.; Scolnick, E.; Scott, L.J.; Shi, J.; Shilling, P.D.; Shyn, S.I.; Silverman, J.M.; Slager, S.L.; Smalley, S.L.; Smit, J.H.; Smith, E.N.; Sonuga-Barke, E.J.; St Clair, D.; State, M.; Steffens, M; Steinhausen, H.C.; Strauss, J.; Strohmaier, J.; Stroup, T.S.; Sutcliffe, J.; Szatmari, P.; Szelinger, S.; Thirumalai, S.; Thompson, R.C.; Todorov, A.A.; Tozzi, F.; Treutlein, J.; Uhr, M.; van den Oord, E.J.C.G.; Grootheest, G.; van Os, J.; Vicente, A.; Vieland, V.; Vincent, J.B.; Visscher, P.M.; Walsh, C.A.; Wassink, T.H.; Watson, S.J.; Weissman, M.M.; Werge, T.; Wienker, T.F.; Wijsman, E.M.; Willemsen, G.; Williams, N.; Willsey, A.J.; Witt, S.H.; Xu, W.; Young, A.H.; Yu, T.W.; Zammit, S.; Zandi, P.P.; Zhang, P.; Zitman, F.G.; Zöllner, S.; Devlin, B.; Kelsoe, J.; Sklar, P.; Daly, M.J.; O'Donovan, M.C.; Craddock, N.; Sullivan, P.F.; Smoller, J.W.; Kendler, K.S.; Wray, N.R.

2013-01-01

Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases

Genome-wide association study identifies 74 loci associated with educational attainment

NARCIS (Netherlands)

A. Okbay (Aysu); J.P. Beauchamp (Jonathan); Fontana, M.A. (Mark Alan); J.J. Lee (James J.); T.H. Pers (Tune); Rietveld, C.A. (Cornelius A.); P. Turley (Patrick); Chen, G.-B. (Guo-Bo); V. Emilsson (Valur); Meddens, S.F.W. (S. Fleur W.); Oskarsson, S. (Sven); Pickrell, J.K. (Joseph K.); Thom, K. (Kevin); Timshel, P. (Pascal); R. de Vlaming (Ronald); A. Abdellaoui (Abdel); T.S. Ahluwalia (Tarunveer Singh); J. Bacelis (Jonas); C. Baumbach (Clemens); Bjornsdottir, G. (Gyda); J.H. Brandsma (Johan); Pina Concas, M. (Maria); J. Derringer; Furlotte, N.A. (Nicholas A.); T.E. Galesloot (Tessel); S. Girotto; Gupta, R. (Richa); L.M. Hall (Leanne M.); S.E. Harris (Sarah); E. Hofer; Horikoshi, M. (Momoko); J.E. Huffman (Jennifer E.); Kaasik, K. (Kadri); I.-P. Kalafati (Ioanna-Panagiota); R. Karlsson (Robert); A. Kong (Augustine); J. Lahti (Jari); S.J. van der Lee (Sven); Deleeuw, C. (Christiaan); P.A. Lind (Penelope); Lindgren, K.-O. (Karl-Oskar); Liu, T. (Tian); M. Mangino (Massimo); J. Marten (Jonathan); E. Mihailov (Evelin); M. Miller (Mike); P.J. van der Most (Peter); C. Oldmeadow (Christopher); A. Payton (Antony); N. Pervjakova (Natalia); W.J. Peyrot (Wouter ); Qian, Y. (Yong); O. Raitakari (Olli); Rueedi, R. (Rico); Salvi, E. (Erika); Schmidt, B. (Börge); Schraut, K.E. (Katharina E.); Shi, J. (Jianxin); A.V. Smith (Albert Vernon); R.A. Poot (Raymond); B. St Pourcain (Beate); A. Teumer (Alexander); G. Thorleifsson (Gudmar); N. Verweij (Niek); D. Vuckovic (Dragana); Wellmann, J. (Juergen); H.J. Westra (Harm-Jan); Yang, J. (Jingyun); Zhao, W. (Wei); Zhu, Z. (Zhihong); B.Z. Alizadeh (Behrooz); N. Amin (Najaf); Bakshi, A. (Andrew); S.E. Baumeister (Sebastian); G. Biino (Ginevra); K. Bønnelykke (Klaus); P.A. Boyle (Patricia); H. Campbell (Harry); Cappuccio, F.P. (Francesco P.); G. Davies (Gail); J.E. de Neve (Jan-Emmanuel); P. Deloukas (Panagiotis); I. Demuth (Ilja); Ding, J. (Jun); Eibich, P. (Peter); Eisele, L. (Lewin); N. Eklund (Niina); D.M. Evans (David); J.D. Faul (Jessica D.); M.F. Feitosa (Mary Furlan); A.J. Forstner (Andreas); I. Gandin (Ilaria); Gunnarsson, B. (Bjarni); B.V. Halldorsson (Bjarni); T.B. Harris (Tamara); E.G. Holliday (Elizabeth); A.C. Heath (Andrew C.); L.J. Hocking; G. Homuth (Georg); M. Horan (Mike); J.J. Hottenga (Jouke Jan); P.L. de Jager (Philip); P.K. Joshi (Peter); A. Juqessur (Astanand); M. Kaakinen (Marika); M. Kähönen (Mika); S. Kanoni (Stavroula); Keltigangas-Järvinen, L. (Liisa); L.A.L.M. Kiemeney (Bart); I. Kolcic (Ivana); Koskinen, S. (Seppo); A. Kraja (Aldi); Kroh, M. (Martin); Z. Kutalik (Zoltán); A. Latvala (Antti); L.J. Launer (Lenore); Lebreton, M.P. (Maël P.); D.F. Levinson (Douglas F.); P. Lichtenstein (Paul); P. Lichtner (Peter); D.C. Liewald (David C.); A. Loukola (Anu); P.A. Madden (Pamela); R. Mägi (Reedik); Mäki-Opas, T. (Tomi); R.E. Marioni (Riccardo); P. Marques-Vidal; Meddens, G.A. (Gerardus A.); G. Mcmahon (George); C. Meisinger (Christa); T. Meitinger (Thomas); Milaneschi, Y. (Yusplitri); L. Milani (Lili); G.W. Montgomery (Grant); R. Myhre (Ronny); C.P. Nelson (Christopher P.); D.R. Nyholt (Dale); W.E.R. Ollier (William); A. Palotie (Aarno); L. Paternoster (Lavinia); N.L. Pedersen (Nancy); K. Petrovic (Katja); D.J. Porteous (David J.); K. Räikkönen (Katri); Ring, S.M. (Susan M.); A. Robino (Antonietta); O. Rostapshova (Olga); I. Rudan (Igor); A. Rustichini (Aldo); V. Salomaa (Veikko); Sanders, A.R. (Alan R.); A.-P. Sarin; R. Schmidt (Reinhold); R.J. Scott (Rodney); B.H. Smith (Blair); J.A. Smith (Jennifer A); J.A. Staessen (Jan); E. Steinhagen-Thiessen (Elisabeth); K. Strauch (Konstantin); A. Terracciano; M.D. Tobin (Martin); S. Ulivi (Shelia); S. Vaccargiu (Simona); L. Quaye (Lydia); F.J.A. van Rooij (Frank); C. Venturini (Cristina); A.A.E. Vinkhuyzen (Anna A.); U. Völker (Uwe); Völzke, H. (Henry); J.M. Vonk (Judith); D. Vozzi (Diego); J. Waage (Johannes); E.B. Ware (Erin B.); G.A.H.M. Willemsen (Gonneke); J. Attia (John); D.A. Bennett (David A.); Berger, K. (Klaus); L. Bertram (Lars); H. Bisgaard (Hans); D.I. Boomsma (Dorret); I.B. Borecki (Ingrid); U. Bültmann (Ute); C.F. Chabris (Christopher F.); F. Cucca (Francesco); D. Cusi (Daniele); I.J. Deary (Ian J.); G.V. Dedoussis (George); C.M. van Duijn (Cornelia); K. Hagen (Knut); B. Franke (Barbara); L. Franke (Lude); P. Gasparini (Paolo); P.V. Gejman (Pablo); C. Gieger (Christian); H.J. Grabe (Hans Jörgen); J. Gratten (Jacob); P.J.F. Groenen (Patrick); V. Gudnason (Vilmundur); P. van der Harst (Pim); C. Hayward (Caroline); D.A. Hinds (David A.); W. Hoffmann (Wolfgang); E. Hypponen (Elina); W.G. Iacono (William); B. Jacobsson (Bo); M.-R. Jarvelin (Marjo-Riitta); K.-H. JöCkel (Karl-Heinz); J. Kaprio (Jaakko); S.L.R. Kardia (Sharon); T. Lehtimäki (Terho); Lehrer, S.F. (Steven F.); P.K. Magnusson (Patrik); N.G. Martin (Nicholas); M. McGue (Matt); A. Metspalu (Andres); N. Pendleton (Neil); B.W.J.H. Penninx (Brenda); M. Perola (Markus); N. Pirastu (Nicola); M. Pirastu (Mario); O. Polasek (Ozren); D. Posthuma (Danielle); C. Power (Christopher); M.A. Province (Mike); N.J. Samani (Nilesh); Schlessinger, D. (David); R. Schmidt (Reinhold); T.I.A. Sørensen (Thorkild); T.D. Spector (Timothy); J-A. Zwart (John-Anker); U. Thorsteinsdottir (Unnur); A.R. Thurik (Roy); Timpson, N.J. (Nicholas J.); H.W. Tiemeier (Henning); J.Y. Tung (Joyce Y.); A.G. Uitterlinden (André); Vitart, V. (Veronique); P. Vollenweider (Peter); D.R. Weir (David); J.F. Wilson (James F.); A.F. Wright (Alan); Conley, D.C. (Dalton C.); R.F. Krueger; G.D. Smith; Hofman, A. (Albert); D. Laibson (David); S.E. Medland (Sarah Elizabeth); M.N. Meyer (Michelle N.); J. Yang (Joanna); M. Johannesson (Magnus); P.M. Visscher (Peter); T. Esko (Tõnu); Ph.D. Koellinger (Philipp); D. Cesarini (David); D.J. Benjamin (Daniel J.)

2016-01-01

textabstractEducational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that

Genome-wide identification of structural variants in genes encoding drug targets

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Dahmcke, Christina Mackeprang

2012-01-01

The objective of the present study was to identify structural variants of drug target-encoding genes on a genome-wide scale. We also aimed at identifying drugs that are potentially amenable for individualization of treatments based on knowledge about structural variation in the genes encoding...

Genome-wide association study identifies 74 loci associated with educational attainment

NARCIS (Netherlands)

Okbay, A.; Beauchamp, J.; Fontana, M.A.; Lee, J.J.; Pers, T.H.; Rietveld, C.A.; Turley, P.; Chen, G.B.; Emilsson, V.; Meddens, S.F.W.; de Vlaming, R.; Abdellaoui, A.; Peyrot, W.; Vinkhuyzen, A.A.E.; Hottenga, J.J.; Willemsen, G.; Boomsma, D.I.; Penninx, B.W.J.H.; Laibson, D.; Medland, S.E.; Meyer, M.N.; Yang, J.; Johannesson, M.; Visscher, P.M.; Esko, T.; Koellinger, P.D.; Cesarini, D.; Benjamin, D.J.

2016-01-01

Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our

Genome-wide association study identifies 74 loci associated with educational attainment

NARCIS (Netherlands)

Okbay, Aysu; Beauchamp, Jonathan P.; Fontana, Mark Alan; Lee, James J.; Pers, Tune H.; Rietveld, Cornelius A.; Turley, Patrick; Chen, Guo-Bo; Emilsson, Valur; Meddens, S. Fleur W.; Oskarsson, Sven; Pickrell, Joseph K.; Thom, Kevin; Timshel, Pascal; de Vlaming, Ronald; Abdellaoui, Abdel; Ahluwalia, Tarunveer S.; Bacelis, Jonas; Baumbach, Clemens; Bjornsdottir, Gyda; Brandsma, Johannes H.; Concas, Maria Pina; Derringer, Jaime; Furlotte, Nicholas A.; Galesloot, Tessel E.; Girotto, Giorgia; Gupta, Richa; Hall, Leanne M.; Harris, Sarah E.; Hofer, Edith; Horikoshi, Momoko; Huffman, Jennifer E.; Kaasik, Kadri; Kalafati, Ioanna P.; Karlsson, Robert; Kong, Augustine; Lahti, Jari; van der Lee, Sven J.; de Leeuw, Christiaan; Lind, Penelope A.; Lindgren, Karl-Oskar; Liu, Tian; van der Most, Peter J.; Verweij, Niek; Alizadeh, Behrooz Z.; Vonk, Judith M.; Bultmann, Ute; Franke, Lude; van der Harst, Pim; Penninx, Brenda W. J. H.

2016-01-01

Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals(1). Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends

Within-culture variations of uniqueness: towards an integrative approach based on social status, gender, life contexts, and interpersonal comparison.

Science.gov (United States)

Causse, Elsa; Félonneau, Marie-Line

2014-01-01

Research on uniqueness is widely focused on cross-cultural comparisons and tends to postulate a certain form of within-culture homogeneity. Taking the opposite course of this classic posture, we aimed at testing an integrative approach enabling the study of within-culture variations of uniqueness. This approach considered different sources of variation: social status, gender, life contexts, and interpersonal comparison. Four hundred seventy-nine participants completed a measure based on descriptions of "self" and "other." Results showed important variations of uniqueness. An interaction between social status and life contexts revealed the expression of uniqueness in the low-status group. This study highlights the complexity of uniqueness that appears to be related to both cultural ideology and social hierarchy.

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.

Characterization of motor units in behaving adult mice shows a wide primary range.

Science.gov (United States)

Ritter, Laura K; Tresch, Matthew C; Heckman, C J; Manuel, Marin; Tysseling, Vicki M

2014-08-01

The mouse is essential for genetic studies of motor function in both normal and pathological states. Thus it is important to consider whether the structure of motor output from the mouse is in fact analogous to that recorded in other animals. There is a striking difference in the basic electrical properties of mouse motoneurons compared with those in rats, cats, and humans. The firing evoked by injected currents produces a unique frequency-current (F-I) function that emphasizes recruitment of motor units at their maximum force. These F-I functions, however, were measured in anesthetized preparations that lacked two key components of normal synaptic input: high levels of synaptic noise and neuromodulatory inputs. Recent studies suggest that the alterations in the F-I function due to these two components are essential for recreating firing behavior of motor units in human subjects. In this study we provide the first data on firing patterns of motor units in the awake mouse, focusing on steady output in quiet stance. The resulting firing patterns did not match the predictions from the mouse F-I behaviors but instead revealed rate modulation across a remarkably wide range (10-60 Hz). The low end of the firing range may be due to changes in the F-I relation induced by synaptic noise and neuromodulatory inputs. The high end of the range may indicate that, unlike other species, quiet standing in the mouse involves recruitment of relatively fast-twitch motor units. Copyright © 2014 the American Physiological Society.

Genetic variation shapes protein networks mainly through non-transcriptional mechanisms.

Directory of Open Access Journals (Sweden)

Eric J Foss

2011-09-01

Full Text Available Networks of co-regulated transcripts in genetically diverse populations have been studied extensively, but little is known about the degree to which these networks cause similar co-variation at the protein level. We quantified 354 proteins in a genetically diverse population of yeast segregants, which allowed for the first time construction of a coherent protein co-variation matrix. We identified tightly co-regulated groups of 36 and 93 proteins that were made up predominantly of genes involved in ribosome biogenesis and amino acid metabolism, respectively. Even though the ribosomal genes were tightly co-regulated at both the protein and transcript levels, genetic regulation of proteins was entirely distinct from that of transcripts, and almost no genes in this network showed a significant correlation between protein and transcript levels. This result calls into question the widely held belief that in yeast, as opposed to higher eukaryotes, ribosomal protein levels are regulated primarily by regulating transcript levels. Furthermore, although genetic regulation of the amino acid network was more similar for proteins and transcripts, regression analysis demonstrated that even here, proteins vary predominantly as a result of non-transcriptional variation. We also found that cis regulation, which is common in the transcriptome, is rare at the level of the proteome. We conclude that most inter-individual variation in levels of these particular high abundance proteins in this genetically diverse population is not caused by variation of their underlying transcripts.

The variational nodal method: some history and recent activity

International Nuclear Information System (INIS)

Lewis, E.E.; Smith, M.A.; Palmiotti, G.

2005-01-01

The variational nodal method combines spherical harmonics expansions in angle with hybrid finite element techniques in space to obtain multigroup transport response matrix algorithms applicable to a wide variety of reactor physics problems. This survey briefly recounts the method's history and reviews its capabilities. Two methods for obtaining discretized equations in the form of response matrices are compared. The first is that contained the widely used VARIANT code, while the second incorporates more recently developed integral transport techniques into the variational nodal framework. The two approaches are combined with a finite sub-element formulation to treat heterogeneous nodes. Results are presented for application to a deep penetration problem and to an OECD benchmark consisting of LWR Mox fuel assemblies. Ongoing work is discussed. (authors)

Structural genomic variation in ischemic stroke

Science.gov (United States)

Matarin, Mar; Simon-Sanchez, Javier; Fung, Hon-Chung; Scholz, Sonja; Gibbs, J. Raphael; Hernandez, Dena G.; Crews, Cynthia; Britton, Angela; Wavrant De Vrieze, Fabienne; Brott, Thomas G.; Brown, Robert D.; Worrall, Bradford B.; Silliman, Scott; Case, L. Douglas; Hardy, John A.; Rich, Stephen S.; Meschia, James F.; Singleton, Andrew B.

2008-01-01

Technological advances in molecular genetics allow rapid and sensitive identification of genomic copy number variants (CNVs). This, in turn, has sparked interest in the function such variation may play in disease. While a role for copy number mutations as a cause of Mendelian disorders is well established, it is unclear whether CNVs may affect risk for common complex disorders. We sought to investigate whether CNVs may modulate risk for ischemic stroke (IS) and to provide a catalog of CNVs in patients with this disorder by analyzing copy number metrics produced as a part of our previous genome-wide single-nucleotide polymorphism (SNP)-based association study of ischemic stroke in a North American white population. We examined CNVs in 263 patients with ischemic stroke (IS). Each identified CNV was compared with changes identified in 275 neurologically normal controls. Our analysis identified 247 CNVs, corresponding to 187 insertions (76%; 135 heterozygous; 25 homozygous duplications or triplications; 2 heterosomic) and 60 deletions (24%; 40 heterozygous deletions;3 homozygous deletions; 14 heterosomic deletions). Most alterations (81%) were the same as, or overlapped with, previously reported CNVs. We report here the first genome-wide analysis of CNVs in IS patients. In summary, our study did not detect any common genomic structural variation unequivocally linked to IS, although we cannot exclude that smaller CNVs or CNVs in genomic regions poorly covered by this methodology may confer risk for IS. The application of genome-wide SNP arrays now facilitates the evaluation of structural changes through the entire genome as part of a genome-wide genetic association study. PMID:18288507

Genome-wide approaches towards identification of susceptibility genes in complex diseases

NARCIS (Netherlands)

Franke, L.H.

2008-01-01

Throughout the human genome millions of places exist where humans differ gentically. The aim of this PhD thesis was to systematically assess this genetic variation and its biological consequences in a genome-wide way, through the utilization of DNA oligonucleotide arrays that assess hundres of

Genome-wide association analysis of symbiotic nitrogen fixation in common bean

Science.gov (United States)

A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean diversity panel (ADP) comprised of 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in...

A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

NARCIS (Netherlands)

Brown, William R A; Liti, Gianni; Rosa, Carlos; James, Steve; Roberts, Ian; Robert, Vincent; Jolly, Neil; Tang, Wen; Baumann, Peter; Green, Carter; Schlegel, Kristina; Young, Jonathan; Hirchaud, Fabienne; Leek, Spencer; Thomas, Geraint; Blomberg, Anders; Warringer, Jonas

2011-01-01

The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe.

Synthesis of styrene/isoprene/butadiene integrated rubber with wide glass transition temperature by reactive extrusion

Science.gov (United States)

Huang, Tianhua; Zheng, Anna; Zhan, Pengfei; Shi, Han; Li, Xiang; Guan, Yong; Wei, Dafu

2018-05-01

In this work, styrene/isoprene/butadiene integrated rubber (SIBR) was synthesized with n-butyllithium as the initiator and tetrahydrofuran as structure modifier in a co-rotating intermeshing twin-screw extruder. The content of diene in these terpolymers reached a surprising 70 wt% by feeding the monomers in two different sites of the twin-screw extruder. 1H-NMR, GPC and TEM results showed that the molecular structures of terpolymers changed with the variation of feeding site. Dynamic mechanical analysis of the vulcanized SIBR showed that the terpolymer had a wide glass transition region, which assured an excellent combination of high antiskid properties and low rolling resistance. Different from traditional solution polymerization, the present work provides a green approach to prepare the SIBR via bulk polymerization without solvent.

Genome-Wide Association Study on Male Genital Shape and Size in Drosophila melanogaster.

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Baku Takahara

Full Text Available Male genital morphology of animals with internal fertilization and promiscuous mating systems have been one of the most diverse and rapidly evolving morphological traits. The male genital morphology in general is known to have low phenotypic and genetic variations, but the genetic basis of the male genital variation remains unclear. Drosophila melanogaster and its closely related species are morphologically very similar, but the shapes of the posterior lobe, a cuticular projection on the male genital arch are distinct from each other, representing a model system for studying the genetic basis of male genital morphology. In this study, we used highly inbred whole genome sequenced strains of D. melanogaster to perform genome wide association analysis on posterior lobe morphology. We quantified the outline shape of posterior lobes with Fourier coefficients obtained from elliptic Fourier analysis and performed principal component analysis, and posterior lobe size. The first and second principal components (PC1 and PC2 explained approximately 88% of the total variation of the posterior lobe shape. We then examined the association between the principal component scores and posterior lobe size and 1902142 single nucleotide polymorphisms (SNPs. As a result, we obtained 15, 14 and 15 SNPs for PC1, PC2 and posterior lobe size with P-values smaller than 10(-5. Based on the location of the SNPs, 13, 13 and six protein coding genes were identified as potential candidates for PC1, PC2 and posterior lobe size, respectively. In addition to the previous findings showing that the intraspecific posterior shape variation are regulated by multiple QTL with strong effects, the present study suggests that the intraspecific variation may be under polygenic regulation with a number of loci with small effects. Further studies are required for investigating whether these candidate genes are responsible for the intraspecific posterior lobe shape variation.

Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

DEFF Research Database (Denmark)

Postmus, Iris; Warren, Helen R; Trompet, Stella

2016-01-01

BACKGROUND: In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation. METHODS AND RESULTS: We performed...... a meta-analysis of genome-wide association studies (GWAS) to identify variants with an effect on statin-induced high density lipoprotein cholesterol (HDL-C) changes. The 123 most promising signals with p

Spatial and Decadal Variations in Potential Evapotranspiration of China Based on Reanalysis Datasets during 1982–2010

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Yunjun Yao

2014-10-01

Full Text Available Potential evapotranspiration (PET is an important indicator of atmospheric evaporation demand and has been widely used to characterize hydrological change. However, sparse observations of pan evaporation (EP prohibit the accurate characterization of the spatial and temporal patterns of PET over large spatial scales. In this study, we have estimated PET of China using the Penman-Monteith (PM method driven by gridded reanalysis datasets to analyze the spatial and decadal variations of PET in China during 1982–2010. The results show that the estimated PET has decreased on average by 3.3 mm per year (p < 0.05 over China during 1982–1993, while PET began to increase since 1994 by 3.4 mm per year (p < 0.05. The spatial pattern of the linear trend in PET of China illustrates that a widely significant increasing trend in PET appears during 1982–2010 in Northwest China, Central China, Northeast China and South China while there are no obvious variations of PET in other regions. Our findings illustrate that incident solar radiation (Rs is the largest contributor to the variation of PET in China, followed by vapor pressure deficit (VPD, air temperature (Tair and wind speed (WS. However, WS is the primary factor controlling inter-annual variation of PET over Northwest China.

Genetic variation of temperature-regulated curd induction in cauliflower: elucidation of floral transition by genome-wide association mapping and gene expression analysis

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Matschegewski, Claudia; Zetzsche, Holger; Hasan, Yaser; Leibeguth, Lena; Briggs, William; Ordon, Frank; Uptmoor, Ralf

2015-01-01

Cauliflower (Brassica oleracea var. botrytis) is a vernalization-responsive crop. High ambient temperatures delay harvest time. The elucidation of the genetic regulation of floral transition is highly interesting for a precise harvest scheduling and to ensure stable market supply. This study aims at genetic dissection of temperature-dependent curd induction in cauliflower by genome-wide association studies and gene expression analysis. To assess temperature-dependent curd induction, two greenhouse trials under distinct temperature regimes were conducted on a diversity panel consisting of 111 cauliflower commercial parent lines, genotyped with 14,385 SNPs. Broad phenotypic variation and high heritability (0.93) were observed for temperature-related curd induction within the cauliflower population. GWA mapping identified a total of 18 QTL localized on chromosomes O1, O2, O3, O4, O6, O8, and O9 for curding time under two distinct temperature regimes. Among those, several QTL are localized within regions of promising candidate flowering genes. Inferring population structure and genetic relatedness among the diversity set assigned three main genetic clusters. Linkage disequilibrium (LD) patterns estimated global LD extent of r2 = 0.06 and a maximum physical distance of 400 kb for genetic linkage. Transcriptional profiling of flowering genes FLOWERING LOCUS C (BoFLC) and VERNALIZATION 2 (BoVRN2) was performed, showing increased expression levels of BoVRN2 in genotypes with faster curding. However, functional relevance of BoVRN2 and BoFLC2 could not consistently be supported, which probably suggests to act facultative and/or might evidence for BoVRN2/BoFLC-independent mechanisms in temperature-regulated floral transition in cauliflower. Genetic insights in temperature-regulated curd induction can underpin genetically informed phenology models and benefit molecular breeding strategies toward the development of thermo-tolerant cultivars. PMID:26442034

[Variations and simulation of stable isotopes in precipitation in the Heihe River basin].

Science.gov (United States)

Wu, Jin-Kui; Yang, Qi-Yue; Ding, Yong-Jian; Ye, Bai-Sheng; Zhang, Ming-Quan

2011-07-01

To study the variations of deltaD and delta18O in precipitation, 301 samples were sampled during 2002-2004 in 6 sites in the Heihe River basin, Northwestern China. The deltaD and delta18O values ranged from 59 per thousand to -254 per thousand and 6.5 per thousand to -33.4 per thousand, respectively. This wide range indicated that stable isotopes in precipitation were controlled by different condensation mechanisms as a function of air temperature and varying sources of moisture. delta18O in precipitation had a close positive relationship with the air temperature, i. e., a clear temperature effect existed in this area. At a monthly scale, no precipitation effect existed. On the other hand, a weak precipitation effect still accrued at precipitation events scale. The spatial variation of delta18O showed that the weighted average delta18O values decreased with the increasing altitude of sampling sites at a gradient of -0. 47 per thousand/100m. A regional Meteoric Water Line, deltaD = 7.82 delta18O + 7.63, was nearly identical to the Meteoric Water Line in the Northern China. The results of backward trajectory of each precipitation day at Xishui showed that the moisture of the precipitation in cold season (October to March) mainly originated from the west while the moisture source was more complicated in warm season (April to September). The simulation of seasonal delta18O variation showed that the stable isotope composition of precipitation tended to a clear sine-wave seasonal variation.

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

Morphological Variation in Anuran Limbs: Constraints and Novelties.

Science.gov (United States)

Fabrezi, Marissa; Goldberg, Javier; Chuliver Pereyra, Mariana

2017-09-01

Anurans have three primary types of locomotion: walking, jumping, and swimming. Additionally, they may dig, climb, grasp, etc. All adult anurans have four limbs, with four fingers on the hands and five toes on the feet. We summarized and updated knowledge on the interspecific variation within anuran limbs, then discuss how developmental constraints (e.g., in size) and novelties may have influenced anuran diversification through the locomotion. We analyze morphological variation from limb bud stages up to the final limb form resulting from certain skeletal organization and growth. We find limited morphometric variations in the skeleton of different developmental modules (i.e., skull, trunk, urostyle, limbs) indicate that the anuran body shape is largely constrained. We identify specializations of the stylopodium, zeugopodium, and proximal carpals/tarsals that have evolved to facilitiate saltatorial locomotion. We show that the anuran prepollex and prehallux are not vestigial digits and that they have come to serve specialized function. Medial rotation of the manus in anurans appears to have evolved to help distribute the force of impact upon landing at the end of a jump. Additional skeletal elements in anuran limbs are intercalary elements and sesamoids. The intercalary elements appear within neobatrachians and are integrated with digital pads in lineages capable of locomotion on smooth vertical surfaces. They have allowed arboreal anurans to occupy a wide range of arboreal habitats. © 2017 Wiley Periodicals, Inc.

Four variations of the Mondini inner ear malformations as seen in microdissections.

Science.gov (United States)

Johnsson, L G; Hawkins, J E; Rouse, R C; Kingsley, T C

1984-01-01

Four variations and degrees of severity of the Mondini malformation were found in the temporal bones from two neonates, one with congenital heart disease and the other with trisomy D, and from one teenager with leukemia: 1) short cochlea and normal vestibular organs; 2) short cochlea and persistent horizontal canal anlage; 3) markedly shortened cochlea with no modiolus, wide internal auditory meatus, and persistent horizontal canal anlage; 4) same as variation 3, but with persistent anlagen in all semicircular canals. Variations 3 and 4 were from the case of trisomy D, in which the left cochlea had a normal hair cell population but few nerve fibers, and the intraganglionic spiral bundle was displaced from Rosenthal's canal to the osseous spiral lamina. The right ear had no cochlear nerve fibers; the organ of Corti was present, but hair cells were unusually small. In the case of trisomy D, both ears showed subtotal loss of vestibular nerve fibers. Although the rudimentary cristae of the right ear had numerous hair cells, the macular hair cells were fewer and malformed. No hydrops was present.

Genome-wide association study identifies chromosome 10q24.32 variants associated with arsenic metabolism and toxicity phenotypes in Bangladesh.

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Brandon L Pierce

Full Text Available Arsenic contamination of drinking water is a major public health issue in many countries, increasing risk for a wide array of diseases, including cancer. There is inter-individual variation in arsenic metabolism efficiency and susceptibility to arsenic toxicity; however, the basis of this variation is not well understood. Here, we have performed the first genome-wide association study (GWAS of arsenic-related metabolism and toxicity phenotypes to improve our understanding of the mechanisms by which arsenic affects health. Using data on urinary arsenic metabolite concentrations and approximately 300,000 genome-wide single nucleotide polymorphisms (SNPs for 1,313 arsenic-exposed Bangladeshi individuals, we identified genome-wide significant association signals (P<5×10(-8 for percentages of both monomethylarsonic acid (MMA and dimethylarsinic acid (DMA near the AS3MT gene (arsenite methyltransferase; 10q24.32, with five genetic variants showing independent associations. In a follow-up analysis of 1,085 individuals with arsenic-induced premalignant skin lesions (the classical sign of arsenic toxicity and 1,794 controls, we show that one of these five variants (rs9527 is also associated with skin lesion risk (P = 0.0005. Using a subset of individuals with prospectively measured arsenic (n = 769, we show that rs9527 interacts with arsenic to influence incident skin lesion risk (P = 0.01. Expression quantitative trait locus (eQTL analyses of genome-wide expression data from 950 individual's lymphocyte RNA suggest that several of our lead SNPs represent cis-eQTLs for AS3MT (P = 10(-12 and neighboring gene C10orf32 (P = 10(-44, which are involved in C10orf32-AS3MT read-through transcription. This is the largest and most comprehensive genomic investigation of arsenic metabolism and toxicity to date, the only GWAS of any arsenic-related trait, and the first study to implicate 10q24.32 variants in both arsenic metabolism and arsenical

Lateral structural variation within the overlying plate and its correlation to the Tonankai earthquake

Science.gov (United States)

Fujie, G.; Nakanishi, A.; Park, J.; Obana, K.; Kodaira, S.; Kaneda, Y.

2009-12-01

Destructive interplate earthquakes have repeatedly occurred every 100-150 years beneath the Kumano-nada, off the Kii peninsula owing to the subduction of the Philippine Sea plate beneath the southwest Japan arc. The last great interplate earthquakes in this seismogenic subduction zone was the 1944 Tonankai earthquakes, and a number of coseismic slip distribution models derived from seismic and tsunami data show remarkable lateral variations along the trough axis. In 2006 and 2007, we conducted extensive wide-angle seismic refraction and reflection surveys in the entire rupture zone of the 1944 Tonankai earthquake. We designed two along-trough and two across-trench seismic survey lines and deployed a number of OBSs (Ocean Bottom Seismometers) with a spacing of 5km and fired an airgun array with a total volume of 200L at every 0.2km. The quality of the obtained wide-angle seismic record section is substantially good and we observed remarkable regional variation in the amplitude of refraction and reflection phases. For example, in some record sections, we can trace seismic signals up to the offset of more than 100 km, but in other sections, the airgun signals become dim at the offset of less than 30km. Such regional variation in the amplitude indicates the lateral variation of the seismic attenuation structure. For revealing lateral structural variation, we developed seismic structure models by the following approach. First, we applied the first arrival tomography for developing P-wave velocity structure models. Then, we imaged structural boundaries by the reflection traveltime mapping method. Finally, we developed seismic attenuation models by using raypaths and amplitude of first arrivals. Our seismic structure models showed remarkable along-trench structural variation. In the P-wave velocity models, we found a height on the subducting Philippine plate at the eastern end of the Kumano basin (south-east off Shima peninsula). In the western area (i.e. Kumano Basin

Speed, speed variation and crash relationships for urban arterials.

Science.gov (United States)

Wang, Xuesong; Zhou, Qingya; Quddus, Mohammed; Fan, Tianxiang; Fang, Shou'en

2018-04-01

Speed and speed variation are closely associated with traffic safety. There is, however, a dearth of research on this subject for the case of urban arterials in general, and in the context of developing nations. In downtown Shanghai, the traffic conditions in each direction are very different by time of day, and speed characteristics during peak hours are also greatly different from those during off-peak hours. Considering that traffic demand changes with time and in different directions, arterials in this study were divided into one-way segments by the direction of flow, and time of day was differentiated and controlled for. In terms of data collection, traditional fixed-based methods have been widely used in previous studies, but they fail to capture the spatio-temporal distributions of speed along a road. A new approach is introduced to estimate speed variation by integrating spatio-temporal speed fluctuation of a single vehicle with speed differences between vehicles using taxi-based high frequency GPS data. With this approach, this paper aims to comprehensively establish a relationship between mean speed, speed variation and traffic crashes for the purpose of formulating effective speed management measures, specifically using an urban dataset. From a total of 234 one-way road segments from eight arterials in Shanghai, mean speed, speed variation, geometric design features, traffic volume, and crash data were collected. Because the safety effects of mean speed and speed variation may vary at different segment lengths, arterials with similar signal spacing density were grouped together. To account for potential correlations among these segments, a hierarchical Poisson log-normal model with random effects was developed. Results show that a 1% increase in mean speed on urban arterials was associated with a 0.7% increase in total crashes, and larger speed variation was also associated with increased crash frequency. Copyright © 2018 Elsevier Ltd. All rights

Maintenance of phenotypic variation: repeatibility, heritability, and size-dependent processes in a wild brook trout population

Science.gov (United States)

Benjamin H. Letcher; Jason A Coombs; Keith H. Nislow

2011-01-01

Phenotypic variation in body size can result from within-cohort variation in birth dates, among-individual growth variation and size-selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream-dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple...

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

Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda

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Andrea Gloria-Soria

2016-06-01

Full Text Available The tsetse fly Glossina fuscipes fuscipes (Gff is the insect vector of the two forms of Human African Trypanosomiasis (HAT that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r2max/2 between 1359 and 2429 bp. The overall LD estimated for the species reaches r2max/2 at 708 bp, an order of magnitude slower than in Drosophila. Using 53 infected (Trypanosoma spp. and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis.

Detection of somaclonal variation in micropropagated Hibiscus ...

African Journals Online (AJOL)

The main objective of micropropagation is to produce clones i.e. plants which are phenotypically and genetically identical to the mother plants. The culture of organized meristems usually guarantees the production of true-to-type plants but variations in the progenies have been widely reported. Hibiscus sabdariffa L. plants ...

Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.

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Angelo Scuteri

2007-07-01

Full Text Available The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 x10(-7, hip circumference (p = 3.4 x 10(-8, and weight (p = 9.1 x 10(-7. In Sardinia, homozygotes for the rare "G" allele of this SNP (minor allele frequency = 0.46 were 1.3 BMI units heavier than homozygotes for the common "A" allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 x 10(-6. Homozygotes for the rare "A" allele of this SNP (minor allele frequency = 0.12 were 1.8 BMI units heavier than homozygotes for the common "G" allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496 and in Hispanic Americans (N = 839, we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001, weight (p = 0.001, and hip circumference (p = 0.0005. We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare "A" allele were, on average, 1.0-3.0 BMI units heavier than homozygotes for the more common "G" allele. In summary, we have completed a whole genome-association scan for

Modelling and validation of a simple and compact wide upper stop band ultra-wideband bandpass filter

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Somdotta Roy Choudhury

2014-09-01

Full Text Available A compact ultra-wideband (UWB bandpass filter (BPF is proposed based on end coupled microstrip transmission line, defected ground structure and defected microstrip structure. The experimental filter shows a fractional bandwidth of 110% at a centre frequency, with two observable transmission zeros (attenuation poles at 2.1 and 11.7 GHz. Measured results exhibit an UWB passband from 3.02 to 10.6 GHz with mid-band insertion loss of 1.8 dB and group delay variation <0.45 ns. The BPF achieves a wide stopband with < −18 dB attenuation up to 20 GHz.

Reference free phasing and representation of complex variation

DEFF Research Database (Denmark)

Jensen, Jacob Malte

2017-01-01

High throughput sequencing has revolutionized our ability to interrogate genomes and entire human genomes are sequenced daily across the world. Mapping of short reads to a reference genome has enhanced our ability to detect genetic variation and is currently the most widely used technology....... Therefore, new methods for detecting variation that reduce reference bias are needed including ways of representing genomes that account for the variability within and between populations. The major histocompatibility complex (MHC) region is one of the most diverse and complex regions of the human genome...... to detect and call variation in humans. However, it has become evident that mapping of short reads to a single reference genome is subject to ascertainment bias (reference bias). This bias is especially pronounced in complex regions of the genome and particularly hampers detection of structural variation...

CoNVaQ: a web tool for copy number variation-based association studies

DEFF Research Database (Denmark)

Larsen, Simon Jonas; do Canto, Luisa Matos; Rogatto, Silvia Regina

2018-01-01

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to diseas...

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

DEFF Research Database (Denmark)

Randall, Joshua C; Winkler, Thomas W; Kutalik, Zoltán

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133...

Genome-Wide Association Study of Serum Selenium Concentrations

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Ulrike Peters

2013-05-01

Full Text Available Selenium is an essential trace element and circulating selenium concentrations have been associated with a wide range of diseases. Candidate gene studies suggest that circulating selenium concentrations may be impacted by genetic variation; however, no study has comprehensively investigated this hypothesis. Therefore, we conducted a two-stage genome-wide association study to identify genetic variants associated with serum selenium concentrations in 1203 European descents from two cohorts: the Prostate, Lung, Colorectal, and Ovarian (PLCO Cancer Screening and the Women’s Health Initiative (WHI. We tested association between 2,474,333 single nucleotide polymorphisms (SNPs and serum selenium concentrations using linear regression models. In the first stage (PLCO 41 SNPs clustered in 15 regions had p < 1 × 10−5. None of these 41 SNPs reached the significant threshold (p = 0.05/15 regions = 0.003 in the second stage (WHI. Three SNPs had p < 0.05 in the second stage (rs1395479 and rs1506807 in 4q34.3/AGA-NEIL3; and rs891684 in 17q24.3/SLC39A11 and had p between 2.62 × 10−7 and 4.04 × 10−7 in the combined analysis (PLCO + WHI. Additional studies are needed to replicate these findings. Identification of genetic variation that impacts selenium concentrations may contribute to a better understanding of which genes regulate circulating selenium concentrations.

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits

NARCIS (Netherlands)

Randall, Joshua C.; Winkler, Thomas W.; Kutalik, Zoltán; Berndt, Sonja I.; Jackson, Anne U.; Monda, Keri L.; Kilpeläinen, Tuomas O.; Esko, Tõnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Grönberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Asa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; van der Klauw, Melanie M.; van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindström, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; Krjutå Kov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Njølstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David; Ingelsson, Erik; Kaplan, Robert; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Abecasis, Gonçalo R.; McCarthy, Mark I.; Hirschhorn, Joel N.; Qi, Lu; Loos, Ruth J. F.; Lindgren, Cecilia M.; North, Kari E.; Heid, Iris M.

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

NARCIS (Netherlands)

Randall, J.C.; Winkler, T.W.; Kutalik, Z.; Berndt, S.I.; Jackson, A.U.; Monda, K.L.; Kilpelainen, T.O.; Esko, T.; Magi, R.; Li, S.; Workalemahu, T.; Feitosa, M.F.; Croteau-Chonka, D.C.; Day, F.R.; Fall, T.; Ferreira, T.; Gustafsson, S.; Locke, A.E.; Mathieson, I.; Scherag, A.; Vedantam, S.; Wood, A.R.; Liang, L.; Steinthorsdottir, V.; Thorleifsson, G.; Dermitzakis, E.T.; Dimas, A.S.; Karpe, F.; Min, J.L.; Nicholson, G.; Clegg, D.J.; Person, T.; Krohn, J.P.; Bauer, S.; Buechler, C.; Eisinger, K.; Bonnefond, A.; Froguel, P.; Hottenga, J.J.; Prokopenko, I.; Waite, L.L.; Harris, T.B.; Smith, A.V.; Shuldiner, A.R.; McArdle, W.L.; Caulfield, M.J.; Munroe, P.B.; Gronberg, H.; Chen, Y.D.; Li, G.; Beckmann, J.S.; Johnson, T.; Thorsteinsdottir, U.; Teder-Laving, M.; Khaw, K.T.; Wareham, N.J.; Zhao, J.H.; Amin, N.; Oostra, B.A.; Kraja, A.T.; Province, M.A.; Cupples, L.A.; Heard-Costa, N.L.; Kaprio, J.; Ripatti, S.; Surakka, I.; Collins, F.S.; Saramies, J.; Tuomilehto, J.; Jula, A.; Salomaa, V.; Erdmann, J.; Hengstenberg, C.; Loley, C.; Schunkert, H.; Lamina, C.; Wichmann, H.E.; Albrecht, E.; Gieger, C.; Hicks, A.A.; Johansson, A; Pramstaller, P.P.; Kathiresan, S.; Speliotes, E.K.; Penninx, B.; Hartikainen, A.L.; Jarvelin, M.R.; Gyllensten, U.; Boomsma, D.I.; Campbell, H.; Wilson, J.F.; Chanock, S.J.; Farrall, M.; Goel, A.; Medina-Gomez, C.; Rivadeneira, F.; Estrada, K.; Uitterlinden, A.G.; Heijer, M. den; Kiemeney, L.A.L.M.; et al.,

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits

NARCIS (Netherlands)

Randall, Joshua C; Winkler, Thomas W; Kutalik, Zoltán; Berndt, Sonja I; Jackson, Anne U; Monda, Keri L; Kilpeläinen, Tuomas O; Esko, Tõnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F; Croteau-Chonka, Damien C; Day, Felix R; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T; Dimas, Antigone S; Karpe, Fredrik; Min, Josine L; Nicholson, George; Clegg, Deborah J; Person, Thomas; Krohn, Jon P; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Smith, Albert Vernon; Zhao, Jing Hua; Penninx, Brenda; Nolte, Ilja M; Snieder, Harold; Van der Klauw, Melanie M; Van Vliet-Ostaptchouk, Jana V; Bakker, Stephan J L; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Kumari, Meena

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723

Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.

Science.gov (United States)

Francisco, Marta; Joseph, Bindu; Caligagan, Hart; Li, Baohua; Corwin, Jason A; Lin, Catherine; Kerwin, Rachel E; Burow, Meike; Kliebenstein, Daniel J

2016-01-01

A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

Genome wide association mapping in Arabidopsis thaliana identifies novel genes involved in linking allyl glucosinolate to altered biomass and defense

Directory of Open Access Journals (Sweden)

Marta Francisco

2016-07-01

Full Text Available A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL, may provide direct feedback regulation, linking defense metabolism outputs to the growth and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 µM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana.

Science.gov (United States)

Tabas-Madrid, Daniel; Méndez-Vigo, Belén; Arteaga, Noelia; Marcer, Arnald; Pascual-Montano, Alberto; Weigel, Detlef; Xavier Picó, F; Alonso-Blanco, Carlos

2018-03-08

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants. © 2018 John Wiley & Sons Ltd.

Variational principles

CERN Document Server

Moiseiwitsch, B L

2004-01-01

This graduate-level text's primary objective is to demonstrate the expression of the equations of the various branches of mathematical physics in the succinct and elegant form of variational principles (and thereby illuminate their interrelationship). Its related intentions are to show how variational principles may be employed to determine the discrete eigenvalues for stationary state problems and to illustrate how to find the values of quantities (such as the phase shifts) that arise in the theory of scattering. Chapter-by-chapter treatment consists of analytical dynamics; optics, wave mecha

Evidence from northwest European bogs shows ‘Little Ice Age’ climatic changes driven by variations in solar activity

NARCIS (Netherlands)

Mauquoy, D; van Geel, B; Blaauw, Maarten; van der Plicht, J

2002-01-01

Fluctuations in Holocene atmospheric radiocarbon concentrations have been shown to be due to variations in solar activity. Analyses of both Be-10 and C-14 nuclides confirm that production-rate changes during the Holocene were largely modulated by solar activity. Analyses of peat samples from two

Genetic variation of piperidine alkaloids in Pinus ponderosa: a common garden study.

Science.gov (United States)

Gerson, Elizabeth A; Kelsey, Rick G; St Clair, J Bradley

2009-02-01

Previous measurements of conifer alkaloids have revealed significant variation attributable to many sources, environmental and genetic. The present study takes a complementary and intensive, common garden approach to examine genetic variation in Pinus ponderosa var. ponderosa alkaloid production. Additionally, this study investigates the potential trade-off between seedling growth and alkaloid production, and associations between topographic/climatic variables and alkaloid production. Piperidine alkaloids were quantified in foliage of 501 nursery seedlings grown from seed sources in west-central Washington, Oregon and California, roughly covering the western half of the native range of ponderosa pine. A nested mixed model was used to test differences among broad-scale regions and among families within regions. Alkaloid concentrations were regressed on seedling growth measurements to test metabolite allocation theory. Likewise, climate characteristics at the seed sources were also considered as explanatory variables. Quantitative variation from seedling to seedling was high, and regional variation exceeded variation among families. Regions along the western margin of the species range exhibited the highest alkaloid concentrations, while those further east had relatively low alkaloid levels. Qualitative variation in alkaloid profiles was low. All measures of seedling growth related negatively to alkaloid concentrations on a natural log scale; however, coefficients of determination were low. At best, annual height increment explained 19.4 % of the variation in ln(total alkaloids). Among the climate variables, temperature range showed a negative, linear association that explained 41.8 % of the variation. Given the wide geographic scope of the seed sources and the uniformity of resources in the seedlings' environment, observed differences in alkaloid concentrations are evidence for genetic regulation of alkaloid secondary metabolism in ponderosa pine. The theoretical

Genome-wide association for sensitivity to chronic oxidative stress in Drosophila melanogaster.

Directory of Open Access Journals (Sweden)

Katherine W Jordan

Full Text Available Reactive oxygen species (ROS are a common byproduct of mitochondrial energy metabolism, and can also be induced by exogenous sources, including UV light, radiation, and environmental toxins. ROS generation is essential for maintaining homeostasis by triggering cellular signaling pathways and host defense mechanisms. However, an imbalance of ROS induces oxidative stress and cellular death and is associated with human disease, including age-related locomotor impairment. To identify genes affecting sensitivity and resistance to ROS-induced locomotor decline, we assessed locomotion of aged flies of the sequenced, wild-derived lines from the Drosophila melanogaster Genetics Reference Panel on standard medium and following chronic exposure to medium supplemented with 3 mM menadione sodium bisulfite (MSB. We found substantial genetic variation in sensitivity to oxidative stress with respect to locomotor phenotypes. We performed genome-wide association analyses to identify candidate genes associated with variation in sensitivity to ROS-induced decline in locomotor performance, and confirmed the effects for 13 of 16 mutations tested in these candidate genes. Candidate genes associated with variation in sensitivity to MSB-induced oxidative stress form networks of genes involved in neural development, immunity, and signal transduction. Many of these genes have human orthologs, highlighting the utility of genome-wide association in Drosophila for studying complex human disease.

Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.

Science.gov (United States)

Ji, Yuan; Schaid, Daniel J; Desta, Zeruesenay; Kubo, Michiaki; Batzler, Anthony J; Snyder, Karen; Mushiroda, Taisei; Kamatani, Naoyuki; Ogburn, Evan; Hall-Flavin, Daniel; Flockhart, David; Nakamura, Yusuke; Mrazek, David A; Weinshilboum, Richard M

2014-08-01

Citalopram (CT) and escitalopram (S-CT) are among the most widely prescribed selective serotonin reuptake inhibitors used to treat major depressive disorder (MDD). We applied a genome-wide association study to identify genetic factors that contribute to variation in plasma concentrations of CT or S-CT and their metabolites in MDD patients treated with CT or S-CT. Our genome-wide association study was performed using samples from 435 MDD patients. Linear mixed models were used to account for within-subject correlations of longitudinal measures of plasma drug/metabolite concentrations (4 and 8 weeks after the initiation of drug therapy), and single-nucleotide polymorphisms (SNPs) were modelled as additive allelic effects. Genome-wide significant associations were observed for S-CT concentration with SNPs in or near the CYP2C19 gene on chromosome 10 (rs1074145, P = 4.1 × 10(-9) ) and with S-didesmethylcitalopram concentration for SNPs near the CYP2D6 locus on chromosome 22 (rs1065852, P = 2.0 × 10(-16) ), supporting the important role of these cytochrome P450 (CYP) enzymes in biotransformation of citalopram. After adjustment for the effect of CYP2C19 functional alleles, the analyses also identified novel loci that will require future replication and functional validation. In vitro and in vivo studies have suggested that the biotransformation of CT to monodesmethylcitalopram and didesmethylcitalopram is mediated by CYP isozymes. The results of our genome-wide association study performed in MDD patients treated with CT or S-CT have confirmed those observations but also identified novel genomic loci that might play a role in variation in plasma levels of CT or its metabolites during the treatment of MDD patients with these selective serotonin reuptake inhibitors. © 2014 The British Pharmacological Society.

Population-genetic properties of differentiated copy number variations in cattle.

Science.gov (United States)

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Zhou, Yang; Hay, El Hamidi Abdel; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Liu, George E

2016-03-23

While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.

Is there much variation in variation? Revisiting statistics of small area variation in health services research

Directory of Open Access Journals (Sweden)

Ibáñez Berta

2009-04-01

Full Text Available Abstract Background The importance of Small Area Variation Analysis for policy-making contrasts with the scarcity of work on the validity of the statistics used in these studies. Our study aims at 1 determining whether variation in utilization rates between health areas is higher than would be expected by chance, 2 estimating the statistical power of the variation statistics; and 3 evaluating the ability of different statistics to compare the variability among different procedures regardless of their rates. Methods Parametric bootstrap techniques were used to derive the empirical distribution for each statistic under the hypothesis of homogeneity across areas. Non-parametric procedures were used to analyze the empirical distribution for the observed statistics and compare the results in six situations (low/medium/high utilization rates and low/high variability. A small scale simulation study was conducted to assess the capacity of each statistic to discriminate between different scenarios with different degrees of variation. Results Bootstrap techniques proved to be good at quantifying the difference between the null hypothesis and the variation observed in each situation, and to construct reliable tests and confidence intervals for each of the variation statistics analyzed. Although the good performance of Systematic Component of Variation (SCV, Empirical Bayes (EB statistic shows better behaviour under the null hypothesis, it is able to detect variability if present, it is not influenced by the procedure rate and it is best able to discriminate between different degrees of heterogeneity. Conclusion The EB statistics seems to be a good alternative to more conventional statistics used in small-area variation analysis in health service research because of its robustness.

Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups.

Science.gov (United States)

Lou, Haiyi; Li, Shilin; Jin, Wenfei; Fu, Ruiqing; Lu, Dongsheng; Pan, Xinwei; Zhou, Huaigu; Ping, Yuan; Jin, Li; Xu, Shuhua

2015-04-01

Xinjiang is geographically located in central Asia, and it has played an important historical role in connecting eastern Eurasian (EEA) and western Eurasian (WEA) people. However, human population genomic studies in this region have been largely underrepresented, especially with respect to studies of copy number variations (CNVs). Here we constructed the first CNV map of the three major ethnic minority groups, the Uyghur, Kazakh and Kirgiz, using Affymetrix Genome-Wide Human SNP Array 6.0. We systematically compared the properties of CNVs we identified in the three groups with the data from representatives of EEA and WEA. The analyses indicated a typical genetic admixture pattern in all three groups with ancestries from both EEA and WEA. We also identified several CNV regions showing significant deviation of allele frequency from the expected genome-wide distribution, which might be associated with population-specific phenotypes. Our study provides the first genome-wide perspective on the CNVs of three major Xinjiang ethnic minority groups and has implications for both evolutionary and medical studies.

Accommodating variation: dialects, idiolects, and speech processing.

Science.gov (United States)

Kraljic, Tanya; Brennan, Susan E; Samuel, Arthur G

2008-04-01

Listeners are faced with enormous variation in pronunciation, yet they rarely have difficulty understanding speech. Although much research has been devoted to figuring out how listeners deal with variability, virtually none (outside of sociolinguistics) has focused on the source of the variation itself. The current experiments explore whether different kinds of variation lead to different cognitive and behavioral adjustments. Specifically, we compare adjustments to the same acoustic consequence when it is due to context-independent variation (resulting from articulatory properties unique to a speaker) versus context-conditioned variation (resulting from common articulatory properties of speakers who share a dialect). The contrasting results for these two cases show that the source of a particular acoustic-phonetic variation affects how that variation is handled by the perceptual system. We also show that changes in perceptual representations do not necessarily lead to changes in production.

A Fast Alternating Minimization Algorithm for Nonlocal Vectorial Total Variational Multichannel Image Denoising

Directory of Open Access Journals (Sweden)

Rubing Xi

2014-01-01

Full Text Available The variational models with nonlocal regularization offer superior image restoration quality over traditional method. But the processing speed remains a bottleneck due to the calculation quantity brought by the recent iterative algorithms. In this paper, a fast algorithm is proposed to restore the multichannel image in the presence of additive Gaussian noise by minimizing an energy function consisting of an l2-norm fidelity term and a nonlocal vectorial total variational regularization term. This algorithm is based on the variable splitting and penalty techniques in optimization. Following our previous work on the proof of the existence and the uniqueness of the solution of the model, we establish and prove the convergence properties of this algorithm, which are the finite convergence for some variables and the q-linear convergence for the rest. Experiments show that this model has a fabulous texture-preserving property in restoring color images. Both the theoretical derivation of the computation complexity analysis and the experimental results show that the proposed algorithm performs favorably in comparison to the widely used fixed point algorithm.

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

Science.gov (United States)

Hormozdiari, Fereydoun; Hajirasouliha, Iman; McPherson, Andrew; Eichler, Evan E.; Sahinalp, S. Cenk

Next generation sequencing technologies have been decreasing the costs and increasing the world-wide capacity for sequence production at an unprecedented rate, making the initiation of large scale projects aiming to sequence almost 2000 genomes [1]. Structural variation detection promises to be one of the key diagnostic tools for cancer and other diseases with genomic origin. In this paper, we study the problem of detecting structural variation events in two or more sequenced genomes through high throughput sequencing . We propose to move from the current model of (1) detecting genomic variations in single next generation sequenced (NGS) donor genomes independently, and (2) checking whether two or more donor genomes indeed agree or disagree on the variations (in this paper we name this framework Independent Structural Variation Discovery and Merging - ISV&M), to a new model in which we detect structural variation events among multiple genomes simultaneously.

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

NARCIS (Netherlands)

Scott, Robert A; Scott, Laura J; Mägi, Reedik; Marullo, Letizia; Gaulton, Kyle J; Kaakinen, Marika; Pervjakova, Natalia; Pers, Tune H; Johnson, Andrew D; Eicher, John D; Jackson, Anne U; Ferreira, Teresa; Lee, Yeji; Ma, Clement; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Qi, Lu; Van Zuydam, Natalie R; Mahajan, Anubha; Chen, Han; Almgren, Peter; Voight, Ben F; Grallert, Harald; Müller-Nurasyid, Martina; Ried, Janina S; Rayner, William N; Robertson, Neil; Karssen, Lennart C; van Leeuwen, Elisabeth M; Willems, Sara M; Fuchsberger, Christian; Kwan, Phoenix; Teslovich, Tanya M; Chanda, Pritam; Li, Man; Lu, Yingchang; Dina, Christian; Thuillier, Dorothee; Yengo, Loic; Jiang, Longda; Sparso, Thomas; Kestler, Hans A; Chheda, Himanshu; Eisele, Lewin; Gustafsson, Stefan; Frånberg, Mattias; Strawbridge, Rona J; Benediktsson, Rafn; Hreidarsson, Astradur B; Kong, Augustine; Sigurðsson, Gunnar; Kerrison, Nicola D; Luan, Jian'an; Liang, Liming; Meitinger, Thomas; Roden, Michael; Thorand, Barbara; Esko, Tõnu; Mihailov, Evelin; Fox, Caroline; Liu, Ching-Ti; Rybin, Denis; Isomaa, Bo; Lyssenko, Valeriya; Tuomi, Tiinamaija; Couper, David J; Pankow, James S; Grarup, Niels; Have, Christian T; Jørgensen, Marit E; Jørgensen, Torben; Linneberg, Allan; Cornelis, Marilyn C; van Dam, Rob M; Hunter, David J; Kraft, Peter; Sun, Qi; Edkins, Sarah; Owen, Katharine R; Perry, John Rb; Wood, Andrew R; Zeggini, Eleftheria; Tajes-Fernandes, Juan; Abecasis, Goncalo R; Bonnycastle, Lori L; Chines, Peter S; Stringham, Heather M; Koistinen, Heikki A; Kinnunen, Leena; Sennblad, Bengt; Mühleisen, Thomas W; Nöthen, Markus M; Pechlivanis, Sonali; Baldassarre, Damiano; Gertow, Karl; Humphries, Steve E; Tremoli, Elena; Klopp, Norman; Meyer, Julia; Steinbach, Gerald; Wennauer, Roman; Eriksson, Johan G; Mӓnnistö, Satu; Peltonen, Leena; Tikkanen, Emmi; Charpentier, Guillaume; Eury, Elodie; Lobbens, Stéphane; Gigante, Bruna; Leander, Karin; McLeod, Olga; Bottinger, Erwin P; Gottesman, Omri; Ruderfer, Douglas; Blüher, Matthias; Kovacs, Peter; Tonjes, Anke; Maruthur, Nisa M; Scapoli, Chiara; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; de Faire, Ulf; Hamsten, Anders; Stumvoll, Michael; Deloukas, Panagiotis; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; Ripatti, Samuli; Salomaa, Veikko; Pedersen, Nancy L; Boehm, Bernhard O; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Tuomilehto, Jaakko; Hansen, Torben; Pedersen, Oluf; Barroso, Inês; Lannfelt, Lars; Ingelsson, Erik; Lind, Lars; Lindgren, Cecilia M; Cauchi, Stephane; Froguel, Philippe; Loos, Ruth Jf; Balkau, Beverley; Boeing, Heiner; Franks, Paul W; Gurrea, Aurelio Barricarte; Palli, Domenico; van der Schouw, Yvonne T; Altshuler, David; Groop, Leif C; Langenberg, Claudia; Wareham, Nicholas J; Sijbrands, Eric; van Duijn, Cornelia M; Florez, Jose C; Meigs, James B; Boerwinkle, Eric; Gieger, Christian; Strauch, Konstantin; Metspalu, Andres; Morris, Andrew D; Palmer, Colin Na; Hu, Frank B; Thorsteinsdottir, Unnur; Stefansson, Kari; Dupuis, Josée; Morris, Andrew P; Boehnke, Michael; McCarthy, Mark I; Prokopenko, Inga

2017-01-01

To characterise type 2 diabetes (T2D) associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D cases and 132,532 controls of European ancestry after imputation using the 1000 Genomes multi-ethnic reference panel.

Natural variations in the geomagnetically trapped electron population

Science.gov (United States)

Vampola, A. L.

1972-01-01

Temporal variations in the trapped natural electron flux intensities and energy spectra are discussed and demonstrated using recent satellite data. These data are intended to acquaint the space systems engineer with the types of natural variations that may be encountered during a mission and to augment the models of the electron environment currently being used in space system design and orbit selection. An understanding of the temporal variations which may be encountered should prove helpful. Some of the variations demonstrated here which are not widely known include: (1) addition of very energetic electrons to the outer zone during moderate magnetic storms: (2) addition of energetic electrons to the inner zone during major magnetic storms; (3) inversions in the outer zone electron energy spectrum during the decay phase of a storm injection event and (4) occasional formation of multiple maxima in the flux vs altitude profile of moderately energetic electrons.

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

Science.gov (United States)

Lv, Weihua; Zheng, Xianhu; Kuang, Youyi; Cao, Dingchen; Yan, Yunqin; Sun, Xiaowen

2016-05-05

Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs

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...

Variation morphogeometrics of Africanized honey bees (Apis mellifera in Brazil

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Lorena A. Nunes

2012-09-01

Full Text Available The morphometrics of the honey bee Apis mellifera L., 1758 has been widely studied mainly because this species has great ecological importance, high adaptation capacity, wide distribution and capacity to effectively adapt to different regions. The current study aimed to investigate the morphometric variations of wings and pollen baskets of honey bees Apis mellifera scutellata Lepeletier, 1836 from the five regions in Brazil. We used geometric morphometrics to identify the existence of patterns of variations of shape and size in Africanized honey bees in Brazil 16 years after the classic study with this species, allowing a temporal and spatial comparative analysis using new technological resources to assess morphometrical data. Samples were collected in 14 locations in Brazil, covering the five geographical regions of the country. The shape analysis and multivariate analyses of the wing allowed to observe that there is a geographical pattern among the population of Apis mellifera in Brazil. The geographical variations may be attributed to the large territorial extension of the country in addition to the differences between the bioregions.

Stress Redistribution Explains Anti-correlated Subglacial Pressure Variations

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Pierre-Marie Lefeuvre

2018-01-01

Full Text Available We used a finite element model to interpret anti-correlated pressure variations at the base of a glacier to demonstrate the importance of stress redistribution in the basal ice. We first investigated two pairs of load cells installed 20 m apart at the base of the 210 m thick Engabreen glacier in Northern Norway. The load cell data for July 2003 showed that pressurisation of a subglacial channel located over one load cell pair led to anti-correlation in pressure between the two pairs. To investigate the cause of this anti-correlation, we used a full Stokes 3D model of a 210 m thick and 25–200 m wide glacier with a pressurised subglacial channel represented as a pressure boundary condition. The model reproduced the anti-correlated pressure response at the glacier bed and variations in pressure of the same order of magnitude as the load cell observations. The anti-correlation pattern was shown to depend on the bed/surface slope. On a flat bed with laterally constrained cross-section, the resulting bridging effect diverted some of the normal forces acting on the bed to the sides. The anti-correlated pressure variations were then reproduced at a distance >10–20 m from the channel. In contrast, when the bed was inclined, the channel support of the overlying ice was vertical only, causing a reduction of the normal stress on the bed. With a bed slope of 5 degrees, the anti-correlation occurred within 10 m of the channel. The model thus showed that the effect of stress redistribution can lead to an opposite response in pressure at the same distance from the channel and that anti-correlation in pressure is reproduced without invoking cavity expansion caused by sliding.

Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans.

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Maxime Rotival

2011-12-01

Full Text Available One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies. So far, few cis expression quantitative trait loci (eQTLs have been reliably related to disease susceptibility. Trans-regulating mechanisms may play a more prominent role in disease susceptibility. We analyzed 12,808 genes detected in at least 5% of circulating monocyte samples from a population-based sample of 1,490 European unrelated subjects. We applied a method of extraction of expression patterns-independent component analysis-to identify sets of co-regulated genes. These patterns were then related to 675,350 SNPs to identify major trans-acting regulators. We detected three genomic regions significantly associated with co-regulated gene modules. Association of these loci with multiple expression traits was replicated in Cardiogenics, an independent study in which expression profiles of monocytes were available in 758 subjects. The locus 12q13 (lead SNP rs11171739, previously identified as a type 1 diabetes locus, was associated with a pattern including two cis eQTLs, RPS26 and SUOX, and 5 trans eQTLs, one of which (MADCAM1 is a potential candidate for mediating T1D susceptibility. The locus 12q24 (lead SNP rs653178, which has demonstrated extensive disease pleiotropy, including type 1 diabetes, hypertension, and celiac disease, was associated to a pattern strongly correlating to blood pressure level. The strongest trans eQTL in this pattern was CRIP1, a known marker of cellular proliferation in cancer. The locus 12q15 (lead SNP rs11177644 was associated with a pattern driven by two cis eQTLs, LYZ and YEATS4, and including 34 trans eQTLs, several of them tumor-related genes. This study shows that a method exploiting the structure of co-expressions among genes can help identify genomic regions involved in trans regulation of sets of genes and can provide clues for understanding the

Natural enemies drive geographic variation in plant defenses

DEFF Research Database (Denmark)

Zuest, Tobias; Heichinger, Christian; Grossniklaus, Ueli

2012-01-01

Plants defend themselves against attack by natural enemies, and these defenses vary widely across populations. However, whether communities of natural enemies are a sufficiently potent force to maintain polymorphisms in defensive traits is largely unknown. Here, we exploit the genetic resources...... of Arabidopsis thaliana, coupled with 39 years of field data on aphid abundance, to (i) demonstrate that geographic patterns in a polymorphic defense locus (GS-ELONG) are strongly correlated with changes in the relative abundance of two specialist aphids; and (ii) demonstrate differential selection by the two...... aphids on GS-ELONG, using a multigeneration selection experiment. We thereby show a causal link between variation in abundance of the two specialist aphids and the geographic pattern at GS-ELONG, which highlights the potency of natural enemies as selective forces....

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.

Science.gov (United States)

Glessner, Joseph T; Wang, Kai; Cai, Guiqing; Korvatska, Olena; Kim, Cecilia E; Wood, Shawn; Zhang, Haitao; Estes, Annette; Brune, Camille W; Bradfield, Jonathan P; Imielinski, Marcin; Frackelton, Edward C; Reichert, Jennifer; Crawford, Emily L; Munson, Jeffrey; Sleiman, Patrick M A; Chiavacci, Rosetta; Annaiah, Kiran; Thomas, Kelly; Hou, Cuiping; Glaberson, Wendy; Flory, James; Otieno, Frederick; Garris, Maria; Soorya, Latha; Klei, Lambertus; Piven, Joseph; Meyer, Kacie J; Anagnostou, Evdokia; Sakurai, Takeshi; Game, Rachel M; Rudd, Danielle S; Zurawiecki, Danielle; McDougle, Christopher J; Davis, Lea K; Miller, Judith; Posey, David J; Michaels, Shana; Kolevzon, Alexander; Silverman, Jeremy M; Bernier, Raphael; Levy, Susan E; Schultz, Robert T; Dawson, Geraldine; Owley, Thomas; McMahon, William M; Wassink, Thomas H; Sweeney, John A; Nurnberger, John I; Coon, Hilary; Sutcliffe, James S; Minshew, Nancy J; Grant, Struan F A; Bucan, Maja; Cook, Edwin H; Buxbaum, Joseph D; Devlin, Bernie; Schellenberg, Gerard D; Hakonarson, Hakon

2009-05-28

Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.

Study on the Diurnal Variation of the Plasma Immunoreactive Glucagon

International Nuclear Information System (INIS)

Lee, Hong Kyu; Hong, Kee Suk; Kim, Byoung Kook; Koh, Chang Soon; Chung, June Key; Kim, Eui Chong

1984-01-01

It is well known that glucagon, like insulin, is very important in the moment-to-moment control of the homeostasis of glucose, and of amino acids. Glucagon has been shown to have potent glycogenolytic, gluconeogenic and lipolytic activities. Attention to its role in the pathogenesis of diabetes mellitus and hypoglycemia has been also advanced recently. To evaluate the diurnal variation of plasma glucagon concentration, we measured serum glucose, insulin, and plasma glucagon every 30 minutes or every hour in 7 normal Korean adults. Results were as follows: 1) Although plasma glucagon concentration showed wide individual variations, it had a tendency to decrease after meals. After lunch and dinner, plasma glucagon concentration had gradually declined and reached its nadir at postprandial 2-2.5 hours. The minimal level of plasma glucagon was at 4 A.M. 2) Serum insulin:plasma glucagon ratios were increased promptly after meals. Especially after lunch, its peak was prominent (3.65 ± 1. 95). The minimal level of serum insulin:plasma glucagon ratio appeared at 6 A.M.

Study on the Diurnal Variation of the Plasma Immunoreactive Glucagon

Energy Technology Data Exchange (ETDEWEB)

Lee, Hong Kyu; Hong, Kee Suk; Kim, Byoung Kook; Koh, Chang Soon [Seoul National University College of Medicine, Seoul (Korea, Republic of); Chung, June Key; Kim, Eui Chong [Seoul District Armed Forces General Hospital, Seoul (Korea, Republic of)

1984-03-15

It is well known that glucagon, like insulin, is very important in the moment-to-moment control of the homeostasis of glucose, and of amino acids. Glucagon has been shown to have potent glycogenolytic, gluconeogenic and lipolytic activities. Attention to its role in the pathogenesis of diabetes mellitus and hypoglycemia has been also advanced recently. To evaluate the diurnal variation of plasma glucagon concentration, we measured serum glucose, insulin, and plasma glucagon every 30 minutes or every hour in 7 normal Korean adults. Results were as follows: 1) Although plasma glucagon concentration showed wide individual variations, it had a tendency to decrease after meals. After lunch and dinner, plasma glucagon concentration had gradually declined and reached its nadir at postprandial 2-2.5 hours. The minimal level of plasma glucagon was at 4 A.M. 2) Serum insulin:plasma glucagon ratios were increased promptly after meals. Especially after lunch, its peak was prominent (3.65 +- 1. 95). The minimal level of serum insulin:plasma glucagon ratio appeared at 6 A.M.

Variation in gene expression within clones of the earthworm Dendrobaena octaedra.

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Marina Mustonen

Full Text Available Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.

Integrated resource planning in the power sector and economy-wide changes in environmental emissions

International Nuclear Information System (INIS)

Shrestha, Ram M.; Marpaung, Charles O.P.

2006-01-01

This paper analyzes the roles of key factors (i.e., changes in structure, fuel mix and final demand) on total economy-wide changes in CO 2 , SO 2 and NO x emissions when power sector development follows the integrated resource planning (IRP) approach instead of traditional supply-based electricity planning (TEP). It also considers the rebound effect (RE) of energy efficiency improvements in the demand side and analyzes the sensitivity of the results to variations in the values of the RE. A framework is developed to decompose the total economy-wide change in the emission of a pollutant into four major components, i.e., structural change-, fuel mix- , final demand- and joint-effects. The final demand effect is further decomposed into three categories, i.e., construction of power plants, electricity final demand and final demand related to electricity using equipments. The factor decomposition framework is then applied in the case of the power sector in Indonesia. A key finding in the case of Indonesia is that in the absence of the RE, there would be total economy-wide reductions in CO 2 , SO 2 and NO x emissions of 431, 1.6 and 1.3 million tons respectively during the planning horizon of 2006-2025 under IRP as compared to that under TEP. The decomposition analysis shows that the final demand effect would account for 38% of the total CO 2 emission reduction followed by the structural change effect (35.1%) and fuel mix effect (27.6%) while the joint effect is negligible. The study also shows that economy-wide CO 2 emission reduction due to IRP considering the RE of 45% would be 241 million tons as compared to 333 million tons when the RE is 25%

Integrated resource planning in the power sector and economy-wide changes in environmental emissions

International Nuclear Information System (INIS)

Shrestha, Ram M.; Marpaung, Charles O.P.

2006-01-01

This paper analyzes the roles of key factors (i.e., changes in structure, fuel mix and final demand) on total economy-wide changes in CO 2 , SO 2 and NO x emissions when power sector development follows the integrated resource planning (IRP) approach instead of traditional supply-based electricity planning (TEP). It also considers the rebound effect (RE) of energy efficiency improvements in the demand side and analyzes the sensitivity of the results to variations in the values of the RE. A framework is developed to decompose the total economy-wide change in the emission of a pollutant into four major components, i.e., structural change-, fuel mix- , final demand- and joint-effects. The final demand effect is further decomposed into three categories, i.e., construction of power plants, electricity final demand and final demand related to electricity using equipment. The factor decomposition framework is then applied in the case of the power sector in Indonesia. A key finding in the case of Indonesia is that in the absence of the RE, there would be total economy-wide reductions in CO 2 , SO 2 and NO x emissions of 431, 1.6 and 1.3 million tons respectively during the planning horizon of 2006-2025 under IRP as compared to that under TEP. The decomposition analysis shows that the final demand effect would account for 38% of the total CO 2 emission reduction followed by the structural change effect (35.1%) and fuel mix effect (27.6%) while the joint effect is negligible. The study also shows that economy-wide CO 2 emission reduction due to IRP considering the RE of 45% would be 241 million tons as compared to 333 million tons when the RE is 25%. (Author)

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...

Variations in the small-scale galactic magnetic field and short time-scale intensity variations of extragalactic radio sources

International Nuclear Information System (INIS)

Simonetti, J.H.

1985-01-01

Structure functions of the Faraday rotation measures (RMs) of extragalactic radio sources are used to investigate variations in the interstellar magnetic field on length scales of approx.0.01 to 100 pc. Model structure functions derived assuming a power-law power spectrum of irregularities in n/sub e/B, are compared with those observed. The results indicate an outer angular scale for RM variations of approximately less than or equal to 5 0 and evidence for RM variations on scales as small as 1'. Differences in the variance of n/sub e/B fluctuations for various lines of sight through the Galaxy are found. Comparison of pulsar scintillations in right- and left-circular polarizations yield an upper limit to the variations in n/sub e/ on a length scale of approx.10 11 cm. RMs were determined through high-velocity molecular flows in galactic star-formation regions, with the goal of constraining magnetic fields in and near the flows. RMs of 7 extragalactic sources with a approx.20 arcmin wide area seen through Cep A, fall in two groups separated by approx.150 rad m -2 - large given our knowledge of RM variations on small angular scales and possibly a result of the anisotropy of the high-velocity material

Random Positional Variation Among the Skull, Mandible, and Cervical Spine With Treatment Progression During Head-and-Neck Radiotherapy

International Nuclear Information System (INIS)

Ahn, Peter H.; Ahn, Andrew I.; Lee, C. Joe; Shen Jin; Miller, Ekeni; Lukaj, Alex; Milan, Elissa; Yaparpalvi, Ravindra; Kalnicki, Shalom; Garg, Madhur K.

2009-01-01

Purpose: With 54 o of freedom from the skull to mandible to C7, ensuring adequate immobilization for head-and-neck radiotherapy (RT) is complex. We quantify variations in skull, mandible, and cervical spine movement between RT sessions. Methods and Materials: Twenty-three sequential head-and-neck RT patients underwent serial computed tomography. Patients underwent planned rescanning at 11, 22, and 33 fractions for a total of 93 scans. Coordinates of multiple bony elements of the skull, mandible, and cervical spine were used to calculate rotational and translational changes of bony anatomy compared with the original planning scan. Results: Mean translational and rotational variations on rescanning were negligible, but showed a wide range. Changes in scoliosis and lordosis of the cervical spine between fractions showed similar variability. There was no correlation between positional variation and fraction number and no strong correlation with weight loss or skin separation. Semi-independent rotational and translation movement of the skull in relation to the lower cervical spine was shown. Positioning variability measured by means of vector displacement was largest in the mandible and lower cervical spine. Conclusions: Although only small overall variations in position between head-and-neck RT sessions exist on average, there is significant random variation in patient positioning of the skull, mandible, and cervical spine elements. Such variation is accentuated in the mandible and lower cervical spine. These random semirigid variations in positioning of the skull and spine point to a need for improved immobilization and/or confirmation of patient positioning in RT of the head and neck

Random Positional Variation Among the Skull, Mandible, and Cervical Spine With Treatment Progression During Head-and-Neck Radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Ahn, Peter H. [Department of Radiation Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY (United States)], E-mail: phahn@mdanderson.org; Ahn, Andrew I [Albert Einstein College of Medicine of Yeshiva University, Bronx, NY (United States); Lee, C Joe; Jin, Shen; Miller, Ekeni; Lukaj, Alex; Milan, Elissa; Yaparpalvi, Ravindra; Kalnicki, Shalom; Garg, Madhur K [Department of Radiation Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY (United States)

2009-02-01

Purpose: With 54{sup o} of freedom from the skull to mandible to C7, ensuring adequate immobilization for head-and-neck radiotherapy (RT) is complex. We quantify variations in skull, mandible, and cervical spine movement between RT sessions. Methods and Materials: Twenty-three sequential head-and-neck RT patients underwent serial computed tomography. Patients underwent planned rescanning at 11, 22, and 33 fractions for a total of 93 scans. Coordinates of multiple bony elements of the skull, mandible, and cervical spine were used to calculate rotational and translational changes of bony anatomy compared with the original planning scan. Results: Mean translational and rotational variations on rescanning were negligible, but showed a wide range. Changes in scoliosis and lordosis of the cervical spine between fractions showed similar variability. There was no correlation between positional variation and fraction number and no strong correlation with weight loss or skin separation. Semi-independent rotational and translation movement of the skull in relation to the lower cervical spine was shown. Positioning variability measured by means of vector displacement was largest in the mandible and lower cervical spine. Conclusions: Although only small overall variations in position between head-and-neck RT sessions exist on average, there is significant random variation in patient positioning of the skull, mandible, and cervical spine elements. Such variation is accentuated in the mandible and lower cervical spine. These random semirigid variations in positioning of the skull and spine point to a need for improved immobilization and/or confirmation of patient positioning in RT of the head and neck.

Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia.

Science.gov (United States)

Chávez-Galarza, Julio; Henriques, Dora; Johnston, J Spencer; Carneiro, Miguel; Rufino, José; Patton, John C; Pinto, M Alice

2015-06-01

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity. © 2015 John Wiley & Sons Ltd.

The variational nodal method: history and recent accomplishments

International Nuclear Information System (INIS)

Lewis, E.E.

2004-01-01

The variational nodal method combines spherical harmonics expansions in angle with hybrid finite element techniques is space to obtain multigroup transport response matrix algorithms applicable to both deep penetration and reactor core physics problems. This survey briefly recounts the method's history and reviews its capabilities. The variational basis for the approach is presented and two methods for obtaining discretized equations in the form of response matrices are detailed. The first is that contained the widely used VARIANT code, while the second incorporates newly developed integral transport techniques into the variational nodal framework. The two approaches are combined with a finite sub element formulation to treat heterogeneous nodes. Applications are presented for both a deep penetration problem and to an OECD benchmark consisting of LWR MOX fuel assemblies. Ongoing work is discussed. (Author)

A Reconfigurable Series Resonant DC-DC Converter for Wide-Input and Wide-Output Voltages

DEFF Research Database (Denmark)

Shen, Yanfeng; Wang, Huai; Qin, Zian

2017-01-01

This paper proposes a dual-bridge based LC series resonant dc-dc converter. The input inverter unit incorporates two bridge structures, i.e., a full-bridge inverter and a half-bridge inverter. For the output rectifier, it can be a full-bridge rectifier or an asymmetric half-bridge rectifier....... Different from the conventional resonant converter, a fixed-frequency PWM control is employed which makes the optimization of magnetic components easier. The primary-side switches can achieve ZVS and the secondary-side diodes turn off with ZCS. In addition, the root-mean-square (RMS) values...... of the transformer currents do not significantly vary with respect to the voltage variation. Therefore, this converter can maintain high efficiency over a wide voltage range. The topology and operating principle are firstly described. Then the dc voltage gain and the RMS current characteristics are detailed. Finally...

Using Balls of Different Sports To Model the Variation of Atomic Sizes

Science.gov (United States)

Pinto, Gabriel

1998-06-01

In this article, an analogy is described about the order of magnitude of the variation of atomic sizes that can be used for discussion in introductory chemistry classes. The order of magnitude of this variation, involving microscopic magnitudes, is difficult for students to imagine. For the most part, the students are very familiar with the world of sports. In any case for example, the teacher can make use of the wide, informative coverage given to the olympic games or similar events, where different sports are televised in a few days. The radii of official balls for seven well-known sports are given, and students must assign an atom to each ball by using tabulated single-bond, covalent radii and by assigning the smallest ball (i.e., corresponding to ping-pong) to the smallest atom (i.e., hydrogen). The balls can also be used to show how the ionic radii change upon ionization.

Genetically contextual effects of smoking on genome wide DNA methylation.

Science.gov (United States)

Dogan, Meeshanthini V; Beach, Steven R H; Philibert, Robert A

2017-09-01

Smoking is the leading cause of death in the United States. It exerts its effects by increasing susceptibility to a variety of complex disorders among those who smoke, and if pregnant, to their unborn children. In prior efforts to understand the epigenetic mechanisms through which this increased vulnerability is conveyed, a number of investigators have conducted genome wide methylation analyses. Unfortunately, secondary to methodological limitations, these studies were unable to examine methylation in gene regions with significant amounts of genetic variation. Using genome wide genetic and epigenetic data from the Framingham Heart Study, we re-examined the relationship of smoking status to genome wide methylation status. When only methylation status is considered, smoking was significantly associated with differential methylation in 310 genes that map to a variety of biological process and cellular differentiation pathways. However, when SNP effects on the magnitude of smoking associated methylation changes are also considered, cis and trans-interaction effects were noted at a total of 266 and 4353 genes with no marked enrichment for any biological pathways. Furthermore, the SNP variation participating in the significant interaction effects is enriched for loci previously associated with complex medical illnesses. The enlarged scope of the methylome shown to be affected by smoking may better explicate the mediational pathways linking smoking with a myriad of smoking related complex syndromes. Additionally, these results strongly suggest that combined epigenetic and genetic data analyses may be critical for a more complete understanding of the relationship between environmental variables, such as smoking, and pathophysiological outcomes. © 2017 Wiley Periodicals, Inc.

Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.

Directory of Open Access Journals (Sweden)

Yuhua Yang

2017-11-01

Full Text Available Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79, followed by paternal effect (mean = 0.21. Analysis of the data using diploid seed embryo–cytoplasmic–maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%, followed by special combining ability of parental combination (37.0%. More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed.

Mixing and Transport of Dust in the Early Solar Nebula as Inferred from Titanium Isotope Variations among Chondrules

Energy Technology Data Exchange (ETDEWEB)

Gerber, Simone; Burkhardt, Christoph; Budde, Gerrit; Metzler, Knut; Kleine, Thorsten, E-mail: burkhardt@uni-muenster.de [Institut für Planetologie, University of Münster, Wilhelm Klemm-Straße 10, D-48149 Münster (Germany)

2017-05-20

Chondrules formed by the melting of dust aggregates in the solar protoplanetary disk and as such provide unique insights into how solid material was transported and mixed within the disk. Here, we show that chondrules from enstatite and ordinary chondrites show only small {sup 50}Ti variations and scatter closely around the {sup 50}Ti composition of their host chondrites. By contrast, chondrules from carbonaceous chondrites have highly variable {sup 50}Ti compositions, which, relative to the terrestrial standard, range from the small {sup 50}Ti deficits measured for enstatite and ordinary chondrite chondrules to the large {sup 50}Ti excesses known from Ca–Al-rich inclusions (CAIs). These {sup 50}Ti variations can be attributed to the addition of isotopically heterogeneous CAI-like material to enstatite and ordinary chondrite-like chondrule precursors. The new Ti isotopic data demonstrate that isotopic variations among carbonaceous chondrite chondrules do not require formation over a wide range of orbital distances, but can instead be fully accounted for by the incorporation of isotopically anomalous “nuggets” into chondrule precursors. As such, these data obviate the need for disk-wide transport of chondrules prior to chondrite parent body accretion and are consistent with formation of chondrules from a given chondrite group in localized regions of the disk. Finally, the ubiquitous presence of {sup 50}Ti-enriched material in carbonaceous chondrites and the lack of this material in the non-carbonaceous chondrites support the idea that these two meteorite groups derive from areas of the disk that remained isolated from each other, probably through the formation of Jupiter.

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.

Amazing variational approach to chemical reactions

OpenAIRE

Fernández, Francisco M.

2009-01-01

In this letter we analyse an amazing variational approach to chemical reactions. Our results clearly show that the variational expressions are unsuitable for the analysis of empirical data obtained from chemical reactions.

Morphometric variation in the Tunisian green frog, Rana saharica ...

African Journals Online (AJOL)

Rana saharica is the most widely distributed anuran in Tunisia. We examined morphological variation in 124 specimens as a function of their geographical origin, using univariate and multivariate statistics with traditional morphometrics. Our results supported the existence of three morphotypes of this species, correctly ...

Resolving three-dimensional shape of sub-50 nm wide lines with nanometer-scale sensitivity using conventional optical microscopes

International Nuclear Information System (INIS)

Attota, Ravikiran; Dixson, Ronald G.

2014-01-01

We experimentally demonstrate that the three-dimensional (3-D) shape variations of nanometer-scale objects can be resolved and measured with sub-nanometer scale sensitivity using conventional optical microscopes by analyzing 4-D optical data using the through-focus scanning optical microscopy (TSOM) method. These initial results show that TSOM-determined cross-sectional (3-D) shape differences of 30 nm–40 nm wide lines agree well with critical-dimension atomic force microscope measurements. The TSOM method showed a linewidth uncertainty of 1.22 nm (k = 2). Complex optical simulations are not needed for analysis using the TSOM method, making the process simple, economical, fast, and ideally suited for high volume nanomanufacturing process monitoring.

Variations and determinants of carbon content in plants: a global synthesis

Science.gov (United States)

Ma, Suhui; He, Feng; Tian, Di; Zou, Dongting; Yan, Zhengbing; Yang, Yulong; Zhou, Tiancheng; Huang, Kaiyue; Shen, Haihua; Fang, Jingyun

2018-02-01

Plant carbon (C) content is one of the most important plant traits and is critical to the assessment of global C cycle and ecological stoichiometry; however, the global variations in plant C content remain poorly understood. In this study, we conducted a global analysis of the plant C content by synthesizing data from 4318 species to document specific values and their variation of the C content across plant organs and life forms. Plant organ C contents ranged from 45.0 % in reproductive organs to 47.9 % in stems at global scales, which were significantly lower than the widely employed canonical value of 50 %. Plant C content in leaves (global mean of 46.9 %) was higher than that in roots (45.6 %). Across life forms, woody plants exhibited higher C content than herbaceous plants. Conifers, relative to broad-leaved woody species, had higher C content in roots, leaves, and stems. Plant C content tended to show a decrease with increasing latitude. The life form explained more variation of the C content than climate. Our findings suggest that specific C content values of different organs and life forms developed in our study should be incorporated into the estimations of regional and global vegetation biomass C stocks.

Variations and determinants of carbon content in plants: a global synthesis

Directory of Open Access Journals (Sweden)

S. Ma

2018-02-01

Full Text Available Plant carbon (C content is one of the most important plant traits and is critical to the assessment of global C cycle and ecological stoichiometry; however, the global variations in plant C content remain poorly understood. In this study, we conducted a global analysis of the plant C content by synthesizing data from 4318 species to document specific values and their variation of the C content across plant organs and life forms. Plant organ C contents ranged from 45.0 % in reproductive organs to 47.9 % in stems at global scales, which were significantly lower than the widely employed canonical value of 50 %. Plant C content in leaves (global mean of 46.9 % was higher than that in roots (45.6 %. Across life forms, woody plants exhibited higher C content than herbaceous plants. Conifers, relative to broad-leaved woody species, had higher C content in roots, leaves, and stems. Plant C content tended to show a decrease with increasing latitude. The life form explained more variation of the C content than climate. Our findings suggest that specific C content values of different organs and life forms developed in our study should be incorporated into the estimations of regional and global vegetation biomass C stocks.

Ladder variational autoencoders

DEFF Research Database (Denmark)

Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

2016-01-01

Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...

Ladder Variational Autoencoder

DEFF Research Database (Denmark)

Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

2016-01-01

Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...

Variation in Women's Preferences Regarding Male Facial Masculinity Is Better Explained by Genetic Differences Than by Previously Identified Context-Dependent Effects.

Science.gov (United States)

Zietsch, Brendan P; Lee, Anthony J; Sherlock, James M; Jern, Patrick

2015-09-01

Women's preferences for masculine versus feminine male faces are highly variable. According to a dominant theory in evolutionary psychology, this variability results from adaptations that optimize preferences by calibrating them to certain contextual factors, including women's self-perceived attractiveness, short- versus long-term relationship orientation, pathogen disgust sensitivity, and stage of the menstrual cycle. The theory does not account for the possible contribution of genetic variation on women's facial masculinity preference. Using a large sample (N = 2,160) of identical and nonidentical female Finnish twins and their siblings, we showed that the proportion of variation in women's preferences regarding male facial masculinity that was attributable to genetic variation (38%) dwarfed the variation due to the combined effect of contextual factors (< 1%). These findings cast doubt on the importance of these context-dependent effects and may suggest a need for refocusing in the field toward understanding the wide genetic variation in these preferences and how this variation relates to the evolution of sexual dimorphism in faces. © The Author(s) 2015.

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.

Variations in the origin of inferior phrenic arteries and their relationship to celiac axis variations on CT angiography

Energy Technology Data Exchange (ETDEWEB)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal [Dept. of Radiology, Tepecik Training and Research Hospital, Izmir (Turkmenistan); Toka, Onur [Dept. of Statistics, Hacettepe University, Ankara (Turkmenistan)

2017-04-15

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18–94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

Variations in the origin of inferior phrenic arteries and their relationship to celiac axis variations on CT angiography

International Nuclear Information System (INIS)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal; Toka, Onur

2017-01-01

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18–94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation

Variations in the Origin of Inferior Phrenic Arteries and Their Relationship to Celiac Axis Variations on CT Angiography.

Science.gov (United States)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal; Toka, Onur

2017-01-01

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18-94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

Science.gov (United States)

Jackson, Anne U.; Monda, Keri L.; Kilpeläinen, Tuomas O.; Esko, Tõnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Grönberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Åsa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; Van der Klauw, Melanie M.; Van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindström, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; KrjutÅ¡kov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Njølstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David; Ingelsson, Erik; Kaplan, Robert; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Abecasis, Gonçalo R.; McCarthy, Mark I.; Hirschhorn, Joel N.; Qi, Lu; Loos, Ruth J. F.; Lindgren, Cecilia M.; North, Kari E.; Heid, Iris M.

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10−8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits. PMID:23754948

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

Directory of Open Access Journals (Sweden)

Joshua C Randall

2013-06-01

Full Text Available Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals and took forward 348 SNPs into follow-up (additional 137,052 individuals in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%, including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9 and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG, all of which were genome-wide significant in women (P<5×10(-8, but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.

Priming as a Motivating Factor in Sociophonetic Variation and Change.

Science.gov (United States)

Clark, Lynn

2018-04-24

Understanding how and why pronunciations vary and change has been a dominant theme in variationist sociolinguistics (Labov, , ). Linguistic variability has also been an area of focus in psychology and cognitive science. Work from these two fields has shown that where variation exists in language, an alternative form, once used, persists in working memory and has a greater chance of reuse (Bock, ; Bock & Loebell, ; Branigan, Pickering, & Cleland, ). While there have been efforts to connect priming research with sociolinguistics at the level of grammar (Poplack, ; Travis, ), there has been less work which explicitly considers the potential role of priming as a motivating factor in accent variation and change. This paper explores the role of priming in a socially conditioned sound change. There are two main findings: (a) phonetic variants with the same voicing tend to cluster together in naturally occurring speech and (b) repetition of phonetic form interacts with widely attested sociolinguistic predictors of variation. I argue that there are benefits to both cognitive science and sociolinguistics from this synergy: Incorporating research from cognitive science into sociolinguistics provides us with a better understanding of the factors underpinning a sound change in progress; incorporating insights from sociolinguistics into cognitive science shows that priming does not always operate in the same way for all speakers. Copyright © 2018 Cognitive Science Society, Inc.

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

NARCIS (Netherlands)

Zhang, Z.; Mao, L.; Chen, Junshi; Bu, F.; Li, G.; Sun, J.; Li, S.; Sun, H.; Jiao, C.; Blakely, R.; Pan, J.; Cai, R.; Luo, R.; Peer, Van de Y.; Jacobsen, E.; Fei, Z.; Huang, S.

2015-01-01

Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep

Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico

Science.gov (United States)

Pompa-García, Marín; Venegas-González, Alejandro

2016-01-01

Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries. PMID:27272519

Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico.

Directory of Open Access Journals (Sweden)

Marín Pompa-García

Full Text Available Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass was estimated from a specific allometric equation for this species based on: (i variation of intra-annual wood density and (ii diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries.

Characterising landscape variation through spatial folksonomies

OpenAIRE

Derungs, Curdin; Purves, Ross S

2016-01-01

Describing current, past and future landscapes for inventory and policy making purposes requires classifications capturing variation in, for example, land use and land cover. Typical land cover classifi- cations for such purposes result from a top-down process and rely on expert conceptualisations, and thus provide limited space for incorporating more widely held views of key landscape elements. In this paper we introduce the notion of spatial folksonomies, which we define as a tuple linking ...

Effect of current and travel speed variation of TIG welding on microstructure and hardness of stainless steel SS 316L

Science.gov (United States)

Jatimurti, Wikan; Abdillah, Fakhri Aulia; Kurniawan, Budi Agung; Rochiem, Rochman

2018-04-01

One of the stainless steel types that widely used in industry is SS 316L, which is austenitic stainless steel. One of the welding methods to join stainless steel is Tungsten Inert Gas (TIG), which can affect its morphology, microstructure, strength, hardness, and even lead to cracks in the weld area due to the given heat input. This research has a purpose of analyzing the relationship between microstructure and hardness value of SS 316L stainless steel after TIG welding with the variation of current and travel speed. The macro observation shows a distinct difference in the weld metal and base metal area, and the weld form is not symmetrical. The metallographic test shows the phases that formed in the specimen are austenite and ferrite, which scattered in three welding areas. The hardness test showed that the highest hardness value found in the variation of travel speed 12 cm/min with current 100 A. Welding process and variation were given do not cause any defects in the microstructure, such as carbide precipitation and sigma phase, means that it does not affect the hardness and corrosion resistance of all welded specimen.

A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data

Directory of Open Access Journals (Sweden)

Scherer Stephen W

2011-05-01

Full Text Available Abstract Background Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. Conclusions The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

Spatiotemporal Variations and Driving Factors of Air Pollution in China.

Science.gov (United States)

Zhan, Dongsheng; Kwan, Mei-Po; Zhang, Wenzhong; Wang, Shaojian; Yu, Jianhui

2017-12-08

In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP) witness the strongest and most significant positive effects on air pollution ratio.

Spatiotemporal Variations and Driving Factors of Air Pollution in China

Directory of Open Access Journals (Sweden)

Dongsheng Zhan

2017-12-01

Full Text Available In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP witness the strongest and most significant positive effects on air pollution ratio.

Kinetic Alfven wave with density variation and loss-cone distribution function of multi-ions in PSBL region

Science.gov (United States)

Tamrakar, Radha; Varma, P.; Tiwari, M. S.

2018-05-01

Kinetic Alfven wave (KAW) generation due to variation of loss-cone index J and density of multi-ions (H+, He+ and O+) in the plasma sheet boundary layer region (PSBL) is investigated. Kinetic approach is used to derive dispersion relation of wave using Vlasov equation. Variation of frequency with respect to wide range of k⊥ρi (where k⊥ is wave vector across the magnetic field, ρi is gyroradius of ions and i denotes H+, He+ and O+ ions) is analyzed. It is found that each ion gyroradius and number density shows different effect on wave generation with varying width of loss-cone. KAW is generated with multi-ions (H+, He+ and O+) over wide regime for J=1 and shows dissimilar effect for J=2. Frequency is reduced with increasing density of gyrating He+ and O+ ions. Wave frequency is obtained within the reported range which strongly supports generation of kinetic Alfven waves. A sudden drop of frequency is also observed for H+ and He+ ion which may be due to heavy penetration of these ions through the loss-cone. The parameters of PSBL region are used for numerical calculation. The application of these results are in understanding the effect of gyrating multi-ions in transfer of energy and Poynting flux losses from PSBL region towards ionosphere and also describing the generation of aurora.

Existence and uniqueness of consistent conjectural variation equilibrium in electricity markets

International Nuclear Information System (INIS)

Liu, Youfei; Cai, Bin; Ni, Y.X.; Wu, Felix F.

2007-01-01

The game-theory based methods are widely applied to analyze the market equilibrium and to study the strategic behavior in the oligopolistic electricity markets. Recently, the conjecture variation approach, one of well-studied methods in game theory, is reported to model the strategic behavior in deregulated electricity markets. Unfortunately, the conjecture variation models have been criticized for the drawback of logical inconsistence and possibility of abundant equilibria. Aiming for this, this paper investigates the existence and uniqueness of consistent conjectural variation equilibrium in electricity markets. With several good characteristics of the electricity market and with an infinite horizon optimization model, it is shown that the consistent conjecture variation will satisfy a set of coupled nonlinear equations and there will be only one equilibrium. This result can provide the fundamentals for further applications of the conjecture variation approach. (author)

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder

Science.gov (United States)

Elia, Josephine; Glessner, Joseph T; Wang, Kai; Takahashi, Nagahide; Shtir, Corina J; Hadley, Dexter; Sleiman, Patrick M A; Zhang, Haitao; Kim, Cecilia E; Robison, Reid; Lyon, Gholson J; Flory, James H; Bradfield, Jonathan P; Imielinski, Marcin; Hou, Cuiping; Frackelton, Edward C; Chiavacci, Rosetta M; Sakurai, Takeshi; Rabin, Cara; Middleton, Frank A; Thomas, Kelly A; Garris, Maria; Mentch, Frank; Freitag, Christine M; Steinhausen, Hans-Christoph; Todorov, Alexandre A; Reif, Andreas; Rothenberger, Aribert; Franke, Barbara; Mick, Eric O; Roeyers, Herbert; Buitelaar, Jan; Lesch, Klaus-Peter; Banaschewski, Tobias; Ebstein, Richard P; Mulas, Fernando; Oades, Robert D; Sergeant, Joseph; Sonuga-Barke, Edmund; Renner, Tobias J; Romanos, Marcel; Romanos, Jasmin; Warnke, Andreas; Walitza, Susanne; Meyer, Jobst; Pálmason, Haukur; Seitz, Christiane; Loo, Sandra K; Smalley, Susan L; Biederman, Joseph; Kent, Lindsey; Asherson, Philip; Anney, Richard J L; Gaynor, J William; Shaw, Philip; Devoto, Marcella; White, Peter S; Grant, Struan F A; Buxbaum, Joseph D; Rapoport, Judith L; Williams, Nigel M; Nelson, Stanley F; Faraone, Stephen V; Hakonarson, Hakon

2014-01-01

Attention deficit hyperactivity disorder (ADHD) is a common, heritable neuropsychiatric disorder of unknown etiology. We performed a whole-genome copy number variation (CNV) study on 1,013 cases with ADHD and 4,105 healthy children of European ancestry using 550,000 SNPs. We evaluated statistically significant findings in multiple independent cohorts, with a total of 2,493 cases with ADHD and 9,222 controls of European ancestry, using matched platforms. CNVs affecting metabotropic glutamate receptor genes were enriched across all cohorts (P = 2.1 × 10−9). We saw GRM5 (encoding glutamate receptor, metabotropic 5) deletions in ten cases and one control (P = 1.36 × 10−6). We saw GRM7 deletions in six cases, and we saw GRM8 deletions in eight cases and no controls. GRM1 was duplicated in eight cases. We experimentally validated the observed variants using quantitative RT-PCR. A gene network analysis showed that genes interacting with the genes in the GRM family are enriched for CNVs in ~10% of the cases (P = 4.38 × 10−10) after correction for occurrence in the controls. We identified rare recurrent CNVs affecting glutamatergic neurotransmission genes that were overrepresented in multiple ADHD cohorts. PMID:22138692

Cryptic Genetic Variation in Evolutionary Developmental Genetics

Directory of Open Access Journals (Sweden)

Annalise B. Paaby

2016-06-01

Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

Variations in breast tangent radiotherapy: a survey of practice in New South Wales and the Australian Capital Territory

International Nuclear Information System (INIS)

Veness, M.J.; Delaney, G.; Berry, M.

1999-01-01

The breast is a complex anatomical structure where achieving a homogeneous dose distribution with radiation treatment is difficult. Despite obvious similarities in the approach to such treatment (using tangents) there is variation in the process of simulation, planning and treatment between radiation oncologists. Previous Australasian studies in the treatment of lung cancer, prostate cancer and Hodgkin's disease highlighted considerable variation in many areas of treatment. As part of a multicentre breast phantom study involving 10 radiation oncology departments throughout New South Wales (NSW) and the Australian Capital Territory (ACT), a 22-question survey was distributed. The aim of the survey was to assess the extent of variation in the approach to the simulation, planning and treatment of early breast cancer using tangents. Responses from 10 different radiation oncology departments revealed variation in most areas of the survey. There is no reason to assume similar variations do not occur Australasia wide. Studies involving overseas radiation oncologists also reveal a wide variation in treating early breast cancer. The consequences of such variations remain unclear. Copyright (1999) Blackwell Science Pty Ltd

Histograms showing variations in oil yield, water yield, and specific gravity of oil from Fischer assay analyses of oil-shale drill cores and cuttings from the Piceance Basin, northwestern Colorado

Science.gov (United States)

Dietrich, John D.; Brownfield, Michael E.; Johnson, Ronald C.; Mercier, Tracey J.

2014-01-01

Recent studies indicate that the Piceance Basin in northwestern Colorado contains over 1.5 trillion barrels of oil in place, making the basin the largest known oil-shale deposit in the world. Previously published histograms display oil-yield variations with depth and widely correlate rich and lean oil-shale beds and zones throughout the basin. Histograms in this report display oil-yield data plotted alongside either water-yield or oil specific-gravity data. Fischer assay analyses of core and cutting samples collected from exploration drill holes penetrating the Eocene Green River Formation in the Piceance Basin can aid in determining the origins of those deposits, as well as estimating the amount of organic matter, halite, nahcolite, and water-bearing minerals. This report focuses only on the oil yield plotted against water yield and oil specific gravity.

Early Paleogene Orbital Variations in Atmospheric CO2 and New Astronomical Solutions

Science.gov (United States)

Zeebe, R. E.

2017-12-01

Geologic records across the globe show prominent variations on orbital time scales during numerous epochs going back hundreds of millions of years. The origin of the Milankovic cycles are variations in orbital parameters of the bodies of the Solar System. On long time scales, the orbital variations can not be computed analytically because of the chaotic nature of the Solar System. Thus, numerical solutions are used to estimate changes in, e.g., Earth's orbital parameters in the past. The orbital solutions represent the backbone of cyclostratigraphy and astrochronology, now widely used in geology and paleoclimatology. Hitherto only two solutions for Earth's eccentricity appear to be used in paleoclimate studies, provided by two different groups that integrated the full Solar System equations over the past >100 Myr. In this presentation, I will touch on the basic physics behind, and present new results of, accurate Solar System integrations for Earth's eccentricity over the past hundred million years. I will discuss various limitations within the framework of the present simulations and compare the results to existing solutions. Furthermore, I will present new results from practical applications of such orbital solutions, including effects of orbital forcing on coupled climate- and carbon cycle variations. For instance, we have recently revealed a mechanism for a large lag between changes in carbon isotope ratios and eccentricity at the 400-kyr period, which has been observed in Paleocene, Oligocene, and Miocene sections. Finally, I will present the first estimates of orbital-scale variations in atmospheric CO2 during the early Paleogene.

Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

2004-02-25

The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

Constitutive and Operational Variation of Learning in Foraging Predatory Mites.

Science.gov (United States)

Seiter, Michael; Schausberger, Peter

2016-01-01

Learning is widely documented across animal taxa but studies stringently scrutinizing the causes of constitutive or operational variation of learning among populations and individuals are scarce. The ability to learn is genetically determined and subject to constitutive variation while the performance in learning depends on the immediate circumstances and is subject to operational variation. We assessed variation in learning ability and performance of plant-inhabiting predatory mites, Amblyseius swirskii, caused by population origin, rearing diet, and type of experience. Using an early learning foraging paradigm, we determined that homogeneous single prey environments did not select for reduced learning ability, as compared to natural prey-diverse environments, whereas a multi-generational pollen diet resulted in loss of learning, as compared to a diet of live prey. Associative learning produced stronger effects than non-associative learning but both types of experience produced persistent memory. Our study represents a key example of environmentally caused variation in learning ability and performance.

Constitutive and Operational Variation of Learning in Foraging Predatory Mites.

Directory of Open Access Journals (Sweden)

Michael Seiter

Full Text Available Learning is widely documented across animal taxa but studies stringently scrutinizing the causes of constitutive or operational variation of learning among populations and individuals are scarce. The ability to learn is genetically determined and subject to constitutive variation while the performance in learning depends on the immediate circumstances and is subject to operational variation. We assessed variation in learning ability and performance of plant-inhabiting predatory mites, Amblyseius swirskii, caused by population origin, rearing diet, and type of experience. Using an early learning foraging paradigm, we determined that homogeneous single prey environments did not select for reduced learning ability, as compared to natural prey-diverse environments, whereas a multi-generational pollen diet resulted in loss of learning, as compared to a diet of live prey. Associative learning produced stronger effects than non-associative learning but both types of experience produced persistent memory. Our study represents a key example of environmentally caused variation in learning ability and performance.

Water quality, Multivariate statistical techniques, submarine out fall, spatial variation, temporal variation

International Nuclear Information System (INIS)

Garcia, Francisco; Palacio, Carlos; Garcia, Uriel

2012-01-01

Multivariate statistical techniques were used to investigate the temporal and spatial variations of water quality at the Santa Marta coastal area where a submarine out fall that discharges 1 m3/s of domestic wastewater is located. Two-way analysis of variance (ANOVA), cluster and principal component analysis and Krigging interpolation were considered for this report. Temporal variation showed two heterogeneous periods. From December to April, and July, where the concentration of the water quality parameters is higher; the rest of the year (May, June, August-November) were significantly lower. The spatial variation reported two areas where the water quality is different, this difference is related to the proximity to the submarine out fall discharge.

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

Directory of Open Access Journals (Sweden)

Victor Renault

Full Text Available Copy number variations (CNV include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information.To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer, a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs Affymetrix SNP Array data (Fig 1A. Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test, validated by another cohort of HCCs (p-value of 5.6e-7 (Fig 2B.aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/.aCNViewer@cephb.fr.

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

Science.gov (United States)

Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

2017-01-01

Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https

Analysis of indel variations in the human disease-associated genes ...

Indian Academy of Sciences (India)

Keywords. insertion–deletion variations; haematological disease; tumours; human genetics. Journal of Genetics ... domly selected healthy Korean individuals using a blood genomic DNA ... Bioinformatics annotation and 3-D protein structure analysis. In this study ..... 2009 A genome-wide meta-analysis identifies. Journal of ...

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...

Stochastic process variation in deep-submicron CMOS circuits and algorithms

CERN Document Server

Zjajo, Amir

2014-01-01

One of the most notable features of nanometer scale CMOS technology is the increasing magnitude of variability of the key device parameters affecting performance of integrated circuits. The growth of variability can be attributed to multiple factors, including the difficulty of manufacturing control, the emergence of new systematic variation-generating mechanisms, and most importantly, the increase in atomic-scale randomness, where device operation must be described as a stochastic process. In addition to wide-sense stationary stochastic device variability and temperature variation, existence of non-stationary stochastic electrical noise associated with fundamental processes in integrated-circuit devices represents an elementary limit on the performance of electronic circuits. In an attempt to address these issues, Stochastic Process Variation in Deep-Submicron CMOS: Circuits and Algorithms offers unique combination of mathematical treatment of random process variation, electrical noise and temperature and ne...

Higher frequency of social learning in China than in the West shows cultural variation in the dynamics of cultural evolution.

Science.gov (United States)

Mesoudi, Alex; Chang, Lei; Murray, Keelin; Lu, Hui Jing

2015-01-07

Cultural evolutionary models have identified a range of conditions under which social learning (copying others) is predicted to be adaptive relative to asocial learning (learning on one's own), particularly in humans where socially learned information can accumulate over successive generations. However, cultural evolution and behavioural economics experiments have consistently shown apparently maladaptive under-utilization of social information in Western populations. Here we provide experimental evidence of cultural variation in people's use of social learning, potentially explaining this mismatch. People in mainland China showed significantly more social learning than British people in an artefact-design task designed to assess the adaptiveness of social information use. People in Hong Kong, and Chinese immigrants in the UK, resembled British people in their social information use, suggesting a recent shift in these groups from social to asocial learning due to exposure to Western culture. Finally, Chinese mainland participants responded less than other participants to increased environmental change within the task. Our results suggest that learning strategies in humans are culturally variable and not genetically fixed, necessitating the study of the 'social learning of social learning strategies' whereby the dynamics of cultural evolution are responsive to social processes, such as migration, education and globalization.

Patterns of morphological variation of extant sloth skulls and their implication for future conservation efforts.

Science.gov (United States)

Hautier, Lionel; Billet, Guillaume; Eastwood, Bethany; Lane, Jemima

2014-06-01

Several studies have shown an increased morphological variability of sloths from mammalian norms, affecting varied phenotypic traits from skeletal parts to soft tissues. We present here the first descriptive comparison of the whole skull morphology within the two extant sloth genera, combining geometric morphometric approaches with comparative anatomy. We used these methods to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as phylogeny, geography, allometry, or sexual dimorphism. Our study first revealed strong phylogenetic and geographical imprints on the cranial and mandibular morphological traits. This result demonstrates the importance of accurate knowledge of species and their geographical distributions; here we show from an example pertaining to Bradypus variegatus populations the implications this has on conservation management. Moreover, in order to control the amount of this detected variation, we tentatively compared sloths to a wide range of mammalian species. Our analysis found no significant increase in the average deviation of skull shape within each investigated sloth species compared to other mammals. This suggests that the intraspecific cranial variation in sloths does not depart significantly from the variation observed in other mammals. This result has positive implications for the demarcation of anatomical regions that maintain high levels of morphological variation in sloths. Copyright © 2014 Wiley Periodicals, Inc.

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

Science.gov (United States)

Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

2014-01-01

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs. PMID:25198154

Sparse linear models: Variational approximate inference and Bayesian experimental design

International Nuclear Information System (INIS)

Seeger, Matthias W

2009-01-01

A wide range of problems such as signal reconstruction, denoising, source separation, feature selection, and graphical model search are addressed today by posterior maximization for linear models with sparsity-favouring prior distributions. The Bayesian posterior contains useful information far beyond its mode, which can be used to drive methods for sampling optimization (active learning), feature relevance ranking, or hyperparameter estimation, if only this representation of uncertainty can be approximated in a tractable manner. In this paper, we review recent results for variational sparse inference, and show that they share underlying computational primitives. We discuss how sampling optimization can be implemented as sequential Bayesian experimental design. While there has been tremendous recent activity to develop sparse estimation, little attendance has been given to sparse approximate inference. In this paper, we argue that many problems in practice, such as compressive sensing for real-world image reconstruction, are served much better by proper uncertainty approximations than by ever more aggressive sparse estimation algorithms. Moreover, since some variational inference methods have been given strong convex optimization characterizations recently, theoretical analysis may become possible, promising new insights into nonlinear experimental design.

Sparse linear models: Variational approximate inference and Bayesian experimental design

Energy Technology Data Exchange (ETDEWEB)

Seeger, Matthias W [Saarland University and Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbruecken (Germany)

2009-12-01

A wide range of problems such as signal reconstruction, denoising, source separation, feature selection, and graphical model search are addressed today by posterior maximization for linear models with sparsity-favouring prior distributions. The Bayesian posterior contains useful information far beyond its mode, which can be used to drive methods for sampling optimization (active learning), feature relevance ranking, or hyperparameter estimation, if only this representation of uncertainty can be approximated in a tractable manner. In this paper, we review recent results for variational sparse inference, and show that they share underlying computational primitives. We discuss how sampling optimization can be implemented as sequential Bayesian experimental design. While there has been tremendous recent activity to develop sparse estimation, little attendance has been given to sparse approximate inference. In this paper, we argue that many problems in practice, such as compressive sensing for real-world image reconstruction, are served much better by proper uncertainty approximations than by ever more aggressive sparse estimation algorithms. Moreover, since some variational inference methods have been given strong convex optimization characterizations recently, theoretical analysis may become possible, promising new insights into nonlinear experimental design.

Ethnic variations in lung cancer.

Science.gov (United States)

Groeger, A M; Mueller, M R; Odocha, O; Dekan, G; Salat, A; Röthy, W; Esposito, V; Caputi, M; Wolner, E; Kaiser, H E

1997-01-01

Cancer of the lung is the most frequent cancer in the world, but with wide geographical variation in risk. It is most spread among males of all races worldwide, the only exception being its incidence among Chinese women aged 70 years and older. When comparing the different ethnic groups we have to consider that besides inhaling cigarette smoke actively or as a passive smoker the exposure to occupational carcinogens varies considerably according to different work places. In our study we compared 10 years of data from African-Americans in Howard University Hospital, Washington D.C. with 20 years of data from the white population in the University Hospital of Vienna, Austria. Ethnic patterns are generally consistent within each group in terms of both incidence and mortality. The difference in susceptibility between the sexes, the three major racial groups and already proven differences in genetic variations indicate the difference between individuals concerning the initiation and progression of lung cancer.

Genome-Wide Interactions with Dairy Intake for Body Mass Index in Adults of European Descent

DEFF Research Database (Denmark)

Smith, Caren E; Follis, Jack L; Dashti, Hassan S

2018-01-01

SCOPE: Body weight responds variably to the intake of dairy foods. Genetic variation may contribute to inter-individual variability in associations between body weight and dairy consumption. METHODS AND RESULTS: A genome-wide interaction study to discover genetic variants that account for variati...

Genetic Variations Involved in Vitamin E Status

Directory of Open Access Journals (Sweden)

Patrick Borel

2016-12-01

Full Text Available Vitamin E (VE is the generic term for four tocopherols and four tocotrienols that exhibit the biological activity of α-tocopherol. VE status, which is usually estimated by measuring fasting blood VE concentration, is affected by numerous factors, such as dietary VE intake, VE absorption efficiency, and VE catabolism. Several of these factors are in turn modulated by genetic variations in genes encoding proteins involved in these factors. To identify these genetic variations, two strategies have been used: genome-wide association studies and candidate gene association studies. Each of these strategies has its advantages and its drawbacks, nevertheless they have allowed us to identify a list of single nucleotide polymorphisms associated with fasting blood VE concentration and α-tocopherol bioavailability. However, much work remains to be done to identify, and to replicate in different populations, all the single nucleotide polymorphisms involved, to assess the possible involvement of other kind of genetic variations, e.g., copy number variants and epigenetic modifications, in order to establish a reliable list of genetic variations that will allow us to predict the VE status of an individual by knowing their genotype in these genetic variations. Yet, the potential usefulness of this area of research is exciting with regard to personalized nutrition and for future clinical trials dedicated to assessing the biological effects of the various isoforms of VE.

Mate-finding as an overlooked critical determinant of dispersal variation in sexually-reproducing animals.

Science.gov (United States)

Gilroy, James J; Lockwood, Julie L

2012-01-01

Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly 'fat-tailed' at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

Collective frequency variation in network synchronization and reverse PageRank.

Science.gov (United States)

Skardal, Per Sebastian; Taylor, Dane; Sun, Jie; Arenas, Alex

2016-04-01

A wide range of natural and engineered phenomena rely on large networks of interacting units to reach a dynamical consensus state where the system collectively operates. Here we study the dynamics of self-organizing systems and show that for generic directed networks the collective frequency of the ensemble is not the same as the mean of the individuals' natural frequencies. Specifically, we show that the collective frequency equals a weighted average of the natural frequencies, where the weights are given by an outflow centrality measure that is equivalent to a reverse PageRank centrality. Our findings uncover an intricate dependence of the collective frequency on both the structural directedness and dynamical heterogeneity of the network, and also reveal an unexplored connection between synchronization and PageRank, which opens the possibility of applying PageRank optimization to synchronization. Finally, we demonstrate the presence of collective frequency variation in real-world networks by considering the UK and Scandinavian power grids.

Collective frequency variation in network synchronization and reverse PageRank

Science.gov (United States)

Skardal, Per Sebastian; Taylor, Dane; Sun, Jie; Arenas, Alex

2016-04-01

A wide range of natural and engineered phenomena rely on large networks of interacting units to reach a dynamical consensus state where the system collectively operates. Here we study the dynamics of self-organizing systems and show that for generic directed networks the collective frequency of the ensemble is not the same as the mean of the individuals' natural frequencies. Specifically, we show that the collective frequency equals a weighted average of the natural frequencies, where the weights are given by an outflow centrality measure that is equivalent to a reverse PageRank centrality. Our findings uncover an intricate dependence of the collective frequency on both the structural directedness and dynamical heterogeneity of the network, and also reveal an unexplored connection between synchronization and PageRank, which opens the possibility of applying PageRank optimization to synchronization. Finally, we demonstrate the presence of collective frequency variation in real-world networks by considering the UK and Scandinavian power grids.

Development and testing of a European Union-wide farm-level carbon calculator.

Science.gov (United States)

Tuomisto, Hanna L; De Camillis, Camillo; Leip, Adrian; Nisini, Luigi; Pelletier, Nathan; Haastrup, Palle

2015-07-01

Direct greenhouse gas (GHG) emissions from agriculture accounted for approximately 10% of total European Union (EU) emissions in 2010. To reduce farming-related GHG emissions, appropriate policy measures and supporting tools for promoting low-C farming practices may be efficacious. This article presents the methodology and testing results of a new EU-wide, farm-level C footprint calculator. The Carbon Calculator quantifies GHG emissions based on international standards and technical specifications on Life Cycle Assessment (LCA) and C footprinting. The tool delivers its results both at the farm level and as allocated to up to 5 main products of the farm. In addition to the quantification of GHG emissions, the calculator proposes mitigation options and sequestration actions that may be suitable for individual farms. The results obtained during a survey made on 54 farms from 8 EU Member States are presented. These farms were selected in view of representing the diversity of farm types across different environmental zones in the EU. The results of the C footprint of products in the data set show wide range of variation between minimum and maximum values. The results of the mitigation actions showed that the tool can help identify practices that can lead to substantial emission reductions. To avoid burden-shifting from climate change to other environmental issues, the future improvements of the tool should include incorporation of other environmental impact categories in place of solely focusing on GHG emissions. © 2015 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of SETAC.

A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs.

Directory of Open Access Journals (Sweden)

Youssef Idaghdour

2008-04-01

Full Text Available The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence. Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression. Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease. Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

Wide-field spectrally resolved quantitative fluorescence imaging system: toward neurosurgical guidance in glioma resection

Science.gov (United States)

Xie, Yijing; Thom, Maria; Ebner, Michael; Wykes, Victoria; Desjardins, Adrien; Miserocchi, Anna; Ourselin, Sebastien; McEvoy, Andrew W.; Vercauteren, Tom

2017-11-01

In high-grade glioma surgery, tumor resection is often guided by intraoperative fluorescence imaging. 5-aminolevulinic acid-induced protoporphyrin IX (PpIX) provides fluorescent contrast between normal brain tissue and glioma tissue, thus achieving improved tumor delineation and prolonged patient survival compared with conventional white-light-guided resection. However, commercially available fluorescence imaging systems rely solely on visual assessment of fluorescence patterns by the surgeon, which makes the resection more subjective than necessary. We developed a wide-field spectrally resolved fluorescence imaging system utilizing a Generation II scientific CMOS camera and an improved computational model for the precise reconstruction of the PpIX concentration map. In our model, the tissue's optical properties and illumination geometry, which distort the fluorescent emission spectra, are considered. We demonstrate that the CMOS-based system can detect low PpIX concentration at short camera exposure times, while providing high-pixel resolution wide-field images. We show that total variation regularization improves the contrast-to-noise ratio of the reconstructed quantitative concentration map by approximately twofold. Quantitative comparison between the estimated PpIX concentration and tumor histopathology was also investigated to further evaluate the system.

Radon in Austrian tourist mines and show caves

International Nuclear Information System (INIS)

Ringer, W.; Graeser, J.

2009-01-01

The radon situation in tourist mines and show caves is barely investigated in Austria. This paper investigates the influence of its determining factors, such as climate, structure and geology. For this purpose, long-term time-resolved measurements over 6 to 12 months in 4 tourist mines and 2 show caves - with 5 to 9 measuring points each - have been carried out to obtain the course of radon concentration throughout the year. In addition, temperature and air-pressure were measured and compared to the data outside where available. Results suggest that the dominating factors of the average radon concentration are structure and location (geology) of the tunnel-system, whereas the diurnal and annual variation is mainly caused by the changing airflow, which is driven by the difference in temperature inside and outside. Downcast air is connected with very low radon concentrations, upcast air with high concentrations. In some locations the maximum values appear when the airflow ceases. But airflow can be different in different parts of mines and caves. Systems close to the surface show generally lower radon levels than the ones located deeper underground. Due to variation of structure, geology and local climate, the radon situation in mines and caves can only be described by simultaneous measurements at several measuring points. (orig.)

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

Science.gov (United States)

2014-01-01

Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

Science.gov (United States)

Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

2014-01-16

The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study

Luminosity Variations in Post-AGB Stars

Science.gov (United States)

Mesler, Robert; Henson, G.

2007-12-01

Although much is known about AGB stars and planetary nebulae, relatively little is known about the phase of a star's life in which it transitions between those two states. We have measured the variations in luminosity of a sample of known Post-AGB stars (as well as several candidates) relative to nearby, non-variable stars in order to compare them with theoretical models. The typical behavior of the observed variations is described and an attempt is made to discern whether any periodicity might be present. Luminosity variations were found to be on the order of a few hundredths to a few tenths of a magnitude for the stars that were surveyed, with occasional fluctuations of up to a magnitude. This agrees with current models of Post-AGB stars. Each star fell into one of three categories, which were termed groups 1, 2, and 3. Group 1 stars showed long term, non-periodic luminosity variations on the scale of weeks or longer and were most likely to display some sort of short term, coherent luminosity oscillation (each of which lasted for only a few cycles). Group 2 stars showed erratic, short-term magnitude variations occurring on scales of several days. Group 3 stars showed little or no variation in magnitude. Of the 27 Post-AGB stars that were sampled, five fell into group 1, fifteen fell into group 2, and seven fell into group 3. The luminosity variations tended to be color-independent, and occurred on timescales ranging nearly continuously from a few days to more than a year. No clear periodic behavior was found in any star in our sample. This project was funded by a partnership between the National Science Foundation (NSF AST-0552798), Research Experiences for Undergraduates (REU), and the Department of Defense (DoD) ASSURE (Awards to Stimulate and Support Undergraduate Research Experiences) programs.

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings.

Directory of Open Access Journals (Sweden)

2006-03-01

Full Text Available The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036. The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within-family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will

Water Vapor, Temperature and Wind Profiles within Maize Canopy under in-Field Rainwater Harvesting with Wide and Narrow Runoff Strips

Directory of Open Access Journals (Sweden)

Weldemichael A. Tesfuhuney

2013-11-01

Full Text Available Micrometeorological measurements were used to evaluate heat and water vapor to describe the transpiration (Ev and soil evaporation (Es processes for wide and narrow runoff strips under in-field rainwater harvesting (IRWH system. The resulting sigmoid-shaped water vapor (ea in wide and narrow runoff strips varied in lower and upper parts of the maize canopy. In wide runoff strips, lapse conditions of ea extended from lowest measurement level (LP to the upper middle section (MU and inversion was apparent at the top of the canopy. The virtual potential temperature (θv profile showed no difference in middle section, but the lower and upper portion (UP had lower  in narrow, compared to wide, strips, and LP-UP changes of 0.6 K and 1.2 K were observed, respectively. The Ev and Es within the canopy increased the ea concentration as determined by the wind order of magnitude. The ea concentration reached peak at about 1.6 kPa at a range of wind speed value of 1.4–1.8 m∙s−1 and 2.0–2.4 m∙s−1 for wide and narrow treatments, respectively. The sparse maize canopy of the wide strips could supply more drying power of the air in response to atmospheric evaporative demand compared to narrow strips. This is due to the variation in air flow in wide and narrow runoff strips that change gradients in ea for evapotranspiration processes.

Patterns of among- and within-species variation in heterospecific pollen receipt: The importance of ecological generalization.

Science.gov (United States)

Arceo-Gómez, Gerardo; Abdala-Roberts, Luis; Jankowiak, Anneka; Kohler, Clare; Meindl, George A; Navarro-Fernández, Carmen M; Parra-Tabla, Víctor; Ashman, Tia-Lynn; Alonso, Conchita

2016-03-01

Coflowering plants are at risk for receiving pollen from heterospecifics as well as conspecifics, yet evidence shows wide variation in the degree that heterospecific pollen transfer occurs. Evaluation of patterns and correlates of among- and within-species variation in heterospecific pollen (HP) receipt is key to understanding its importance for floral evolution and species coexistence; however, the rarity of deeply sampled multispecies comparisons has precluded such an evaluation. We evaluated patterns of among- and within-species variation in HP load size and diversity in 19 species across three distinct plant communities. We assessed the importance of phenotypic specialization (floral phenotype), ecological specialization (contemporary visitor assemblage), and conspecific flower density as determinants of among-species variation. We present hypotheses for different accrual patterns of HP within species based on the evenness and quality of floral visitors and evaluated these by characterizing the relationship between conspecific pollen (CP) and HP receipt. We found that within-species variation in HP receipt was greater than among-species and among-communities variation. Among species, ecological generalization emerged as the strongest driver of variation in HP receipt irrespective of phenotypic specialization. Within-species variation in HP load size and diversity was predicted most often from two CP-HP relationships (linear or exponentially decreasing), suggesting that two distinct types of plant-pollinator interactions prevail. Our results give important insights into the potential drivers of among- and within-species variation in HP receipt. They also highlight the value of explorations of patterns at the intraspecific level, which can ultimately shed light on plant-pollinator-mediated selection in diverse plant communities. © 2016 Botanical Society of America.

Genome-wide association study identifies five new schizophrenia loci.

LENUS (Irish Health Repository)

Ripke, Stephan

2011-10-01

We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10(-9)), ANK3 (rs10994359, P = 2.5 × 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10(-9)).

Medication and volume delivery by gravity-driven micro-drip intravenous infusion: potential variations during "wide-open" flow.

Science.gov (United States)

Pierce, Eric T; Kumar, Vikram; Zheng, Hui; Peterfreund, Robert A

2013-03-01

Gravity-driven micro-drip infusion sets allow control of medication dose delivery by adjusting drops per minute. When the roller clamp is fully open, flow in the drip chamber can be a continuous fluid column rather than discrete, countable, drops. We hypothesized that during this "wide-open" state, drug delivery becomes dependent on factors extrinsic to the micro-drip set and is therefore difficult to predict. We conducted laboratory experiments to characterize volume delivery under various clinically relevant conditions of wide-open flow in an in vitro laboratory model. A micro-drip infusion set, plugged into a bag of normal saline, was connected to a high-flow stopcock at the distal end. Vertically oriented IV catheters (gauges 14-22) were connected to the stopcock. The fluid meniscus height in the bag was fixed (60-120 cm) above the outflow point. The roller clamp on the infusion set was in fully open position for all experiments resulting in a continuous column of fluid in the drip chamber. Fluid volume delivered in 1 minute was measured 4 times with each condition. To model resistive effects of carrier flow, volumetric infusion pumps were used to deliver various flow rates of normal saline through a carrier IV set into which a micro-drip infusion was "piggybacked." We also compared delivery by micro-drip infusion sets from 3 manufacturers. The volume of fluid delivered by gravity-driven infusion under wide-open conditions (continuous fluid column in drip chamber) varied 2.9-fold (95% confidence interval, 2.84-2.96) depending on catheter size and fluid column height. Total model resistance of the micro-drip with stopcock and catheter varied with flow rate. Volume delivered by the piggybacked micro-drip decreased up to 29.7% ± 0.8% (mean ± SE) as the carrier flow increased from 0 to 1998 mL/min. Delivery characteristics of the micro-drip infusion sets from 3 different manufacturers were similar. Laboratory simulation of clinical situations with gravity

Genome-wide quantitative trait loci mapping of the human cerebrospinal fluid proteome.

Science.gov (United States)

Sasayama, Daimei; Hattori, Kotaro; Ogawa, Shintaro; Yokota, Yuuki; Matsumura, Ryo; Teraishi, Toshiya; Hori, Hiroaki; Ota, Miho; Yoshida, Sumiko; Kunugi, Hiroshi

2017-01-01

Cerebrospinal fluid (CSF) is virtually the only one accessible source of proteins derived from the central nervous system (CNS) of living humans and possibly reflects the pathophysiology of a variety of neuropsychiatric diseases. However, little is known regarding the genetic basis of variation in protein levels of human CSF. We examined CSF levels of 1,126 proteins in 133 subjects and performed a genome-wide association analysis of 514,227 single nucleotide polymorphisms (SNPs) to detect protein quantitative trait loci (pQTLs). To be conservative, Spearman's correlation was used to identify an association between genotypes of SNPs and protein levels. A total of 421 cis and 25 trans SNP-protein pairs were significantly correlated at a false discovery rate (FDR) of less than 0.01 (nominal P genome-wide association studies. The present findings suggest that genetic variations play an important role in the regulation of protein expression in the CNS. The obtained database may serve as a valuable resource to understand the genetic bases for CNS protein expression pattern in humans. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic Dissection of the Canq1 Locus Governing Variation in Extent of the Collateral Circulation

Science.gov (United States)

Wang, Shiliang; Zhang, Hua; Wiltshire, Tim; Sealock, Robert; Faber, James E.

2012-01-01

Background Native (pre-existing) collaterals are arteriole-to-arteriole anastomoses that interconnect adjacent arterial trees and serve as endogenous bypass vessels that limit tissue injury in ischemic stroke, myocardial infarction, coronary and peripheral artery disease. Their extent (number and diameter) varies widely among mouse strains and healthy humans. We previously identified a major quantitative trait locus on chromosome 7 (Canq1, LOD = 29) responsible for 37% of the heritable variation in collateral extent between C57BL/6 and BALB/c mice. We sought to identify candidate genes in Canq1 responsible for collateral variation in the cerebral pial circulation, a tissue whose strain-dependent variation is shared by similar variation in other tissues. Methods and Findings Collateral extent was intermediate in a recombinant inbred line that splits Canq1 between the C57BL/6 and BALB/c strains. Phenotyping and SNP-mapping of an expanded panel of twenty-one informative inbred strains narrowed the Canq1 locus, and genome-wide linkage analysis of a SWRxSJL-F2 cross confirmed its haplotype structure. Collateral extent, infarct volume after cerebral artery occlusion, bleeding time, and re-bleeding time did not differ in knockout mice for two vascular-related genes located in Canq1, IL4ra and Itgal. Transcript abundance of 6 out of 116 genes within the 95% confidence interval of Canq1 were differentially expressed >2-fold (p-valuecollateral formation. Conclusions These findings refine the Canq1 locus and identify several genes as high-priority candidates important in specifying native collateral formation and its wide variation. PMID:22412848

Analysis of Diffusion Problems using Homotopy Perturbation and Variational Iteration Methods

DEFF Research Database (Denmark)

Barari, Amin; Poor, A. Tahmasebi; Jorjani, A.

2010-01-01

In this paper, variational iteration method and homotopy perturbation method are applied to different forms of diffusion equation. The diffusion equations have found wide applications in heat transfer problems, theory of consolidation and many other problems in engineering. The methods proposed...

Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection

Directory of Open Access Journals (Sweden)

Cho Won

2012-05-01

Full Text Available Abstract Background Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21 is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessary for preventing damage caused by F. graminearum. Therefore, we investigated important cellular regulatory processes in a host containing FgV1-DK21 as compared to an uninfected parent using a transcriptional approach. Results Using a 3′-tiling microarray covering all known F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum at two different time points. At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. In addition, genes required for transcription and signal transduction, including fungal-specific transcription factors and cAMP signaling, respectively, were actively up-regulated. In contrast, genes involved in various metabolic pathways, particularly in producing carboxylic acids, aromatic amino acids, nitrogen compounds, and polyamines, showed dramatic down-regulation at the early time point. Moreover, genes associated with transport systems localizing to transmembranes were down-regulated at both time points. Conclusion This is the first report of global change in the prominent cellular pathways in the Fusarium host containing FgV1-DK21. The significant increase in transcripts for transcription and translation machinery in fungal host cells seems to be related to virus replication. In addition, significant down-regulation of genes required for metabolism and transporting systems in a fungal host containing the virus appears to be related to the host defense mechanism and fungal virulence. Taken together

Applications of low lift to drag ratio aerobrakes using angle of attack variation for control

Science.gov (United States)

Mulqueen, J. A.

1991-01-01

Several applications of low lift to drag ratio aerobrakes are investigated which use angle of attack variation for control. The applications are: return from geosynchronous or lunar orbit to low Earth orbit; and planetary aerocapture at Earth and Mars. A number of aerobrake design considerations are reviewed. It was found that the flow impingement behind the aerobrake and the aerodynamic heating loads are the primary factors that control the sizing of an aerobrake. The heating loads and other loads, such as maximum acceleration, are determined by the vehicle ballistic coefficient, the atmosphere entry conditions, and the trajectory design. Several formulations for defining an optimum trajectory are reviewed, and the various performance indices that can be used are evaluated. The 'nearly grazing' optimal trajectory was found to provide the best compromise between the often conflicting goals of minimizing the vehicle propulsive requirements and minimizing vehicle loads. The relationship between vehicle and trajectory design is investigated further using the results of numerical simulations of trajectories for each aerobrake application. The data show the sensitivity of the trajectories to several vehicle parameters and atmospheric density variations. The results of the trajectory analysis show that low lift to drag ratio aerobrakes, which use angle of attack variation for control, can potentially be used for a wide range of aerobrake applications.

Genome-wide association analysis of oxidative stress resistance in Drosophila melanogaster.

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Allison L Weber

Full Text Available Aerobic organisms are susceptible to damage by reactive oxygen species. Oxidative stress resistance is a quantitative trait with population variation attributable to the interplay between genetic and environmental factors. Drosophila melanogaster provides an ideal system to study the genetics of variation for resistance to oxidative stress.We used 167 wild-derived inbred lines of the Drosophila Genetic Reference Panel for a genome-wide association study of acute oxidative stress resistance to two oxidizing agents, paraquat and menadione sodium bisulfite. We found significant genetic variation for both stressors. Single nucleotide polymorphisms (SNPs associated with variation in oxidative stress resistance were often sex-specific and agent-dependent, with a small subset common for both sexes or treatments. Associated SNPs had moderately large effects, with an inverse relationship between effect size and allele frequency. Linear models with up to 12 SNPs explained 67-79% and 56-66% of the phenotypic variance for resistance to paraquat and menadione sodium bisulfite, respectively. Many genes implicated were novel with no known role in oxidative stress resistance. Bioinformatics analyses revealed a cellular network comprising DNA metabolism and neuronal development, consistent with targets of oxidative stress-inducing agents. We confirmed associations of seven candidate genes associated with natural variation in oxidative stress resistance through mutational analysis.We identified novel candidate genes associated with variation in resistance to oxidative stress that have context-dependent effects. These results form the basis for future translational studies to identify oxidative stress susceptibility/resistance genes that are evolutionary conserved and might play a role in human disease.

Head shape variation in eastern and western Montpellier snakes

Directory of Open Access Journals (Sweden)

Marco Mangiacotti

2014-12-01

Full Text Available The Montpellier snake Malpolon monspessulanus is a wide-ranging species that inhabits Western and Eastern Europe, North Africa and Middle East. Four clades have been recognised as two species, M. insignitus and M. monspessulanus, each with two subspecies. Clades have been substantially identified on the basis of molecular data, pholidosis and colouration, while morphometric traits have been ignored. We compared head shape of 54 specimens belonging to three out of the four clades (M. insignitus insignitus, M. i. fuscus, and M. monspessulanus monspessulanus by means of geometric morphometrics. We found a significant differentiation: the supraocular and frontal area showed the largest amount of variation, being respectively much thinner in M. i. insignitus, a bit less thin in M. i. fuscus and definitely wider in M. m. monspessulanus. Our findings are fully in agreement with the genetic studies and phylogeny explains more than 20% of the observed variation, supporting the taxonomic distinction inside the genus Malpolon. The functional and/or adaptive meaning of the observed differences is not clear, but it seems unlikely that it may be related to diet. Combining morphological data with phylogeography and environmental features, we formulated an explanatory hypothesis that allowed a precise and testable prediction.

Transformation of natural genetic variation into Haemophilus influenzae genomes.

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Joshua Chang Mell

2011-07-01

Full Text Available Many bacteria are able to efficiently bind and take up double-stranded DNA fragments, and the resulting natural transformation shapes bacterial genomes, transmits antibiotic resistance, and allows escape from immune surveillance. The genomes of many competent pathogens show evidence of extensive historical recombination between lineages, but the actual recombination events have not been well characterized. We used DNA from a clinical isolate of Haemophilus influenzae to transform competent cells of a laboratory strain. To identify which of the ~40,000 polymorphic differences had recombined into the genomes of four transformed clones, their genomes and their donor and recipient parents were deep sequenced to high coverage. Each clone was found to contain ~1000 donor polymorphisms in 3-6 contiguous runs (8.1±4.5 kb in length that collectively comprised ~1-3% of each transformed chromosome. Seven donor-specific insertions and deletions were also acquired as parts of larger donor segments, but the presence of other structural variation flanking 12 of 32 recombination breakpoints suggested that these often disrupt the progress of recombination events. This is the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, connecting experimental studies of transformation with the high levels of natural genetic variation found in isolates of the same species.

Genome-wide single-generation signatures of local selection in the panmictic European eel

DEFF Research Database (Denmark)

Pujolar, J. M.; Jacobsen, M. W.; Als, Thomas Damm

2014-01-01

Next-generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from eight locations between 34 and 64oN, we examined the patterns...... of genome-wide genetic diversity across locations. We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables. The overall low genetic differentiation...... with single-generation signatures of spatially varying selection acting on glass eels. After screening 50 354 SNPs, a total of 754 potentially locally selected SNPs were identified. Candidate genes for local selection constituted a wide array of functions, including calcium signalling, neuroactive ligand...

Application of the control variate technique to estimation of total sensitivity indices

International Nuclear Information System (INIS)

Kucherenko, S.; Delpuech, B.; Iooss, B.; Tarantola, S.

2015-01-01

Global sensitivity analysis is widely used in many areas of science, biology, sociology and policy planning. The variance-based methods also known as Sobol' sensitivity indices has become the method of choice among practitioners due to its efficiency and ease of interpretation. For complex practical problems, estimation of Sobol' sensitivity indices generally requires a large number of function evaluations to achieve reasonable convergence. To improve the efficiency of the Monte Carlo estimates for the Sobol' total sensitivity indices we apply the control variate reduction technique and develop a new formula for evaluation of total sensitivity indices. Presented results using well known test functions show the efficiency of the developed technique. - Highlights: • We analyse the efficiency of the Monte Carlo estimates of Sobol' sensitivity indices. • The control variate technique is applied for estimation of total sensitivity indices. • We develop a new formula for evaluation of Sobol' total sensitivity indices. • We present test results demonstrating the high efficiency of the developed formula

Statistical survey of widely spread out solar electron events observed with STEREO and ACE with special attention to anisotropies

Science.gov (United States)

Dresing, N.; Gómez-Herrero, R.; Heber, B.; Klassen, A.; Malandraki, O.; Dröge, W.; Kartavykh, Y.

2014-07-01

Context. In February 2011, the two STEREO spacecrafts reached a separation of 180 degrees in longitude, offering a complete view of the Sun for the first time ever. When the full Sun surface is visible, source active regions of solar energetic particle (SEP) events can be identified unambiguously. STEREO, in combination with near-Earth observatories such as ACE or SOHO, provides three well separated viewpoints, which build an unprecedented platform from which to investigate the longitudinal variations of SEP events. Aims: We show an ensemble of SEP events that were observed between 2009 and mid-2013 by at least two spacecrafts and show a remarkably wide particle spread in longitude (wide-spread events). The main selection criterion for these events was a longitudinal separation of at least 80 degrees between active region and spacecraft magnetic footpoint for the widest separated spacecraft. We investigate the events statistically in terms of peak intensities, onset delays, and rise times, and determine the spread of the longitudinal events, which is the range filled by SEPs during the events. Energetic electron anisotropies are investigated to distinguish the source and transport mechanisms that lead to the observed wide particle spreads. Methods: According to the anisotropy distributions, we divided the events into three classes depending on different source and transport scenarios. One potential mechanism for wide-spread events is efficient perpendicular transport in the interplanetary medium that competes with another scenario, which is a wide particle spread that occurs close to the Sun. In the latter case, the observations at 1 AU during the early phase of the events are expected to show significant anisotropies because of the wide injection range at the Sun and particle-focusing during the outward propagation, while in the first case only low anisotropies are anticipated. Results: We find events for both of these scenarios in our sample that match the

Complex Kohn variational principle for the solution of Lippmann-Schwinger equations

International Nuclear Information System (INIS)

Adhikari, S.K.

1992-07-01

A recently proposed version of the Kohn variational principle for the t matrix incorporating the correct boundary condition is applied for the first time to the study of nucleon-nucleon scattering. Analytic expressions can be obtained for all the integrals in the method for a wide class of potentials and for a suitable choice of trial functions. Closed-form analytic expressions for these integrals are given for Yakawa and exponential potentials. Calculations with two commonly used S-wave nucleon-nucleon potentials show that the method may converge faster than other solution schemes not only for the phase-shifts but also for the off-shell t matrix elements if the freedom in the choice of the trial function is exploited. (author)

A genome-wide characterization of microRNA genes in maize.

Directory of Open Access Journals (Sweden)

Lifang Zhang

2009-11-01

Full Text Available MicroRNAs (miRNAs are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

geomagnetic secular variation and the 1969–1970 secular jerk

African Journals Online (AJOL)

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The plots of D rather strongly suggest the presence of a jerk around 1980 at most of the stations. Key words/phrases: Magnetic observatories, polynomial fitting, residuals, secular variation, secular jerk. INTRODUCTION. The magnetic field of the Earth has been observed to exhibit changes of remarkably wide spectral.

Solution of problems in calculus of variations via He's variational iteration method

International Nuclear Information System (INIS)

Tatari, Mehdi; Dehghan, Mehdi

2007-01-01

In the modeling of a large class of problems in science and engineering, the minimization of a functional is appeared. Finding the solution of these problems needs to solve the corresponding ordinary differential equations which are generally nonlinear. In recent years He's variational iteration method has been attracted a lot of attention of the researchers for solving nonlinear problems. This method finds the solution of the problem without any discretization of the equation. Since this method gives a closed form solution of the problem and avoids the round off errors, it can be considered as an efficient method for solving various kinds of problems. In this research He's variational iteration method will be employed for solving some problems in calculus of variations. Some examples are presented to show the efficiency of the proposed technique

Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee.

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Gabriele Greve

Full Text Available BACKGROUND: We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia and CDY (chromodomain protein Y varied with respect to copy number and position among chimpanzees (Pan troglodytes. In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus, the chimpanzee's closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla and orangutans (Pongo pygmaeus, and examine the resulting patterns in the light of the species' markedly different social and mating behaviors. METHODOLOGY/PRINCIPAL FINDINGS: Fluorescence in situ hybridization analysis (FISH of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla and a single lineage of the eastern lowland gorilla (G. beringei graueri showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus, and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii. We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR in chimpanzee and bonobo. CONCLUSION/SIGNIFICANCE: High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans-species that are not subject to sperm competition-showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA

Infrared variation reduction by simultaneous background suppression and target contrast enhancement for deep convolutional neural network-based automatic target recognition

Science.gov (United States)

Kim, Sungho

2017-06-01

Automatic target recognition (ATR) is a traditionally challenging problem in military applications because of the wide range of infrared (IR) image variations and the limited number of training images. IR variations are caused by various three-dimensional target poses, noncooperative weather conditions (fog and rain), and difficult target acquisition environments. Recently, deep convolutional neural network-based approaches for RGB images (RGB-CNN) showed breakthrough performance in computer vision problems, such as object detection and classification. The direct use of RGB-CNN to the IR ATR problem fails to work because of the IR database problems (limited database size and IR image variations). An IR variation-reduced deep CNN (IVR-CNN) to cope with the problems is presented. The problem of limited IR database size is solved by a commercial thermal simulator (OKTAL-SE). The second problem of IR variations is mitigated by the proposed shifted ramp function-based intensity transformation. This can suppress the background and enhance the target contrast simultaneously. The experimental results on the synthesized IR images generated by the thermal simulator (OKTAL-SE) validated the feasibility of IVR-CNN for military ATR applications.

An Easy Way to Show Memory Color Effects.

Science.gov (United States)

Witzel, Christoph

2016-01-01

This study proposes and evaluates a simple stimulus display that allows one to measure memory color effects (the effect of object knowledge and memory on color perception). The proposed approach is fast and easy and does not require running an extensive experiment. It shows that memory color effects are robust to minor variations due to a lack of color calibration.

An Easy Way to Show Memory Color Effects

OpenAIRE

Witzel, Christoph

2016-01-01

This study proposes and evaluates a simple stimulus display that allows one to measure memory color effects (the effect of object knowledge and memory on color perception). The proposed approach is fast and easy and does not require running an extensive experiment. It shows that memory color effects are robust to minor variations due to a lack of color calibration.

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

Science.gov (United States)

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

2012-10-05

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

Genome-wide association study of Arabidopsis thaliana leaf microbial community.

Science.gov (United States)

Horton, Matthew W; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D; Subramanian, Sathish; Vetter, M Madlen; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Gordon, Jeffrey I; Bergelson, Joy

2014-11-10

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

Crustal structure of the North Iberian continental margin from seismic refraction/wide-angle reflection profiles

Science.gov (United States)

Ruiz, M.; Díaz, J.; Pedreira, D.; Gallart, J.; Pulgar, J. A.

2017-10-01

The structure and geodynamics of the southern margin of the Bay of Biscay have been investigated from a set of 11 multichannel seismic reflection profiles, recorded also at wide angle offsets in an onshore-offshore network of 24 OBS/OBH and 46 land sites. This contribution focuses on the analysis of the wide-angle reflection/refraction data along representative profiles. The results document strong lateral variations of the crustal structure along the margin and provide an extensive test of the crustal models previously proposed for the northern part of the Iberian Peninsula. Offshore, the crust has a typical continental structure in the eastern tip of the bay, which disappears smoothly towards the NW to reach crustal thickness close to 10 km at the edge of the studied area ( 45°N, 6°W). The analysis of the velocity-depth profiles, altogether with additional information provided by the multichannel seismic data and magnetic surveys, led to the conclusion that the crust in this part of the bay should be interpreted as transitional from continental to oceanic. Typical oceanic crust has not been imaged in the investigated area. Onshore, the new results are in good agreement with previous results and document the indentation of the Bay of Biscay crust into the Iberian crust, forcing its subduction to the North. The interpreted profiles show that the extent of the southward indentation is not uniform, with an Alpine root less developed in the central and western sector of the Basque-Cantabrian Basin. N-S to NE-SW transfer structures seem to control those variations in the indentation degree.

Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer

DEFF Research Database (Denmark)

Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils

2013-01-01

Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212...... of rare CNVs related to cell migration (false-discovery rate = 0.021, 1.8% of cases and 1.1% of controls). Dysregulation during migration of primordial germ cells has previously been suspected to be a part of TGCC development and this set of multiple rare variants may thereby have a minor contribution...

Branch xylem density variations across the Amazon Basin

Science.gov (United States)

Patiño, S.; Lloyd, J.; Paiva, R.; Baker, T. R.; Quesada, C. A.; Mercado, L. M.; Schmerler, J.; Schwarz, M.; Santos, A. J. B.; Aguilar, A.; Czimczik, C. I.; Gallo, J.; Horna, V.; Hoyos, E. J.; Jimenez, E. M.; Palomino, W.; Peacock, J.; Peña-Cruz, A.; Sarmiento, C.; Sota, A.; Turriago, J. D.; Villanueva, B.; Vitzthum, P.; Alvarez, E.; Arroyo, L.; Baraloto, C.; Bonal, D.; Chave, J.; Costa, A. C. L.; Herrera, R.; Higuchi, N.; Killeen, T.; Leal, E.; Luizão, F.; Meir, P.; Monteagudo, A.; Neil, D.; Núñez-Vargas, P.; Peñuela, M. C.; Pitman, N.; Priante Filho, N.; Prieto, A.; Panfil, S. N.; Rudas, A.; Salomão, R.; Silva, N.; Silveira, M.; Soares Dealmeida, S.; Torres-Lezama, A.; Vásquez-Martínez, R.; Vieira, I.; Malhi, Y.; Phillips, O. L.

2009-04-01

Xylem density is a physical property of wood that varies between individuals, species and environments. It reflects the physiological strategies of trees that lead to growth, survival and reproduction. Measurements of branch xylem density, ρx, were made for 1653 trees representing 598 species, sampled from 87 sites across the Amazon basin. Measured values ranged from 218 kg m-3 for a Cordia sagotii (Boraginaceae) from Mountagne de Tortue, French Guiana to 1130 kg m-3 for an Aiouea sp. (Lauraceae) from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average ρx across regions and sampled plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that species identity (family, genera and species) accounted for 33% with environment (geographic location and plot) accounting for an additional 26%; the remaining "residual" variance accounted for 41% of the total variance. Variations in plot means, were, however, not only accountable by differences in species composition because xylem density of the most widely distributed species in our dataset varied systematically from plot to plot. Thus, as well as having a genetic component, branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing in a predictable manner. Within the analysed taxa, exceptions to this general rule seem to be pioneer species belonging for example to the Urticaceae whose branch xylem density is more constrained than most species sampled in this study. These patterns of variation of branch xylem density across Amazonia suggest a large functional diversity amongst Amazonian trees which is not well understood.

Colonizing the world in spite of reduced MHC variation

Science.gov (United States)

Gangoso, L.; Alcaide, M.; Grande, J.M.; Muñoz, J.; Talbot, Sandra L.; Sonsthagen, Sarah A.; Sage, Kevin; Figuerola, J.

2012-01-01

Reduced immune gene diversity is thought to negatively affect the capacity of organisms to adapt to pathogen challenges, which represent a major force in natural selection. Genes of the Major Histocompatibility Complex (MHC) are the most widely invoked adaptive loci in conservation biology, and have become the most popular genetic markers to investigate pathogen-host interactions in vertebrates. Although MHC genes are the most polymorphic genes described in the vertebrate genome, the extent to which MHC diversity determines the long-term persistence of populations is, unclear and often debated, as recent studies have documented the occurrence of natural populations thriving even after a depletion of MHC diversity caused by genetic drift. Here, we show that some phylogenetically related species belonging to the Falco genus (Aves: Falconidae) present a dramatically low MHC variability that has not precluded, nevertheless, the successful colonization of almost all existing regions and habitats worldwide. We found evidence for two remarkably different patterns of MHC variation within the genus. While kestrels show a high MHC variation according to the general theory, falcons exhibit an ancestrally low intra- and inter-specific MHC allelic diversity. We provide compelling evidence that this pattern is not caused by the degeneration of functional genes into pseudogenes, the inadvertent analyses of paralogous MHC genes, or the devastating action of genetic drift. Instead, our results strongly support the idea of an evolutionary transition driven and maintained by natural selection from primarily highly variable towards low polymorphic, but functional and expressed, MHC genes with species-specific pathogen-recognition capabilities.

Sequence variation in TgROP7 gene among Toxoplasma gondii ...

African Journals Online (AJOL)

Yomi

2012-03-27

Mar 27, 2012 ... Toxoplasma gondii can infect a wide range of hosts including mammals and birds, causing toxoplasmosis which is one of the most common parasitic zoonoses worldwide. The present study examined sequence variation in rhoptry 7 (ROP7) gene among different T. gondii isolates from different hosts and ...

Venomics of New World pit vipers: genus-wide comparisons of venom proteomes across Agkistrodon.

Science.gov (United States)

Lomonte, Bruno; Tsai, Wan-Chih; Ureña-Diaz, Juan Manuel; Sanz, Libia; Mora-Obando, Diana; Sánchez, Elda E; Fry, Bryan G; Gutiérrez, José María; Gibbs, H Lisle; Sovic, Michael G; Calvete, Juan J

2014-01-16

We report a genus-wide comparison of venom proteome variation across New World pit vipers in the genus Agkistrodon. Despite the wide variety of habitats occupied by this genus and that all its taxa feed on diverse species of vertebrates and invertebrate prey, the venom proteomes of copperheads, cottonmouths, and cantils are remarkably similar, both in the type and relative abundance of their different toxin families. The venoms from all the eleven species and subspecies sampled showed relatively similar proteolytic and PLA2 activities. In contrast, quantitative differences were observed in hemorrhagic and myotoxic activities in mice. The highest myotoxic activity was observed with the venoms of A. b. bilineatus, followed by A. p. piscivorus, whereas the venoms of A. c. contortrix and A. p. leucostoma induced the lowest myotoxic activity. The venoms of Agkistrodon bilineatus subspecies showed the highest hemorrhagic activity and A. c. contortrix the lowest. Compositional and toxicological analyses agree with clinical observations of envenomations by Agkistrodon in the USA and Central America. A comparative analysis of Agkistrodon shows that venom divergence tracks phylogeny of this genus to a greater extent than in Sistrurus rattlesnakes, suggesting that the distinct natural histories of Agkistrodon and Sistrurus clades may have played a key role in molding the patterns of evolution of their venom protein genes. A deep understanding of the structural and functional profiles of venoms and of the principles governing the evolution of venomous systems is a goal of venomics. Isolated proteomics analyses have been conducted on venoms from many species of vipers and pit vipers. However, making sense of these large inventories of data requires the integration of this information across multiple species to identify evolutionary and ecological trends. Our genus-wide venomics study provides a comprehensive overview of the toxic arsenal across Agkistrodon and a ground for

Venomics of New World pit vipers: Genus-wide comparisons of venom proteomes across Agkistrodon

Science.gov (United States)

Lomonte, Bruno; Tsai, Wan-Chih; Ureña-Diaz, Juan Manuel; Sanz, Libia; Mora-Obando, Diana; Sánchez, Elda E.; Fry, Bryan G.; Gutiérrez, José María; Gibbs, H. Lisle; Sovic, Michael G.; Calvete, Juan J.

2015-01-01

We report a genus-wide comparison of venom proteome variation across New World pit vipers in the genus Agkistrodon. Despite the wide variety of habitats occupied by this genus and that all its taxa feed on diverse species of vertebrates and invertebrate prey, the venom proteomes of copperheads, cottonmouths, and cantils are remarkably similar, both in the type and relative abundance of their different toxin families. The venoms from all the eleven species and subspecies sampled showed relatively similar proteolytic and PLA2 activities. In contrast, quantitative differences were observed in hemorrhagic and myotoxic activities in mice. The highest myotoxic activity was observed with the venoms of A. b. bilineatus, followed by A. p. piscivorus, whereas the venoms of A. c. contortrix and A. p. leucostoma induced the lowest myotoxic activity. The venoms of Agkistrodon bilineatus subspecies showed the highest hemorrhagic activity and A. c. contortrix the lowest. Compositional and toxicological analyses agree with clinical observations of envenomations by Agkistrodon in the USA and Central America. A comparative analysis of Agkistrodon shows that venom divergence tracks phylogeny of this genus to a greater extent than in Sistrurus rattlesnakes, suggesting that the distinct natural histories of Agkistrodon and Sistrurus clades may have played a key role in molding the patterns of evolution of their venom protein genes. Biological significance A deep understanding of the structural and functional profiles of venoms and of the principles governing the evolution of venomous systems is a goal of venomics. Isolated proteomics analyses have been conducted on venoms from many species of vipers and pit vipers. However, making sense of these large inventories of data requires the integration of this information across multiple species to identify evolutionary and ecological trends. Our genus-wide venomics study provides a comprehensive overview of the toxic arsenal across

Variational principles for locally variational forms

International Nuclear Information System (INIS)

Brajercik, J.; Krupka, D.

2005-01-01

We present the theory of higher order local variational principles in fibered manifolds, in which the fundamental global concept is a locally variational dynamical form. Any two Lepage forms, defining a local variational principle for this form, differ on intersection of their domains, by a variationally trivial form. In this sense, but in a different geometric setting, the local variational principles satisfy analogous properties as the variational functionals of the Chern-Simons type. The resulting theory of extremals and symmetries extends the first order theories of the Lagrange-Souriau form, presented by Grigore and Popp, and closed equivalents of the first order Euler-Lagrange forms of Hakova and Krupkova. Conceptually, our approach differs from Prieto, who uses the Poincare-Cartan forms, which do not have higher order global analogues

Variation in diagnosis and management of common foot problems by GPs

NARCIS (Netherlands)

Gorter, K; de Melker, R; Kuyvenhoven, M; de Poel, S.

2001-01-01

Background. There are indications that the diagnosis and management of common foot problems vary widely in general practice. Objectives. Our aim was to explore the variation of GPs' diagnosis and management of common foot problems and the possible correlation between GPs' characteristics and their

Variations in brain DNA

Directory of Open Access Journals (Sweden)

Jesus eAvila

2014-11-01

Full Text Available It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.

Fluctuating survival selection explains variation in avian group size.

Science.gov (United States)

Brown, Charles R; Brown, Mary Bomberger; Roche, Erin A; O'Brien, Valerie A; Page, Catherine E

2016-05-03

Most animal groups vary extensively in size. Because individuals in certain sizes of groups often have higher apparent fitness than those in other groups, why wide group size variation persists in most populations remains unexplained. We used a 30-y mark-recapture study of colonially breeding cliff swallows (Petrochelidon pyrrhonota) to show that the survival advantages of different colony sizes fluctuated among years. Colony size was under both stabilizing and directional selection in different years, and reversals in the sign of directional selection regularly occurred. Directional selection was predicted in part by drought conditions: birds in larger colonies tended to be favored in cooler and wetter years, and birds in smaller colonies in hotter and drier years. Oscillating selection on colony size likely reflected annual differences in food availability and the consequent importance of information transfer, and/or the level of ectoparasitism, with the net benefit of sociality varying under these different conditions. Averaged across years, there was no net directional change in selection on colony size. The wide range in cliff swallow group size is probably maintained by fluctuating survival selection and represents the first case, to our knowledge, in which fitness advantages of different group sizes regularly oscillate over time in a natural vertebrate population.

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

Science.gov (United States)

Wain, Louise V; Verwoert, Germaine C; O’Reilly, Paul F; Shi, Gang; Johnson, Toby; Johnson, Andrew D; Bochud, Murielle; Rice, Kenneth M; Henneman, Peter; Smith, Albert V; Ehret, Georg B; Amin, Najaf; Larson, Martin G; Mooser, Vincent; Hadley, David; Dörr, Marcus; Bis, Joshua C; Aspelund, Thor; Esko, Tõnu; Janssens, A Cecile JW; Zhao, Jing Hua; Heath, Simon; Laan, Maris; Fu, Jingyuan; Pistis, Giorgio; Luan, Jian’an; Arora, Pankaj; Lucas, Gavin; Pirastu, Nicola; Pichler, Irene; Jackson, Anne U; Webster, Rebecca J; Zhang, Feng; Peden, John F; Schmidt, Helena; Tanaka, Toshiko; Campbell, Harry; Igl, Wilmar; Milaneschi, Yuri; Hotteng, Jouke-Jan; Vitart, Veronique; Chasman, Daniel I; Trompet, Stella; Bragg-Gresham, Jennifer L; Alizadeh, Behrooz Z; Chambers, John C; Guo, Xiuqing; Lehtimäki, Terho; Kühnel, Brigitte; Lopez, Lorna M; Polašek, Ozren; Boban, Mladen; Nelson, Christopher P; Morrison, Alanna C; Pihur, Vasyl; Ganesh, Santhi K; Hofman, Albert; Kundu, Suman; Mattace-Raso, Francesco US; Rivadeneira, Fernando; Sijbrands, Eric JG; Uitterlinden, Andre G; Hwang, Shih-Jen; Vasan, Ramachandran S; Wang, Thomas J; Bergmann, Sven; Vollenweider, Peter; Waeber, Gérard; Laitinen, Jaana; Pouta, Anneli; Zitting, Paavo; McArdle, Wendy L; Kroemer, Heyo K; Völker, Uwe; Völzke, Henry; Glazer, Nicole L; Taylor, Kent D; Harris, Tamara B; Alavere, Helene; Haller, Toomas; Keis, Aime; Tammesoo, Mari-Liis; Aulchenko, Yurii; Barroso, Inês; Khaw, Kay-Tee; Galan, Pilar; Hercberg, Serge; Lathrop, Mark; Eyheramendy, Susana; Org, Elin; Sõber, Siim; Lu, Xiaowen; Nolte, Ilja M; Penninx, Brenda W; Corre, Tanguy; Masciullo, Corrado; Sala, Cinzia; Groop, Leif; Voight, Benjamin F; Melander, Olle; O’Donnell, Christopher J; Salomaa, Veikko; d’Adamo, Adamo Pio; Fabretto, Antonella; Faletra, Flavio; Ulivi, Sheila; Del Greco, M Fabiola; Facheris, Maurizio; Collins, Francis S; Bergman, Richard N; Beilby, John P; Hung, Joseph; Musk, A William; Mangino, Massimo; Shin, So-Youn; Soranzo, Nicole; Watkins, Hugh; Goel, Anuj; Hamsten, Anders; Gider, Pierre; Loitfelder, Marisa; Zeginigg, Marion; Hernandez, Dena; Najjar, Samer S; Navarro, Pau; Wild, Sarah H; Corsi, Anna Maria; Singleton, Andrew; de Geus, Eco JC; Willemsen, Gonneke; Parker, Alex N; Rose, Lynda M; Buckley, Brendan; Stott, David; Orru, Marco; Uda, Manuela; van der Klauw, Melanie M; Zhang, Weihua; Li, Xinzhong; Scott, James; Chen, Yii-Der Ida; Burke, Gregory L; Kähönen, Mika; Viikari, Jorma; Döring, Angela; Meitinger, Thomas; Davies, Gail; Starr, John M; Emilsson, Valur; Plump, Andrew; Lindeman, Jan H; ’t Hoen, Peter AC; König, Inke R; Felix, Janine F; Clarke, Robert; Hopewell, Jemma C; Ongen, Halit; Breteler, Monique; Debette, Stéphanie; DeStefano, Anita L; Fornage, Myriam; Mitchell, Gary F; Smith, Nicholas L; Holm, Hilma; Stefansson, Kari; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Samani, Nilesh J; Preuss, Michael; Rudan, Igor; Hayward, Caroline; Deary, Ian J; Wichmann, H-Erich; Raitakari, Olli T; Palmas, Walter; Kooner, Jaspal S; Stolk, Ronald P; Jukema, J Wouter; Wright, Alan F; Boomsma, Dorret I; Bandinelli, Stefania; Gyllensten, Ulf B; Wilson, James F; Ferrucci, Luigi; Schmidt, Reinhold; Farrall, Martin; Spector, Tim D; Palmer, Lyle J; Tuomilehto, Jaakko; Pfeufer, Arne; Gasparini, Paolo; Siscovick, David; Altshuler, David; Loos, Ruth JF; Toniolo, Daniela; Snieder, Harold; Gieger, Christian; Meneton, Pierre; Wareham, Nicholas J; Oostra, Ben A; Metspalu, Andres; Launer, Lenore; Rettig, Rainer; Strachan, David P; Beckmann, Jacques S; Witteman, Jacqueline CM; Erdmann, Jeanette; van Dijk, Ko Willems; Boerwinkle, Eric; Boehnke, Michael; Ridker, Paul M; Jarvelin, Marjo-Riitta; Chakravarti, Aravinda; Abecasis, Goncalo R; Gudnason, Vilmundur; Newton-Cheh, Christopher; Levy, Daniel; Munroe, Patricia B; Psaty, Bruce M; Caulfield, Mark J; Rao, Dabeeru C

2012-01-01

Numerous genetic loci influence systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans 1-3. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N=74,064) and follow-up studies (N=48,607), we identified at genome-wide significance (P= 2.7×10-8 to P=2.3×10-13) four novel PP loci (at 4q12 near CHIC2/PDGFRAI, 7q22.3 near PIK3CG, 8q24.12 in NOV, 11q24.3 near ADAMTS-8), two novel MAP loci (3p21.31 in MAP4, 10q25.3 near ADRB1) and one locus associated with both traits (2q24.3 near FIGN) which has recently been associated with SBP in east Asians. For three of the novel PP signals, the estimated effect for SBP was opposite to that for DBP, in contrast to the majority of common SBP- and DBP-associated variants which show concordant effects on both traits. These findings indicate novel genetic mechanisms underlying blood pressure variation, including pathways that may differentially influence SBP and DBP. PMID:21909110

Genome-wide association study identifies 74 loci associated with educational attainment

OpenAIRE

Okbay, Aysu; Beauchamp, Jonathan; Fontana, M.A. (Mark Alan); Lee, James J.; Pers, Tune; Rietveld, C.A. (Cornelius A.); Turley, Patrick; Chen, G.-B. (Guo-Bo); Emilsson, Valur; Meddens, S.F.W. (S. Fleur W.); Oskarsson, S. (Sven); Pickrell, J.K. (Joseph K.); Thom, K. (Kevin); Timshel, P. (Pascal); Vlaming, Ronald

2016-01-01

textabstractEducational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 geno...

Assessment and reduction of comet assay variation in relation to DNA damage: studies from the European Comet Assay Validation Group

DEFF Research Database (Denmark)

Møller, Peter; Möller, Lennart; Godschalk, Roger W L

2010-01-01

The alkaline single cell gel electrophoresis (comet) assay has become a widely used method for the detection of DNA damage and repair in cells and tissues. Still, it has been difficult to compare results from different investigators because of differences in assay conditions and because the data...... are reported in different units. The European Comet Assay Validation Group (ECVAG) was established for the purpose of validation of the comet assay with respect to measures of DNA damage formation and its repair. The results from this inter-laboratory validation trail showed a large variation in measured level...... reliability for the measurement of DNA damage by the comet assay but there is still a need for further validation to reduce both assay and inter-laboratory variation....

Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation

Science.gov (United States)

Tsai, Chia-Ti; Hsieh, Chia-Shan; Chang, Sheng-Nan; Chuang, Eric Y.; Ueng, Kwo-Chang; Tsai, Chin-Feng; Lin, Tsung-Hsien; Wu, Cho-Kai; Lee, Jen-Kuang; Lin, Lian-Yu; Wang, Yi-Chih; Yu, Chih-Chieh; Lai, Ling-Ping; Tseng, Chuen-Den; Hwang, Juey-Jen; Chiang, Fu-Tien; Lin, Jiunn-Lee

2016-01-01

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Previous genome-wide association studies had identified single-nucleotide polymorphisms in several genomic regions to be associated with AF. In human genome, copy number variations (CNVs) are known to contribute to disease susceptibility. Using a genome-wide multistage approach to identify AF susceptibility CNVs, we here show a common 4,470-bp diallelic CNV in the first intron of potassium interacting channel 1 gene (KCNIP1) is strongly associated with AF in Taiwanese populations (odds ratio=2.27 for insertion allele; P=6.23 × 10−24). KCNIP1 insertion is associated with higher KCNIP1 mRNA expression. KCNIP1-encoded protein potassium interacting channel 1 (KCHIP1) is physically associated with potassium Kv channels and modulates atrial transient outward current in cardiac myocytes. Overexpression of KCNIP1 results in inducible AF in zebrafish. In conclusions, a common CNV in KCNIP1 gene is a genetic predictor of AF risk possibly pointing to a functional pathway. PMID:26831368

Determinants of intra-specific variation in basal metabolic rate.

Science.gov (United States)

Konarzewski, Marek; Książek, Aneta

2013-01-01

Basal metabolic rate (BMR) provides a widely accepted benchmark of metabolic expenditure for endotherms under laboratory and natural conditions. While most studies examining BMR have concentrated on inter-specific variation, relatively less attention has been paid to the determinants of within-species variation. Even fewer studies have analysed the determinants of within-species BMR variation corrected for the strong influence of body mass by appropriate means (e.g. ANCOVA). Here, we review recent advancements in studies on the quantitative genetics of BMR and organ mass variation, along with their molecular genetics. Next, we decompose BMR variation at the organ, tissue and molecular level. We conclude that within-species variation in BMR and its components have a clear genetic signature, and are functionally linked to key metabolic process at all levels of biological organization. We highlight the need to integrate molecular genetics with conventional metabolic field studies to reveal the adaptive significance of metabolic variation. Since comparing gene expressions inter-specifically is problematic, within-species studies are more likely to inform us about the genetic underpinnings of BMR. We also urge for better integration of animal and medical research on BMR; the latter is quickly advancing thanks to the application of imaging technologies and 'omics' studies. We also suggest that much insight on the biochemical and molecular underpinnings of BMR variation can be gained from integrating studies on the mammalian target of rapamycin (mTOR), which appears to be the major regulatory pathway influencing the key molecular components of BMR.

Natural Variation in Synthesis and Catabolism Genes Influences Dhurrin Content in Sorghum

Directory of Open Access Journals (Sweden)

Chad M. Hayes

2015-07-01

Full Text Available Cyanogenic glucosides are natural compounds found in more than 1000 species of angiosperms that produce HCN and are deemed undesirable for agricultural use. However, these compounds are important components of the primary defensive mechanisms of many plant species. One of the best-studied cyanogenic glucosides is dhurrin [(--hydroxymandelonitrile-β--glucopyranoside], which is produced primarily in sorghum [ (L. Moench]. The biochemical basis for dhurrin metabolism is well established; however, little information is available on its genetic control. Here, we dissect the genetic control of leaf dhurrin content through a genome-wide association study (GWAS using a panel of 700 diverse converted sorghum lines (conversion panel previously subjected to pre-breeding and selected for short stature (∼1 m in height and photoperiod insensitivity. The conversion panel was grown for 2 yr in three environments. Wide variation for leaf dhurrin content was found in the sorghum conversion panel, with the Caudatum group exhibiting the highest dhurrin content and the Guinea group showing the lowest dhurrin content. A GWAS using a mixed linear model revealed significant associations (a false discovery rate [FDR] < 0.05 close to both UGT 185B1 in the canonical biosynthetic gene cluster on chromosome 1 and close to the catabolic dhurrinase loci on chromosome 8. Dhurrin content was associated consistently with biosynthetic genes in the two N-fertilized environments, while dhurrin content was associated with catabolic loci in the environment without supplemental N. These results suggest that genes for both biosynthesis and catabolism are important in determining natural variation for leaf dhurrin in sorghum in different environments.

Super-Planckian spatial field variations and quantum gravity

Energy Technology Data Exchange (ETDEWEB)

Klaewer, Daniel; Palti, Eran [Institut für Theoretische Physik, Ruprecht-Karls-Universität,Philosophenweg 19, 69120 Heidelberg (Germany)

2017-01-20

We study scenarios where a scalar field has a spatially varying vacuum expectation value such that the total field variation is super-Planckian. We focus on the case where the scalar field controls the coupling of a U(1) gauge field, which allows us to apply the Weak Gravity Conjecture to such configurations. We show that this leads to evidence for a conjectured property of quantum gravity that as a scalar field variation in field space asymptotes to infinity there must exist an infinite tower of states whose mass decreases as an exponential function of the scalar field variation. We determine the rate at which the mass of the states reaches this exponential behaviour showing that it occurs quickly after the field variation passes the Planck scale.

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

DEFF Research Database (Denmark)

Lee, S Hong; Ripke, Stephan; Neale, Benjamin M

2013-01-01

Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases...... and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17......-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD...

Genetic variations in the Dravidian population of South West coast of India: Implications in designing case-control studies.

Science.gov (United States)

D'Cunha, Anitha; Pandit, Lekha; Malli, Chaithra

2017-06-01

Indian data have been largely missing from genome-wide databases that provide information on genetic variations in different populations. This hinders association studies for complex disorders in India. This study was aimed to determine whether the complex genetic structure and endogamy among Indians could potentially influence the design of case-control studies for autoimmune disorders in the south Indian population. A total of 12 single nucleotide variations (SNVs) related to genes associated with autoimmune disorders were genotyped in 370 healthy individuals belonging to six different caste groups in southern India. Allele frequencies were estimated; genetic divergence and phylogenetic relationship within the various caste groups and other HapMap populations were ascertained. Allele frequencies for all genotyped SNVs did not vary significantly among the different groups studied. Wright's FSTwas 0.001 per cent among study population and 0.38 per cent when compared with Gujarati in Houston (GIH) population on HapMap data. The analysis of molecular variance results showed a 97 per cent variation attributable to differences within the study population and variation due to differences between castes. Phylogenetic analysis showed a separation of Dravidian population from other HapMap populations and particularly from GIH population. Despite the complex genetic origins of the Indian population, our study indicated a low level of genetic differentiation among Dravidian language-speaking people of south India. Case-control studies of association among Dravidians of south India may not require stratification based on language and caste.

Variational integrators for electric circuits

International Nuclear Information System (INIS)

Ober-Blöbaum, Sina; Tao, Molei; Cheng, Mulin; Owhadi, Houman; Marsden, Jerrold E.

2013-01-01

In this contribution, we develop a variational integrator for the simulation of (stochastic and multiscale) electric circuits. When considering the dynamics of an electric circuit, one is faced with three special situations: 1. The system involves external (control) forcing through external (controlled) voltage sources and resistors. 2. The system is constrained via the Kirchhoff current (KCL) and voltage laws (KVL). 3. The Lagrangian is degenerate. Based on a geometric setting, an appropriate variational formulation is presented to model the circuit from which the equations of motion are derived. A time-discrete variational formulation provides an iteration scheme for the simulation of the electric circuit. Dependent on the discretization, the intrinsic degeneracy of the system can be canceled for the discrete variational scheme. In this way, a variational integrator is constructed that gains several advantages compared to standard integration tools for circuits; in particular, a comparison to BDF methods (which are usually the method of choice for the simulation of electric circuits) shows that even for simple LCR circuits, a better energy behavior and frequency spectrum preservation can be observed using the developed variational integrator

Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana

NARCIS (Netherlands)

Davila Olivas, Nelson H.; Kruijer, Willem; Gort, Gerrit; Wijnen, Cris L.; Loon, van Joop J.A.; Dicke, Marcel

2017-01-01

Plants are commonly exposed to abiotic and biotic stresses. We used 350 Arabidopsis thaliana accessions grown under controlled conditions. We employed genome-wide association analysis to investigate the genetic architecture and underlying loci involved in genetic variation in resistance to: two

Size variation in Middle Pleistocene humans.

Science.gov (United States)

Arsuaga, J L; Carretero, J M; Lorenzo, C; Gracia, A; Martínez, I; Bermúdez de Castro, J M; Carbonell, E

1997-08-22

It has been suggested that European Middle Pleistocene humans, Neandertals, and prehistoric modern humans had a greater sexual dimorphism than modern humans. Analysis of body size variation and cranial capacity variation in the large sample from the Sima de los Huesos site in Spain showed instead that the sexual dimorphism is comparable in Middle Pleistocene and modern populations.

Finite element approximation of a new variational principle for compressible and incompressible linear isotropic elasticity

International Nuclear Information System (INIS)

Franca, L.P.; Stenberg, R.

1989-06-01

Stability conditions are described to analyze a variational formulation emanating from a variational principle for linear isotropic elasticity. The variational principle is based on four dependent variables (namely, the strain tensor, augmented stress, pressure and displacement) and is shown to be valid for any compressibility including the incompressible limit. An improved convergence error analysis is established for a Galerkin-least-squares method based upon these four variables. The analysis presented establishes convergence for a wide choice of combinations of finite element interpolations. (author) [pt

AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana

Science.gov (United States)

Chen, Zi-Ru; Kuang, Lu; Gao, Yi-Qun; Wang, Ya-Ling; Salt, David E.; Chao, Dai-Yin

2018-01-01

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 (HMA4) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation. PMID:29545819

AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana.

Science.gov (United States)

Chen, Zi-Ru; Kuang, Lu; Gao, Yi-Qun; Wang, Ya-Ling; Salt, David E; Chao, Dai-Yin

2018-01-01

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 ( HMA4 ) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation.

A novel statistic for genome-wide interaction analysis.

Directory of Open Access Journals (Sweden)

Xuesen Wu

2010-09-01

Full Text Available Although great progress in genome-wide association studies (GWAS has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked. The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001wide interaction analysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

Error estimation for variational nodal calculations

International Nuclear Information System (INIS)

Zhang, H.; Lewis, E.E.

1998-01-01

Adaptive grid methods are widely employed in finite element solutions to both solid and fluid mechanics problems. Either the size of the element is reduced (h refinement) or the order of the trial function is increased (p refinement) locally to improve the accuracy of the solution without a commensurate increase in computational effort. Success of these methods requires effective local error estimates to determine those parts of the problem domain where the solution should be refined. Adaptive methods have recently been applied to the spatial variables of the discrete ordinates equations. As a first step in the development of adaptive methods that are compatible with the variational nodal method, the authors examine error estimates for use in conjunction with spatial variables. The variational nodal method lends itself well to p refinement because the space-angle trial functions are hierarchical. Here they examine an error estimator for use with spatial p refinement for the diffusion approximation. Eventually, angular refinement will also be considered using spherical harmonics approximations

Genetic variation in bovine milk fat composition

NARCIS (Netherlands)

Stoop, W.M.

2009-01-01

In her thesis, Stoop shows that there is considerable genetic variation in milk fat composition, which opens opportunities to improve milk fat composition by selective breeding. Short and medium chain fatty acids had high heritabilities, whereas variation due to herd (mainly feed effects) was

Integrating common and rare genetic variation in diverse human populations.

Science.gov (United States)

Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Dermitzakis, Emmanouil; Schaffner, Stephen F; Yu, Fuli; Peltonen, Leena; Dermitzakis, Emmanouil; Bonnen, Penelope E; Altshuler, David M; Gibbs, Richard A; de Bakker, Paul I W; Deloukas, Panos; Gabriel, Stacey B; Gwilliam, Rhian; Hunt, Sarah; Inouye, Michael; Jia, Xiaoming; Palotie, Aarno; Parkin, Melissa; Whittaker, Pamela; Yu, Fuli; Chang, Kyle; Hawes, Alicia; Lewis, Lora R; Ren, Yanru; Wheeler, David; Gibbs, Richard A; Muzny, Donna Marie; Barnes, Chris; Darvishi, Katayoon; Hurles, Matthew; Korn, Joshua M; Kristiansson, Kati; Lee, Charles; McCarrol, Steven A; Nemesh, James; Dermitzakis, Emmanouil; Keinan, Alon; Montgomery, Stephen B; Pollack, Samuela; Price, Alkes L; Soranzo, Nicole; Bonnen, Penelope E; Gibbs, Richard A; Gonzaga-Jauregui, Claudia; Keinan, Alon; Price, Alkes L; Yu, Fuli; Anttila, Verneri; Brodeur, Wendy; Daly, Mark J; Leslie, Stephen; McVean, Gil; Moutsianas, Loukas; Nguyen, Huy; Schaffner, Stephen F; Zhang, Qingrun; Ghori, Mohammed J R; McGinnis, Ralph; McLaren, William; Pollack, Samuela; Price, Alkes L; Schaffner, Stephen F; Takeuchi, Fumihiko; Grossman, Sharon R; Shlyakhter, Ilya; Hostetter, Elizabeth B; Sabeti, Pardis C; Adebamowo, Clement A; Foster, Morris W; Gordon, Deborah R; Licinio, Julio; Manca, Maria Cristina; Marshall, Patricia A; Matsuda, Ichiro; Ngare, Duncan; Wang, Vivian Ota; Reddy, Deepa; Rotimi, Charles N; Royal, Charmaine D; Sharp, Richard R; Zeng, Changqing; Brooks, Lisa D; McEwen, Jean E

2010-09-02

Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

Genetic variations and relationships of cultivated and weedy types of perilla species in Korea and Japan using multi DNA markers

International Nuclear Information System (INIS)

Sun, Y.; Zheng, S.; Lee, J.; Hong, S.

2017-01-01

The genus Perilla, known as an oil crop or a Chinese medicine, vegetable crop, is widely cultivated in East Asia. It occurs in two distinct varieties, var. frutescens and var. crispa, and their genetic relationship is still obscure. To understand the genetic diversity and relationships of the cultivated and weedy types of Perilla crops in Korea, Japan and China, we evaluated the genetic variation of 20 accessions by 3 rDNA markers. Among these three markers, the nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) region of Perilla crops showed less sequence variations than the 5S and 18S genes. There were abundant variable nucleotide sites appearing in the 5S and 18S genes. Especially in the 18S gene, the variable nucleotide sites showed specificity between some Perilla type and other varieties. JPN1 showed 6 special variable nucleotide sites differing from other varieties, resulting in the farthest phylogenetic relationship in the 18S tree. CHI15 shared 8 special variable sites, also showing far phylogenetic relationship with other varieties. According to the sequence analysis result, the cultivated types of Korean var. frutescens showed relatively more genetic diversity than those of Japanese var. frutescens, while Korean var. crispa showed lower genetic diversity than those of Japanese var. crispa. However, the intra- or inter-variety genetic distance did not have significant difference. This work provided more sequence resources of Perilla crops and evidences to evaluate the genetic variation and relationships. Our result would help molecular type identification, functional plant breeding and trait improvement of Perilla crops. (author)

A map of human genome variation from population-scale sequencing.

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Abecasis, Gonçalo R; Altshuler, David; Auton, Adam; Brooks, Lisa D; Durbin, Richard M; Gibbs, Richard A; Hurles, Matt E; McVean, Gil A

2010-10-28

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

Analysis of natural variation in bermudagrass (Cynodon dactylon) reveals physiological responses underlying drought tolerance.

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Shi, Haitao; Wang, Yanping; Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

2012-01-01

Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H₂O₂ content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system.

Genome-Wide Association Study (GWAS) and Genome-Wide Environment Interaction Study (GWEIS) of Depressive Symptoms in African American and Hispanic/Latina Women

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Dunn, Erin C.; Wiste, Anna; Radmanesh, Farid; Almli, Lynn M.; Gogarten, Stephanie M.; Sofer, Tamar; Faul, Jessica D.; Kardia, Sharon L.R.; Smith, Jennifer A.; Weir, David R.; Zhao, Wei; Soare, Thomas W.; Mirza, Saira S.; Hek, Karin; Tiemeier, Henning W.; Goveas, Joseph S.; Sarto, Gloria E.; Snively, Beverly M.; Cornelis, Marilyn; Koenen, Karestan C.; Kraft, Peter; Purcell, Shaun; Ressler, Kerry J.; Rosand, Jonathan; Wassertheil-Smoller, Sylvia; Smoller, Jordan W.

2016-01-01

Background Genome-wide association studies (GWAS) have been unable to identify variants linked to depression. We hypothesized that examining depressive symptoms and considering gene-environment interaction (G×E) might improve efficiency for gene discovery. We therefore conducted a GWAS and genome-wide environment interaction study (GWEIS) of depressive symptoms. Methods Using data from the SHARe cohort of the Women’s Health Initiative, comprising African Americans (n=7179) and Hispanics/Latinas (n=3138), we examined genetic main effects and G×E with stressful life events and social support. We also conducted a heritability analysis using genome-wide complex trait analysis (GCTA). Replication was attempted in four independent cohorts. Results No SNPs achieved genome-wide significance for main effects in either discovery sample. The top signals in African Americans were rs73531535 (located 20kb from GPR139, p=5.75×10−8) and rs75407252 (intronic to CACNA2D3, p=6.99×10−7). In Hispanics/Latinas, the top signals were rs2532087 (located 27kb from CD38, p=2.44×10−7) and rs4542757 (intronic to DCC, p=7.31×10−7). In the GWEIS with stressful life events, one interaction signal was genome-wide significant in African Americans (rs4652467; p=4.10×10−10; located 14kb from CEP350). This interaction was not observed in a smaller replication cohort. Although heritability estimates for depressive symptoms and stressful life events were each less than 10%, they were strongly genetically correlated (rG=0.95), suggesting that common variation underlying depressive symptoms and stressful life event exposure, though modest on their own, were highly overlapping in this sample. Conclusions Our results underscore the need for larger samples, more GWEIS, and greater investigation into genetic and environmental determinants of depressive symptoms in minorities. PMID:27038408

A systematic review of genome-wide research on psychotic experiences and negative symptom traits: New revelations and implications for psychiatry.

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Ronald, Angelica; Pain, Oliver

2018-05-08

We present a systematic review of genome-wide research on psychotic experience and negative symptom traits (PENS) in the community. We integrate these new findings, most of which have emerged over the last four years, with more established behaviour genetic and epidemiological research. The review includes the first genome-wide association studies of PENS, including a recent meta-analysis, and the first SNP heritability estimates. Sample sizes of < 10,000 participants mean that no genome-wide significant variants have yet been replicated. Importantly, however, in the most recent and well-powered studies, polygenic risk score prediction and linkage disequilibrium (LD) score regression analyses show that all types of PENS share genetic influences with diagnosed schizophrenia and that negative symptom traits also share genetic influences with major depression. These genetic findings corroborate other evidence in supporting a link between PENS in the community and psychiatric conditions. Beyond the systematic review, we highlight recent work on gene-environment correlation, which appears to be a relevant process for psychotic experiences. Genes that influence risk factors such as tobacco use and stressful life events are likely to be harbouring 'hits' that also influence PENS. We argue for the acceptance of PENS within the mainstream, as heritable traits in the same vein as other subclinical psychopathology and personality styles such as neuroticism. While acknowledging some mixed findings, new evidence shows genetic overlap between PENS and psychiatric conditions. In sum, normal variations in adolescent and adult thinking styles, such as feeling paranoid, are heritable and show genetic associations with schizophrenia and major depression.

SNP-based pathway enrichment analysis for genome-wide association studies

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Potkin Steven G

2011-04-01

Full Text Available Abstract Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs, have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1 for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2 ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one

Human Variome Project Quality Assessment Criteria for Variation Databases.

Science.gov (United States)

Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

2016-06-01

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

Wide wavelength range tunable one-dimensional silicon nitride nano-grating guided mode resonance filter based on azimuthal rotation

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Ryoji Yukino

2017-01-01

Full Text Available We describe wavelength tuning in a one dimensional (1D silicon nitride nano-grating guided mode resonance (GMR structure under conical mounting configuration of the device. When the GMR structure is rotated about the axis perpendicular to the surface of the device (azimuthal rotation for light incident at oblique angles, the conditions for resonance are different than for conventional GMR structures under classical mounting. These resonance conditions enable tuning of the GMR peak position over a wide range of wavelengths. We experimental demonstrate tuning over a range of 375 nm between 500 nm˜875 nm. We present a theoretical model to explain the resonance conditions observed in our experiments and predict the peak positions with show excellent agreement with experiments. Our method for tuning wavelengths is simpler and more efficient than conventional procedures that employ variations in the design parameters of structures or conical mounting of two-dimensional (2D GMR structures and enables a single 1D GMR device to function as a high efficiency wavelength filter over a wide range of wavelengths. We expect tunable filters based on this technique to be applicable in a wide range of fields including astronomy and biomedical imaging.

The circadian variation of premature atrial contractions

DEFF Research Database (Denmark)

Larsen, Bjørn Strøier; Kumarathurai, Preman; Nielsen, Olav W

2016-01-01

AIMS: The aim of the study was to assess a possible circadian variation of premature atrial contractions (PACs) in a community-based population and to determine if the daily variation could be used to assess a more vulnerable period of PACs in predicting later incidence of atrial fibrillation (AF...... variation in heart rate. After adjusting for relevant risk factors, the risk of AF was equal in all time intervals throughout the day. CONCLUSION: Premature atrial contractions showed a circadian variation in subjects with frequent PACs. No specific time interval of the day was more predictive of AF than...

An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity

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Struchalin Maksim V

2012-01-01

Full Text Available Abstract Background Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties. We and Pare with colleagues (2010 developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants. Results In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests. Conclusions Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context.

Variational Approach to Enhanced Sampling and Free Energy Calculations

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Valsson, Omar; Parrinello, Michele

2014-08-01

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

Solar UV Variations During the Decline of Cycle 23

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DeLand, Matthew, T.; Cebula, Richard P.

2011-01-01

Characterization of temporal and spectral variations in solar ultraviolet irradiance over a solar cycle is essential for understanding the forcing of Earth's atmosphere and climate. Satellite measurements of solar UV variability for solar cycles 21, 22, and 23 show consistent solar cycle irradiance changes at key wavelengths (e.g. 205 nm, 250 nm) within instrumental uncertainties. All historical data sets also show the same relative spectral dependence for both short-term (rotational) and long-term (solar cycle) variations. Empirical solar irradiance models also produce long-term solar UV variations that agree well with observational data. Recent UV irradiance data from the Solar Radiation and Climate Experiment (SORCE) Spectral Irradiance Monitor (SIM) and Solar Stellar Irradiance Comparison Experiment (SOLSTICE) instruments covering the declining phase of Cycle 23 present a different picture oflong-term solar variations from previous results. Time series of SIM and SOLSTICE spectral irradiance data between 2003 and 2007 show solar variations that greatly exceed both previous measurements and predicted irradiance changes over this period, and the spectral dependence of the SIM and SOLSTICE variations during these years do not show features expected from solar physics theory. The use of SORCE irradiance variations in atmospheric models yields substantially different middle atmosphere ozone responses in both magnitude and vertical structure. However, short-term solar variability derived from SIM and SOLSTICE UV irradiance data is consistent with concurrent solar UV measurements from other instruments, as well as previous results, suggesting no change in solar physics. Our analysis of short-term solar variability is much less sensitive to residual instrument response changes than the observations of long-term variations. The SORCE long-term UV results can be explained by under-correction of instrument response changes during the first few years of measurements

Single-Nucleotide Variations in Cardiac Arrhythmias: Prospects for Genomics and Proteomics Based Biomarker Discovery and Diagnostics

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Ayman Abunimer

2014-03-01

Full Text Available Cardiovascular diseases are a large contributor to causes of early death in developed countries. Some of these conditions, such as sudden cardiac death and atrial fibrillation, stem from arrhythmias—a spectrum of conditions with abnormal electrical activity in the heart. Genome-wide association studies can identify single nucleotide variations (SNVs that may predispose individuals to developing acquired forms of arrhythmias. Through manual curation of published genome-wide association studies, we have collected a comprehensive list of 75 SNVs associated with cardiac arrhythmias. Ten of the SNVs result in amino acid changes and can be used in proteomic-based detection methods. In an effort to identify additional non-synonymous mutations that affect the proteome, we analyzed the post-translational modification S-nitrosylation, which is known to affect cardiac arrhythmias. We identified loss of seven known S-nitrosylation sites due to non-synonymous single nucleotide variations (nsSNVs. For predicted nitrosylation sites we found 1429 proteins where the sites are modified due to nsSNV. Analysis of the predicted S-nitrosylation dataset for over- or under-representation (compared to the complete human proteome of pathways and functional elements shows significant statistical over-representation of the blood coagulation pathway. Gene Ontology (GO analysis displays statistically over-represented terms related to muscle contraction, receptor activity, motor activity, cystoskeleton components, and microtubule activity. Through the genomic and proteomic context of SNVs and S-nitrosylation sites presented in this study, researchers can look for variation that can predispose individuals to cardiac arrhythmias. Such attempts to elucidate mechanisms of arrhythmia thereby add yet another useful parameter in predicting susceptibility for cardiac diseases.

Genome-wide DNA polymorphism analyses using VariScan

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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.

Matter tensor from the Hilbert variational principle

International Nuclear Information System (INIS)

Pandres, D. Jr.

1976-01-01

We consider the Hilbert variational principle which is conventionally used to derive Einstein's equations for the source-free gravitational field. We show that at least one version of the equivalence principle suggests an alternative way of performing the variation, resulting in a different set of Einstein equations with sources automatically present. This illustrates a technique which may be applied to any theory that is derived from a variational principle and that admits a gauge group. The essential point is that, if one first imposes a gauge condition and then performs the variation, one obtains field equations with source terms which do not appear if one first performs the variation and then imposes the gauge condition. A second illustration is provided by the variational principle conventionally used to derive Maxwell's equations for the source-free electromagnetic field. If one first imposes the Lorentz gauge condition and then performs the variation, one obtains Maxwell's equations with sources present

Branch xylem density variations across the Amazon Basin

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S. Patiño

2009-04-01

Full Text Available Xylem density is a physical property of wood that varies between individuals, species and environments. It reflects the physiological strategies of trees that lead to growth, survival and reproduction. Measurements of branch xylem density, ρ_x, were made for 1653 trees representing 598 species, sampled from 87 sites across the Amazon basin. Measured values ranged from 218 kg m⁻³ for a Cordia sagotii (Boraginaceae from Mountagne de Tortue, French Guiana to 1130 kg m⁻³ for an Aiouea sp. (Lauraceae from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average ρ_x across regions and sampled plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that species identity (family, genera and species accounted for 33% with environment (geographic location and plot accounting for an additional 26%; the remaining "residual" variance accounted for 41% of the total variance. Variations in plot means, were, however, not only accountable by differences in species composition because xylem density of the most widely distributed species in our dataset varied systematically from plot to plot. Thus, as well as having a genetic component, branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing in a predictable manner. Within the analysed taxa, exceptions to this general rule seem to be pioneer species belonging for example to the Urticaceae whose branch xylem density is more constrained than most species sampled in this study. These patterns of variation of branch xylem density across Amazonia suggest a large functional diversity amongst Amazonian trees which is not well understood.

High responders and low responders: factors associated with individual variation in response to standardized training.

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Mann, Theresa N; Lamberts, Robert P; Lambert, Michael I

2014-08-01

The response to an exercise intervention is often described in general terms, with the assumption that the group average represents a typical response for most individuals. In reality, however, it is more common for individuals to show a wide range of responses to an intervention rather than a similar response. This phenomenon of 'high responders' and 'low responders' following a standardized training intervention may provide helpful insights into mechanisms of training adaptation and methods of training prescription. Therefore, the aim of this review was to discuss factors associated with inter-individual variation in response to standardized, endurance-type training. It is well-known that genetic influences make an important contribution to individual variation in certain training responses. The association between genotype and training response has often been supported using heritability estimates; however, recent studies have been able to link variation in some training responses to specific single nucleotide polymorphisms. It would appear that hereditary influences are often expressed through hereditary influences on the pre-training phenotype, with some parameters showing a hereditary influence in the pre-training phenotype but not in the subsequent training response. In most cases, the pre-training phenotype appears to predict only a small amount of variation in the subsequent training response of that phenotype. However, the relationship between pre-training autonomic activity and subsequent maximal oxygen uptake response appears to show relatively stronger predictive potential. Individual variation in response to standardized training that cannot be explained by genetic influences may be related to the characteristics of the training program or lifestyle factors. Although standardized programs usually involve training prescribed by relative intensity and duration, some methods of relative exercise intensity prescription may be more successful in creating

Solar cycle variations of geocoronal balmer α emission

International Nuclear Information System (INIS)

Nossal, S.; Reynolds, R.J.; Roesler, F.L.; Scherb, F.

1993-01-01

Observations of the geocoronal Balmer in nightglow have been made from Wisconsin for more than a solar cycle with an internally consistent intensity reference to standard astronomical nebulae. These measurements were made with a double etalon, pressure-scanned, 15-cm aperture Fabry-Perot interferometer. The resulting long time data provides an opportunity to examine solar cycle influence on the mid-latitude exosphere and to address accompanying questions concerning the degree to which the exosphere is locally static or changing. The exospheric Balmer α absolute intensity measurements reported here show no statistically significant variations throughout the solar cycle when the variation with viewing geometry is removed by normalizing the data to reference exospheric model predictions by Anderson et al. However, the relative intensity dependence on solar depression angle does show a solar cycle variation. This variation suggests a possible related variation in the exospheric hydrogen density profile, although other interpretations are also possible. The results suggest that additional well-calibrated data taken over a longer time span could probe low-amplitude variations over the solar cycle and test predictions of a slow monotonic increase in exospheric hydrogen arising from greenhouse gases. 21 refs., 9 figs., 2 tabs

Survey of the variation in ultraviolet outputs from ultraviolet A sunbeds in Bradford.

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Wright, A L; Hart, G C; Kernohan, E; Twentyman, G

1996-02-01

Concerns have been expressed for some time regarding the growth of the cosmetic suntanning industry and the potential harmful effects resulting from these exposures. Recently published work has appeared to confirm a link between sunbed use and skin cancer. A previous survey in Oxford some years ago demonstrated significant output variations, and we have attempted to extend and update that work. Ultraviolet A, UVB and blue-light output measurements were made on 50 sunbeds using a radiometer fitted with broad-band filters and detectors. A number of irradiance measurements were made on each sunbed within each waveband so that the uniformity of the output could also be assessed. UVA outputs varied by a factor of 3, with a mean of 13.5 mW/cm2; UVB outputs varied by a factor of 60, with a mean of 19.2 microW/cm2; and blue-light outputs varied by a factor of 2.5, with a mean of 2.5 mW/cm2. Outputs fall on average to 80% of the central value at either end of the sunbed. Facial units in sunbeds ranged in output between 18 and 45 mW/cm2. Output uniformity shows wide variation, with 16% of the sunbeds having an axial coefficient of variation > 10%. UVB output is highly tube-specific. Eyewear used in sunbeds should also protect against blue light.

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure.

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Hao, Dapeng; Ren, Cong; Li, Chuanxing

2012-05-01

A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling). Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn't show dependence of degree. Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to "deterministic model" of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Directory of Open Access Journals (Sweden)

Jorge Urrestarazu

2017-11-01

Full Text Available Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM, which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16 which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe, and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated

Pre-analytical and analytical variation of drug determination in segmented hair using ultra-performance liquid chromatography-tandem mass spectrometry.

Science.gov (United States)

Nielsen, Marie Katrine Klose; Johansen, Sys Stybe; Linnet, Kristian

2014-01-01

Assessment of total uncertainty of analytical methods for the measurements of drugs in human hair has mainly been derived from the analytical variation. However, in hair analysis several other sources of uncertainty will contribute to the total uncertainty. Particularly, in segmental hair analysis pre-analytical variations associated with the sampling and segmentation may be significant factors in the assessment of the total uncertainty budget. The aim of this study was to develop and validate a method for the analysis of 31 common drugs in hair using ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) with focus on the assessment of both the analytical and pre-analytical sampling variations. The validated method was specific, accurate (80-120%), and precise (CV≤20%) across a wide linear concentration range from 0.025-25 ng/mg for most compounds. The analytical variation was estimated to be less than 15% for almost all compounds. The method was successfully applied to 25 segmented hair specimens from deceased drug addicts showing a broad pattern of poly-drug use. The pre-analytical sampling variation was estimated from the genuine duplicate measurements of two bundles of hair collected from each subject after subtraction of the analytical component. For the most frequently detected analytes, the pre-analytical variation was estimated to be 26-69%. Thus, the pre-analytical variation was 3-7 folds larger than the analytical variation (7-13%) and hence the dominant component in the total variation (29-70%). The present study demonstrated the importance of including the pre-analytical variation in the assessment of the total uncertainty budget and in the setting of the 95%-uncertainty interval (±2CVT). Excluding the pre-analytical sampling variation could significantly affect the interpretation of results from segmental hair analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries).

Science.gov (United States)

Johnston, Susan E; Bérénos, Camillo; Slate, Jon; Pemberton, Josephine M

2016-05-01

Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h(2) = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3 A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals. Copyright © 2016 by the Genetics Society of America.

Satellite-derived SIF and CO2 Observations Show Coherent Responses to Interannual Climate Variations

Science.gov (United States)

Butterfield, Z.; Hogikyan, A.; Kulawik, S. S.; Keppel-Aleks, G.

2017-12-01

Gross primary production (GPP) is the single largest carbon flux in the Earth system, but its sensitivity to changes in climate is subject to significant uncertainty. Satellite measurements of solar-induced chlorophyll fluorescence (SIF) offer insight into spatial and temporal patterns in GPP at a global scale and, combined with other satellite-derived datasets, provide unprecedented opportunity to explore interactions between atmospheric CO2, GPP, and climate variability. To explore potential drivers of GPP in the Northern Hemisphere (NH), we compare monthly-averaged SIF data from the Global Ozone Monitoring Experiment 2 (GOME-2) with observed anomalies in temperature (T; CRU-TS), liquid water equivalent (LWE) from the Gravity Recovery and Climate Experiment (GRACE), and photosynthetically active radiation (PAR; CERES SYN1deg). Using observations from 2007 through 2015 for several NH regions, we calculate month-specific sensitivities of SIF to variability in T, LWE, and PAR. These sensitivities provide insight into the seasonal progression of how productivity is affected by climate variability and can be used to effectively model the observed SIF signal. In general, we find that high temperatures are beneficial to productivity in the spring, but detrimental in the summer. The influences of PAR and LWE are more heterogeneous between regions; for example, higher LWE in North American temperate forest leads to decreased springtime productivity, while exhibiting a contrasting effect in water-limited regions. Lastly, we assess the influence of variations in terrestrial productivity on atmospheric carbon using a new lower tropospheric CO2 product derived from the Greenhouse Gases Observing Satellite (GOSAT). Together, these data shed light on the drivers of interannual variability in the annual cycle of NH atmospheric CO2, and may provide improved constraints on projections of long-term carbon cycle responses to climate change.

Extensive Variation in Chromatin States Across Humans

KAUST Repository

Kasowski, M.

2013-10-17

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

Extensive Variation in Chromatin States Across Humans

KAUST Repository

Kasowski, M.; Kyriazopoulou-Panagiotopoulou, S.; Grubert, F.; Zaugg, J. B.; Kundaje, A.; Liu, Y.; Boyle, A. P.; Zhang, Q. C.; Zakharia, F.; Spacek, D. V.; Li, J.; Xie, D.; Olarerin-George, A.; Steinmetz, L. M.; Hogenesch, J. B.; Kellis, M.; Batzoglou, S.; Snyder, M.

2013-01-01

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

Preschool Language Variation, Growth, and Predictors in Children on the Autism Spectrum

Science.gov (United States)

Ellis Weismer, Susan; Kover, Sara T.

2015-01-01

Background: There is wide variation in language abilities among young children with autism spectrum disorders (ASD), with some toddlers developing age-appropriate language while others remain minimally verbal after age 5. Conflicting findings exist regarding predictors of language outcomes in ASD and various methodological issues limit the…

Active feedback wide-field optical low-coherence interferometry for ultrahigh-speed three-dimensional morphometry

International Nuclear Information System (INIS)

Choi, Woo June; Choi, Hae Young; Lee, Byeong Ha; Na, Jihoon; Eom, Jonghyun

2010-01-01

A novel optical interferometric scheme for ultrahigh-speed three-dimensional morphometry is proposed. The system is based on wide-field optical coherence tomography (WF-OCT) but with optically chopped illumination. The chopping frequency is feedback-controlled to be always matched with the Doppler frequency of the OCT interferometer, which provides an efficient page-wide demodulation suitable for ultrahigh-speed volumetric imaging. To compensate the unwanted variation in the OCT Doppler frequency of the system, the illumination frequency is phase-locked with an auxiliary laser interferometer which shares the reference arm with the OCT interferometer. The two-dimensional (2D) interference signals projected on the 2D array pixels of a 200 Hz CCD are accumulated during one imaging frame of the CCD. Then, each pixel of the CCD demodulates the OCT signal automatically. Owing to the proposed active frequency-locked illumination scheme, the demodulation does not depend on the variation in the axial scanning speed. Volumetric topograms or/and tomograms of several samples were achieved and rendered with a sensitivity of 58 dB at an axial scan speed of 0.805 mm s −1

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

OpenAIRE

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gen...

Wandel und Variation in der Morphosyntax der schweizerdeutschen Dialekte

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Elvira Glaser

2014-12-01

Full Text Available Syntactic Variation and change in Swiss German dialects The article deals with the areal distribution of morphosyntactic variants in Swiss German dialects. The Zurich project “Syntaktischer Atlas der deutschen Schweiz” (SADS has provided a lot of evidence for the existence of syntactic isoglosses within the German-speaking regions of Switzerland. In the following, we will discuss several types of variant distribution. There are syntactic variables showing a division of Western and Eastern Swiss German dialects, a division well known from phonology and lexis. In addition, we find few archaic variants restricted to southern Highest Alemannic, again in line with other linguistic levels. Most interesting are some variants showing up in quite small – and differing – regions. These regions usually do not only show these specific variants but variation with a more common variant. This leads to a discussion of the implications of variation. Variation is not only seen as an indication of an ongoing change, but it is argued that there is evidence for a long lasting variational situation and largely stable variation respectively. Several possible types of comparison with older data and between age groups (apparent time analysis within the data are presented. There are relatively few cases where we can show larger shifts between two regional variants and there seem to be only some rare cases of syntactic influence by Standard German introducing new variants. With respect to the old question of morphosyntactic borrowing, Swiss German dialects show cases of resistance as well as cases of interference, the latter concerning loan translation and semantic adaptation if the structure favors it.

Background selection as baseline for nucleotide variation across the Drosophila genome.

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Josep M Comeron

2014-06-01

Full Text Available The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS. Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms at 100-kb scale, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and, thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and

A cost-effective method to characterize variation in clinical practice.

Science.gov (United States)

Chang, K; Sauereisen, S; Dlutowski, M; Veloski, J J; Nash, D B

1999-06-01

This study's objective was to measure variation in physicians' practice styles and policies. Family physicians and general internists were surveyed about evidence-based medicine in the areas of asthma, congestive heart failure, and diabetes mellitus. They were asked about clinical recommendations where standards of practice were uncertain, controversial, or changing in response to published guidelines. Also included were items dealing with managed care. Although there was wide variation in responses to 20 of 36 items, some responses were consistent with practice guidelines. Responses to several items indicated a tendency to overuse expensive tests. Overall, the results indicate that a brief, open-ended survey can assess practice variation quickly and economically, as contrasted with more expensive analyses of medical records or claims data. With proper validation such assessments can be used as baselines to guide interventions, as well as measures of the outcomes of these interventions to change practice styles.

Measurement of isotope abundance variations in nature by gravimetric spiking isotope dilution analysis (GS-IDA).

Science.gov (United States)

Chew, Gina; Walczyk, Thomas

2013-04-02

Subtle variations in the isotopic composition of elements carry unique information about physical and chemical processes in nature and are now exploited widely in diverse areas of research. Reliable measurement of natural isotope abundance variations is among the biggest challenges in inorganic mass spectrometry as they are highly sensitive to methodological bias. For decades, double spiking of the sample with a mix of two stable isotopes has been considered the reference technique for measuring such variations both by multicollector-inductively coupled plasma mass spectrometry (MC-ICPMS) and multicollector-thermal ionization mass spectrometry (MC-TIMS). However, this technique can only be applied to elements having at least four stable isotopes. Here we present a novel approach that requires measurement of three isotope signals only and which is more robust than the conventional double spiking technique. This became possible by gravimetric mixing of the sample with an isotopic spike in different proportions and by applying principles of isotope dilution for data analysis (GS-IDA). The potential and principle use of the technique is demonstrated for Mg in human urine using MC-TIMS for isotopic analysis. Mg is an element inaccessible to double spiking methods as it consists of three stable isotopes only and shows great potential for metabolically induced isotope effects waiting to be explored.

Ecological and evolutionary variation in community nitrogen use traits during tropical dry forest secondary succession.

Science.gov (United States)

Bhaskar, Radika; Porder, Stephen; Balvanera, Patricia; Edwards, Erika J

2016-05-01

We assessed the role of ecological and evolutionary processes in driving variation in leaf and litter traits related to nitrogen (N) use among tropical dry forest trees in old-growth and secondary stands in western Mexico. Our expectation was that legumes (Fabaceae), a dominant component of the regional flora, would have consistently high leaf N and therefore structure phylogenetic variation in N-related traits. We also expected ecological selection during succession for differences in nitrogen use strategies, and corresponding shifts in legume abundance. We used phylogenetic analyses to test for trait conservatism in foliar and litter N, C:N, and N resorption. We also evaluated differences in N-related traits between old-growth and secondary forests. We found a weak phylogenetic signal for all traits, partly explained by wide variation within legumes. Across taxa we observed a positive relationship between leaf and litter N, but no shift in resorption strategies along the successional gradient. Despite species turnover, N-resorption, and N-related traits showed little change across succession, suggesting that, at least for these traits, secondary forests rapidly recover ecosystem function. Collectively, our results also suggest that legumes should not be considered a single functional group from a biogeochemical perspective.

Millennial-scale Climate Variations Recorded As Far Back As The Early Pliocene

Science.gov (United States)

Steenbrink, J.; Hilgen, F. J.; Lourens, L. J.

Quaternary climate proxy records show compelling evidence for climate variability on time scales of a few thousand years. The causes for these millennial-scale or sub- Milankovitch cycles are yet poorly understood, not in the least due to the complex feedback mechanisms of large ice-sheets during the Quaternary. We present evidence of millennial-scale climate variability in Early Pliocene lacustrine sediments from the intramontane Ptolemais Basin in northwestern Greece. The sediments are well ex- posed in a series of open-pit lignite mines and exhibit a distinct m-scale sedimentary cyclicity of alternating lignites and lacustrine marl beds that result from precession- induced variations in climate. A higher-frequency cyclicity is particular prominent within the marl segment of individual cycles. A stratigraphic interval of~115 kyr, cov- ering five precession-induced sedimentary cycles, was studied in nine parallel sections from two quarries located several km apart. Colour reflectance records were used to quantify the within-cycle variability and to determine its lateral continuity. Much of the within-cycle variability could be correlated between the parallel sections, even in fine detail, which suggests that these changes reflect basin-wide variations in environ- mental conditions related to (regional) climate fluctuations. Interbedded volcanic ash beds demonstrate the synchronicity of these fluctuations and spectral analysis of the reflectance time series shows a significant concentration of variability at periods of ~11,~5.5 and~2 kyr. Their occurrence at times before the intensification of the North- ern Hemisphere glaciation suggests that they cannot solely have resulted from internal ice-sheet dynamics. Possible candidates include harmonics or combination tones of the main orbital cycles, variations in solar output or periodic motions of the Earth and moon.

Camouflage and individual variation in shore crabs (Carcinus maenas from different habitats.

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Martin Stevens

Full Text Available Camouflage is widespread throughout the natural world and conceals animals from predators in a vast range of habitats. Because successful camouflage usually involves matching aspects of the background environment, species and populations should evolve appearances tuned to their local habitat, termed phenotype-environment associations. However, although this has been studied in various species, little work has objectively quantified the appearances of camouflaged animals from different habitats, or related this to factors such as ontogeny and individual variation. Here, we tested for phenotype-environment associations in the common shore crab (Carcinus maenas, a species highly variable in appearance and found in a wide range of habitats. We used field surveys and digital image analysis of the colors and patterns of crabs found in four locations around Cornwall in the UK to quantify how individuals vary with habitat (predominantly rockpool, mussel bed, and mudflat. We find that individuals from sites comprising different backgrounds show substantial differences in several aspects of color and pattern, and that this is also dependent on life stage (adult or juvenile. Furthermore, the level of individual variation is dependent on site and life stage, with juvenile crabs often more variable than adults, and individuals from more homogenous habitats less diverse. Ours is the most comprehensive study to date exploring phenotype-environment associations for camouflage and individual variation in a species, and we discuss the implications of our results in terms of the mechanisms and selection pressures that may drive this.

Camouflage and individual variation in shore crabs (Carcinus maenas) from different habitats.

Science.gov (United States)

Stevens, Martin; Lown, Alice E; Wood, Louisa E

2014-01-01

Camouflage is widespread throughout the natural world and conceals animals from predators in a vast range of habitats. Because successful camouflage usually involves matching aspects of the background environment, species and populations should evolve appearances tuned to their local habitat, termed phenotype-environment associations. However, although this has been studied in various species, little work has objectively quantified the appearances of camouflaged animals from different habitats, or related this to factors such as ontogeny and individual variation. Here, we tested for phenotype-environment associations in the common shore crab (Carcinus maenas), a species highly variable in appearance and found in a wide range of habitats. We used field surveys and digital image analysis of the colors and patterns of crabs found in four locations around Cornwall in the UK to quantify how individuals vary with habitat (predominantly rockpool, mussel bed, and mudflat). We find that individuals from sites comprising different backgrounds show substantial differences in several aspects of color and pattern, and that this is also dependent on life stage (adult or juvenile). Furthermore, the level of individual variation is dependent on site and life stage, with juvenile crabs often more variable than adults, and individuals from more homogenous habitats less diverse. Ours is the most comprehensive study to date exploring phenotype-environment associations for camouflage and individual variation in a species, and we discuss the implications of our results in terms of the mechanisms and selection pressures that may drive this.

SABER (TIMED) and MLS (UARS) Temperature Observations of Mesospheric and Stratospheric QBO and Related Tidal Variations

Science.gov (United States)

Huang, Frank T.; Mayr, Hans G.; Reber, Carl A.; Russell, James; Mlynczak, Marty; Mengel, John

2006-01-01

More than three years of temperature observations from the SABER (TIMED) and MLS WARS) instruments are analyzed to study the annual and inter-annual variations extending from the stratosphere into the upper mesosphere. The SABER measurements provide data from a wide altitude range (15 to 95 km) for the years 2002 to 2004, while the MLS data were taken in the 16 to 55 km altitude range a decade earlier. Because of the sampling properties of SABER and MLS, the variations with local solar time must be accounted for when estimating the zonal mean variations. An algorithm is thus applied that delineates with Fourier analysis the year-long variations of the migrating tides and zonal mean component. The amplitude of the diurnal tide near the equator shows a strong semiannual periodicity with maxima near equinox, which vary from year to year to indicate the influence from the Quasi-biennial Oscillation (QBO) in the zonal circulation. The zonal mean QBO temperature variations are analyzed over a range of latitudes and altitudes, and the results are presented for latitudes from 48"s to 48"N. New results are obtained for the QBO, especially in the upper stratosphere and mesosphere, and at mid-latitudes. At Equatorial latitudes, the QBO amplitudes show local peaks, albeit small, that occur at different altitudes. From about 20 to 40 km, and within about 15" of the Equator, the amplitudes can approach 3S K for the stratospheric QBO or SQBO. For the mesospheric QBO or MQBO, we find peaks near 70 km, with temperature amplitudes reaching 3.5"K, and near 85 km, the amplitudes approach 2.5OK. Morphologically, the amplitude and phase variations derived from the SABER and MLS measurements are in qualitative agreement. The QBO amplitudes tend to peak at the Equator but then increase again pole-ward of about 15" to 20'. The phase progression with altitude varies more gradually at the Equator than at mid-latitudes. A comparison of the observations with results from the Numerical Spectral

COELIAC TRUNK BRANCHING PATTERN AND VARIATION

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Jude Jose Thomson

2017-01-01

Full Text Available BACKGROUND Anatomical variations involving the visceral arteries are common. However, variations in coeliac trunk are usually asymptomatic, they may become important in patients undergoing diagnostic angiography for gastrointestinal bleeding or prior to an operative procedure. This study was useful for knowing the possible morphological variations before an upper abdominal surgery. MATERIALS AND METHODS This was a descriptive study done by cadaveric dissection, conducted on thirty cadavers. The coeliac trunk being examined for its origin, branching pattern, distribution, and variations. Results were statistically analysed and compared with the previous studies. RESULTS In our study, 60% of the coeliac trunk shows variations and 40% have normal branching pattern. A complete absence of coeliac trunk was observed in one case. In the present study the Right inferior phrenic artery arising from coeliac trunk in 2 cases (6.6% and left inferior phrenic artery arising from coeliac trunk in 3 cases (9.9%. Both inferior phrenic arteries are arising from coeliac trunk in 2 cases (6.6%. The common hepatomesenteric trunk and gastro splenic trunk was found in 1 case (3.3%. Hepatosplenic trunk was found in 2 cases (6.6%. In another 2 cases (6.6% gastric and hepatic artery originate from coeliac trunk but splenic artery has a separate origin from abdominal aorta. An absent trunk was also found in 1 case (3.3%. In 5 cases (16.7% showed trifurcation with variation in the branching pattern. CONCLUSION The branching pattern and extreme degree variability in coeliac trunk as brought out in the observations of the present study make it obvious that the present study almost falls in description with previous studies.

Frequency variations of discrete cranial traits in major human populations. I. Supernumerary ossicle variations.

Science.gov (United States)

Hanihara, T; Ishida, H

2001-06-01

Four supernumerary ossicle variations-the ossicle at the lambda, the parietal notch bone, the asterionic bone, and the occipitomastoid bone-were examined for laterality differences, intertrait correlations, sex differences, and between group variations in the samples from around the world. Significant laterality differences were not detected in almost all samples. In some pairs of traits, significant association of occurrence were found. Several geographic samples were sexually dimorphic with respect to the asterionic bone and to a lesser extent for the parietal notch bone. East/Northeast Asians including the Arctic populations in general had lower frequencies of the 4 accessory ossicles. Australians, Melanesians and the majority of the New World peoples, on the other hand, generally had high frequencies. In the western hemisphere of the Old World, Subsaharan Africans had relatively high frequencies. Except for the ossicle at the lambda, the distribution pattern in incidence showed clinal variation from south to north. Any identifiable adaptive value related to environmental or subsistence factors may be expressed in such clinal variation. This may allow us to hypothesise that not only mechanical factors but a founder effect, genetic drift, and population structure could have been the underlying causes for interregional variation and possible clines in the incidences of the accessory ossicles.

Variations in the male genitalia of Aedes (Stegomyia Albopictus (Skuse from Chandigarh and its surrounding areas (Diptera: Culicidae

Directory of Open Access Journals (Sweden)

Sagandeep Kaur

2014-09-01

Full Text Available The Asian tiger mosquito Aedes albopictus is the most dominant species of subgenus Stegomyia and is medically important from the standpoint of transmitting wide range of human pathogens of deadly diseases like dengue, yellow fever and chikungunya. During present investigations, it has been observed that IX tergum in the male genitalia of Aedes albopictus varies greatly. It shows variations with respect to the presence or absence of lateral projections on the IX tergum, as well as in the shape and size of median and lateral projections. The shape of IX tergum in the male genitalia of Aedes species is of great taxonomic importance as it is a diagnostic character of the species. These variations have been observed both in natural populations collected from various breeding sites as well as in the adults reared in laboratory. The observed differences have not been noticed by any of the previous workers.

Characteristics of seasonal variation and solar activity dependence of the geomagnetic solar quiet daily variation

Science.gov (United States)

Shinbori, A.; Koyama, Y.; Nose, M.; Hori, T.

2017-12-01

Characteristics of seasonal variation and solar activity dependence of the X- and Y-components of the geomagnetic solar quiet (Sq) daily variation at Memanbetsu in mid-latitudes and Guam near the equator have been investigated using long-term geomagnetic field data with 1-h time resolution from 1957 to 2016. In this analysis, we defined the quiet day when the maximum value of the Kp index is less than 3 for that day. In this analysis, we used the monthly average of the adjusted daily F10.7 corresponding to geomagnetically quiet days. For identification of the monthly mean Sq variation in the X and Y components (Sq-X and Sq-Y), we first determined the baseline of the X and Y components from the average value from 22 to 2 h (LT: local time) for each quiet day. Next, we calculated a deviation from the baseline of the X- and Y-components of the geomagnetic field for each quiet day, and computed the monthly mean value of the deviation for each local time. As a result, Sq-X and Sq-Y shows a clear seasonal variation and solar activity dependence. The amplitude of seasonal variation increases significantly during high solar activities, and is proportional to the solar F10.7 index. The pattern of the seasonal variation is quite different between Sq-X and Sq-Y. The result of the correlation analysis between the solar F10.7 index and Sq-X and Sq-Y shows almost the linear relationship, but the slope and intercept of the linear fitted line varies as function of local time and month. This implies that the sensitivity of Sq-X and Sq-Y to the solar activity is different for different local times and seasons. The local time dependence of the offset value of Sq-Y at Guam and its seasonal variation suggest a magnetic field produced by inter-hemispheric field-aligned currents (FACs). From the sign of the offset value of Sq-Y, it is infer that the inter-hemispheric FACs flow from the summer to winter hemispheres in the dawn and dusk sectors and from the winter to summer hemispheres in

Variations in stable hydrogen and oxygen isotopes in atmospheric water vapor in the marine boundary layer across a wide latitude range.

Science.gov (United States)

Liu, Jingfeng; Xiao, Cunde; Ding, Minghu; Ren, Jiawen

2014-11-01

The newly-developed cavity ring-down laser absorption spectroscopy analyzer with special calibration protocols has enabled the direct measurement of atmospheric vapor isotopes at high spatial and temporal resolution. This paper presents real-time hydrogen and oxygen stable isotope data for atmospheric water vapor above the sea surface, over a wide range of latitudes spanning from 38°N to 69°S. Our results showed relatively higher values of δ(18)O and δ(2)H in the subtropical regions than those in the tropical and high latitude regions, and also a notable decreasing trend in the Antarctic coastal region. By combining the hydrogen and oxygen isotope data with meteoric water line and backward trajectory model analysis, we explored the kinetic fractionation caused by subsiding air masses and related saturated vapor pressure in the subtropics, and the evaporation-driven kinetic fractionation in the Antarctic region. Simultaneous observations of meteorological and marine variables were used to interpret the isotopic composition characteristics and influential factors, indicating that d-excess is negatively correlated with humidity across a wide range of latitudes and weather conditions worldwide. Coincident with previous studies, d-excess is also positively correlated with sea surface temperature and air temperature (Tair), with greater sensitivity to Tair. Thus, atmospheric vapor isotopes measured with high accuracy and good spatial-temporal resolution could act as informative tracers for exploring the water cycle at different regional scales. Such monitoring efforts should be undertaken over a longer time period and in different regions of the world. Copyright © 2014. Published by Elsevier B.V.

Cosmological constants and variations

International Nuclear Information System (INIS)

Barrow, John D

2005-01-01

We review properties of theories for the variation of the gravitation and fine structure 'constants'. We highlight some general features of the cosmological models that exist in these theories with reference to recent quasar data that is consistent with time-variation in the fine structure 'constant' since a redshift of 3.5. The behaviour of a simple class of varying alpha cosmologies is outlined in the light of all the observational constraints. We also discuss some of the consequences of varying 'constants' for oscillating universes and show by means of exact solutions that they appear to evolve monotonically in time even though the scale factor of the universe oscillates

Variation in recruitment across sites in a consent-based clinical data registry: lessons from the Canadian Stroke Network

Directory of Open Access Journals (Sweden)

Richards Janice A

2006-05-01

Full Text Available Abstract Background In earlier work, we found important selection biases when we tried to obtain consent for participation in a national stroke registry. Recognizing that not all registries will be exempt from requiring consent for participation, we examine here in greater depth the reasons for the poor accrual of patients from a systems perspective with a view to obtaining as representative sample as possible. Methods We determined the percent of eligible patients who were approached to participate and, among those approached, the percent who actually consented to participate. In addition we examined the reasons why people were not approached or did not consent and the variation across sites in the percent of patients approached and consented. We also considered site variation in restrictions on the accrual and data collection process imposed by either the local research ethics board or the hospital. Results Seventy percent of stroke patients were approached, with wide variations in approach rates across sites (from: 41% to 86%, and considerable inter-site variation in hospital policies governing patient accrual. Chief reasons for not approaching were discharge or death before being approached for consent. Seventeen percent of those approached refused to participate (range: 5% to 75%. Finally, 11% of those approached did not participate due to language or communication difficulties. Conclusion We found wide variation in approach and agree rates across sites that were accounted for, in part, by different approaches to accrual and idiosyncratic policies of the hospitals. This wide variation in approach and agree rates raises important challenges for research ethics boards and data protection authorities in determining when to waive consent requirements, when to press for increased quality control, when to permit local adaptation of the consent process, and when to permit alternatives to individual express consent. We offer several suggestions for

Skin care practice in German nursing homes: a German-wide cross-sectional study.

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Kottner, Jan; Rahn, Yasmin; Blume-Peytavi, Ulrike; Lahmann, Nils

2013-04-01

Due to anatomical and physiological changes in the course of aging and due to increased vulnerability, there are special skin care needs in elderly and care-dependent persons. Little is known about skin care practice in German long-term care facilities. The aim of the study was to gather epidemiological data about skin care practice in German nursing homes. In spring 2012 a German-wide cross sectional study was conducted in 47 nursing homes. Based on standardized data collection sheets. demographics and variables about methods and frequencies of skin cleansing and application of skin care products for 3 552 nursing home residents were collected and analyzed. The variables age, gender and level of care dependency was representative for the group of all German nursing home residents. More than 90% of investigated nursing home residents required skin care assistance. Washing body parts or the whole body were conducted most frequently (89.1%, 95% CI 88.0- 90.1). Skin care leave-on products were used in 91.7% (95% CI 90.7-92.6), whereas there were large variations between individuals. In total, more than 100 brands were used. Skin care practice in multimorbid care dependent persons shows large variations. How skin care products meet the special requirements of aged skin and whether they enhance the skin barrier function and prevent cuteneous skin damage is unknown. © The Authors • Journal compilation © Blackwell Verlag GmbH, Berlin.

Variation of global DNA methylation levels with age and in autistic children.

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Tsang, Shui-Ying; Ahmad, Tanveer; Mat, Flora W K; Zhao, Cunyou; Xiao, Shifu; Xia, Kun; Xue, Hong

2016-09-23

The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2-97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us. Genome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = -0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41-55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001). The multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation.

Structural variations and physical properties of lignin coke

International Nuclear Information System (INIS)

Otani, C.

1986-01-01

The studied lignin is a by-product of the process of ethanol production from eucaliptus. It was heat-treated under inert atmosphere conditions at increasing temperatures from 300 0 C up to 2600 0 C. This material has about 35 weight % of carbon yield and low ash content (0.70 w %). The structural variations were studied by wide-angle X-ray diffraction, small-angle X-ray scattering and infra-red spectroscopy. The bulk and the ''real'' density of the samples have also been determined as a function of the heat treatment temperatures. These experimental results enabled us to establish a mechanism of structure variation based on the formation of a graphite-like and porous structure within the initially amorphous lignin matrix. It has been possible to specify the adequate heat treatment temperature based upon the lignin coke applications. (author) [pt

Variation tolerant SoC design

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Kozhikkottu, Vivek J.

performance distribution. This task is particularly complex and challenging due to the inter-dependencies between components' execution, indirect effects of shared resources, and interactions between multiple system-level "execution paths". We argue that accurate variation-aware performance analysis requires Monte-Carlo based repeated system execution. Our proposed analysis framework leverages emulation to significantly speedup performance analysis without sacrificing the generality and accuracy achieved by Monte-Carlo based simulations. Our experiments show performance improvements of around 60x compared to state-of-the-art hardware-software co-simulation tools and also underscore the framework's potential to enable variation-aware design and exploration at the system level. Our second contribution addresses the problem of designing variation-tolerant SoCs using recovery based design, a popular circuit design paradigm that addresses variations by eliminating guard-bands and operating circuits at close to "zero margins" while detecting and recovering from timing errors. While previous efforts have demonstrated the potential benefits of recovery based design, we identify several challenges that need to be addressed in order to apply this technique to SoCs. We present a systematic design framework to apply recovery based design at the system level. We propose to partition SoCs into "recovery islands", wherein each recovery island consists of one or more SoC components that can recover independent of the rest of the SoC. We present a variation-aware design methodology that partitions a given SoC into recovery islands and computes the optimal operating points for each island, taking into account the various trade-offs involved. Our experiments demonstrate that the proposed design framework achieves an average of 32% energy savings over conventional worst-case designs, with negligible losses in performance. The third contribution of this thesis introduces disproportionate

Wide-focus subject-verb inversion in Ibero-Romance: A locative account

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Alice Corr

2016-06-01

Full Text Available This paper explores the hypothesis that wide-focus subject-verb inversion in Ibero-Romance is a type of locative inversion, involving a null locative argument. Ibero-Romance displays fine-grained, systematic variation determined by verbal class and variety, offering evidence that Ibero-Romance neutral word order is SVO, rather than VSO as claimed by some null-subject accounts. It is proposed that ‘locative’ subject-verb inversion is a consequence of grammatically-encoded deictic features correlating with the semantic properties of the verbs involved. The locative element, available unequally across Ibero-Romance, can surface in different positions in the left periphery, yielding the variation encountered. The data indicate that the licensing of these constructions depends neither on the null-subject parameter, since this type of inversion also occurs in non- and partial null-subject varieties, nor on the unaccusative/unergative division, though in both cases a degree of correspondence exists.

Tobacco Surcharges on 2015 Health Insurance Plans Sold in Federally Facilitated Marketplaces: Variations by Age and Geography and Implications for Health Equity.

Science.gov (United States)

Liber, Alex C; Drope, Jeffrey M; Graetz, Ilana; Waters, Teresa M; Kaplan, Cameron M

2015-11-01

In 2014, few health insurance plans sold in the Affordable Care Act's Federally Facilitated Marketplaces had age-dependent tobacco surcharges, possibly because of a system glitch. The 2015 tobacco surcharges show wide variation, with more plans implementing tobacco surcharges that increase with age. This underscores concerns that older tobacco users will find postsubsidy health insurance premiums difficult to afford. Future monitoring of enrollment will determine whether tobacco surcharges cause adverse selection by dissuading tobacco users, particularly older users, from buying health insurance.

Outdoor radon variation in Romania

International Nuclear Information System (INIS)

Simion, Elena; Simion, Florin

2008-01-01

Full text: The results of a long-term survey (1992 - 2006) of the variations of outdoor radon concentrations in semi-natural location from Romania are reported in the present paper. Measurements, covering between two and four sessions of the day (morning, afternoon, evening and night), were performed on a daily bases by 37 Environmental Radioactivity Monitoring Stations from National Environmental Radioactivity Survey Network. The method used was based on indirect determination of outdoor radon from aerosol samples collected on glass micro-fibre filters by drawing the air through the filters. The sampling was performed in a fixed place at a height of 2 m above the ground surface. Total beta counting of aerosol samples collected was performed immediately and after 20 hours. Values recorded during the years of continuous measurement indicated the presence of several patterns in the long-term variation of outdoor radon concentration: diurnal, seasonal and annual variation. For diurnal variation, outdoor radon concentration shows a maximum values in the night (early hours) and minimum values by day (in the afternoon). On average, this maximum is a factor of 2 higher than the minimum. Late autumn - beginning of winter maximum and an early spring minimum are characteristic for seasonal patterns. In the long term a seasonal pattern was observed for diurnal variation, with an average diurnal maximum to minimum ratio of 1.33 in winter compared with 3.0 in the summer months. The variations of outdoor radon levels showed little correlation with the uranium concentration of the ground and were attributed to changes in soil moisture content. In dry seasons, because of the low precipitation, the soil was drying out in the summer allowing fractures to develop and radon to migrate easily through the ground. Depending on micro-climatic and geological conditions, outdoor radon average concentrations in different regions of Romania are from 1200 mBq/mc to 13065 mBq/mc. The smallest

Seasonal variations of indoor radon concentrations

International Nuclear Information System (INIS)

Majborn, B.

1990-01-01

Seasonal variations of indoor radon concentrations have been studied in a cluster of 10 single-family houses. Eight of the houses are of a similar construction with slab-on-grade foundations. The remaining two houses have different substructures, one of them having a crawl space, and the other having partly a basement and partly a crawl space. A 'normal' seasonal variation of the radon concentration with a maximum in winter and a minimum in summer was observed in most of the houses. In these houses the variation showed a strong correlation with the indoor-outdoor temperature difference on a 2-month basis. However, deviating seasonal variations were observed in some of the houses, notably in the two houses having different substructures. This paper reports that a re-examination of the data obtained in a previous study indicates that winter/summer ratios of indoor radon concentrations in Danish houses depend on the house substructure. The mean winter/summer ratios were about 2.1 for houses with slab-on-grade foundations, 1.5 for houses having a basement, and 1.0 for houses with a crawl space (geometric mean values). However, a study with more houses in each substructure category will be needed to show whether or not the indicated differences are generally valid for Danish houses

Strain Variation along Cimandiri Fault, West Java Based on Continuous and Campaign GPS Observation From 2006-2016

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Safitri, A. A.; Meilano, I.; Gunawan, E.; Abidin, H. Z.; Efendi, J.; Kriswati, E.

2018-03-01

The Cimandiri fault which is running in the direction from Pelabuhan Ratu to Padalarang is the longest fault in West Java with several previous shallow earthquakes in the last 20 years. By using continues and campaign GPS observation from 2006-2016, we obtain the deformation pattern along the fault through the variation of strain tensor. We use the velocity vector of GPS station which is fixed in stable International Terrestrial Reference Frame 2008 to calculate horizontal strain tensor. Least Square Collocation is applied to produce widely dense distributed velocity vector and optimum scale factor for the Least Square Weighting matrix. We find that the strain tensor tend to change from dominantly contraction in the west to dominantly extension to the east of fault. Both the maximum shear strain and dilatation show positive value along the fault and increasing from the west to the east. The findings of strain tensor variation along Cimandiri Fault indicate the post seismic effect of the 2006 Java Earthquake.

Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation.

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Mishra, Anshuman; Nizammuddin, Sheikh; Mallick, Chandana Basu; Singh, Sakshi; Prakash, Satya; Siddiqui, Niyamat Ali; Rai, Niraj; Carlus, S Justin; Sudhakar, Digumarthi V S; Tripathi, Vishnu P; Möls, Märt; Kim-Howard, Xana; Dewangan, Hemlata; Mishra, Abhishek; Reddy, Alla G; Roy, Biswajit; Pandey, Krishna; Chaubey, Gyaneshwer; Das, Pradeep; Nath, Swapan K; Singh, Lalji; Thangaraj, Kumarasamy

2017-03-01

Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Dopa decarboxylase (Ddc) affects variation in Drosophila longevity.

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De Luca, Maria; Roshina, Nataliya V; Geiger-Thornsberry, Gretchen L; Lyman, Richard F; Pasyukova, Elena G; Mackay, Trudy F C

2003-08-01

Mutational analyses in model organisms have shown that genes affecting metabolism and stress resistance regulate life span, but the genes responsible for variation in longevity in natural populations are largely unidentified. Previously, we mapped quantitative trait loci (QTLs) affecting variation in longevity between two Drosophila melanogaster strains. Here, we show that the longevity QTL in the 36E;38B cytogenetic interval on chromosome 2 contains multiple closely linked QTLs, including the Dopa decarboxylase (Ddc) locus. Complementation tests to mutations show that Ddc is a positional candidate gene for life span in these strains. Linkage disequilibrium (LD) mapping in a sample of 173 alleles from a single population shows that three common molecular polymorphisms in Ddc account for 15.5% of the genetic contribution to variance in life span from chromosome 2. The polymorphisms are in strong LD, and the effects of the haplotypes on longevity suggest that the polymorphisms are maintained by balancing selection. DDC catalyzes the final step in the synthesis of the neurotransmitters, dopamine and serotonin. Thus, these data implicate variation in the synthesis of bioamines as a factor contributing to natural variation in individual life span.

Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin.

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Jennifer L Bolton

2014-07-01

Full Text Available Variation in plasma levels of cortisol, an essential hormone in the stress response, is associated in population-based studies with cardio-metabolic, inflammatory and neuro-cognitive traits and diseases. Heritability of plasma cortisol is estimated at 30-60% but no common genetic contribution has been identified. The CORtisol NETwork (CORNET consortium undertook genome wide association meta-analysis for plasma cortisol in 12,597 Caucasian participants, replicated in 2,795 participants. The results indicate that <1% of variance in plasma cortisol is accounted for by genetic variation in a single region of chromosome 14. This locus spans SERPINA6, encoding corticosteroid binding globulin (CBG, the major cortisol-binding protein in plasma, and SERPINA1, encoding α1-antitrypsin (which inhibits cleavage of the reactive centre loop that releases cortisol from CBG. Three partially independent signals were identified within the region, represented by common SNPs; detailed biochemical investigation in a nested sub-cohort showed all these SNPs were associated with variation in total cortisol binding activity in plasma, but some variants influenced total CBG concentrations while the top hit (rs12589136 influenced the immunoreactivity of the reactive centre loop of CBG. Exome chip and 1000 Genomes imputation analysis of this locus in the CROATIA-Korcula cohort identified missense mutations in SERPINA6 and SERPINA1 that did not account for the effects of common variants. These findings reveal a novel common genetic source of variation in binding of cortisol by CBG, and reinforce the key role of CBG in determining plasma cortisol levels. In turn this genetic variation may contribute to cortisol-associated degenerative diseases.

Spatial and temporal variation in proportional stock density and relative weight of smallmouth bass in a reservoir

Science.gov (United States)

Mesa, Matthew G.; Duke, S.D.; Ward, David L.

1990-01-01

Population data for smallmouth bass Micropterus dolomieui in 20,235 ha John Day Reservoir on the Columbia River were used to (1) determine whether Proportional Stock Density (PSD) and Relative Weight (Wr) varied spatially and temporally in two areas of the reservoir with established smallmouth bass fisheries; (2) explore possible causes of any observed variation; and (3) discuss some management implications and recommendations. Both PSD and Wr varied spatially and monthly in all years examined. On an annual basis, PSD varied at one area but not at the other, whereas Wr showed little variation. Possible explanations for the variation in PSD and Wr are differences in growth, mortality, recruitment, and exploitation. Our data suggested that regulations established or changed on a reservoir-wide basis may have different effects on the fishery, depending on location in the reservoir. Also, pooling data from various areas within a reservoir to yield point estimates of structural indices may not represent the variation present in the population as a whole. The significant temporal variability reflects the importance of determining the proper time to sample fish to yield representative estimates of the variable of interest. In areas with valuable fisheries or markedly different population structures, we suggest that an area-specific approach be made to reservoir fishery management, and that efforts be made toward effecting consistent harvest regulations in interstate waters.

Cryptic Plutella species show deep divergence despite the capacity to hybridize.

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Perry, Kym D; Baker, Gregory J; Powis, Kevin J; Kent, Joanne K; Ward, Christopher M; Baxter, Simon W

2018-05-29

Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays. The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1

Variational iteration method for one dimensional nonlinear thermoelasticity

International Nuclear Information System (INIS)

Sweilam, N.H.; Khader, M.M.

2007-01-01

This paper applies the variational iteration method to solve the Cauchy problem arising in one dimensional nonlinear thermoelasticity. The advantage of this method is to overcome the difficulty of calculation of Adomian's polynomials in the Adomian's decomposition method. The numerical results of this method are compared with the exact solution of an artificial model to show the efficiency of the method. The approximate solutions show that the variational iteration method is a powerful mathematical tool for solving nonlinear problems

Analysis of Natural Variation in Bermudagrass (Cynodon dactylon) Reveals Physiological Responses Underlying Drought Tolerance

Science.gov (United States)

Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

2012-01-01

Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H2O2 content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system. PMID:23285294

Incidence, time trends and regional variation of childhood leukaemia in Germany and Europe

International Nuclear Information System (INIS)

Kaatsch, P.; Mergenthaler, A.

2008-01-01

This paper presents data on the German and Europe-wide incidence, time trends and regional variations of childhood leukaemia. Data were provided by the German Childhood Cancer Registry (GCCR), a population-based cancer registry recording all cases of malignant diseases in children under 15 y of age residing in Germany and by the Automated Childhood Cancer Information System (ACCIS) co-ordinated at International Agency for Research on Cancer, Lyon, that combines and evaluates data from several European population-based cancer registries. The incidence of leukaemia (44.0 per million) has increased in Europe as well as in Germany in the last decades (0.6% annually on average). Germany shows no systematic aggregation of regions with low or high cancer incidence in terms of regional clustering. Incidence rates differ between European regions with the highest rates in Northern Europe (48.0 per million) and the lowest rates in Eastern Europe (39.1). Altogether, the results from ACCIS and the GCCR show good agreement. (authors)

Variation in human recombination rates and its genetic determinants.

Directory of Open Access Journals (Sweden)

Adi Fledel-Alon

Full Text Available Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution.Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation.These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.

Activation of AMP-activated protein kinase in response to temperature elevation shows seasonal variation in the zebra mussel, Dreissena polymorpha.

Science.gov (United States)

Jost, Jennifer A; Keshwani, Sarah S; Abou-Hanna, Jacob J

2015-04-01

Global climate change is affecting ectothermic species, and a variety of studies are needed on thermal tolerances, especially from cellular and physiological perspectives. This study utilized AMP-activated protein kinase (AMPK), a key regulator of cellular energy levels, to examine the effects of high water temperatures on zebra mussel (Dreissena polymorpha) physiology. During heating, AMPK activity increased as water temperature increased to a point, and maximum AMPK activity was detected at high, but sublethal, water temperatures. This pattern varied with season, suggesting that cellular mechanisms of seasonal thermal acclimatization affect basic metabolic processes during sublethal heat stress. There was a greater seasonal variation in the water temperature at which maximum AMPK activity was measured than in lethal water temperature. Furthermore, baseline AMPK activity varied significantly across seasons, most likely reflecting altered metabolic states during times of growth and reproduction. In addition, when summer-collected mussels were lab-acclimated to winter and spring water temperatures, patterns of heat stress mirrored those of field-collected animals. These data suggest that water temperature is the main driver of the seasonal variation in physiology. This study concluded that AMPK activity, which reflects changes in energy supply and demand during heat stress, can serve as a sensitive and early indicator of temperature stress in mussels. Copyright © 2014 Elsevier Inc. All rights reserved.

Diversity evaluation based on morphological, physiological and isozyme variation in genetic resources of garlic (Allium sativum L.) collected worldwide.

Science.gov (United States)

Hirata, Sho; Abdelrahman, Mostafa; Yamauchi, Naoki; Shigyo, Masayoshi

2016-11-26

The aim of this study was to obtain primary information about the global diversity of garlic (Allium sativum L.) by evaluating morphological, physiological and isozyme variation. A total of 107 garlic accessions collected worldwide were grown in Yamaguchi, Japan. Five morphological traits (bulb weight, bulb diameter, number of cloves per bulb, number of bulbils and scape length) and one physiological trait (bolting period) of the collected garlic showed wide variation. Meanwhile, a total of 140 garlic accessions, including the 107 mentioned above, were characterized by leucine aminopeptidase (LAP) and phosphoglucoisomerase (PGI) isozyme analyses; they clearly showed polymorphisms in putative isozyme loci (Lap-1, Lap-2 and Pgi-1). Allelic frequencies were estimated in each group of accessions categorized by their geographical origin, and the observed (H o ) and expected (H e ) heterozygosities were calculated. The allelic frequencies differed between groups. A principal component analysis based on morpho-physiological data indicated a grouping of the garlic accessions into Central Asian and Northern Mediterranean groups as well as others. We discuss the roles of artificial and natural selection that may have caused differentiation in these traits, on the assumption that ancestral domesticated garlic populations have adapted in various regions using standing variation or mutations that accumulated during expansion, and have evolved along with human-preferred traits over a long history of cultivation.

Wide-bandwidth bilateral control using two-stage actuator system

International Nuclear Information System (INIS)

Kokuryu, Saori; Izutsu, Masaki; Kamamichi, Norihiro; Ishikawa, Jun

2015-01-01

This paper proposes a two-stage actuator system that consists of a coarse actuator driven by a ball screw with an AC motor (the first stage) and a fine actuator driven by a voice coil motor (the second stage). The proposed two-stage actuator system is applied to make a wide-bandwidth bilateral control system without needing expensive high-performance actuators. In the proposed system, the first stage has a wide moving range with a narrow control bandwidth, and the second stage has a narrow moving range with a wide control bandwidth. By consolidating these two inexpensive actuators with different control bandwidths in a complementary manner, a wide bandwidth bilateral control system can be constructed based on a mechanical impedance control. To show the validity of the proposed method, a prototype of the two-stage actuator system has been developed and basic performance was evaluated by experiment. The experimental results showed that a light mechanical impedance with a mass of 10 g and a damping coefficient of 2.5 N/(m/s) that is an important factor to establish good transparency in bilateral control has been successfully achieved and also showed that a better force and position responses between a master and slave is achieved by using the proposed two-stage actuator system compared with a narrow bandwidth case using a single ball screw system. (author)

Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music.

Science.gov (United States)

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

2013-01-01

Music perception and practice represent complex cognitive functions of the human brain. Recently, evidence for the molecular genetic background of music related phenotypes has been obtained. In order to further elucidate the molecular background of musical phenotypes we analyzed genome wide copy number variations (CNVs) in five extended pedigrees and in 172 unrelated subjects characterized for musical aptitude and creative functions in music. Musical aptitude was defined by combination of the scores of three music tests (COMB scores): auditory structuring ability, Seashores test for pitch and for time. Data on creativity in music (herein composing, improvising and/or arranging music) was surveyed using a web-based questionnaire.Several CNVRs containing genes that affect neurodevelopment, learning and memory were detected. A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis. Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin release and membrane trafficking of the human serotonin transporter. Interestingly, genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. Finally, a 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24. No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. In summary, CNVs and genes found in this study are related to cognitive functions. Our result suggests new candidate genes for music perception

Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music.

Directory of Open Access Journals (Sweden)

Liisa Ukkola-Vuoti

Full Text Available Music perception and practice represent complex cognitive functions of the human brain. Recently, evidence for the molecular genetic background of music related phenotypes has been obtained. In order to further elucidate the molecular background of musical phenotypes we analyzed genome wide copy number variations (CNVs in five extended pedigrees and in 172 unrelated subjects characterized for musical aptitude and creative functions in music. Musical aptitude was defined by combination of the scores of three music tests (COMB scores: auditory structuring ability, Seashores test for pitch and for time. Data on creativity in music (herein composing, improvising and/or arranging music was surveyed using a web-based questionnaire.Several CNVRs containing genes that affect neurodevelopment, learning and memory were detected. A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9 was found co-segregating with low music test scores (COMB in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis. Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM at 2p22. GALM has influence on serotonin release and membrane trafficking of the human serotonin transporter. Interestingly, genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. Finally, a 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP at 8q24. No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. In summary, CNVs and genes found in this study are related to cognitive functions. Our result suggests new candidate genes for

Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music

Science.gov (United States)

Oikkonen, Jaana; Buck, Gemma; Blancher, Christine; Raijas, Pirre; Karma, Kai; Lähdesmäki, Harri; Järvelä, Irma

2013-01-01

Music perception and practice represent complex cognitive functions of the human brain. Recently, evidence for the molecular genetic background of music related phenotypes has been obtained. In order to further elucidate the molecular background of musical phenotypes we analyzed genome wide copy number variations (CNVs) in five extended pedigrees and in 172 unrelated subjects characterized for musical aptitude and creative functions in music. Musical aptitude was defined by combination of the scores of three music tests (COMB scores): auditory structuring ability, Seashores test for pitch and for time. Data on creativity in music (herein composing, improvising and/or arranging music) was surveyed using a web-based questionnaire. Several CNVRs containing genes that affect neurodevelopment, learning and memory were detected. A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis. Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin release and membrane trafficking of the human serotonin transporter. Interestingly, genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. Finally, a 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24. No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. In summary, CNVs and genes found in this study are related to cognitive functions. Our result suggests new candidate genes for music

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure

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Hao Dapeng

2012-05-01

Full Text Available Abstract Background A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling. Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. Results We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn’t show dependence of degree. Conclusions Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to “deterministic model” of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

Solving Ratio-Dependent Predatorprey System with Constant Effort Harvesting Using Variational Iteration Method

DEFF Research Database (Denmark)

Ghotbi, Abdoul R; Barari, Amin

2009-01-01

Due to wide range of interest in use of bio-economic models to gain insight in to the scientific management of renewable resources like fisheries and forestry, variational iteration method (VIM) is employed to approximate the solution of the ratio-dependent predator-prey system with constant effort...

Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity

DEFF Research Database (Denmark)

Thorleifsson, Gudmar; Walters, G Bragi; Gudbjartsson, Daniel F

2009-01-01

Obesity results from the interaction of genetic and environmental factors. To search for sequence variants that affect variation in two common measures of obesity, weight and body mass index (BMI), both of which are highly heritable, we performed a genome-wide association (GWA) study with 305......,846 SNPs typed in 25,344 Icelandic, 2,998 Dutch, 1,890 European Americans and 1,160 African American subjects and combined the results with previously published results from the Diabetes Genetics Initiative (DGI) on 3,024 Scandinavians. We selected 43 variants in 19 regions for follow-up in 5,586 Danish...... individuals and compared the results to a genome-wide study on obesity-related traits from the GIANT consortium. In total, 29 variants, some correlated, in 11 chromosomal regions reached a genome-wide significance threshold of P

Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation

OpenAIRE

Shedrack Reuben Kitimu; Shedrack Reuben Kitimu; Julian eTaylor; Timothy J March; Fred eTairo; Mike J Wilkinson; Carlos Marcelino Rodriguez Lopez

2015-01-01

There is great interest in the phenotypic, genetic and epigenetic changes associated with plant in vitro culture known as somaclonal variation. In vitro propagation systems that are based on the use of microcuttings or meristem cultures are considered analogous to clonal cuttings and so widely viewed to be largely free from such somaclonal effects. In this study, we surveyed for epigenetic changes during propagation by meristem culture and by field cuttings in five cassava (Manihot esculenta...

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

DEFF Research Database (Denmark)

Scott, Robert A; Scott, Laura J; Mägi, Reedik

2017-01-01

To characterise type 2 diabetes (T2D) associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D cases and 132,532 controls of European ancestry after imputation using the 1000 Genomes multi-ethnic reference panel. Promi...... secretion, and in adipocytes, monocytes and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology....

Within-individual variation in bullfrog vocalizations: implications for a vocally mediated social recognition system.

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Bee, Mark A

2004-12-01

Acoustic signals provide a basis for social recognition in a wide range of animals. Few studies, however, have attempted to relate the patterns of individual variation in signals to behavioral discrimination thresholds used by receivers to discriminate among individuals. North American bullfrogs (Rana catesbeiana) discriminate among familiar and unfamiliar individuals based on individual variation in advertisement calls. The sources, patterns, and magnitudes of variation in eight acoustic properties of multiple-note advertisement calls were examined to understand how patterns of within-individual variation might either constrain, or provide additional cues for, vocal recognition. Six of eight acoustic properties exhibited significant note-to-note variation within multiple-note calls. Despite this source of within-individual variation, all call properties varied significantly among individuals, and multivariate analyses indicated that call notes were individually distinct. Fine-temporal and spectral call properties exhibited less within-individual variation compared to gross-temporal properties and contributed most toward statistically distinguishing among individuals. Among-individual differences in the patterns of within-individual variation in some properties suggest that within-individual variation could also function as a recognition cue. The distributions of among-individual and within-individual differences were used to generate hypotheses about the expected behavioral discrimination thresholds of receivers.

Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray

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Rempei Yanagawa

2001-01-01

Full Text Available In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions.

On Bi-Dimensional Second µ-Variation

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Ereú Jurancy

2014-12-01

Full Text Available In this paper, we present a generalization of the notion of bounded slope variation for functions defined on a rectangle Iba in ℝ2. Given a strictly increasing function µ-defined in a closed real interval, we introduce the class BVµ,2 (Iba , of functions of bounded second µ-variation on Iba ; and show that this class can be equipped with a norm with respect to which it is a Banach space. We also deal with the important case of factorizable functions in BVµ,2 (Iba and finally we exhibit a relation between this class and the one of double Riemann-Stieltjes integrals of functions of bi-dimensional bounded variation.

Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum

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Jing Zhao

2016-07-01

Full Text Available Sorghum [ (L Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA biosynthesis and signaling genes with these phenotypes. A total of 101 single-nucleotide polymorphism (SNP representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, ( and (, affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation ( and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

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Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Accounting for between-study variation in incremental net benefit in value of information methodology.

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Willan, Andrew R; Eckermann, Simon

2012-10-01

Previous applications of value of information methods for determining optimal sample size in randomized clinical trials have assumed no between-study variation in mean incremental net benefit. By adopting a hierarchical model, we provide a solution for determining optimal sample size with this assumption relaxed. The solution is illustrated with two examples from the literature. Expected net gain increases with increasing between-study variation, reflecting the increased uncertainty in incremental net benefit and reduced extent to which data are borrowed from previous evidence. Hence, a trial can become optimal where current evidence is sufficient assuming no between-study variation. However, despite the expected net gain increasing, the optimal sample size in the illustrated examples is relatively insensitive to the amount of between-study variation. Further percentage losses in expected net gain were small even when choosing sample sizes that reflected widely different between-study variation. Copyright © 2011 John Wiley & Sons, Ltd.

State variations in women's socioeconomic status and use of modern contraceptives in Nigeria.

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Lamidi, Esther O

2015-01-01

According to the 2014 World Population Data Sheet, Nigeria has one of the highest fertility and lowest contraceptive prevalence rates around the world. However, research suggests that national contraceptive prevalence rate overshadows enormous spatial variations in reproductive behavior in the country. I examined the variations in women's socioeconomic status and modern contraceptive use across states in Nigeria. Using the 2013 Nigeria Demographic and Health Survey data (n = 18,910), I estimated the odds of modern contraceptive use among sexually active married and cohabiting women in a series of multilevel logistic regression models. The share of sexually active, married and cohabiting women using modern contraceptives widely varied, from less than one percent in Kano, Yobe, and Jigawa states, to 40 percent in Osun state. Most of the states with low contraceptive prevalence rates also ranked low on women's socioeconomic attributes. Results of multilevel logistic regression analyses showed that women residing in states with greater shares of women with secondary or higher education, higher female labor force participation rates, and more women with health care decision-making power, had significantly higher odds of using modern contraceptives. Differences in women's participation in health care decisions across states remained significantly associated with modern contraceptive use, net of individual-level socioeconomic status and other covariates of modern contraceptive use. Understanding of state variations in contraceptive use is crucial to the design and implementation of family planning programs. The findings reinforce the need for state-specific family planning programs in Nigeria.

SU-F-T-284: The Effect of Linear Accelerator Output Variation On the Quality of Patient Specific Rapid Arc Verification Plans

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Sandhu, G; Cao, F; Szpala, S; Kohli, K [Fraser Valley Cancer Centre, BC Cancer Agency, Surrey, British Columbia (Canada)

2016-06-15

Purpose: The aim of the current study is to investigate the effect of machine output variation on the delivery of the RapidArc verification plans. Methods: Three verification plans were generated using Eclipse™ treatment planning system (V11.031) with plan normalization value 100.0%. These plans were delivered on the linear accelerators using ArcCHECK− device, with machine output 1.000 cGy/MU at calibration point. These planned and delivered dose distributions were used as reference plans. Additional plans were created in Eclipse− with normalization values ranging 92.80%–102% to mimic the machine output ranging 1.072cGy/MU-0.980cGy/MU, at the calibration point. These plans were compared against the reference plans using gamma indices (3%, 3mm) and (2%, 2mm). Calculated gammas were studied for its dependence on machine output. Plans were considered passed if 90% of the points satisfy the defined gamma criteria. Results: The gamma index (3%, 3mm) was insensitive to output fluctuation within the output tolerance level (2% of calibration), and showed failures, when the machine output exceeds ≥3%. Gamma (2%, 2mm) was found to be more sensitive to the output variation compared to the gamma (3%, 3mm), and showed failures, when output exceeds ≥1.7%. The variation of the gamma indices with output variability also showed dependence upon the plan parameters (e.g. MLC movement and gantry rotation). The variation of the percentage points passing gamma criteria with output variation followed a non-linear decrease beyond the output tolerance level. Conclusion: Data from the limited plans and output conditions showed that gamma (2%, 2mm) is more sensitive to the output fluctuations compared to Gamma (3%,3mm). Work under progress, including detail data from a large number of plans and a wide range of output conditions, may be able to conclude the quantitative dependence of gammas on machine output, and hence the effect on the quality of delivered rapid arc plans.

Variation as a main feature of norm

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S. Poladova

2017-09-01

Full Text Available The past half-century has witnessed remarkable growth in the study of language variation, and it has now become a highly productive subfield of research in sociolinguistics. Variability is everywhere in language, from the unique details in each production of a sound or sign to the auditory or visual processing of the linguistic signal. All languages that we can observe today show variation; what is more, they vary in identical ways, namely geographically and socially. It’s no secret that languages like English are full of variation. So, the aim of the article is to detect the reasons of variation and to uncover rates of usage of different free variations for a given set of lexical items. The research work is carried out by using the descriptive, comparative methods by subjecting to analysis the specific language materials. The discovery of law of variation became a starting point for the evolution of linguistics. The problem of search of variation facts and its role in the functioning of language system concerns many specialists from the outset. The scope of the investigation was to set up a system out of chaos of phenomena. Currently, the fact of conditionality of variation by system relations existing in the language is considered to be established.

Effects of range-wide variation in climate and isolation on floral traits and reproductive output of Clarkia pulchella.

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Bontrager, Megan; Angert, Amy L

2016-01-01

Plant mating systems and geographic range limits are conceptually linked by shared underlying drivers, including landscape-level heterogeneity in climate and in species' abundance. Studies of how geography and climate interact to affect plant traits that influence mating system and population dynamics can lend insight to ecological and evolutionary processes shaping ranges. Here, we examined how spatiotemporal variation in climate affects reproductive output of a mixed-mating annual, Clarkia pulchella. We also tested the effects of population isolation and climate on mating-system-related floral traits across the range. We measured reproductive output and floral traits on herbarium specimens collected across the range of C. pulchella. We extracted climate data associated with specimens and derived a population isolation metric from a species distribution model. We then examined how predictors of reproductive output and floral traits vary among populations of increasing distance from the range center. Finally, we tested whether reproductive output and floral traits vary with increasing distance from the center of the range. Reproductive output decreased as summer precipitation decreased, and low precipitation may contribute to limiting the southern and western range edges of C. pulchella. High spring and summer temperatures are correlated with low herkogamy, but these climatic factors show contrasting spatial patterns in different quadrants of the range. Limiting factors differ among different parts of the range. Due to the partial decoupling of geography and environment, examining relationships between climate, reproductive output, and mating-system-related floral traits reveals spatial patterns that might be missed when focusing solely on geographic position. © 2016 Botanical Society of America.

A primer on the calculus of variations and optimal control theory

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Mesterton-Gibbons, Mike

2009-01-01

The calculus of variations is used to find functions that optimize quantities expressed in terms of integrals. Optimal control theory seeks to find functions that minimize cost integrals for systems described by differential equations. This book is an introduction to both the classical theory of the calculus of variations and the more modern developments of optimal control theory from the perspective of an applied mathematician. It focuses on understanding concepts and how to apply them. The range of potential applications is broad: the calculus of variations and optimal control theory have been widely used in numerous ways in biology, criminology, economics, engineering, finance, management science, and physics. Applications described in this book include cancer chemotherapy, navigational control, and renewable resource harvesting. The prerequisites for the book are modest: the standard calculus sequence, a first course on ordinary differential equations, and some facility with the use of mathematical softwa...

Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

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Cameron Palmer

2017-07-01

Full Text Available Genome-wide association studies (GWAS have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14, even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16. We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94. In contrast, ancestry differences between replication and discovery (13 studies, 385 loci cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.

Dynamics of nonholonomic systems from variational principles embedded variation identity

International Nuclear Information System (INIS)

Guo Yongxin; Liu Shixing; Liu Chang; Chang Peng

2009-01-01

Nondeterminacy of dynamics, i.e., the nonholonomic or the vakonomic, fundamental variational principles, e.g., the Lagrange-d'Alembert or Hamiltonian, and variational operators, etc., of nonholonomic mechanical systems can be attributed to the non-uniqueness of ways how to realize nonholonomic constraints. Making use of a variation identity of nonholonomic constraints embedded into the Hamilton's principle with the method of Lagrange undetermined multipliers, three kinds of dynamics for the nonholonomic systems including the vakonomic and nonholonomic ones and a new one are obtained if the variation is respectively reduced to three conditional variations: vakonomic variation, Hoelder's variation and Suslov's variation, defined by the identity. Therefore, different dynamics of nonholonomic systems can be derived from an integral variational principle, utilizing one way of embedding constraints into the principle, with different variations. It is verified that the similar embedding of the identity into the Lagrange-d'Alembert principle gives rise to the nonholonomic dynamics but fails to give the vakonomic one unless the constraints are integrable.

Wide Angle of Incidence-Insensitive Polarization-Independent THz Metamaterial Absorber for Both TE and TM Mode Based on Plasmon Hybridizations

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Xiu Tao Huang

2018-04-01

Full Text Available An ultra-wide-angle THz metamaterial absorber (MA utilizing sixteen-circular-sector (SCR resonator for both transverse electric (TE and transverse magnetic (TM mode is designed and investigated numerically. At normal incidence, the absorptivity of the proposed MA is higher than 93.7% at 9.05 THz for different polarization angles, due to the rotational symmetry structure of the unit cell. Under oblique incidence, the absorptivity can still exceed 90%, even when the incident angle is up to 70° for both TE and TM mode. Especially, the frequency variation in TE mode is less than 0.25% for different incident angles from 0° to 70°. The electric field (Ez distributions are used to explain the absorption mechanism. Numerical simulation results show that the high absorption with wide-angle independence stems from fundamental dipole resonance and gap surface plasmons. The broadband deep-infrared MA is also obtained by stacking three metal-dielectric layers. The designed MA has great potential in bolometric pixel elements, biomedical sensors, THz imaging, and solar cells.

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

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Nicola K Petty

2011-04-01

Full Text Available Citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC and enterohaemorrhagic E. coli (EHEC and is widely used to model this route of pathogenesis. We previously reported the complete genome sequence of C. rodentium ICC168, where we found that the genome displayed many characteristics of a newly evolved pathogen. In this study, through PFGE, sequencing of isolates showing variation, whole genome transcriptome analysis and examination of the mobile genetic elements, we found that, consistent with our previous hypothesis, the genome of C. rodentium is unstable as a result of repeat-mediated, large-scale genome recombination and because of active transposition of mobile genetic elements such as the prophages. We sequenced an additional C. rodentium strain, EX-33, to reveal that the reference strain ICC168 is representative of the species and that most of the inactivating mutations were common to both isolates and likely to have occurred early on in the evolution of this pathogen. We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease.

Age-related variation in foraging behaviour in the wandering albatross at South Georgia: no evidence for senescence.

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Hannah Froy

Full Text Available Age-related variation in demographic rates is now widely documented in wild vertebrate systems, and has significant consequences for population and evolutionary dynamics. However, the mechanisms underpinning such variation, particularly in later life, are less well understood. Foraging efficiency is a key determinant of fitness, with implications for individual life history trade-offs. A variety of faculties known to decline in old age, such as muscular function and visual acuity, are likely to influence foraging performance. We examine age-related variation in the foraging behaviour of a long-lived, wide-ranging oceanic seabird, the wandering albatross Diomedea exulans. Using miniaturised tracking technologies, we compared foraging trip characteristics of birds breeding at Bird Island, South Georgia. Based on movement and immersion data collected during the incubation phase of a single breeding season, and from extensive tracking data collected in previous years from different stages of the breeding cycle, we found limited evidence for age-related variation in commonly reported trip parameters, and failed to detect signs of senescent decline. Our results contrast with the limited number of past studies that have examined foraging behaviour in later life, since these have documented changes in performance consistent with senescence. This highlights the importance of studies across different wild animal populations to gain a broader perspective on the processes driving variation in ageing rates.

Illness as a source of variation of laterality in lions (Panthera leo).

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Zucca, Paolo; Baciadonna, Luigi; Masci, Stefano; Mariscoli, Massimo

2011-05-01

Brain asymmetry--i.e. the specialisation of each cerebral hemisphere for sensorimotor processing mechanisms and for specific cognitive functions-is widely distributed among vertebrates. Several factors, such as embryological manipulations, sex, age, and breeds, can influence the maintenance, strength, and direction of laterality within a certain vertebrate species. Brain lateralisation is a universal phenomenon characterising not only cerebral control of cognitive or emotion-related functions but also cerebral regulation of somatic processes, and its evolution is strongly influenced by social selection pressure. Diseases are well known to be a cost of sociality but their role in influencing behaviour has received very little attention. The present study investigates the influence of illness conditions as a source of variation on laterality in a social keystone vertebrate predator model, the lion. In a preliminary stage, the clinical conditions of 24 adult lions were assessed. The same animals were scored for forelimb preference when in the quadrupedal standing position. Lions show a marked forelimb preference with a population bias towards the use of the right forelimb. Illness conditions strongly influenced the strength of laterality bias, with a significant difference between clinically healthy and sick lions. According to these results, health conditions should be recognised as an important source of variation in brain lateralisation.

A genome-wide methylation study on obesity: differential variability and differential methylation.

Science.gov (United States)

Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Hidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

2013-05-01

Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common complex disease. We analyzed genome-wide methylation profiles of over 470,000 CpGs in peripheral blood samples from 48 obese and 48 lean African-American youth aged 14-20 y old. A substantial number of differentially variable CpG sites (DVCs), using statistics based on variances, as well as a substantial number of differentially methylated CpG sites (DMCs), using statistics based on means, were identified. Similar to the findings in cancers, DVCs generally exhibited an outlier structure and were more variable in cases than in controls. By randomly splitting the current sample into a discovery and validation set, we observed that both the DVCs and DMCs identified from the first set could independently predict obesity status in the second set. Furthermore, both the genes harboring DMCs and the genes harboring DVCs showed significant enrichment of genes identified by genome-wide association studies on obesity and related diseases, such as hypertension, dyslipidemia, type 2 diabetes and certain types of cancers, supporting their roles in the etiology and pathogenesis of obesity. We generalized the recent finding on methylation variability in cancer research to obesity and demonstrated that differential variability is also an important feature of obesity-related methylation changes. Future studies on the epigenetics of obesity will benefit from both statistics based on means and statistics based on variances.

Seasonal Variation in Epidemiology

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Marrero, Osvaldo

2013-01-01

Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

A new Mumford-Shah total variation minimization based model for sparse-view x-ray computed tomography image reconstruction.

Science.gov (United States)

Chen, Bo; Bian, Zhaoying; Zhou, Xiaohui; Chen, Wensheng; Ma, Jianhua; Liang, Zhengrong

2018-04-12

Total variation (TV) minimization for the sparse-view x-ray computer tomography (CT) reconstruction has been widely explored to reduce radiation dose. However, due to the piecewise constant assumption for the TV model, the reconstructed images often suffer from over-smoothness on the image edges. To mitigate this drawback of TV minimization, we present a Mumford-Shah total variation (MSTV) minimization algorithm in this paper. The presented MSTV model is derived by integrating TV minimization and Mumford-Shah segmentation. Subsequently, a penalized weighted least-squares (PWLS) scheme with MSTV is developed for the sparse-view CT reconstruction. For simplicity, the proposed algorithm is named as 'PWLS-MSTV.' To evaluate the performance of the present PWLS-MSTV algorithm, both qualitative and quantitative studies were conducted by using a digital XCAT phantom and a physical phantom. Experimental results show that the present PWLS-MSTV algorithm has noticeable gains over the existing algorithms in terms of noise reduction, contrast-to-ratio measure and edge-preservation.

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

Coupled variations of fundamental couplings and primordial nucleosynthesis

International Nuclear Information System (INIS)

Coc, Alain; Nunes, Nelson J.; Olive, Keith A.; Uzan, Jean-Philippe; Vangioni, Elisabeth

2006-10-01

The effect of variations of the fundamental nuclear parameters on big-bang nucleosynthesis are modeled and discussed in detail taking into account the interrelations between the fundamental parameters arising in unified theories. Considering only 4 He, strong constraints on the variation of the neutron lifetime, neutron-proton mass difference are set. These constraints are then translated into constraints on the time variation of the Yukawa couplings and the fine structure constant. Furthermore, we show that a variation of the deuterium binding energy is able to reconcile the 7 Li abundance deduced from the WMAP analysis with its spectroscopically determined value while maintaining concordance with D and 4 He. (authors)

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...

Regularization of Nonmonotone Variational Inequalities

International Nuclear Information System (INIS)

Konnov, Igor V.; Ali, M.S.S.; Mazurkevich, E.O.

2006-01-01

In this paper we extend the Tikhonov-Browder regularization scheme from monotone to rather a general class of nonmonotone multivalued variational inequalities. We show that their convergence conditions hold for some classes of perfectly and nonperfectly competitive economic equilibrium problems