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Sample records for revealed substantial variation

  1. Immunity traits in pigs: substantial genetic variation and limited covariation.

    Directory of Open Access Journals (Sweden)

    Laurence Flori

    Full Text Available BACKGROUND: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs. Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. METHODOLOGY/PRINCIPAL FINDINGS: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10, phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.10.4 heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection

  2. 'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

    Science.gov (United States)

    Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

    2018-01-01

    A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

  3. Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA.

    Science.gov (United States)

    Li, Lu; Wu, Xiangyun; Yu, Ziniu

    2013-09-01

    The Hong Kong oyster, Crassostrea hongkongensis, is an important fisheries resource that is cultivated in the coastal waters of the South China Sea. Despite significant advances in understanding biological and taxonomic aspects of this species, no detailed study of its population genetic diversity in regions of extensive cultivation are available. Direct sequencing of the mtDNA cox1 gene region was used to investigate genetic variation within and between eleven C. hongkongensis populations collected from typical habitats. Sixty-two haplotypes were identified; only haplotype 2 (21.74% of total haplotypes) was shared among all the eleven populations, and most of the observed haplotypes were restricted to individual populations. Both AMOVA and FST analyses revealed significant population structure, and the isolation by distance (IBD) was confirmed. The highest local differentiation was observed between the sample pools from Guangxi versus Guangdong and Fujian, which are separated by a geographic barrier, the Leizhou Peninsula. Current knowledge from seed management suggests that seed transfer from Guangxi province has likely reduced the divergence that somewhat naturally exists between these pools. The findings from the present study could be useful for genetic management and may serve as a baseline by which to monitor future changes in genetic diversity, either due to natural or anthropogenic impacts. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

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    Jinliang Yang

    2017-09-01

    Full Text Available Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

  5. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

    Science.gov (United States)

    Yang, Jinliang; Mezmouk, Sofiane; Baumgarten, Andy; Buckler, Edward S; Guill, Katherine E; McMullen, Michael D; Mumm, Rita H; Ross-Ibarra, Jeffrey

    2017-09-01

    Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

  6. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

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    Ashley S. Chaffin

    2016-07-01

    Full Text Available Hexaploid oat ( L., 2 = 6 = 42 is a member of the Poaceae family and has a large genome (∼12.5 Gb containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP array and genotyping-by-sequencing (GBS were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L. reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

  7. Substantial variation in the interpretation of financial disclosure policies for orthopaedic society meetings.

    Science.gov (United States)

    Jegede, Kolawole; Whang, Peter; Grauer, Jonathan N

    2011-07-06

    Physician disclosure of potential conflicts of interest is currently controversial. To address this issue, orthopaedic societies have implemented a variety of guidelines related to potential conflict-of-interest disclosure. Transparency is crucial to address the concerns about potential conflict-of-interest disclosure. Nonetheless, prior studies have noted substantial discrepancies in disclosures to societies for individual authors who present their research work at multiple conferences. Our goal was to evaluate the ability of orthopaedic surgeons to interpret disclosure policy statements regarding project-specific or global disclosure instructions. The disclosure policy statements of the ten conferences most frequently attended by this group were collected, and selected statements were compiled into a questionnaire survey that was administered to orthopaedic faculty and trainees at our institution. Subjects were asked to read each statement and identify whether they interpreted the policy to be requesting project-specific disclosures (potential conflict of interest related to the research work in the abstract being submitted) or global disclosure (inclusive of all potential conflicts of interest, including those not associated with the abstract being submitted). The correct responses were identified by communicating with the individual societies and determining the responses desired by the society. The study had a 100% return rate from seventeen orthopaedic faculty, twenty-five orthopaedic residents and fellows, and twenty-five medical students. The average number of incorrect responses to the ten questions was 2.8. Forty-six percent of respondents had three or more incorrect responses, 24% had two incorrect responses, 19% had one incorrect response, and 10% had no incorrect responses. There was no significant difference in responses between those of different training levels. Subjects were no more likely to answer a project-specific question incorrectly than they

  8. Applications of Pharmacogenetics in Revealing Variations in ...

    African Journals Online (AJOL)

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    taking place in molecular biology techniques. Drug action is now more ... the latest findings of genetic variations in pharmacological targets related to disorders of major .... Similarly, Gly 9 allele. (Ser9Gly) of the dopamine D3 receptor gene.

  9. Sewage-treatment under substantial load variations in winter tourism areas--a full case study.

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    Winkler, S; Matsché, N; Gamperer, T; Dum, M

    2004-01-01

    The sewage-load variations in winter tourism areas are characterized by sudden increases--in the range of a factor two to three--within only a few days at the start and the end of the tourist season, especially at Christmas. The sudden load increases occur during periods of low wastewater temperatures, which is an additional demanding factor with respect to nitrogen removal. A full case study was carried out at WWTP Saalfelden, which is located near one of Austria's largest skiing resorts. The plant is designed for 80,000 PE and built according to the HYBRID-concept, which is a special two stage activated sludge process for extensive nutrient removal.

  10. Applications of Pharmacogenetics in Revealing Variations in ...

    African Journals Online (AJOL)

    This review article presents the latest findings of genetic variations in pharmacological targets related to disorders of major systems such as central nervous system, cardiovascular system, and the respiratory system especially in relation to asthma and the HLA antigen genotype in hypersensitivity reactions. East and Central ...

  11. Patterns of phenotypic variation reveal substantial differentiation in sexual dimorphism of three Psammodromus (Squamata, Lacertidae) species

    NARCIS (Netherlands)

    San-Jose, L.M.; Gonzalez-Jimena, V.; Fitze, P.S.

    2012-01-01

    The Spanish sand racer (Psammodromus hispanicus) has been recently split into three distinct species: P. hispanicus, P. edwardsianus, and P. occidentalis. Some morphological differences have been reported but there is as yet no description allowing unambiguous identification of the three species.

  12. Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

    Science.gov (United States)

    D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.

    2016-01-01

    Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical population connectivity and genetic diversity showing: (1) a substantial loss of haplotypes, which is consistent with the hypothesis that condors were relatively abundant in the nineteenth century, but declined rapidly as a result of human-caused mortality; and (2) no evidence of historical population segregation, meaning that the available genetic data offer no cause to avoid releasing condors in unoccupied portions of their historical range.

  13. Transcriptomic variation in a coral reveals pathways of clonal organisation

    DEFF Research Database (Denmark)

    K Bay, Line; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard

    2009-01-01

    A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base......) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with energy...... of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels...

  14. Indirect genetic effects contribute substantially to heritable variation in aggression-related traits in group-housed mink (Neovison vison)

    DEFF Research Database (Denmark)

    Alemu, Setegn Worku; Bijma, Peter; Møller, Steen Henrik

    2014-01-01

    Background Since the recommendations on group housing of mink (Neovison vison) were adopted by the Council of Europe in 1999, it has become common in mink production in Europe. Group housing is advantageous from a production perspective, but can lead to aggression between animals and thus raises...... a welfare issue. Bite marks on the animals are an indicator of this aggressive behaviour and thus selection against frequency of bite marks should reduce aggression and improve animal welfare. Bite marks on one individual reflect the aggression of its group members, which means that the number of bite marks...... genetic effects contribute to variation in number of bite marks in group-housed mink. Thus, a genetic selection design that includes both direct genetic and indirect genetic effects could reduce the frequency of bite marks and probably aggression behaviour in group-housed mink....

  15. Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis

    Science.gov (United States)

    Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq

    2018-01-01

    AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the “3′UTR” region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits. PMID:29862252

  16. Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis.

    Science.gov (United States)

    Ullah, Farman; Bhattarai, Dinesh; Cheng, Zhangrui; Liang, Xianwei; Deng, Tingxian; Rehman, Zia Ur; Talpur, Hira Sajjad; Worku, Tesfaye; Brohi, Rahim Dad; Safdar, Muhammad; Ahmad, Muhammad Jamil; Salim, Mohammad; Khan, Momen; Ahmad, Hafiz Ishfaq; Zhang, Shujun

    2018-01-01

    AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP). AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the "3'UTR" region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits.

  17. Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3 Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis

    Directory of Open Access Journals (Sweden)

    Farman Ullah

    2018-01-01

    Full Text Available AKT3 gene is a constituent of the serine/threonine protein kinase family and plays a crucial role in synthesis of milk fats and cholesterol by regulating activity of the sterol regulatory element binding protein (SREBP. AKT3 is highly conserved in mammals and its expression levels during the lactation periods of cattle are markedly increased. AKT3 is highly expressed in the intestine followed by mammary gland and it is also expressed in immune cells. It is involved in the TLR pathways as effectively as proinflammatory cytokines. The aims of this study were to investigate the sequences differences between buffalo and cow. Our results showed that there were substantial differences between buffalo and cow in some exons and noteworthy differences of the gene size in different regions. We also identified the important consensus sequence motifs, variation in 2000 upstream of ATG, substantial difference in the “3′UTR” region, and miRNA association in the buffalo sequences compared with the cow. In addition, genetic analyses, such as gene structure, phylogenetic tree, position of different motifs, and functional domains, were performed to establish their correlation with other species. This may indicate that a buffalo breed has potential resistance to disease, environment changes, and airborne microorganisms and some good production and reproductive traits.

  18. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability

    OpenAIRE

    White, John; Mascarenhas, Anjali; Pereira, Ligia; Dash, Rashmi; Walke, Jayashri T.; Gawas, Pooja; Sharma, Ambika; Manoharan, Suresh Kumar; Guler, Jennifer L.; Maki, Jennifer N.; Kumar, Ashwani; Mahanta, Jagadish; Valecha, Neena; Dubhashi, Nagesh; Vaz, Marina

    2016-01-01

    Background Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. Methods Venous blood was collected f...

  19. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability.

    Science.gov (United States)

    White, John; Mascarenhas, Anjali; Pereira, Ligia; Dash, Rashmi; Walke, Jayashri T; Gawas, Pooja; Sharma, Ambika; Manoharan, Suresh Kumar; Guler, Jennifer L; Maki, Jennifer N; Kumar, Ashwani; Mahanta, Jagadish; Valecha, Neena; Dubhashi, Nagesh; Vaz, Marina; Gomes, Edwin; Chery, Laura; Rathod, Pradipsinh K

    2016-01-22

    Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. Venous blood was collected from 33 P. falciparum-infected individuals at Goa Medical College and Hospital (Bambolim, Goa, India). Culture variables such as whole blood versus washed blood, heat-inactivated plasma versus Albumax, and different starting haematocrit levels were tested on fresh blood samples from patients. In vitro adaptation was considered successful when two four-fold or greater increases in parasitaemia were observed within, at most, 33 days of attempted culture. Subsequently, parasites from the same patients, which were originally cryopreserved following blood draw, were retested for adaptability for 45 days using identical host red blood cells (RBCs) and culture media. At a new endemic area research site, ~65% of tested patient samples, with varied patient history and clinical presentation, were successfully culture-adapted immediately after blood collection. Cultures set up at 1% haematocrit and 0.5% Albumax adapted most rapidly, but no single test condition was uniformly fatal to culture adaptation. Success was not limited by low patient parasitaemia nor by patient age. Some parasites emerged even after significant delays in sample processing and even after initiation of treatment with anti-malarials. When 'day 0' cryopreserved samples were retested in parallel many months later using identical host RBCs and media, speed to adaptation appeared to be an intrinsic property of the parasites collected from individual patients. Culture adaptation of P. falciparum in a field setting is formally shown to be

  20. Molar macrowear reveals Neanderthal eco-geographic dietary variation.

    Directory of Open Access Journals (Sweden)

    Luca Fiorenza

    Full Text Available Neanderthal diets are reported to be based mainly on the consumption of large and medium sized herbivores, while the exploitation of other food types including plants has also been demonstrated. Though some studies conclude that early Homo sapiens were active hunters, the analyses of faunal assemblages, stone tool technologies and stable isotopic studies indicate that they exploited broader dietary resources than Neanderthals. Whereas previous studies assume taxon-specific dietary specializations, we suggest here that the diet of both Neanderthals and early Homo sapiens is determined by ecological conditions. We analyzed molar wear patterns using occlusal fingerprint analysis derived from optical 3D topometry. Molar macrowear accumulates during the lifespan of an individual and thus reflects diet over long periods. Neanderthal and early Homo sapiens maxillary molar macrowear indicates strong eco-geographic dietary variation independent of taxonomic affinities. Based on comparisons with modern hunter-gatherer populations with known diets, Neanderthals as well as early Homo sapiens show high dietary variability in Mediterranean evergreen habitats but a more restricted diet in upper latitude steppe/coniferous forest environments, suggesting a significant consumption of high protein meat resources.

  1. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    OpenAIRE

    Wei Tong; Qiang He; Yong-Jin Park

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucle...

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

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    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.

  3. Small-scale density variations in the lunar crust revealed by GRAIL

    Science.gov (United States)

    Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W.; Milbury, C.; Kiefer, W. S.; Soderblom, J. M.; Zuber, M. T.

    2017-07-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that ∼98% of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2% of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10‧s of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by ± 10% over scales ranging from centimeters to 100‧s of kilometers.

  4. Small-Scale Density Variations in the Lunar Crust Revealed by GRAIL

    Science.gov (United States)

    Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W., III; Milbury, C.; hide

    2017-01-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that approximately 98 percent of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2 percent of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10's of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by plus or minus 10 percent over scales ranging from centimeters to 100’s of kilometers.

  5. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    Science.gov (United States)

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc]. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  7. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

    Directory of Open Access Journals (Sweden)

    James B Pease

    2016-02-01

    Full Text Available Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon, we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

  8. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

    NARCIS (Netherlands)

    Hoedjes, K.M.; Smid, H.M.; Vet, L.E.M.; Werren, J.H.

    2014-01-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the

  9. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

    Science.gov (United States)

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

    2015-11-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  10. Genetic variability of environmental sensitivity revealed by phenotypic variation in body weight and (its correlations to physiological and behavioral traits.

    Directory of Open Access Journals (Sweden)

    Delphine Lallias

    Full Text Available Adaptive phenotypic plasticity is a key component of the ability of organisms to cope with changing environmental conditions. Fish have been shown to exhibit a substantial level of phenotypic plasticity in response to abiotic and biotic factors. In the present study, we investigate the link between environmental sensitivity assessed globally (revealed by phenotypic variation in body weight and more targeted physiological and behavioral indicators that are generally used to assess the sensitivity of a fish to environmental stressors. We took advantage of original biological material, the rainbow trout isogenic lines, which allowed the disentangling of the genetic and environmental parts of the phenotypic variance. Ten lines were characterized for the changes of body weight variability (weight measurements taken every month during 18 months, the plasma cortisol response to confinement stress (3 challenges and a set of selected behavioral indicators. This study unambiguously demonstrated the existence of genetic determinism of environmental sensitivity, with some lines being particularly sensitive to environmental fluctuations and others rather insensitive. Correlations between coefficient of variation (CV for body weight and behavioral and physiological traits were observed. This confirmed that CV for body weight could be used as an indicator of environmental sensitivity. As the relationship between indicators (CV weight, risk-taking, exploration and cortisol was shown to be likely depending on the nature and intensity of the stressor, the joint use of several indicators should help to investigate the biological complexity of environmental sensitivity.

  11. Revisiting diversity: cultural variation reveals the constructed nature of emotion perception.

    Science.gov (United States)

    Gendron, Maria

    2017-10-01

    The extent of cultural variation in emotion perception has long been assumed to be bounded by underlying universality. A growing body of research reveals, however, that evidence of universality in emotion perception is method-bound. Without the assumption of underlying universality, new lines of inquiry become relevant. Accumulating evidence suggests that cultures vary in what cues are relevant to perceptions of emotion. Further, cultural groups vary in their spontaneous inferences; mental state inference does not appear to be the only, or even most routine, mode of perception across cultures. Finally, setting universality assumptions aside requires innovation in the theory and measurement of culture. Recent studies reveal the promise of refinements in psychological approaches to culture. Together, the available evidence is consistent with a view of emotion perceptions as actively constructed by perceivers to fit the social and physical constraints of their cultural worlds. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.

    Science.gov (United States)

    Simon, Lauriane; Rabanal, Fernando A; Dubos, Tristan; Oliver, Cecilia; Lauber, Damien; Poulet, Axel; Vogt, Alexander; Mandlbauer, Ariane; Le Goff, Samuel; Sommer, Andreas; Duborjal, Hervé; Tatout, Christophe; Probst, Aline V

    2018-04-06

    Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.

  13. Metabolomics reveals variation and correlation among different tissues of olive (Olea europaea L.

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    Rao Guodong

    2017-09-01

    Full Text Available Metabolites in olives are associated with nutritional value and physiological properties. However, comprehensive information regarding the olive metabolome is limited. In this study, we identified 226 metabolites from three different tissues of olive using a non-targeted metabolomic profiling approach, of which 76 named metabolites were confirmed. Further statistical analysis revealed that these 76 metabolites covered different types of primary metabolism and some of the secondary metabolism pathways. One-way analysis of variance (ANOVA statistical assay was performed to calculate the variations within the detected metabolites, and levels of 65 metabolites were differentially expressed in different samples. Hierarchical cluster analysis (HCA dendrograms showed variations among different tissues that were similar to the metabolite profiles observed in new leaves and fruit. Additionally, 5776 metabolite-metabolite correlations were detected by a Pearson correlation coefficient approach. Screening of the calculated correlations revealed 3136, 3025, and 5184 were determined to metabolites and had significant correlations in three different combinations, respectively. This work provides the first comprehensive metabolomic of olive, which will provide new insights into understanding the olive metabolism, and potentially help advance studies in olive metabolic engineering.

  14. Latitudinal and seasonal variations of lower atmospheric inertial gravity wave energy revealed by US radiosonde data

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, S.D.; Yi, F. [Wuhan Univ., Hubei (China). School of Electronic Information; Ministry of Education, Wuhan, Hubei (China). Key Lab. of Geospace Environment and Geodesy; State Observatory for Atmospheric Remote Sensing, Wuhan (China); Huang, C.M. [Wuhan Univ., Hubei (China). School of Electronic Information; Ministry of Education, Wuhan, Hubei (China). Key Lab. of Geospace Environment and Geodesy; State Observatory for Atmospheric Remote Sensing, Wuhan (China); Miami Univ., Oxford, OH (United States). Electrical and Computer Engineering Dept.; Zhou, Q. [Miami Univ., Oxford, OH (United States). Electrical and Computer Engineering Dept.

    2010-07-01

    The latitudinal and seasonal variations of gravity wave (GW) potential energy density (E{sub P}), kinetic energy density (E{sub K}), and total energy density (E{sub T}), i.e, the sum of potential and kinetic energy densities in the tropospheric (typically 2-10 km) and lower stratospheric (typically 18- 25 km) segments have been derived from 10 years (1998- 2007) of radiosonde observations over 92 United States stations in the Northern Hemisphere. The latitudinal variation of E{sub P} in the lower stratosphere is in good agreement with satellite observations. However, E{sub K} and E{sub T} in the lower stratosphere are different from satellite observations and the difference is believed to be linked with the latitudinal dependence of GW sources. Our analysis reveals that GW energy properties exhibit distinctive latitudinal and seasonal variations. The upward-propagating GW energy in the troposphere is larger than that in the lower stratosphere at low latitudes but the opposite holds true at high latitudes. The transition latitude, where the upward- propagating energies in the two altitude regions are the same, occurs at 35 N throughout the year. So striking differences between GW activity in the troposphere and lower stratosphere are not likely explained only by the background wind Doppler shifting due to strong tropospheric jets. Our analysis indicates that the region around tropopause, roughly from 10 km to 18 km, is an important source region, especially at latitudes below 35 N. Our studies strongly suggest that in order to fully understand the global GW activity in the lower atmosphere, the GW kinetic energy and its geographical and seasonal variations should be included, and more attention should be given to GWs in the troposphere and GW sources within the intermediate region, especially the upper troposphere. (orig.)

  15. Latitudinal and seasonal variations of lower atmospheric inertial gravity wave energy revealed by US radiosonde data

    Directory of Open Access Journals (Sweden)

    S. D. Zhang

    2010-05-01

    Full Text Available The latitudinal and seasonal variations of gravity wave (GW potential energy density (EP, kinetic energy density (EK, and total energy density (ET, i.e, the sum of potential and kinetic energy densities in the tropospheric (typically 2–10 km and lower stratospheric (typically 18–25 km segments have been derived from 10 years (1998–2007 of radiosonde observations over 92 United States stations in the Northern Hemisphere. The latitudinal variation of EP in the lower stratosphere is in good agreement with satellite observations. However, EK and ET in the lower stratosphere are different from satellite observations and the difference is believed to be linked with the latitudinal dependence of GW sources. Our analysis reveals that GW energy properties exhibit distinctive latitudinal and seasonal variations. The upward-propagating GW energy in the troposphere is larger than that in the lower stratosphere at low latitudes but the opposite holds true at high latitudes. The transition latitude, where the upward- propagating energies in the two altitude regions are the same, occurs at 35° N throughout the year. So striking differences between GW activity in the troposphere and lower stratosphere are not likely explained only by the background wind Doppler shifting due to strong tropospheric jets. Our analysis indicates that the region around tropopause, roughly from 10 km to 18 km, is an important source region, especially at latitudes below 35° N. Our studies strongly suggest that in order to fully understand the global GW activity in the lower atmosphere, the GW kinetic energy and its geographical and seasonal variations should be included, and more attention should be given to GWs in the troposphere and GW sources within the intermediate region, especially the upper troposphere.

  16. Diurnal microstructural variations in healthy adult brain revealed by diffusion tensor imaging.

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    Chunxiang Jiang

    Full Text Available Biorhythm is a fundamental property of human physiology. Changes in the extracellular space induced by cell swelling in response to the neural activity enable the in vivo characterization of cerebral microstructure by measuring the water diffusivity using diffusion tensor imaging (DTI. To study the diurnal microstructural alterations of human brain, fifteen right-handed healthy adult subjects were recruited for DTI studies in two repeated sessions (8∶30 AM and 8∶30 PM within a 24-hour interval. Fractional anisotropy (FA, apparent diffusion coefficient (ADC, axial (λ// and radial diffusivity (λ⊥ were compared pixel by pixel between the sessions for each subject. Significant increased morning measurements in FA, ADC, λ// and λ⊥ were seen in a wide range of brain areas involving frontal, parietal, temporal and occipital lobes. Prominent evening dominant λ⊥ (18.58% was detected in the right inferior temporal and ventral fusiform gyri. AM-PM variation of λ⊥ was substantially left side hemisphere dominant (p<0.05, while no hemispheric preference was observed for the same analysis for ADC (p = 0.77, λ// (p = 0.08 or FA (p = 0.25. The percentage change of ADC, λ//, λ⊥, and FA were 1.59%, 2.15%, 1.20% and 2.84%, respectively, for brain areas without diurnal diffusivity contrast. Microstructural variations may function as the substrates of the phasic neural activities in correspondence to the environment adaptation in a light-dark cycle. This research provided a baseline for researches in neuroscience, sleep medicine, psychological and psychiatric disorders, and necessitates that diurnal effect should be taken into account in following up studies using diffusion tensor quantities.

  17. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  18. Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition.

    Science.gov (United States)

    Diboun, Ilhame; Mathew, Sweety; Al-Rayyashi, Maryam; Elrayess, Mohamed; Torres, Maria; Halama, Anna; Méret, Michaël; Mohney, Robert P; Karoly, Edward D; Malek, Joel; Suhre, Karsten

    2015-12-16

    Dates are tropical fruits with appreciable nutritional value. Previous attempts at global metabolic characterization of the date metabolome were constrained by small sample size and limited geographical sampling. In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabolome. Multivariate analysis revealed a first principal component (PC1) significantly associated with the dates' countries of production. The availability of a smaller dataset featuring immature dates from different development stages served to build a model of the ripening process in dates, which helped reveal a strong ripening signature in PC1. Analysis revealed enrichment in the dry type of dates amongst fruits with early ripening profiles at one end of PC1 as oppose to an overrepresentation of the soft type of dates with late ripening profiles at the other end of PC1. Dry dates are typical to the North African region whilst soft dates are more popular in the Gulf region, which partly explains the observed association between PC1 and geography. Analysis of the loading values, expressing metabolite correlation levels with PC1, revealed enrichment patterns of a comprehensive range of metabolite classes along PC1. Three distinct metabolic phases corresponding to known stages of date ripening were observed: An early phase enriched in regulatory hormones, amines and polyamines, energy production, tannins, sucrose and anti-oxidant activity, a second phase with on-going phenylpropanoid secondary metabolism, gene expression and phospholipid metabolism and a late phase with marked sugar dehydration activity and degradation reactions leading to increased volatile synthesis. These data indicate the importance of date ripening as a main driver of variation in the date metabolome responsible for their diverse nutritional and

  19. Illumina based whole mitochondrial genome of Junonia iphita reveals minor intraspecific variation

    Directory of Open Access Journals (Sweden)

    Catherine Vanlalruati

    2015-12-01

    Full Text Available In the present study, the near complete mitochondrial genome (mitogenome of Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae was determined to be 14,892 bp. The gene order and orientation are identical to those in other butterfly species. The phylogenetic tree constructed from the whole mitogenomes using the 13 protein coding genes (PCGs defines the genetic relatedness of the two J. iphita species collected from two different regions. All the Junonia species clustered together, and were further subdivided into clade one consisting of J. almana and J. orithya and clade two comprising of the two J. iphita which were collected from Indo and Indochinese subregions separated by river barrier. Comparison between the two J. iphita sequences revealed minor variations and Single Nucleotide Polymorphisms were identified at 51 sites amounting to 0.4% of the entire mitochondrial genome.

  20. Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions.

    Science.gov (United States)

    Stange, Madlen; Aguirre-Fernández, Gabriel; Salzburger, Walter; Sánchez-Villagra, Marcelo R

    2018-03-27

    Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats. 3D geometric morphometrics was applied for the first time in catfish skulls and phylogenetically informed statistical analyses were performed to test for the impact of habitat on skull diversification after habitat transition in this lineage. We found that skull shape is conserved throughout phylogeny. A morphospace analysis revealed that freshwater and marine species occupy extreme ends of the first principal component axis and that they exhibit similar Procrustes variances. Yet freshwater species occupy the smallest shape space compared to marine and brackish species (based on partial disparity), and marine and freshwater species have the largest Procrustes distance to each other. We observed a single case of shape convergence as derived from 'C-metrics', which cannot be explained by the occupation of the same habitat. Although Ariidae occupy such a broad spectrum of different habitats from sea to freshwater, the morphospace analysis and analyses of shape and co-variation with habitat in a phylogenetic context shows that conservatism dominates skull shape evolution among ariid genera.

  1. Genome-size Variation in Switchgrass (Panicum virgatum: Flow Cytometry and Cytology Reveal Rampant Aneuploidy

    Directory of Open Access Journals (Sweden)

    Denise E. Costich

    2010-11-01

    Full Text Available Switchgrass ( L., a native perennial dominant of the prairies of North America, has been targeted as a model herbaceous species for biofeedstock development. A flow-cytometric survey of a core set of 11 primarily upland polyploid switchgrass accessions indicated that there was considerable variation in genome size within each accession, particularly at the octoploid (2 = 8 = 72 chromosome ploidy level. Highly variable chromosome counts in mitotic cell preparations indicated that aneuploidy was more common in octoploids (86.3% than tetraploids (23.2%. Furthermore, the incidence of hyper- versus hypoaneuploidy is equivalent in tetraploids. This is clearly not the case in octoploids, where close to 90% of the aneuploid counts are lower than the euploid number. Cytogenetic investigation using fluorescent in situ hybridization (FISH revealed an unexpected degree of variation in chromosome structure underlying the apparent genomic instability of this species. These results indicate that rapid advances in the breeding of polyploid biofuel feedstocks, based on the molecular-genetic dissection of biomass characteristics and yield, will be predicated on the continual improvement of our understanding of the cytogenetics of these species.

  2. Revealing metabolomic variations in Cortex Moutan from different root parts using HPLC-MS method.

    Science.gov (United States)

    Xiao, Chaoni; Wu, Man; Chen, Yongyong; Zhang, Yajun; Zhao, Xinfeng; Zheng, Xiaohui

    2015-01-01

    The distribution of metabolites in the different root parts of Cortex Moutan (the root bark of Paeonia suffruticosa Andrews) is not well understood, therefore, scientific evidence is not available for quality assessment of Cortex Moutan. To reveal metabolomic variations in Cortex Moutan in order to gain deeper insights to enable quality control. Metabolomic variations in the different root parts of Cortex Moutan were characterised using high-performance liquid chromatography combined with mass spectrometry (HPLC-MS) and multivariate data analysis. The discriminating metabolites in different root parts were evaluated by the one-way analysis of variance and a fold change parameter. The metabolite profiles of Cortex Moutan were largely dominated by five primary and 41 secondary metabolites . Higher levels of malic acid, gallic acid and mudanoside-B were mainly observed in the second lateral roots, whereas dihydroxyacetophenone, benzoyloxypaeoniflorin, suffruticoside-A, kaempferol dihexoside, mudanpioside E and mudanpioside J accumulated in the first lateral and axial roots. The highest contents of paeonol, galloyloxypaeoniflorin and procyanidin B were detected in the axial roots. Accordingly, metabolite compositions of Cortex Moutan were found to vary among different root parts. The axial roots have higher quality than the lateral roots in Cortex Moutan due to the accumulation of bioactive secondary metabolites associated with plant physiology. These findings provided important scientific evidence for grading Cortex Moutan on the general market. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Within-Host Variations of Human Papillomavirus Reveal APOBEC-Signature Mutagenesis in the Viral Genome.

    Science.gov (United States)

    Hirose, Yusuke; Onuki, Mamiko; Tenjimbayashi, Yuri; Mori, Seiichiro; Ishii, Yoshiyuki; Takeuchi, Takamasa; Tasaka, Nobutaka; Satoh, Toyomi; Morisada, Tohru; Iwata, Takashi; Miyamoto, Shingo; Matsumoto, Koji; Sekizawa, Akihiko; Kukimoto, Iwao

    2018-03-28

    Persistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied with the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here we explored within-host genetic diversity of HPV by performing deep sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52 and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC), and were deep-sequenced. After constructing a reference vial genome sequence for each specimen, nucleotide positions showing changes with > 0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1, n = 56; CIN2/3, n = 68; ICC, n = 27), with varying numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the tri-nucleotides context encompassing substituted bases revealed that Tp C pN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions. IMPORTANCE HPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep sequencing analyses, we show for the first time a comprehensive snapshot of the "within

  4. Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

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    Kristoffer T Bæk

    Full Text Available Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47 required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75% steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3, a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.

  5. Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Carneiro, Ana [Vanderbilt University; Airey, David [University of Tennessee Health Science Center, Memphis; Thompson, Brent [Vanderbilt University; Zhu, C [Vanderbilt University; Rinchik, Eugene M [ORNL; Lu, Lu [University of Tennessee Health Science Center, Memphis; Chesler, Elissa J [ORNL; Erikson, Keith [University of North Carolina; Blakely, Randy [Vanderbilt University

    2009-01-01

    The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.

  6. Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Han, Leng; Luo, Zhenwu; Hu, Fang; Tieu, Roger; Gan, Lin

    2014-01-01

    Schizophrenia is a common mental disorder with high heritability and strong genetic heterogeneity. Common disease-common variants hypothesis predicts that schizophrenia is attributable in part to common genetic variants. However, recent studies have clearly demonstrated that copy number variations (CNVs) also play pivotal roles in schizophrenia susceptibility and explain a proportion of missing heritability. Though numerous CNVs have been identified, many of the regions affected by CNVs show poor overlapping among different studies, and it is not known whether the genes disrupted by CNVs contribute to the risk of schizophrenia. By using cumulative scoring, we systematically prioritized the genes affected by CNVs in schizophrenia. We identified 8 top genes that are frequently disrupted by CNVs, including NRXN1, CHRNA7, BCL9, CYFIP1, GJA8, NDE1, SNAP29, and GJA5. Integration of genes affected by CNVs with known schizophrenia susceptibility genes (from previous genetic linkage and association studies) reveals that many genes disrupted by CNVs are also associated with schizophrenia. Further protein-protein interaction (PPI) analysis indicates that protein products of genes affected by CNVs frequently interact with known schizophrenia-associated proteins. Finally, systematic integration of CNVs prioritization data with genetic association and PPI data identifies key schizophrenia candidate genes. Our results provide a global overview of genes impacted by CNVs in schizophrenia and reveal a densely interconnected molecular network of de novo CNVs in schizophrenia. Though the prioritized top genes represent promising schizophrenia risk genes, further work with different prioritization methods and independent samples is needed to confirm these findings. Nevertheless, the identified key candidate genes may have important roles in the pathogenesis of schizophrenia, and further functional characterization of these genes may provide pivotal targets for future therapeutics and

  7. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  8. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

    Directory of Open Access Journals (Sweden)

    Aurélien Chateigner

    2015-07-01

    Full Text Available Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%. K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs. Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential.

  9. Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting

    NARCIS (Netherlands)

    Agbo, E.E.C.; Majiwa, P.A.O.; Claassen, H.J.H.M.; Pas, te M.F.W.

    2002-01-01

    Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple

  10. Striking variations in consultation rates with general practice reveal family influence.

    NARCIS (Netherlands)

    Cardol, M.; Dijk, L. van; Bosch, W.J.H.M. van den; Spreeuwenberg, P.; Bakker, D.H. de; Groenewegen, P.P.

    2007-01-01

    BACKGROUND: The reasons why patients decide to consult a general practitioner vary enormously. While there may be individual reasons for this variation, the family context has a significant and unique influence upon the frequency of individuals' visits. The objective of this study was to explore

  11. Striking variations in consultation rates with general practice reveal family influence

    NARCIS (Netherlands)

    Cardol, Mieke; Dijk, Liset van; Bosch, Wil J.H.M. van den; Spreeuwenberg, Peter; Bakker, Dinny H. de; Groenewegen, Peter P.

    2007-01-01

    Background: The reasons why patients decide to consult a general practitioner vary enormously. While there may be individual reasons for this variation, the family context has a significant and unique influence upon the frequency of individuals' visits. The objective of this study was to explore

  12. Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

    Directory of Open Access Journals (Sweden)

    Hines Heather M

    2012-06-01

    Full Text Available Abstract Background Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. Results We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. Conclusions This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.

  13. Anglo-Saxon animal husbandry techniques revealed though isotope and chemical variations in cattle teeth

    International Nuclear Information System (INIS)

    Evans, J.A.; Tatham, S.; Chenery, S.R.; Chenery, C.A.

    2007-01-01

    The Sr concentration and isotope composition of tooth enamel from domesticated animals from two neighbouring Anglo-Saxon settlements, at Empingham (6-7th century) and Ketton (10-12th century) in Rutland, central England, are compared both with each other, and with associated human populations. Data from the Empingham II site form discrete fields in Sr concentration and isotope composition space for cattle, pig and sheep with a partial overlap of the human and pig fields. By contrast there is significant overlap in all the animal and human data fields from the Ketton site. The differences in data distribution between the two sites are attributed to animal husbandry techniques, as the surface geology of the two areas is very similar, implying geological factors are an unlikely cause of the difference. It is suggested that the grazing and feeding patterns of animals at the Empingham II site were controlled and restricted, whereas at the Ketton site the animals grazed and foraged freely over a common area. Strontium isotope variation within cattle molars from the two settlements show marked differences that reflect the nature of their feeding and rearing. The enamel from a cattle molar from the Empingham II site has a well-defined, systematic variation of Sr isotope composition with Sr concentration, whereas no such patterns exist in a comparable cattle molar from Ketton. Chemical and O isotope variations in the cattle tooth from Empingham II show sympathetic variation of Sr and Ba concentrations with Sr isotope composition from cusp to cervix. The cusp has higher Sr and Ba concentrations log (Sr/Ca) ratio of -3.1 and 87 Sr/ 86 Sr ratio of 0.71151 where as the cervical region of the enamel has log (Sr/Ca) = -3.3 and 87 Sr/ 86 Sr = 0.71061

  14. Anglo-Saxon animal husbandry techniques revealed though isotope and chemical variations in cattle teeth

    Energy Technology Data Exchange (ETDEWEB)

    Evans, J.A. [NERC Isotope Geosciences Laboratory, BGS, Keyworth, Nottingham NG12 5GG (United Kingdom)], E-mail: je@nigl.nerc.ac.uk; Tatham, S. [School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH (United Kingdom); Chenery, S.R. [British Geological Survey, Keyworth, Nottingham NG12 5GG (United Kingdom); Chenery, C.A. [NERC Isotope Geosciences Laboratory, BGS, Keyworth, Nottingham NG12 5GG (United Kingdom)

    2007-09-15

    The Sr concentration and isotope composition of tooth enamel from domesticated animals from two neighbouring Anglo-Saxon settlements, at Empingham (6-7th century) and Ketton (10-12th century) in Rutland, central England, are compared both with each other, and with associated human populations. Data from the Empingham II site form discrete fields in Sr concentration and isotope composition space for cattle, pig and sheep with a partial overlap of the human and pig fields. By contrast there is significant overlap in all the animal and human data fields from the Ketton site. The differences in data distribution between the two sites are attributed to animal husbandry techniques, as the surface geology of the two areas is very similar, implying geological factors are an unlikely cause of the difference. It is suggested that the grazing and feeding patterns of animals at the Empingham II site were controlled and restricted, whereas at the Ketton site the animals grazed and foraged freely over a common area. Strontium isotope variation within cattle molars from the two settlements show marked differences that reflect the nature of their feeding and rearing. The enamel from a cattle molar from the Empingham II site has a well-defined, systematic variation of Sr isotope composition with Sr concentration, whereas no such patterns exist in a comparable cattle molar from Ketton. Chemical and O isotope variations in the cattle tooth from Empingham II show sympathetic variation of Sr and Ba concentrations with Sr isotope composition from cusp to cervix. The cusp has higher Sr and Ba concentrations log (Sr/Ca) ratio of -3.1 and {sup 87}Sr/{sup 86}Sr ratio of 0.71151 where as the cervical region of the enamel has log (Sr/Ca) = -3.3 and {sup 87}Sr/{sup 86}Sr = 0.71061.

  15. Developmental constraints revealed by co-variation within and among molar rows in two murine rodents.

    Science.gov (United States)

    Renaud, Sabrina; Pantalacci, Sophie; Quéré, Jean-Pierre; Laudet, Vincent; Auffray, Jean-Christophe

    2009-01-01

    Morphological integration corresponds to interdependency between characters that can arise from several causes. Proximal causes of integration include that different phenotypic features may share common genetic sets and/or interact during their development. Ultimate causes may be the prolonged effect of selection favoring integration of functionally interacting characters, achieved by the molding of these proximal causes. Strong and direct interactions among successive teeth of a molar row are predicted by genetic and developmental evidences. Functional constraints related to occlusion, however, should have selected more strongly for a morphological integration of occluding teeth and a corresponding evolution of the underlying developmental and genetic pathways. To investigate how these predictions match the patterns of phenotypic integration, we studied the co-variation among the six molars of the murine molar row, focusing on two populations of house mice (Mus musculus domesticus) and wood mice (Apodemus sylvaticus). The size and shape of the three upper and lower molars were quantified and compared. Our results evidenced similar patterns in both species, size being more integrated than shape among all the teeth, and both size and shape co-varying strongly between adjacent teeth, but also between occluding teeth. Strong co-variation within each molar row is in agreement with developmental models showing a cascade influence of the first molar on the subsequent molars. In contrast, the strong co-variation between molars of the occluding tooth rows confirms that functional constraints molded patterns of integration and probably the underlying developmental pathways despite the low level of direct developmental interactions occurring among molar rows. These patterns of co-variation are furthermore conserved between the house mouse and the wood mouse that diverged >10 Ma, suggesting that they may constitute long-running constraints to the diversification of the murine

  16. 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

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

    Science.gov (United States)

    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.

  18. 1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    International Nuclear Information System (INIS)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D.

    2011-01-01

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1 H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  19. {sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

    2011-04-15

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  20. Arabian Sea GEOSECS stations revisited: Tracer-depth profiles reveal temporal variations?

    International Nuclear Information System (INIS)

    Mulsow, S.; Povinec, P.P.; Somayajulu, B.L.K.

    2002-01-01

    In March-April 1998, the Physical Research Laboratory and the Regional Research Laboratory (Ahmedabad, India) together with the IAEA Marine Environment Laboratory, Monaco, participated in the research mission to visit GEOSECS (Geochemical Ocean Sections Study) stations in the Arabian Sea. The main objective was to reoccupy these stations which were sampled in the early seventies to observe possible time variations in trace behaviour in this region. It is generally accepted that both natural (climate variations) and anthropogenic (greenhouse effect) changes can cause modifications of the oceanic characteristics and properties of deep waters on yearly and decadal scales. For long time-scales (100 to 1000 years) one needs to look at the sediments where these changes are subtly recorded. Tracers such as 14 C and 3 H (deep waters) and 228 Ra surface waters are useful markers of water circulation patterns and changes. Also man-made radiotracers such as 90 Sr, 137 Cs, 99 Tc, 238 Pu, 239 , 240 Pu and 241 Am, can give information on air-sea exchange as well as penetration (vertical change) rates in the open ocean [2]. We visited GEOSECS stations 415 to 419. In each station, CTD profiles, 3 H, 14 C, 90 Sr, 137 Cs, Pu and Am profiles, nutrients, Be, TOC and oxygen were determined from surface to bottom. Also uranium and trace elements were sampled in function of the oxygen minimum zone. In this paper we report the findings on the physical properties as well as the variations in water circulation patterns and also vertical exchange rates in the Arabian Sea. PSU profiles collected in this mission compared with those PSU profiles measured in 1974 (GEOSECS) showed marked differences in those stations located in the southeast part of the Arabian Sea. In contrast, those located more towards the north (415-416) showed little temporal variation. We think these changes may be real given that the PSU values at depth are comparable and reflect the presence of deep Antarctic bottom

  1. Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

    Science.gov (United States)

    Young, Jodi N.; Heureux, Ana M.C.; Sharwood, Robert E.; Rickaby, Rosalind E.M.; Morel, François M.M.; Whitney, Spencer M.

    2016-01-01

    While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat c), oxygenation (k cat o), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23–68 µM), SC/O (57–116mol mol−1), and K O (413–2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat c for each diatom Rubisco showed less variation (2.1–3.7s−1), thus averting the canonical trade-off typically observed between K C and k cat c for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily. PMID:27129950

  2. Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Jensen, Annette Bruun; Eilenberg, Jørgen

    2017-01-01

    of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar...

  3. Seismic tomography with P and S data reveals lateral variations in the rigidity of slabs

    NARCIS (Netherlands)

    Widiyantoro, S.; Kennett, B.L.N.; Hilst, R.D. van der

    1999-01-01

    Regional seismic tomography of the northwest Pacific island arcs using P- and S-wave arrival time data with similar path coverage reveals an oceanic lithospheric slab deflected in the mantle transition zone beneath the Izu Bonin region in good agreement with the results of earlier tomographic and

  4. Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage

    NARCIS (Netherlands)

    van der Reijden, Wil A.; Brunner, Jorg; Bosch-Tijhof, Carolien J.; van Trappen, Stefanie; Rijnsburger, Martine C.; de Graaff, Marcel P. W.; van Winkelhoff, Arie J.; Cleenwerck, Ilse; de Vos, Paul

    2010-01-01

    The periodontal pathogen Aggregatibacter actinomycetemcomitans that comprises six serotypes (a-f), is often identified by PCR-based techniques targeting the 16S rRNA gene. In this study, 16S rRNA gene sequence analysis revealed an aberrant cluster of 19 strains within serotype e, denoted as serotype

  5. A first glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping

    Directory of Open Access Journals (Sweden)

    Karolina Susek

    2016-07-01

    Full Text Available Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52, basic chromosome numbers (x=5-7, 9, 13 and in nuclear genome size (2C DNA=0.97-2.68 pg. Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution.In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

  6. Complex pattern of variation in neurocranial ontogeny revealed by CT-scanning.

    Science.gov (United States)

    Anzelmo, Marisol; Ventrice, Fernando; Kelmansky, Diana; Sardi, Marina

    2018-05-01

    The neurocranium of hominid species has been largely studied with reference to the midsagittal plane, with variations being attributed to brain evolution. By contrast, there is limited information on variation in non-midsagittal regions, which are the points of insertion of muscles and bony structures related to mastication. This work aims to analyze ontogenetic changes and sexual dimorphism (SD) in midsagittal and non-midsagittal neurocranial structures from a contemporary human sample comprising 138 computed tomography (CT) cranial images of individuals ranging from infants to adults. Morphology of the vault and the base was assessed by registering landmarks and semilandmarks, which were analyzed by geometric morphometrics, and the endocranial volume (EV). The results of regressions and Kruskal-Wallis test indicate that the major size and shape changes in both midsagittal and non-midsagittal regions occur during infancy and juvenility; shape changes are also associated with an increase in EV. The size of the midsagittal vault, the shape of the non-midsagittal vault and the size of the base show an extension of ontogenetic trajectories. Sexes show similar changes in shape but different changes in size. We conclude that brain growth appears to be an important factor influencing the morphology of the neurocranium, at least during infancy and childhood. Subsequent changes may be attributed to osteogenic activity and the differential growth of the brain lobes. Masticatory-related bony structures and muscles may not be strong enough factors to induce independent modifications in non-midsagittal structures. The small influence of the cranial muscles would explain why the human neurocranium is a quite integrated structure.

  7. Indifference to dissonance in native Amazonians reveals cultural variation in music perception.

    Science.gov (United States)

    McDermott, Josh H; Schultz, Alan F; Undurraga, Eduardo A; Godoy, Ricardo A

    2016-07-28

    by biology remains debated. One widely discussed phenomenon is that some combinations of notes are perceived by Westerners as pleasant, or consonant, whereas others are perceived as unpleasant,or dissonant. The contrast between consonance and dissonance is central to Western music and its origins have fascinated scholars since the ancient Greeks. Aesthetic responses to consonance are commonly assumed by scientists to have biological roots, and thus to be universally present in humans. Ethnomusicologists and composers, in contrast, have argued that consonance is a creation of Western musical culture. The issue has remained unresolved, partly because little is known about the extent of cross-cultural variation in consonance preferences. Here we report experiments with the Tsimane'--a native Amazonian society with minimal exposure to Western culture--and comparison populations in Bolivia and the United States that varied in exposure to Western music. Participants rated the pleasantness of sounds. Despite exhibiting Western-like discrimination abilities and Western-like aesthetic responses to familiar sounds and acoustic roughness, the Tsimane' rated consonant and dissonant chords and vocal harmonies as equally pleasant. By contrast, Bolivian city- and town-dwellers exhibited significant preferences for consonance,albeit to a lesser degree than US residents. The results indicate that consonance preferences can be absent in cultures sufficiently isolated from Western music, and are thus unlikely to reflect innate biases or exposure to harmonic natural sounds. The observed variation in preferences is presumably determined by exposure to musical harmony, suggesting that culture has a dominant role in shaping aesthetic responses to music.

  8. Long-term changes in abundances of Sonoran Desert lizards reveal complex responses to climatic variation.

    Science.gov (United States)

    Flesch, Aaron D; Rosen, Philip C; Holm, Peter

    2017-12-01

    Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short-lived, winter-spring breeder increased markedly by an estimated 237%-285% across time, while two larger spring-summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (1-1.5 years) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (2-4 years) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (T max ) are expected to drive global declines of lizards, associations with T max were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines in species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicates that evaluating and responding to the influence of climate change

  9. Experimental reintroduction reveals novel life-history variation in Laysan Ducks (Anas laysanensis)

    Science.gov (United States)

    Walters, Jeffrey R.; Reynolds, Michelle H.

    2013-01-01

    Subfossil remains indicate that the Laysan Duck (Anas laysanensis) formerly occurred throughout the Hawaiian archipelago, but for more than 150 years it has been confined to a single, small atoll in the northwestern chain, Laysan Island. In 2004–2005, 42 ducks were reintroduced from Laysan to Midway Atoll, where they exhibited variation in life history never observed on Laysan. On Laysan, females have never been observed to breed successfully at age 1 year and few attempt it, whereas on Midway, females routinely raised young at study; n = 21 and 19, respectively) and triple brooding has never been observed. Other novel life history on Midway included early cessation of parental care to renest. Altered life history on Midway is likely related to better feeding conditions and low population density compared with Laysan. An especially intriguing possibility is that the phenotypic plasticity observed represents exposure of hidden reaction norms evolved when the species inhabited a range of environments, but several alternative explanations exist. Future reintroductions of this species may provide opportunities to test hypotheses about mechanisms underlying phenotypic plasticity.

  10. 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.

  11. Variations in the Phytophthora infestans Population in Nepal as Revealed by Nuclear and Mitochondrial DNA Polymorphisms.

    Science.gov (United States)

    Ghimire, S R; Hyde, K D; Hodgkiss, I J; Shaw, D S; Liew, E C Y

    2003-02-01

    ABSTRACT Phytophthora infestans isolates collected from potato and tomato crops from various parts of Nepal during the 1999 and 2000 crop seasons were characterized for nuclear and mitochondrial DNA polymorphisms using restriction fragment length polymorphism markers. The nuclear DNA probe RG57 detected 11 multilocus genotypes among 280 isolates. Three genotypes were detected 21 times or more, constituting 94% of the total population, whereas frequencies of other genotypes ranged from 0.004 to 0.014. The overall genotypic diversity as estimated by the Gleason index was 1.78. Most of the overall diversity was present at the highest level (i.e., interregional, 46%), indicating limited gene flow among regions. Cluster analysis of multilocus genotypes derived from RG57 and mating type data for Nepalese isolates and representative isolates worldwide showed Nepalese isolates grouping into four clusters. Characterization of 67 isolates for mitochondrial DNA polymorphisms revealed the presence of two mt-haplotypes, Ia and Ib with the proportions of 0.88 and 0.12, respectively. Polymorphisms in nuclear and mitochondrial DNA revealed a moderate level of diversity in this population. Genotype NP3 had an identical RG57 fingerprint to US1 and had mt-haplotype Ib, confirming the presence of an old population in Nepal. Most of the genotypes had a different RG57 fingerprint than that of US1 and mt-haplotype Ia, the common characteristics of new populations. The presence of a new population at high proportions in Nepal was consistent with the global trend of mt-haplotype distribution, and suggests the displacement of old populations. This study indicates at least three possible introductions of P. infestans to Nepal.

  12. Expression of cytokeratins in odontogenic jaw cysts: monoclonal antibodies reveal distinct variation between different cyst types.

    Science.gov (United States)

    Hormia, M; Ylipaavalniemi, P; Nagle, R B; Virtanen, I

    1987-08-01

    Immunostaining with monoclonal antibodies was used to study and compare the cytokeratin content of odontogenic cysts and normal gingival epithelium. Two monoclonal antibodies, PKK2 and KA1, stained the whole epithelium in all cyst samples. In gingiva, PKK2 gave a suprabasal staining and KA1 reacted with all epithelial cell layers. Antibodies PKK1, KM 4.62 and KS 8.12 gave a heterogeneous staining in follicular and radicular cysts. In keratocysts and in gingiva PKK1 and KM 4.62 reacted mainly with basal cells and KS 8.12 gave a suprabasal staining. Antibodies reacting with the simple epithelial cytokeratin polypeptide No. 18 (PKK3, KS 18.18) recognized in gingiva only solitary cells compatible with Merkel cells. In a case of follicular ameloblastoma a distinct staining of tumor epithelium was revealed with these antibodies. In 2 follicular cysts, but not in other cyst types, a layer of cytokeratin 18-positive cells was revealed. KA5 and KK 8.60 antibodies, reacting exclusively with keratinizing epithelia, including normal gingiva, gave no reaction in radicular cysts, keratocysts and ameloblastoma. Two of the follicular cysts, were negative for PKK3 and KS 18.18, but reacted strongly with KA5 and KK 8.60. The present results show that odontogenic jaw cysts have distinct differences in their cytokeratin content. With the exception of some follicular cysts, they lack signs of keratinizing epithelial differentiation. Only follicular cysts appear to share with some types of ameloblastoma the expression of cytokeratin polypeptide No. 18.

  13. GPS-tracking and colony observations reveal variation in offshore habitat use and foraging ecology of breeding Sandwich Terns

    Science.gov (United States)

    Fijn, R. C.; de Jong, J.; Courtens, W.; Verstraete, H.; Stienen, E. W. M.; Poot, M. J. M.

    2017-09-01

    Breeding success of seabirds critically depends on their foraging success offshore. However, studies combining at-sea tracking and visual provisioning observations are scarce, especially for smaller species of seabirds. This study is the first in which breeding Sandwich Terns were tracked with GPS-loggers to collect detailed data on foraging habitat use in four breeding seasons. The maximum home range of individual Sandwich Terns comprised approximately 1900 km2 and the average foraging range was 27 km. Trip durations were on average 135 min with average trip lengths of 67 km. Actual foraging behaviour comprised 35% of the time budget of a foraging trip. Substantial year-to-year variation was found in habitat use and trip variables, yet with the exception of 2012, home range size remained similar between years. Food availability, chick age and environmental conditions are proposed as the main driving factors between inter- and intra-annual variations in trip variables. Our multi-method approach also provided geo-referenced information on prey presence and we conclude that future combining of colony observations and GPS-loggers deployments can potentially provide a near complete insight into the feeding ecology of breeding Sandwich Terns, including the behaviour of birds at sea.

  14. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance

    Directory of Open Access Journals (Sweden)

    Nicolas eBerthod

    2015-10-01

    Full Text Available Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice (SRC willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec to determine their bioenergy potential in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood, suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50 % of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry

  15. SPATIAL VARIATIONS OF PAH PROPERTIES IN M17SW REVEALED BY SPITZER /IRS SPECTRAL MAPPING

    Energy Technology Data Exchange (ETDEWEB)

    Yamagishi, M. [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Chuo-ku, Sagamihara 252-5210 (Japan); Kaneda, H.; Ishihara, D.; Oyabu, S.; Suzuki, T.; Nishimura, A.; Kohno, M. [Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Onaka, T.; Ohashi, S. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nagayama, T.; Matsuo, M. [Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065 (Japan); Umemoto, T.; Minamidani, T.; Fujita, S. [Nobeyama Radio Observatory, National Astronomical Observatory of Japan (NAOJ), National Institutes of Natural Sciences (NINS), 462-2, Nobeyama, Minamimaki, Minamisaku, Nagano 384-1305 (Japan); Tsuda, Y., E-mail: yamagish@ir.isas.jaxa.jp [Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-0042 (Japan)

    2016-12-20

    We present Spitzer /IRS mid-infrared spectral maps of the Galactic star-forming region M17 as well as IRSF/SIRIUS Br γ and Nobeyama 45 m/FOREST {sup 13}CO ( J = 1–0) maps. The spectra show prominent features due to polycyclic aromatic hydrocarbons (PAHs) at wavelengths of 6.2, 7.7, 8.6, 11.3, 12.0, 12.7, 13.5, and 14.2  μ m. We find that the PAH emission features are bright in the region between the H ii region traced by Br γ and the molecular cloud traced by {sup 13}CO, supporting that the PAH emission originates mostly from photo-dissociation regions. Based on the spatially resolved Spitzer /IRS maps, we examine spatial variations of the PAH properties in detail. As a result, we find that the interband ratio of PAH 7.7  μ m/PAH 11.3  μ m varies locally near M17SW, but rather independently of the distance from the OB stars in M17, suggesting that the degree of PAH ionization is mainly controlled by local conditions rather than the global UV environments determined by the OB stars in M17. We also find that the interband ratios of the PAH 12.0  μ m, 12.7  μ m, 13.5  μ m, and 14.2  μ m features to the PAH 11.3  μ m feature are high near the M17 center, which suggests structural changes of PAHs through processing due to intense UV radiation, producing abundant edgy irregular PAHs near the M17 center.

  16. Fish habitat selection in a large hydropeaking river: Strong individual and temporal variations revealed by telemetry.

    Science.gov (United States)

    Capra, Hervé; Plichard, Laura; Bergé, Julien; Pella, Hervé; Ovidio, Michaël; McNeil, Eric; Lamouroux, Nicolas

    2017-02-01

    Modeling individual fish habitat selection in highly variable environments such as hydropeaking rivers is required for guiding efficient management decisions. We analyzed fish microhabitat selection in the heterogeneous hydraulic and thermal conditions (modeled in two-dimensions) of a reach of the large hydropeaking Rhône River locally warmed by the cooling system of a nuclear power plant. We used modern fixed acoustic telemetry techniques to survey 18 fish individuals (five barbels, six catfishes, seven chubs) signaling their position every 3s over a three-month period. Fish habitat selection depended on combinations of current microhabitat hydraulics (e.g. velocity, depth), past microhabitat hydraulics (e.g. dewatering risk or maximum velocities during the past 15days) and to a lesser extent substrate and temperature. Mixed-effects habitat selection models indicated that individual effects were often stronger than specific effects. In the Rhône, fish individuals appear to memorize spatial and temporal environmental changes and to adopt a "least constraining" habitat selection. Avoiding fast-flowing midstream habitats, fish generally live along the banks in areas where the dewatering risk is high. When discharge decreases, however, they select higher velocities but avoid both dewatering areas and very fast-flowing midstream habitats. Although consistent with the available knowledge on static fish habitat selection, our quantitative results demonstrate temporal variations in habitat selection, depending on individual behavior and environmental history. Their generality could be further tested using comparative experiments in different environmental configurations. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. 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.

  18. In situ cardiac perfusion reveals interspecific variation of intraventricular flow separation in reptiles.

    Science.gov (United States)

    Joyce, William; Axelsson, Michael; Altimiras, Jordi; Wang, Tobias

    2016-07-15

    The ventricles of non-crocodilian reptiles are incompletely divided and provide an opportunity for mixing of oxygen-poor blood and oxygen-rich blood (intracardiac shunting). However, both cardiac morphology and in vivo shunting patterns exhibit considerable interspecific variation within reptiles. In the present study, we develop an in situ double-perfused heart approach to characterise the propensity and capacity for shunting in five reptile species: the turtle Trachemys scripta, the rock python Python sebae, the yellow anaconda Eunectes notaeus, the varanid lizard Varanus exanthematicus and the bearded dragon Pogona vitticeps To simulate changes in vascular bed resistance, pulmonary and systemic afterloads were independently manipulated and changes in blood flow distribution amongst the central outflow tracts were monitored. As previously demonstrated in Burmese pythons, rock pythons and varanid lizards exhibited pronounced intraventricular flow separation. As pulmonary or systemic afterload was raised, flow in the respective circulation decreased. However, flow in the other circulation, where afterload was constant, remained stable. This correlates with the convergent evolution of intraventricular pressure separation and the large intraventricular muscular ridge, which compartmentalises the ventricle, in these species. Conversely, in the three other species, the pulmonary and systemic flows were strongly mutually dependent, such that the decrease in pulmonary flow in response to elevated pulmonary afterload resulted in redistribution of perfusate to the systemic circuit (and vice versa). Thus, in these species, the muscular ridge appeared labile and blood could readily transverse the intraventricular cava. We conclude that relatively minor structural differences between non-crocodilian reptiles result in the fundamental changes in cardiac function. Further, our study emphasises that functionally similar intracardiac flow separation evolved independently in

  19. Pauses in Striatal Cholinergic Interneurons: What is Revealed by Their Common Themes and Variations?

    Directory of Open Access Journals (Sweden)

    Yan-Feng Zhang

    2017-10-01

    Full Text Available Striatal cholinergic interneurons, the so-called tonically active neurons (TANs, pause their firing in response to sensory cues and rewards during classical conditioning and instrumental tasks. The respective pause responses observed can demonstrate many commonalities, such as constant latency and duration, synchronous occurrence in a population of cells, and coincidence with phasic activities of midbrain dopamine neurons (DANs that signal reward predictions and errors. Pauses can however also show divergent properties. Pause latencies and durations can differ in a given TAN between appetitive vs. aversive outcomes in classical conditioning, initial excitation can be present or absent, and a second pause can variably follow a rebound. Despite more than 20 years of study, the functions of these pause responses are still elusive. Our understanding of pause function is hindered by an incomplete understanding of how pauses are generated. In this mini-review article, we compare pause types, as well as current key hypotheses for inputs underlying pauses that include dopamine-induced inhibition through D2-receptors, a GABA input from ventral tegmental area, and a prolonged afterhyperpolarization induced by excitatory input from the cortex or from the thalamus. We review how each of these mechanisms alone explains some but not all aspects of pause responses. These mechanisms might need to operate in specific but variable sets of sequences to generate a full range of pause responses. Alternatively, these mechanisms might operate in conjunction with an underlying control mechanism within cholinergic interneurons which could potentially provide a framework to generate the common themes and variations seen amongst pause responses.

  20. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars.

    Science.gov (United States)

    Lin, Hong; Rao, Jun; Shi, Jianxin; Hu, Chaoyang; Cheng, Fang; Wilson, Zoe A; Zhang, Dabing; Quan, Sheng

    2014-09-01

    Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While "omics" studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield. © 2014 Institute of Botany, Chinese Academy of Sciences.

  1. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

    Institute of Scientific and Technical Information of China (English)

    Hong Lin; Jun Rao; Jianxin Shi; Chaoyang Hu; Fang Cheng; Zoe AWilson; Dabing Zhang; Sheng Quan

    2014-01-01

    Soybean [Glycine max (L.) Merr.] is one of the world’s major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics”studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especial y in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetical y related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  2. Spatiotemporal mechanical variation reveals critical role for rho kinase during primitive streak morphogenesis.

    Science.gov (United States)

    Henkels, Julia; Oh, Jaeho; Xu, Wenwei; Owen, Drew; Sulchek, Todd; Zamir, Evan

    2013-02-01

    Large-scale morphogenetic movements during early embryo development are driven by complex changes in biochemical and biophysical factors. Current models for amniote primitive streak morphogenesis and gastrulation take into account numerous genetic pathways but largely ignore the role of mechanical forces. Here, we used atomic force microscopy (AFM) to obtain for the first time precise biomechanical properties of the early avian embryo. Our data reveal that the primitive streak is significantly stiffer than neighboring regions of the epiblast, and that it is stiffer than the pre-primitive streak epiblast. To test our hypothesis that these changes in mechanical properties are due to a localized increase of actomyosin contractility, we inhibited actomyosin contractility via the Rho kinase (ROCK) pathway using the small-molecule inhibitor Y-27632. Our results using several different assays show the following: (1) primitive streak formation was blocked; (2) the time-dependent increase in primitive streak stiffness was abolished; and (3) convergence of epiblast cells to the midline was inhibited. Taken together, our data suggest that actomyosin contractility is necessary for primitive streak morphogenesis, and specifically, ROCK plays a critical role. To better understand the underlying mechanisms of this fundamental process, future models should account for the findings presented in this study.

  3. Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

    DEFF Research Database (Denmark)

    Kaas, Christian Schrøder; Kristensen, Claus; Betenbaugh, Michael J.

    2015-01-01

    Background: The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins.  Results: Here we present the genomic sequence...... of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC -> AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing...... in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find similar to 2...

  4. Striking variations in consultation rates with general practice reveal family influence

    Directory of Open Access Journals (Sweden)

    Spreeuwenberg Peter

    2007-01-01

    Full Text Available Abstract Background The reasons why patients decide to consult a general practitioner vary enormously. While there may be individual reasons for this variation, the family context has a significant and unique influence upon the frequency of individuals' visits. The objective of this study was to explore which family factors can explain the differences between strikingly high, and correspondingly low, family consultation rates in families with children aged up to 21. Methods Data were used from the second Dutch national survey of general practice. This survey extracted from the medical records of 96 practices in the Netherlands, information on all consultations with patients during 2001. We defined, through multilevel analysis, two groups of families. These had respectively, predominantly high, and low, contact frequencies due to a significant family influence upon the frequency of the individual's first contacts. Binomial logistic regression analyses were used to analyse which of the family factors, related to shared circumstances and socialisation conditions, can explain the differences in consultation rates between the two groups of families. Results In almost 3% of all families, individual consultation rates decrease significantly due to family influence. In 11% of the families, individual consultation rates significantly increase due to family influence. While taking into account the health status of family members, family factors can explain family consultation rates. These factors include circumstances such as their economic status and number of children, as well as socialisation conditions such as specific health knowledge and family beliefs. The chance of significant low frequencies of contact due to family influences increases significantly with factors such as, paid employment of parents in the health care sector, low expectations of general practitioners' care for minor ailments and a western cultural background. Conclusion Family

  5. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

    Directory of Open Access Journals (Sweden)

    McGuire Patrick E

    2010-12-01

    chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

  6. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

    Directory of Open Access Journals (Sweden)

    Yanliang Jiang

    Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  7. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

    Science.gov (United States)

    Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

    2014-01-01

    The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  8. Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

    Science.gov (United States)

    Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

    2011-01-01

    Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

  9. 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.

  10. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

    Science.gov (United States)

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-04

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

  11. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    Science.gov (United States)

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA 2 s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA 2 s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not

  12. How does a carnivore guild utilise a substantial but unpredictable anthropogenic food source? Scavenging on hunter-shot ungulate carcasses by wild dogs/dingoes, red foxes and feral cats in south-eastern Australia revealed by camera traps.

    Directory of Open Access Journals (Sweden)

    David M Forsyth

    Full Text Available There is much interest in understanding how anthropogenic food resources subsidise carnivore populations. Carcasses of hunter-shot ungulates are a potentially substantial food source for mammalian carnivores. The sambar deer (Rusa unicolor is a large (≥ 150 kg exotic ungulate that can be hunted throughout the year in south-eastern Australia, and hunters are not required to remove or bury carcasses. We investigated how wild dogs/dingoes and their hybrids (Canis lupus familiaris/dingo, red foxes (Vulpes vulpes and feral cats (Felis catus utilised sambar deer carcasses during the peak hunting seasons (i.e. winter and spring. We placed carcasses at 1-km intervals along each of six transects that extended 4-km into forest from farm boundaries. Visits to carcasses were monitored using camera traps, and the rate of change in edible biomass estimated at ∼ 14-day intervals. Wild dogs and foxes fed on 70% and 60% of 30 carcasses, respectively, but feral cats seldom (10% fed on carcasses. Spatial and temporal patterns of visits to carcasses were consistent with the hypothesis that foxes avoid wild dogs. Wild dog activity peaked at carcasses 2 and 3 km from farms, a likely legacy of wild dog control, whereas fox activity peaked at carcasses 0 and 4 km from farms. Wild dog activity peaked at dawn and dusk, whereas nearly all fox activity occurred after dusk and before dawn. Neither wild dogs nor foxes remained at carcasses for long periods and the amount of feeding activity by either species was a less important predictor of the loss of edible biomass than season. Reasons for the low impacts of wild dogs and foxes on sambar deer carcass biomass include the spatially and temporally unpredictable distribution of carcasses in the landscape, the rapid rate of edible biomass decomposition in warm periods, low wild dog densities and the availability of alternative food resources.

  13. How does a carnivore guild utilise a substantial but unpredictable anthropogenic food source? Scavenging on hunter-shot ungulate carcasses by wild dogs/dingoes, red foxes and feral cats in south-eastern Australia revealed by camera traps.

    Science.gov (United States)

    Forsyth, David M; Woodford, Luke; Moloney, Paul D; Hampton, Jordan O; Woolnough, Andrew P; Tucker, Mark

    2014-01-01

    There is much interest in understanding how anthropogenic food resources subsidise carnivore populations. Carcasses of hunter-shot ungulates are a potentially substantial food source for mammalian carnivores. The sambar deer (Rusa unicolor) is a large (≥ 150 kg) exotic ungulate that can be hunted throughout the year in south-eastern Australia, and hunters are not required to remove or bury carcasses. We investigated how wild dogs/dingoes and their hybrids (Canis lupus familiaris/dingo), red foxes (Vulpes vulpes) and feral cats (Felis catus) utilised sambar deer carcasses during the peak hunting seasons (i.e. winter and spring). We placed carcasses at 1-km intervals along each of six transects that extended 4-km into forest from farm boundaries. Visits to carcasses were monitored using camera traps, and the rate of change in edible biomass estimated at ∼ 14-day intervals. Wild dogs and foxes fed on 70% and 60% of 30 carcasses, respectively, but feral cats seldom (10%) fed on carcasses. Spatial and temporal patterns of visits to carcasses were consistent with the hypothesis that foxes avoid wild dogs. Wild dog activity peaked at carcasses 2 and 3 km from farms, a likely legacy of wild dog control, whereas fox activity peaked at carcasses 0 and 4 km from farms. Wild dog activity peaked at dawn and dusk, whereas nearly all fox activity occurred after dusk and before dawn. Neither wild dogs nor foxes remained at carcasses for long periods and the amount of feeding activity by either species was a less important predictor of the loss of edible biomass than season. Reasons for the low impacts of wild dogs and foxes on sambar deer carcass biomass include the spatially and temporally unpredictable distribution of carcasses in the landscape, the rapid rate of edible biomass decomposition in warm periods, low wild dog densities and the availability of alternative food resources.

  14. How Does a Carnivore Guild Utilise a Substantial but Unpredictable Anthropogenic Food Source? Scavenging on Hunter-Shot Ungulate Carcasses by Wild Dogs/Dingoes, Red Foxes and Feral Cats in South-Eastern Australia Revealed by Camera Traps

    Science.gov (United States)

    Forsyth, David M.; Woodford, Luke; Moloney, Paul D.; Hampton, Jordan O.; Woolnough, Andrew P.; Tucker, Mark

    2014-01-01

    There is much interest in understanding how anthropogenic food resources subsidise carnivore populations. Carcasses of hunter-shot ungulates are a potentially substantial food source for mammalian carnivores. The sambar deer (Rusa unicolor) is a large (≥150 kg) exotic ungulate that can be hunted throughout the year in south-eastern Australia, and hunters are not required to remove or bury carcasses. We investigated how wild dogs/dingoes and their hybrids (Canis lupus familiaris/dingo), red foxes (Vulpes vulpes) and feral cats (Felis catus) utilised sambar deer carcasses during the peak hunting seasons (i.e. winter and spring). We placed carcasses at 1-km intervals along each of six transects that extended 4-km into forest from farm boundaries. Visits to carcasses were monitored using camera traps, and the rate of change in edible biomass estimated at ∼14-day intervals. Wild dogs and foxes fed on 70% and 60% of 30 carcasses, respectively, but feral cats seldom (10%) fed on carcasses. Spatial and temporal patterns of visits to carcasses were consistent with the hypothesis that foxes avoid wild dogs. Wild dog activity peaked at carcasses 2 and 3 km from farms, a likely legacy of wild dog control, whereas fox activity peaked at carcasses 0 and 4 km from farms. Wild dog activity peaked at dawn and dusk, whereas nearly all fox activity occurred after dusk and before dawn. Neither wild dogs nor foxes remained at carcasses for long periods and the amount of feeding activity by either species was a less important predictor of the loss of edible biomass than season. Reasons for the low impacts of wild dogs and foxes on sambar deer carcass biomass include the spatially and temporally unpredictable distribution of carcasses in the landscape, the rapid rate of edible biomass decomposition in warm periods, low wild dog densities and the availability of alternative food resources. PMID:24918425

  15. Airborne LiDAR analysis and geochronology of faulted glacial moraines in the Tahoe-Sierra frontal fault zone reveal substantial seismic hazards in the Lake Tahoe region, California-Nevada USA

    Science.gov (United States)

    Howle, James F.; Bawden, Gerald W.; Schweickert, Richard A.; Finkel, Robert C.; Hunter, Lewis E.; Rose, Ronn S.; von Twistern, Brent

    2012-01-01

    We integrated high-resolution bare-earth airborne light detection and ranging (LiDAR) imagery with field observations and modern geochronology to characterize the Tahoe-Sierra frontal fault zone, which forms the neotectonic boundary between the Sierra Nevada and the Basin and Range Province west of Lake Tahoe. The LiDAR imagery clearly delineates active normal faults that have displaced late Pleistocene glacial moraines and Holocene alluvium along 30 km of linear, right-stepping range front of the Tahoe-Sierra frontal fault zone. Herein, we illustrate and describe the tectonic geomorphology of faulted lateral moraines. We have developed new, three-dimensional modeling techniques that utilize the high-resolution LiDAR data to determine tectonic displacements of moraine crests and alluvium. The statistically robust displacement models combined with new ages of the displaced Tioga (20.8 ± 1.4 ka) and Tahoe (69.2 ± 4.8 ka; 73.2 ± 8.7 ka) moraines are used to estimate the minimum vertical separation rate at 17 sites along the Tahoe-Sierra frontal fault zone. Near the northern end of the study area, the minimum vertical separation rate is 1.5 ± 0.4 mm/yr, which represents a two- to threefold increase in estimates of seismic moment for the Lake Tahoe basin. From this study, we conclude that potential earthquake moment magnitudes (Mw) range from 6.3 ± 0.25 to 6.9 ± 0.25. A close spatial association of landslides and active faults suggests that landslides have been seismically triggered. Our study underscores that the Tahoe-Sierra frontal fault zone poses substantial seismic and landslide hazards.

  16. Molecular modelling studies of kdr mutations in voltage gated sodium channel revealed significant conformational variations contributing to insecticide resistance.

    Science.gov (United States)

    Yellapu, Nanda Kumar; Gopal, Jeyakodi; Kasinathan, Gunasekaran; Purushothaman, Jambulingam

    2018-06-01

    Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of dichlorodiphenyltrichloroethane (DDT) and other synthetic pyrethroids used in public health programmes. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions. The comparative molecular modelling studies of wild type and mutant models of STD-VGSC revealed that L1014F mutant was observed to be near native to the wild type model in all the respects, but, L1014S and L1014H mutations showed drastic variations in the energy levels, root mean square fluctuations (RMSF) that resulted in conformational variations. The predicted binding sites also showed variable cavity volumes and RMSF in L1014S and L1014H mutants. Further, DDT also found be bound in near native manner to wild type in L1014F mutant and with variable orientation and affinities in L1014S and L1014H mutants. The variations and fluctuations observed in mutant structures explained that each mutation has its specific impact on the conformation of VGSC and its binding with DDT. The study provides new insights into the structure-function-correlations of mutant STD-VGSC structures and demonstrates the role and effects of kdr mutations on insecticide resistance in mosquito vectors.

  17. High-density SNP genotyping of tomato (Solanum lycopersicum L. reveals patterns of genetic variation due to breeding.

    Directory of Open Access Journals (Sweden)

    Sung-Chur Sim

    Full Text Available The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA and pairwise estimates of F(st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage, particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  18. Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

    Science.gov (United States)

    Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

    2012-02-24

    Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

  19. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    Science.gov (United States)

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  20. Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers.

    Science.gov (United States)

    Elsheikha, H M; Schott, H C; Mansfield, L S

    2006-06-01

    Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

  1. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  2. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    2011-03-01

    Full Text Available Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

  3. Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors.

    Directory of Open Access Journals (Sweden)

    Vítor Borges

    Full Text Available Research on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC, and the functionality of the cytotoxin (CT166 through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations and rapidly increasing in frequency (~23% mutants per 10 passages. RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1. This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to

  4. Lateral Variations of the Mantle Transition Zone Structure beneath the Southeastern Tibetan Plateau Revealed by P-wave Receiver Functions

    Science.gov (United States)

    Bai, Y.; Ai, Y.; Jiang, M.; He, Y.; Chen, Q.

    2017-12-01

    The deep structure of the southeastern Tibetan plateau is of great scientific importance to a better understanding of the India-Eurasia collision as well as the evolution of the magnificent Tibetan plateau. In this study, we collected 566 permanent and temporary seismic stations deployed in SE Tibet, with a total of 77853 high quality P-wave receiver functions been extracted by maximum entropy deconvolution method. On the basis of the Common Conversion Point (CCP) stacking technique, we mapped the topography of the 410km and 660km discontinuities (hereinafter called the `410' and the `660'), and further investigated the lateral variation of the mantle transition zone (MTZ) thickness beneath this region. The background velocity model deduced from H-κ stacking results and a previous body-wave tomographic research was applied for the correction of the crustal and upper mantle heterogeneities beneath SE Tibet for CCP stacking. Our results reveal two significantly thickened MTZ anomalies aligned nearly in the south-north direction. The magnitude of both anomalies are 30km above the global average of 250km. The southern anomaly located beneath the Dianzhong sub-block and the Indo-China block is characterized by a slightly deeper `410' and a greater-than-normal `660', while the northern anomaly beneath western Sichuan has an uplifted `410' and a depressed `660'. Combining with previous studies in the adjacent region, we suggest that slab break-off may occurred during the eastward subduction of the Burma plate, with the lower part of the cold slab penetrated into the MTZ and stagnated at the bottom of the `660' which may cause the southern anomaly in our receiver function images. The origin of the Tengchong volcano is probably connected to the upwelling of the asthenospheric material caused by the slab break-off or to the ascending of the hot and wet material triggered by the dehydration of stagnant slab in the MTZ. The anomaly in the north, on the other hand, might be

  5. Comparative genomic sequence variation of Toxoplasma gondii reveals local admixture drives concerted expansion and diversification of secreted pathogenesis determinants

    Science.gov (United States)

    Toxoplasma gondii is among the most abundant parasites world-wide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its distribution from closely related parasites that typically have narrow, specialized host ranges. We undertook...

  6. Seasonal and Daily Variations of Subsurface Velocity Revealed by the Air-gun Source in Binchuan, Yunnan, China

    Science.gov (United States)

    Luan, Y.; Yang, H.; Wang, B.

    2017-12-01

    We derive temporal variations of subsurface structure using a large-volume air-gun source excited in Binchuan, Yunnan, southwest China, the first transmitting seismic station that can generate high-quality repeating waveforms. The data were collected between January 2013 and December 2015 that were recorded by 40 stations within 150 km, including permanent and newly deployed air-gun array stations. Firstly, we conduct cluster analysis using the waveforms at the nearest station and find the clustering result is not only governed by the water level of the reservoir, but also has seasonal variations. Furthermore, we use the records of the nearest station to approximate the source time functions and then retrieve empirical Green's functions (EGF) by deconvolution. Then we obtain travel time difference by comparing the EGF. The travel time difference exhibits clear seasonal variation, and the pattern correlates the best with surface air temperature. The increasing temperature coincides with increasing delay time i.e. decreasing seismic velocity. We interpret the observed seasonal variation of subsurface velocity is partly caused by thermo-elastic strain. However, our calculated thermo-elastic strain is only half in amplitude of the observed strain, indicating other factors such as precipitation and ground water level may play a role in the subsurface changes. Moreover, we derive the daily variation of subsurface velocity in December 2015 when air-gun shots were made in every hour. The delay time clearly correlates with the barometric pressure change and the tidal strain. Here we demonstrate that both long-term (seasonal) and short-term (daily) structural variations can be derived using the newly constructed active source, which is a powerful tool to advance our understanding of rheological properties of the crust as well as well processes associated with earthquakes and other natural hazards.

  7. Multi-tissue analyses reveal limited inter-annual and seasonal variation in mercury exposure in an Antarctic penguin community.

    Science.gov (United States)

    Brasso, Rebecka L; Polito, Michael J; Emslie, Steven D

    2014-10-01

    Inter-annual variation in tissue mercury concentrations in birds can result from annual changes in the bioavailability of mercury or shifts in dietary composition and/or trophic level. We investigated potential annual variability in mercury dynamics in the Antarctic marine food web using Pygoscelis penguins as biomonitors. Eggshell membrane, chick down, and adult feathers were collected from three species of sympatrically breeding Pygoscelis penguins during the austral summers of 2006/2007-2010/2011. To evaluate the hypothesis that mercury concentrations in penguins exhibit significant inter-annual variation and to determine the potential source of such variation (dietary or environmental), we compared tissue mercury concentrations with trophic levels as indicated by δ(15)N values from all species and tissues. Overall, no inter-annual variation in mercury was observed in adult feathers suggesting that mercury exposure, on an annual scale, was consistent for Pygoscelis penguins. However, when examining tissues that reflected more discrete time periods (chick down and eggshell membrane) relative to adult feathers, we found some evidence of inter-annual variation in mercury exposure during penguins' pre-breeding and chick rearing periods. Evidence of inter-annual variation in penguin trophic level was also limited suggesting that foraging ecology and environmental factors related to the bioavailability of mercury may provide more explanatory power for mercury exposure compared to trophic level alone. Even so, the variable strength of relationships observed between trophic level and tissue mercury concentrations across and within Pygoscelis penguin species suggest that caution is required when selecting appropriate species and tissue combinations for environmental biomonitoring studies in Antarctica.

  8. Intra- and interspecific trait variations reveal functional relationships between specific leaf area and soil niche within a subtropical forest.

    Science.gov (United States)

    He, Dong; Chen, Yongfa; Zhao, Kangning; Cornelissen, J H C; Chu, Chengjin

    2018-02-03

    How functional traits vary with environmental conditions is of fundamental importance in trait-based community ecology. However, how intraspecific variability in functional traits is connected to species distribution is not well understood. This study investigated inter- and intraspecific variation of a key functional trait, i.e. specific leaf area (leaf area per unit dry mass; SLA), in relation to soil factors and tested if trait variation is more closely associated with specific environmental regimes for low-variability species than for high-variability species. In a subtropical evergreen forest plot (50 ha, southern China), 106 700 leaves from 5335 individuals of 207 woody species were intensively collected, with 30 individuals sampled for most species to ensure a sufficient sample size representative of intraspecific variability. Soil conditions for each plant were estimated by kriging from more than 1700 observational soil locations across the plot. Intra- and interspecific variation in SLA were separately related to environmental factors. Based on the species-specific variation of SLA, species were categorized into three groups: low-, intermediate- and high-intraspecific variability. Intraspecific habitat ranges and the strength of SLA-habitat relationships were compared among these three groups. Interspecific variation in SLA overrides the intraspecific variation (77 % vs. 8 %). Total soil nitrogen (TN, positively) and total organic carbon (TOC, negatively) are the most important explanatory factors for SLA variation at both intra- and interspecific levels. SLA, both within and between species, decreases with decreasing soil nitrogen availability. As predicted, species with low intraspecific variability in SLA have narrower habitat ranges with respect to soil TOC and TN and show a stronger SLA-habitat association than high-variability species. For woody plants low SLA is a phenotypic and probably adaptive response to nitrogen stress, which drives the

  9. CpDNA haplotype variation reveals strong human influence on oak stands of the Veluwe forest in the Netherlands

    NARCIS (Netherlands)

    Buiteveld, J.; Koelewijn, H.P.

    2006-01-01

    We examined chloroplast DNA (cpDNA) variation in 78 oak stands of an important forest complex (the Veluwe) in The Netherlands. Based on historical maps and information oak stands were classified as planted or autochthonous. A genetic study by means of cpDNA haplotype characterisation was carried out

  10. 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

  11. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.; Yang, J.; Bougouffa, S.; Wang, Y.; Batang, Zenon B.; Tian, R.; Al-Suwailem, A.; Qian, P.-Y.

    2012-01-01

    -pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than

  12. Trophic calculations reveal the mechanism of population-level variation in mercury concentrations between marine ecosystems: Case studies of two polar seabirds

    International Nuclear Information System (INIS)

    Brasso, Rebecka L.; Polito, Michael J.

    2013-01-01

    Highlights: • Ecosystem-specific baseline and consumer δ 15 N paired for population-specific trophic level. • Source of population-level variation in mercury exposure identified in two seabirds. • High mercury and trophic position suggests trophic driver of population-level variation. • Trophic similarities, differing mercury reveals geographic differences in bioavailability. -- Abstract: The incorporation of quantitative trophic level analysis in ecotoxicological studies provides explanatory power to identify the factors, trophic or environmental, driving population-level variation in mercury exposure at large geographic scales. In the Antarctic marine ecosystem, mercury concentrations and stable isotope values in Adélie penguins (Pygoscelis adeliae) were compared between the Antarctic Peninsula and the Ross Sea. Correcting tissue δ 15 N values for baseline δ 15 N values revealed population-level differences in trophic position which contributes to differences in mercury. Data from Thick-billed murres (Uria lomvia) were synthesized from published values from Baffin Bay and Svalbard to demonstrate the utility of baseline δ 15 N values in identifying differences in environmental mercury exposure independent of diet. Here, we demonstrate the importance of calculating population-specific trophic level data to uncover the source of variation in mercury concentrations between geographically distinct populations of marine predators

  13. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

    Directory of Open Access Journals (Sweden)

    Zhu Tong

    2009-10-01

    Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

  14. Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

    Science.gov (United States)

    Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

    2014-03-01

    Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population.

    Science.gov (United States)

    Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K

    2014-07-01

    Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong.

  16. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Science.gov (United States)

    Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

    2015-01-01

    The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  17. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

    Directory of Open Access Journals (Sweden)

    Jiří Macas

    Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

  18. 24 CFR 902.79 - Substantial default.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Substantial default. 902.79 Section... PUBLIC HOUSING ASSESSMENT SYSTEM PHAS Incentives and Remedies § 902.79 Substantial default. (a) Events or conditions that constitute substantial default. The following events or conditions shall constitute...

  19. Revealing the physical insight of a length-scale parameter in metamaterials by exploiting the variational formulation

    Science.gov (United States)

    Abali, B. Emek

    2018-04-01

    For micro-architectured materials with a substructure, called metamaterials, we can realize a direct numerical simulation in the microscale by using classical mechanics. This method is accurate, however, computationally costly. Instead, a solution of the same problem in the macroscale is possible by means of the generalized mechanics. In this case, no detailed modeling of the substructure is necessary; however, new parameters emerge. A physical interpretation of these metamaterial parameters is challenging leading to a lack of experimental strategies for their determination. In this work, we exploit the variational formulation based on action principles and obtain a direct relation between a parameter used in the kinetic energy and a metamaterial parameter in the case of a viscoelastic model.

  20. Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

    Science.gov (United States)

    Popovsky-Sarid, Sigal; Borovsky, Yelena; Faigenboim, Adi; Parsons, Eugene P; Lohrey, Gregory T; Alkalai-Tuvia, Sharon; Fallik, Elazar; Jenks, Matthew A; Paran, Ilan

    2017-02-01

    Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.

  1. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).

    Science.gov (United States)

    Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G

    2017-04-01

    Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum Leaves Affected by Climate, Soil, and Tillage Factors

    Directory of Open Access Journals (Sweden)

    Bo Lei

    2014-04-01

    Full Text Available The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs, soil factors (SFs, and tillage factors (TFs. We detected 4980, 2916, and 1605 differentially expressed genes (DEGs that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs, respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

  3. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

    Science.gov (United States)

    Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

    2014-07-04

    Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was

  4. Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep.

    Science.gov (United States)

    Harbison, Susan T; Serrano Negron, Yazmin L; Hansen, Nancy F; Lobell, Amanda S

    2017-12-01

    Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways-EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.

  5. Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep.

    Directory of Open Access Journals (Sweden)

    Susan T Harbison

    2017-12-01

    Full Text Available Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways-EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.

  6. Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

    Directory of Open Access Journals (Sweden)

    D. LOUKOVITIS

    2014-10-01

    Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

  7. Regional variation of white matter development in the cat brain revealed by ex vivo diffusion MR tractography.

    Science.gov (United States)

    Dai, Guangping; Das, Avilash; Hayashi, Emiko; Chen, Qin; Takahashi, Emi

    2016-11-01

    Three-dimensional reconstruction of developing fiber pathways is essential to assessing the developmental course of fiber pathways in the whole brain. We applied diffusion spectrum imaging (DSI) tractography to five juvenile ex vivo cat brains at postnatal day (P) 35, when the degree of myelination varies across brain regions. We quantified diffusion properties (fractional anisotropy [FA] and apparent diffusion coefficient [ADC]) and other measurements (number, volume, and voxel count) on reconstructed pathways for projection (cortico-spinal and thalamo-cortical), corpus callosal, limbic (cingulum and fornix), and association (cortico-cortical) pathways, and characterized regional differences in maturation patterns by assessing diffusion properties. FA values were significantly higher in cortico-cortical pathways within the right hemisphere compared to those within the left hemisphere, while the other measurements for the cortico-cortical pathways within the hemisphere did not show asymmetry. ADC values were not asymmetric in both types of pathways. Interestingly, tract count and volume were significantly larger in the left thalamo-cortical pathways compared to the right thalamo-cortical pathways. The bilateral thalamo-cortical pathways showed high FA values compared to the other fiber pathways. On the other hand, ADC values did not show any differences across pathways studied. These results demonstrate that DSI tractography successfully depicted regional variations of white matter tracts during development when myelination is incomplete. Low FA and high ADC values in the cingulum bundle suggest that the cingulum bundle is less mature than the others at this developmental stage. Copyright © 2016 ISDN. Published by Elsevier Ltd. All rights reserved.

  8. Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex

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    Jason R. Gerstner

    2016-10-01

    Full Text Available Abstract Background Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep. Results In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV. RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1–3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h do so on average with a time constant that is similar to the time constant for the discharge of sleep need. Conclusions We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally

  9. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.

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    Zhen-Hui Wang

    Full Text Available BACKGROUND: Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs and 17,839 homozygous insertions/deletions (indels were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a

  10. Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

    Science.gov (United States)

    Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

    2015-10-01

    Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Genetic characterisation of farmed rainbow trout in Norway: intra- and inter-strain variation reveals potential for identification of escapees

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    Glover Kevin A

    2008-12-01

    Full Text Available Abstract Background The rainbow trout (Oncorhynchus mykiss is one of the most important aquaculture species in the world, and Norway is one of the largest producers. The present study was initiated in response to a request from the Norwegian police authority to identify the farm of origin for 35 escaped rainbow trout captured in a fjord. Eleven samples, each consisting of approximately 47 fish, were collected from the three farms operating in the fjord where the escapees were captured. In order to gain a better general understanding of the genetic structure of rainbow trout strains used in Norwegian aquaculture, seven samples (47 fish per sample were collected from six farms located outside the region where the escapees were captured. All samples, including the escapees, were genotyped with 12 microsatellite loci. Results All samples displayed considerable genetic variability at all loci (mean number of alleles per locus per sample ranged from 5.4–8.6. Variable degrees of genetic differentiation were observed among the samples, with pair-wise FST values ranging from 0–0.127. Self-assignment tests conducted among the samples collected from farms outside the fjord where the escapees were observed gave an overall correct assignment of 82.5%, demonstrating potential for genetic identification of escapees. In the "real life" assignment of the 35 captured escapees, all were excluded from two of the samples included as controls in the analysis, and 26 were excluded from the third control sample. In contrast, only 1 of the escapees was excluded from the 11 pooled samples collected on the 3 farms operating in the fjord. Conclusion Considerable genetic variation exists within and among rainbow trout strains farmed in Norway. Together with modern statistical methods, this will provide commercial operators with a tool to monitor breeding and fish movements, and management authorities with the ability to identify the source of escapees. The data

  12. Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

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    Marco Scortichini

    2010-11-01

    Full Text Available Forty-five Xanthomonas arboricola pv. juglandis (Xaj strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST, using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity.

  13. Genetic variation in Rhodomyrtus tomentosa (Kemunting) populations from Malaysia as revealed by inter-simple sequence repeat markers.

    Science.gov (United States)

    Hue, T S; Abdullah, T L; Abdullah, N A P; Sinniah, U R

    2015-12-14

    Kemunting (Rhodomyrtus tomentosa) from the Myrtaceae family, is native to Malaysia. It is widely used in traditional medicine to treat various illnesses and possesses significant antibacterial properties. In addition, it has great potential as ornamental in landscape design. Genetic variability studies are important for the rational management and conservation of genetic material. In the present study, inter-simple sequence repeat markers were used to assess the genetic diversity of 18 R. tomentosa populations collected from ten states of Peninsular Malaysia. The 11 primers selected generated 173 bands that ranged in size from 1.6 kb to 130 bp, which corresponded to an average of 15.73 bands per primer. Of these bands, 97.69% (169 in total) were polymorphic. High genetic diversity was documented at the species level (H(T) = 0.2705; I = 0.3973; PPB = 97.69%) but there was a low diversity at population level (H(S) = 0.0073; I = 0 .1085; PPB = 20.14%). The high level of genetic differentiation revealed by G(ST) (73%) and analysis of molecular variance (63%), together with the limited gene flow among population (N(m) = 0.1851), suggests that the populations examined are isolated. Results from an unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis clearly grouped the populations into two geographic groups. This clear grouping can also be demonstrated by the significant Mantel test (r = 0.581, P = 0.001). We recommend that all the R. tomentosa populations be preserved in conservation program.

  14. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions.

    Science.gov (United States)

    Dulik, Matthew C; Osipova, Ludmila P; Schurr, Theodore G

    2011-03-11

    Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th) century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.

  15. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions.

    Directory of Open Access Journals (Sweden)

    Matthew C Dulik

    Full Text Available Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*. In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.

  16. Large regional-scale variation in C3/C4 distribution pattern of Inner Mongolia steppe is revealed by grazer wool carbon isotope composition

    Directory of Open Access Journals (Sweden)

    K. Auerswald

    2009-05-01

    Full Text Available This work explored the spatial variation of C3/C4 distribution in the Inner Mongolia, P. R. China, steppe by geostatistical analysis of carbon isotope data of vegetation and sheep wool. Standing community biomass (n=118 and sheep wool (n=146 were sampled in a ~0.2 Mio km2 area. Samples from ten consecutive years (1998–2007 were obtained. Community biomass samples represented the carbon isotopic composition of standing vegetation on about 1000 m2 ("community-scale", whereas the spatio-temporal scale of wool reflected the isotope composition of the entire area grazed by the herd during a 1-yr period (~5–10 km2, "farm-scale". Pair wise sampling of wool and vegetation revealed a 13C-enrichment of 2.7±0.7‰ (95% confidence interval in wool relative to vegetation, but this shift exhibited no apparent relationships with environmental parameters or stocking rate. The proportion of C4 plants in above-ground biomass (PC4, % was estimated with a two-member mixing model of 13C discrimination by C3 and C4 vegetation (13Δ3 and 13Δ4, respectively, in accounting for the effects of changing 13C in atmospheric CO2 on sample isotope composition, and of altitude and aridity on 13Δ3. PC4 averaged 19%, but the variation was enormous: full-scale (0% to 100% at community-scale, and 0% to 85% at farm-scale. The farm-scale variation of PC4 exhibited a clear regional pattern over a range of ~250 km. Importantly PC4 was significantly higher above the 22°C isotherm of the warmest month, which was obtained from annual high-resolution maps and averaged over the different sampling years. This is consistent with predictions from C3/C4 crossover temperature of quantum yield or light use efficiency in C3 and C4 plants. Still, temperature gradients accounted for only 10% of

  17. Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus.

    Science.gov (United States)

    Wang, Lina; Cao, Chenxing; Zheng, Shuangshuang; Zhang, Haiyang; Liu, Panjing; Ge, Qian; Li, Jinrui; Ren, Zhonghai

    2017-06-07

    Fruit size is an important quality trait in different market classes of Cucumis sativus L., an economically important vegetable cultivated worldwide, but the genetic and molecular mechanisms that control fruit size are largely unknown. In this study, we isolated a natural cucumber mutant, short fruit 1 (sf1), caused by a single recessive Mendelian factor, from the North China-type inbred line CNS2. In addition to significantly decreased fruit length, other fruit-related phenotypic variations were also observed in sf1 compared to the wild-type (WT) phenotype, indicating that sf1 might have pleiotropic effects. Microscopic imaging showed that fruit cell size in sf1 was much larger than that in WT, suggesting that the short fruit phenotype in sf1 is caused by decreased cell number. Fine mapping revealed that sf1 was localized to a 174.3 kb region on chromosome 6. Similarly, SNP association analysis of bulked segregant RNA-Seq data showed increased SNP frequency in the same region of chromosome 6. In addition, transcriptomic analysis revealed that sf1 might control fruit length through the fine-tuning of cytokinin and auxin signalling, gibberellin biosynthesis and signal transduction in cucumber fruits. Overall, our results provide important information for further study of fruit length and other fruit-related features in cucumber.

  18. Increased greenhouse effect substantiated through measurements

    International Nuclear Information System (INIS)

    Skartveit, Arvid

    2001-01-01

    The article presents studies on the greenhouse effect which substantiates the results from satellite measurements during the period 1970 - 1997. These show an increased effect due to increase in the concentration of the climatic gases CO 2 , methane, CFC-11 and CFC-12 in the atmosphere

  19. 21 CFR 514.4 - Substantial evidence.

    Science.gov (United States)

    2010-04-01

    ... adequate and well-controlled studies, such as a study in a target species, study in laboratory animals... and conditions of use. Substantial evidence of effectiveness of a new animal drug shall demonstrate that the new animal drug is effective for each intended use and associated conditions of use for and...

  20. Toward More Substantial Theories of Language Acquisition

    Science.gov (United States)

    Jenson, Cinnamon Ann

    2015-01-01

    Cognitive linguists argue that certain sets of knowledge of language are innate. However, critics have argued that the theoretical concept of "innateness" should be eliminated since it is ambiguous and insubstantial. In response, I aim to strengthen theories of language acquisition and identify ways to make them more substantial. I…

  1. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

    Directory of Open Access Journals (Sweden)

    Rajani Rai

    2015-11-01

    Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

  2. High sensitivity detection of Plasmodium species reveals positive correlations between infections of different species, shifts in age distribution and reduced local variation in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Smith Thomas A

    2009-03-01

    Full Text Available Abstract Background When diagnosed by standard light microscopy (LM, malaria prevalence can vary significantly between sites, even at local scale, and mixed species infections are consistently less common than expect in areas co-endemic for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae. The development of a high-throughput molecular species diagnostic assay now enables routine PCR-based surveillance of malaria infections in large field and intervention studies, and improves resolution of species distribution within and between communities. Methods This study reports differences in the prevalence of infections with all four human malarial species and of mixed infections as diagnosed by LM and post-PCR ligase detection reaction – fluorescent microsphere (LDR-FMA assay in 15 villages in the central Sepik area of Papua New Guinea. Results Significantly higher rates of infection by P. falciparum, P. vivax, P. malariae and Plasmodium ovale were observed in LDR-FMA compared to LM diagnosis (p P. malariae (3.9% vs 13.4% and P. ovale (0.0% vs 4.8%. In contrast to LM diagnosis, which suggested a significant deficit of mixed species infections, a significant excess of mixed infections over expectation was detected by LDR-FMA (p P. falciparum (LM: 7–9 yrs 47.5%, LDR-FMA: 10–19 yrs 74.2% and P. vivax (LM: 4–6 yrs 24.2%, LDR-FMA: 7–9 yrs 50.9% but not P. malariae infections (10–19 yrs, LM: 7.7% LDR-FMA: 21.6%. Significant geographical variation in prevalence was found for all species (except for LM-diagnosed P. falciparum, with the extent of this variation greater in LDR-FMA than LM diagnosed infections (overall, 84.4% vs. 37.6%. Insecticide-treated bednet (ITN coverage was also the dominant factor linked to geographical differences in Plasmodium species infection prevalence explaining between 60.6% – 74.5% of this variation for LDR-FMA and 81.8% – 90.0% for LM (except P. falciparum, respectively. Conclusion The present study

  3. Inter- and intra-specific cuticle variation between amphimictic and parthenogenetic species of root-knot nematode (Meloidogyne spp.) as revealed by a bacterial parasite (Pasteuria penetrans).

    Science.gov (United States)

    Davies, K G; Rowe, J A; Williamson, V M

    2008-06-01

    Specific host-parasite interactions exist between species and strains of plant parasitic root-knot nematodes and the Gram-positive bacterial hyperparasite Pasteuria penetrans. This bacterium produces endospores that adhere to the cuticle of migrating juveniles, germinate and colonise the developing female within roots. Endospore attachment of P. penetrans populations to second-stage juveniles of the root-knot nematode species Meloidogyne incognita and Meloidogyne hapla showed there were interactive differences between bacterial populations and nematode species. Infected females of M. incognita produced a few progeny which were used to establish two nematode lines from single infective juveniles encumbered with either three or 26 endospores. Single juvenile descent lines of each nematode species were produced to test whether cuticle variation was greater within M. hapla lines that reproduce by facultative meiotic parthenogenesis than within lines of M. incognita, which reproduces by obligate parthenogenesis. Assays revealed variability between broods of individual females derived from single second-stage juvenile descent lines of both M. incognita and M. hapla suggesting that progeny derived from a single individual can differ in spore adhesion in both sexual and asexual nematode species. These results suggest that special mechanisms that produced these functional differences in the cuticle surface may have evolved in both sexually and asexually reproducing nematodes as a strategy to circumvent infection by this specialised hyperparasite.

  4. Variation in the Asian monsoon intensity and dry-wet conditions since the Little Ice Age in central China revealed by an aragonite stalagmite

    Science.gov (United States)

    Yin, J.-J.; Yuan, D.-X.; Li, H.-C.; Cheng, H.; Li, T.-Y.; Edwards, R. L.; Lin, Y.-S.; Qin, J.-M.; Tang, W.; Zhao, Z.-Y.; Mii, H.-S.

    2014-10-01

    This paper focuses on the climate variability in central China since AD 1300, involving: (1) a well-dated, 1.5-year resolution stalagmite δ18O record from Lianhua Cave, central China (2) links of the δ18O record with regional dry-wet conditions, monsoon intensity, and temperature over eastern China (3) correlations among drought events in the Lianhua record, solar irradiation, and ENSO (El Niño-Southern Oscillation) variation. We present a highly precise, 230Th / U-dated, 1.5-year resolution δ18O record of an aragonite stalagmite (LHD1) collected from Lianhua Cave in the Wuling Mountain area of central China. The comparison of the δ18O record with the local instrumental record and historical documents indicates that (1) the stalagmite δ18O record reveals variations in the summer monsoon intensity and dry-wet conditions in the Wuling Mountain area. (2) A stronger East Asian summer monsoon (EASM) enhances the tropical monsoon trough controlled by ITCZ (Intertropical Convergence Zone), which produces higher spring quarter rainfall and isotopically light monsoonal moisture in the central China. (3) The summer quarter/spring quarter rainfall ratio in central China can be a potential indicator of the EASM strength: a lower ratio corresponds to stronger EASM and higher spring rainfall. The ratio changed from 1 after 1950, reflecting that the summer quarter rainfall of the study area became dominant under stronger influence of the Northwestern Pacific High. Eastern China temperatures varied with the solar activity, showing higher temperatures under stronger solar irradiation, which produced stronger summer monsoons. During Maunder, Dalton and 1900 sunspot minima, more severe drought events occurred, indicating a weakening of the summer monsoon when solar activity decreased on decadal timescales. On an interannual timescale, dry conditions in the study area prevailed under El Niño conditions, which is also supported by the spectrum analysis. Hence, our record

  5. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes.

    Science.gov (United States)

    Mesoudi, Alex; Magid, Kesson; Hussain, Delwar

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal 'natural experiment' for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i) 1st-generation British Bangladeshi immigrants; (ii) 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii) non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media), with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact) and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission), or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly) despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly). Further consideration of cultural transmission mechanisms, in conjunction with the study of migrant

  6. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes.

    Directory of Open Access Journals (Sweden)

    Alex Mesoudi

    Full Text Available Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal 'natural experiment' for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i 1st-generation British Bangladeshi immigrants; (ii 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media, with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission, or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly. Further consideration of cultural transmission mechanisms, in conjunction with the study of

  7. How Do People Become W.E.I.R.D.? Migration Reveals the Cultural Transmission Mechanisms Underlying Variation in Psychological Processes

    Science.gov (United States)

    Mesoudi, Alex; Magid, Kesson; Hussain, Delwar

    2016-01-01

    Cultural psychologists have shown that people from Western, Educated, Industrialised, Rich, Democratic (WEIRD) countries often exhibit different psychological processing to people from less-WEIRD countries. The former exhibit more individualistic and less collectivistic social orientation, and more analytic and less holistic cognition, than non-Westerners. Yet the mechanisms responsible for maintaining this cultural variation are unclear. Immigration is an ideal ‘natural experiment’ for uncovering such mechanisms. We used a battery of psychological measures previously shown to vary cross-culturally to compare the social orientation and cognitive style of 286 residents of East London from three cultural backgrounds: (i) 1st-generation British Bangladeshi immigrants; (ii) 2nd-generation British Bangladeshis raised in the UK to Bangladeshi-raised parents; and (iii) non-migrants whose parents were born and raised in the UK. Model comparison revealed that individualism and dispositional attribution, typical of Western societies, are driven primarily by horizontal cultural transmission (e.g. via mass media), with parents and other family members having little or no effect, while collectivism, social closeness and situational attribution were driven by a mix of vertical/oblique cultural transmission (e.g. via family contact) and horizontal cultural transmission. These individual-level transmission dynamics can explain hitherto puzzling population-level phenomena, such as the partial acculturation of 2nd-generation immigrants on measures such as collectivism (due to the mix of vertical and horizontal cultural transmission), or the observation in several countries of increasing individualism (which is transmitted horizontally and therefore rapidly) despite little corresponding change in collectivism (which is transmitted partly vertically and therefore more slowly). Further consideration of cultural transmission mechanisms, in conjunction with the study of migrant

  8. The potential of Tillandsia dune ecosystems for revealing past and present variations in advective fog along the coastal Atacama Desert, northern Chile

    Science.gov (United States)

    Latorre Hidalgo, C.; García, J. L.; Gonzalez, A. L.; Marquet, P. A.

    2015-12-01

    The coastal Atacama Desert is home to a complex geo-ecosystem supported by fog with multiple atmospheric and oceanic drivers. Fog collectors in place for the last 17 years reveal that monthly fog intensity and amount are significantly linked to the El Niño-Southern Oscillation (ENSO 1+2) with cold (warm) anomalies correlated to increased (decreased) fog (R2 = 0.41). Rainfall, however, can occur during extreme positive ENSO anomalies. Tillandsia landbeckii is an epiarenitic plant common to the coastal Atacama where fog is intercepted by the coastal escarpment between 950-1250 m.a.s.l. These plants possess multiple adaptations to survive exclusively on fog, including the construction of "dune" ecosystems known as "tillandsiales". Buried T. landbeckii layers in such dunes contain a record of past variations of fog over time (dunes can top 3 m in height) and alternating plant and sand layers are readily visible in dune stratigraphy. Stable N isotopes on modern plants and fog indicate that these plants reflect δ15N values of total N dissolved in fog. We measured δ15N values from buried T. landbeckii layers from five different tillandsiales found across c. 50 km the coastal escarpment. The isotope values in these buried plants indicate a prominent c. 8.0 ‰ shift towards more negative δ15N values on average over the last 3,200 years. Based on differences in δ15N between modern and more extensive "paleo" tillandsiales at one of our lowest elevation study sites, we interpret this shift as an increase in available moisture due to increased fog input during the late Holocene. Increased variability in ENSO as well as increased upwelling and southerly winds along the coastal Atacama would explain in part this increase. Clearly, the Atacama tillandsiales have considerable potential for monitoring past and present change of these large-scale ocean-atmosphere systems.

  9. Substantiating the Incurred but not Reported Reserve

    Directory of Open Access Journals (Sweden)

    Georgeta Vintilã

    2009-12-01

    Full Text Available In order to handle past and future liability taken by insurance contracts concluded, any insurance company must constitute and maintain technical reserves. Substantiating technical reserves is done through actuarial methods and its over-evaluation or under-evaluation influence solvency and financial performance of the insurance companies, in the sense of reducing solvency through over-evaluating reserves and, respectively, influencing profit (hence of outstanding tax through under-evaluating reserves. An important reserve for insurance companies is represented by the incurred but not reported reserve, as it allows the estimation of the liability the company may confront in the future, generated by events occurred in the past, which are not currently known in the present but will be reported in the future.

  10. Mitochondrial and nuclear DNA reveals a complete lineage sorti ng ...

    African Journals Online (AJOL)

    Glossogobius callidus exhibits broad salinity tolerance and is distributed in both estuarine and freshwater environments in southern Africa. Previous studies revealed substantial morphological and molecular variation among populations, suggesting they constitute a species complex. The present study utilised phylogenetic ...

  11. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar; Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; Nair, Mridul; Clark, Taane G.; Zaver, Ambreen; Jafri, Sana; Hasan, Rumina

    2015-01-01

    Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  12. Substantial nitrogen pollution embedded in international trade

    Science.gov (United States)

    Oita, Azusa; Malik, Arunima; Kanemoto, Keiichiro; Geschke, Arne; Nishijima, Shota; Lenzen, Manfred

    2016-02-01

    Anthropogenic emissions of reactive nitrogen to the atmosphere and water bodies can damage human health and ecosystems. As a measure of a nation’s contribution to this potential damage, a country’s nitrogen footprint has been defined as the quantity of reactive nitrogen emitted during the production, consumption and transportation of commodities consumed within that country, whether those commodities are produced domestically or internationally. Here we use global emissions databases, a global nitrogen cycle model, and a global input-output database of domestic and international trade to calculate the nitrogen footprints for 188 countries as the sum of emissions of ammonia, nitrogen oxides and nitrous oxide to the atmosphere, and of nitrogen potentially exportable to water bodies. Per-capita footprints range from under 7 kg N yr-1 in some developing countries to over 100 kg N yr-1 in some wealthy nations. Consumption in China, India, the United States and Brazil is responsible for 46% of global emissions. Roughly a quarter of the global nitrogen footprint is from commodities that were traded across country borders. The main net exporters have significant agricultural, food and textile exports, and are often developing countries, whereas important net importers are almost exclusively developed economies. We conclude that substantial local nitrogen pollution is driven by demand from consumers in other countries.

  13. Variation in the Asian monsoon intensity and dry-wet condition since the Little Ice Age in central China revealed by an aragonite stalagmite

    Science.gov (United States)

    Yin, J.-J.; Yuan, D.-X.; Li, H.-C.; Cheng, H.; Li, T.-Y.; Edwards, R. L.; Lin, Y.-S.; Qin, J.-M.; Tang, W.; Zhao, Z.-Y.; Mii, H.-S.

    2014-04-01

    Highlight: this paper focuses on the climate variability in central China since 1300 AD, involving: 1. A well-dated, 1.5 year resolution stalagmite δ18O record from Lianhua Cave, central China; 2. Links of the δ18O record with regional dry-wet condition, monsoon intensity, and temperature over eastern China; 3. Correlations among drought events in the Lianhua record, solar irradiation, and ENSO index. We present a highly precisely 230Th/U dated, 1.5 year resolution δ18O record of an aragonite stalagmite (LHD1) collected from Lianhua Cave in Wuling mountain area of central China. The comparison of the δ18O record with the local instrumental record and historical documents exhibits at least 15 drought events in the Wuling mountain and adjacent areas during the Little Ice Age, in which some of them were corresponding to megadrought events in the broad Asian monsoonal region of China. Thus, the stalagmite δ18O record reveals variations in the summer monsoon precipitation and dry-wet condition in Wuling mountain area. The eastern China temperature varied with the solar activity, showing higher temperature under stronger solar irradiation which produces stronger summer monsoon. During Maunder, Dalton and 1900 sunspot minima, more severe drought events occurred, indicating weakening of the summer monsoon when solar activity decreased on decadal time scales. On interannual time scale, dry conditions in the studying area were prevailing under El Niño condition, which is also supported by the spectrum analysis. Hence, our record illustrates the linkage of Asian summer monsoon precipitation to solar irradiation and ENSO: wetter condition under stronger summer monsoon during warm periods and vice versa; During cold periods, the Walker circulation will shift toward central Pacific under El Niño condition, resulting further weakening of Asian summer monsoon. However, the δ18O of LHD1 record is positively correlated with temperature after ~1940 AD which is opposite to the

  14. Natural variation at the FRD3 MATE transporter locus reveals cross-talk between Fe homeostasis and Zn tolerance in Arabidopsis thaliana

    OpenAIRE

    Pineau, Christophe; Loubet, Stéphanie; Lefoulon, Cécile; Chaliès, Claude; Fizames, Cécile; Lacombe, Benoît; Ferrand, Marina; Loudet, Olivier; Berthomieu, Pierre; Richard, Odile

    2012-01-01

    Author Summary Plants are adapted to soils in which the amounts of different nutrients vary widely, like Zn-deficient or Zn-contaminated soils. Exploring the molecular bases of plant adaptation to Zn-contaminated soils is important in determining strategies for phytoremediation. Here, we describe the mapping and characterization of a QTL for Zn tolerance in A. thaliana that underlies the natural variation of the root response to excess Zn. This physiological variation is controlled by differe...

  15. 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

  16. Substantial Union or Substantial Distinction of Mind and Body in Descartes' Metaphysics

    Directory of Open Access Journals (Sweden)

    Fahime Jamei

    2009-01-01

    Full Text Available According to Descartes’ metaphysics there are two different kinds of substances in the world of creatures: “thinking substance” and “extended substance” or soul and matter. In Descartes’ philosophy the soul is equal to the mind and considered as a “thinking substance”. This immaterial substance is the essence of the human being. Body, being considered as a “matter“, is an “extended substance” and entirely distinct from the soul. The soul, therefore, exists and may be known prior to body and, not being corporeal, can exist after human death. Hence, Descartes can prove the immortality of human soul in the framework of the principle of substantial distinction. On the other hand, as a physiologist and psychologist, Descartes indeed believes in mind-body union, so that some causal interactions between mind and body show their substantial union. In this essay, the authors show that Descartes faces a serious problem in combining substantial union of mind and body with their substantial distinction; despite of his efforts in introducing the idea of pineal gland, the problem remains unsolved. Therefore it seems that as he cannot dispense with his only reason for proving the immortality of human soul, he has to hold the mind-body distinction theory in his metaphysics. Indeed, Descartes prefers to support the distinction theory rather than union theory in confronting a thesis and an antithesis stating one of two theories

  17. Substantial :union: or Substantial Distinction of Mind and Body in Descartes\\' Metaphysics

    Directory of Open Access Journals (Sweden)

    f Jamei

    2009-06-01

    Full Text Available According to Descartes’ metaphysics there are two different kinds of substances in the world of creatures: “thinking substance” and “extended substance” or soul and matter. In Descartes’ philosophy the soul is equal to the mind and considered as a “thinking substance”. This immaterial substance is the essence of the human being. Body, being considered as a “matter“, is an “extended substance” and entirely distinct from the soul. The soul, therefore, exists and may be known prior to body and, not being corporeal, can exist after human death. Hence, Descartes can prove the immortality of human soul in the framework of the principle of substantial distinction. On the other hand, as a physiologist and psychologist, Descartes indeed believes in mind-body :union:, so that some causal interactions between mind and body show their substantial :union:. In this essay, the authors show that Descartes faces a serious problem in combining substantial :union: of mind and body with their substantial distinction despite of his efforts in introducing the idea of pineal gland, the problem remains unsolved. Therefore it seems that as he cannot dispense with his only reason for proving the immortality of human soul, he has to hold the mind-body distinction theory in his metaphysics. Indeed, Descartes prefers to support the distinction theory rather than :union: theory in confronting a thesis and an antithesis stating one of two theories.

  18. Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    S.M. Zakiur Rahman

    2009-01-01

    Full Text Available Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822 in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001 departure from homogeneity and the F ST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.

  19. Standardized deceased donor kidney donation rates in the UK reveal marked regional variation and highlight the potential for increasing kidney donation: a prospective cohort study†

    Science.gov (United States)

    Summers, D. M.; Johnson, R. J.; Hudson, A. J.; Collett, D.; Murphy, P.; Watson, C. J. E.; Neuberger, J. M.; Bradley, J. A.

    2014-01-01

    Background The UK has implemented a national strategy for organ donation that includes a centrally coordinated network of specialist nurses in organ donation embedded in all intensive care units and a national organ retrieval service for deceased organ donors. We aimed to determine whether despite the national approach to donation there is significant regional variation in deceased donor kidney donation rates. Methods The UK prospective audit of deaths in critical care was analysed for a cohort of patients who died in critical care between April 2010 and December 2011. Multivariate logistic regression was used to identify the factors associated with kidney donation. The logistic regression model was then used to produce risk-adjusted funnel plots describing the regional variation in donation rates. Results Of the 27 482 patients who died in a critical care setting, 1528 (5.5%) became kidney donors. Factors found to influence donation rates significantly were: type of critical care [e.g. neurointensive vs general intensive care: OR 1.53, 95% confidence interval (CI) 1.34–1.75, P69 vs age 18–39 yr: OR 0.2, 0.15–0.25, Pdonation rates for the 20 UK kidney donor regions showed marked variation. The overall standardized donation rate ranged from 3.2 to 7.5%. Four regions had donation rates of >2 standard deviations (sd) from the mean (two below and two above). Regional variation was most marked for donation after circulatory death (DCD) kidney donors with 9 of the 20 regions demonstrating donation rates of >2 sd from the mean (5 below and 4 above). Conclusions The marked regional variation in kidney donation rates observed in this cohort after adjustment for factors strongly associated with donation rates suggests that there is considerable scope for further increasing kidney donation rates in the UK, particularly DCD. PMID:24335581

  20. COMPOSITIONAL AND SUBSTANTIAL STRUCTURE OF THE MEDICAL DOCUMENT: FORMATION STAGES

    Directory of Open Access Journals (Sweden)

    Romashova Olga Vladimirovna

    2015-03-01

    Full Text Available The article deals with the compositional and substantial structure of the ambulatory medical record, or "case history", which has being formed for a long time. The author allocates the three main periods in the formation of this medical document: the first period (the beginning of the 19th century – 1920s is connected with the origin and formation; the second period (1920-1980s is marked by emergence of the normative legal acts regulating registration and maintaining; the third period (1980s – up to the present is associated with the cancellation of regulations and the introduction of the new order of the Ministry of Health of the USSR that changed the document's form and name. It is determined that the composition of the case history consists of the title page and the main part. The following processes take place in the course of ambulatory medical record's formation: strengthening formalization, increase in the number of pattern text fragments, increase in the text's volume, and the implementation of bigger number of functions. The author reveals the main (informative and cumulative, accounting and additional (scientific, controlling, legal, financial functions of the document. The implementation of these functions is reflected in the compositional and substantial structure of the document text and is conditioned by a number of extralinguistic factors.

  1. Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut.

    Directory of Open Access Journals (Sweden)

    Vincent Raquin

    2017-12-01

    Full Text Available Dengue virus (DENV causes more human infections than any other mosquito-borne virus. The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity. Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti used inbred laboratory colonies and/or pools of mosquitoes that erase individual variation. Here, we performed transcriptome sequencing on individual midguts in a field-derived Ae. aegypti population to identify new candidate host factors modulating DENV replication. We analyzed the transcriptomic data using an approach that accounts for individual co-variation between viral RNA load and gene expression. This approach generates a prediction about the agonist or antagonist effect of candidate genes on DENV replication based on the sign of the correlation between gene expression and viral RNA load. Using this method, we identified 39 candidate genes that went undetected by conventional pairwise comparison of gene expression levels between DENV-infected midguts and uninfected controls. Only four candidate genes were detected by both methods, emphasizing their complementarity. We demonstrated the value of our approach by functional validation of a candidate agonist gene encoding a sterol regulatory element-binding protein (SREBP, which was identified by correlation analysis but not by pairwise comparison. We confirmed that SREBP promotes DENV infection in the midgut by RNAi-mediated gene knockdown in vivo. We suggest that our approach for transcriptomic analysis can empower genome-wide screens for potential agonist or antagonist factors by leveraging inter-individual variation in gene expression. More generally, this method is applicable to a wide range of phenotypic traits displaying inter-individual variation.

  2. 20 CFR 416.1075 - Finding of substantial failure.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Finding of substantial failure. 416.1075... AGED, BLIND, AND DISABLED Determinations of Disability Substantial Failure § 416.1075 Finding of substantial failure. A finding of substantial failure with respect to a State may not be made unless and until...

  3. 20 CFR 404.1675 - Finding of substantial failure.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Finding of substantial failure. 404.1675... DISABILITY INSURANCE (1950- ) Determinations of Disability Substantial Failure § 404.1675 Finding of substantial failure. A finding of substantial failure with respect to a State may not be made unless and until...

  4. Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps

    NARCIS (Netherlands)

    Vugt, van J.J.F.A.; Hoedjes, K.M.; Geest, van de H.C.; Schijlen, E.G.W.M.; Vet, L.E.M.; Smid, H.M.

    2015-01-01

    Even though learning and memory are universal traits in the Animal Kingdom, closely related species reveal substantial variation in learning rate and memory dynamics. To determine the genetic background of this natural variation, we studied two congeneric parasitic wasp species, Cotesia glomerata

  5. Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps

    NARCIS (Netherlands)

    Van Vugt, Joke J. F. A.; Hoedjes, Katja M.; Van de Geest, Henri C.; Schijlen, Elio W. G. M.; Vet, Louise E. M.; Smid, Hans M.

    2015-01-01

    BACKGROUND: Even though learning and memory are universal traits in the Animal Kingdom, closely related species reveal substantial variation in learning rate and memory dynamics. To determine the genetic background of this natural variation, we studied two congeneric parasitic wasp species, Cotesia

  6. Not everything is black and white: color and behavioral variation reveal a continuum between cryptic and aposematic strategies in a polymorphic poison frog.

    Science.gov (United States)

    Willink, Beatriz; Brenes-Mora, Esteban; Bolaños, Federico; Pröhl, Heike

    2013-10-01

    Aposematism and crypsis are often viewed as two extremes of a continuum of visual conspicuousness to predators. Theory predicts that behavioral and coloration conspicuousness should vary in tandem along the conspicuousness spectrum for antipredator strategies to be effective. Here we used visual modeling of contrast and behavioral observations to examine the conspicuousness of four populations of the granular poison frog, Oophaga granulifera, which exhibits almost continuous variation in dorsal color. The patterns of geographic variation in color, visual contrast, and behavior support a gradient of overall conspicuousness along the distribution of O. granulifera. Red and green populations, at the extremes of the color distribution, differ in all elements of color, contrast, and behavior, strongly reflecting aposematic and cryptic strategies. However, there is no smooth cline in any elements of behavior or coloration between the two extremes. Instead populations of intermediate colors attain intermediate conspicuousness by displaying different combinations of aposematic and cryptic traits. We argue that coloration divergence among populations may be linked to the evolution of a gradient of strategies to balance the costs of detection by predators and the benefits of learned aversion. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  7. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Novák, Petr; Pellicer, J.; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Vrbová, Iva; Doležel, Jaroslav; Kelly, L.J.; Leitch, I.J.

    2015-01-01

    Roč. 10, č. 11 (2015), e0143424 E-ISSN 1932-6203 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:60077344 ; RVO:61389030 Keywords : Generation sequencing reveals * transposable elements * satellite repeats * retrotransposons Subject RIV: EB - Genetics ; Molecular Biology; EB - Genetics ; Molecular Biology (UEB-Q) Impact factor: 3.057, year: 2015

  8. Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

    Science.gov (United States)

    De Laere, Bram; van Dam, Pieter-Jan; Whitington, Tom; Mayrhofer, Markus; Diaz, Emanuela Henao; Van den Eynden, Gert; Vandebroek, Jean; Del-Favero, Jurgen; Van Laere, Steven; Dirix, Luc; Grönberg, Henrik; Lindberg, Johan

    2017-08-01

    Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy. We performed profiling of circulating tumour DNA via low-pass whole-genome sequencing and targeted sequencing of the entire AR gene, including introns. Targeted RNA sequencing was performed on enriched circulating tumour cell fractions to assess the expression levels of seven AR splice variants (ARVs). Somatic AR variations, including copy-number alterations, structural variations, and point mutations, were combined with ARV expression patterns and correlated to clinicopathologic parameters. Collectively, any AR perturbation, including ARV, was detected in 25/30 patients. Surprisingly, intra-AR structural variation was present in 15/30 patients, of whom 14 expressed ARVs. The majority of ARV-positive patients expressed multiple ARVs, with AR-V3 the most abundantly expressed. The presence of any ARV was associated with progression-free survival after second-line endocrine treatment (hazard ratio 4.53, 95% confidence interval 1.424-14.41; p=0.0105). Six out of 17 poor responders were AR-V7-negative, but four carried other AR perturbations. Comprehensive AR profiling, which is feasible using liquid biopsies, is necessary to increase our understanding of the mechanisms underpinning resistance to endocrine treatment. Alterations in the androgen receptor are associated with endocrine treatment outcomes. This study demonstrates that it is possible to identify different types of alterations via simple blood draws. Follow-up studies are needed to determine the effect of

  9. Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico.

    Science.gov (United States)

    Martínez-Cruzado, J C; Toro-Labrador, G; Ho-Fung, V; Estévez-Montero, M A; Lobaina-Manzanet, A; Padovani-Claudio, D A; Sánchez-Cruz, H; Ortiz-Bermúdez, P; Sánchez-Crespo, A

    2001-08-01

    To estimate the maternal contribution of Native Americans to the human gene pool of Puerto Ricans--a population of mixed African, European, and Amerindian ancestry--the mtDNAs of two sample sets were screened for restriction fragment length polymorphisms (RFLPs) defining the four major Native American haplogroups. The sample set collected from people who claimed to have a maternal ancestor with Native American physiognomic traits had a statistically significant higher frequency of Native American mtDNAs (69.6%) than did the unbiased sample set (52.6%). This higher frequency suggests that, despite the fact that the native Taíno culture has been extinct for centuries, the Taíno contribution to the current population is considerable and some of the Taíno physiognomic traits are still present. Native American haplogroup frequency analysis shows a highly structured distribution, suggesting that the contribution of Native Americans foreign to Puerto Rico is minimal. Haplogroups A and C cover 56.0% and 35.6% of the Native American mtDNAs, respectively. No haplogroup D mtDNAs were found. Most of the linguistic, biological, and cultural evidence suggests that the Ceramic culture of the Taínos originated in or close to the Yanomama territory in the Amazon. However, the absence of haplogroup A in the Yanomami suggests that the Yanomami are not the only Taíno ancestors.

  10. Fourier transform infrared imaging microspectroscopy and tissue-level mechanical testing reveal intraspecies variation in mouse bone mineral and matrix composition.

    Science.gov (United States)

    Courtland, Hayden-William; Nasser, Philip; Goldstone, Andrew B; Spevak, Lyudmila; Boskey, Adele L; Jepsen, Karl J

    2008-11-01

    Fracture susceptibility is heritable and dependent upon bone morphology and quality. However, studies of bone quality are typically overshadowed by emphasis on bone geometry and bone mineral density. Given that differences in mineral and matrix composition exist in a variety of species, we hypothesized that genetic variation in bone quality and tissue-level mechanical properties would also exist within species. Sixteen-week-old female A/J, C57BL/6J (B6), and C3H/HeJ (C3H) inbred mouse femora were analyzed using Fourier transform infrared imaging and tissue-level mechanical testing for variation in mineral composition, mineral maturity, collagen cross-link ratio, and tissue-level mechanical properties. A/J femora had an increased mineral-to-matrix ratio compared to B6. The C3H mineral-to-matrix ratio was intermediate of A/J and B6. C3H femora had reduced acid phosphate and carbonate levels and an increased collagen cross-link ratio compared to A/J and B6. Modulus values paralleled mineral-to-matrix values, with A/J femora being the most stiff, B6 being the least stiff, and C3H having intermediate stiffness. In addition, work-to-failure varied among the strains, with the highly mineralized and brittle A/J femora performing the least amount of work-to-failure. Inbred mice are therefore able to differentially modulate the composition of their bone mineral and the maturity of their bone matrix in conjunction with tissue-level mechanical properties. These results suggest that specific combinations of bone quality and morphological traits are genetically regulated such that mechanically functional bones can be constructed in different ways.

  11. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-01-21

    Background Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multigene family. Although the function of PE_PGRS genes is unknown, it is hypothesized that the PE_PGRS genes may be associated with antigenic variability in MTB. Material and methods Whole genome sequencing analysis was performed on (n = 37) extensively drug-resistant (XDR) MTB strains from Pakistan, which included Lineage 1 (East African Indian, n = 2); Other lineage 1 (n = 3); Lineage 3 (Central Asian, n = 24); Other lineage 3 (n = 4); Lineage 4 (X3, n = 1) and T group (n = 3) MTB strains. Results There were 107 SNPs identified from the analysis of 42 PE_PGRS genes; of these, 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in PE_PGRS genes – 6, 9 and 10 – were common in all EAI, CAS, Other lineages (1 and 3), T1 and X3. Deletions (DELs) in PE_PGRS genes – 3 and 19 – were observed in 17 (80.9%) CAS1 and 6 (85.7%) in Other lineages (1 and 3) XDR MTB strains, while DELs in the PE_PGRS49 were observed in all CAS1, CAS, CAS2 and Other lineages (1 and 3) XDR MTB strains. All CAS, EAI and Other lineages (1 and 3) strains showed insertions (INS) in PE_PGRS6 gene, while INS in the PE_PGRS genes 19 and 33 were observed in 20 (95.2%) CAS1, all CAS, CAS2, EAI and Other lineages (1 and 3) XDR MTB strains. Conclusion Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs and INDELs in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  12. Olivine-melt relationships and syneruptive redox variations in the 1959 eruption of K$\\bar{i}$lauea Volcano as revealed by XANES

    Energy Technology Data Exchange (ETDEWEB)

    Helz, R. T.; Cottrell, E.; Brounce, M. N.; Kelley, K. A.

    2017-03-01

    The 1959 summit eruption of K$\\bar{i}$lauea Volcano exhibited high lava fountains of gas-rich, primitive magma, containing olivine + chromian spinel in highly vesicular brown glass. Microprobe analysis of these samples shows that euhedral rims on olivine phenocrysts, in direct contact with glass, vary significantly in forsterite (Fo) content, at constant major-element melt composition, as do unzoned groundmass olivine crystals. Ferric/total iron (Fe+ 3/FeT)ratios for matrix and interstitial glasses, plus olivine-hosted glass inclusions in eight 1959 scoria samples have been determined by micro X-ray absorption near-edge structure spectroscopy (μ-XANES). These data show that much of the variation in Fo content reflects variation in oxidation state of iron in the melt, which varies with sulfur concentration in the glass and (locally) with proximity to scoria edges in contact with air. Data for 24 olivine-melt pairs in the better-equilibrated samples from later in the eruption show KD averaging 0.280 ± 0.03 for the exchange of Fe and Mg between olivine and melt, somewhat displaced from the value of 0.30 ± 0.03 given by Roeder and Emslie (1970). This may reflect the low SiO2 content of the 1959 magmas, which is lower than that in most K$\\bar{i}$lauea tholeiites. More broadly, we show the potential of μ-XANES and electron microprobe to revisit and refine the value of KD in natural systems.

  13. Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

    Directory of Open Access Journals (Sweden)

    Magdalena Szczepaniak

    2011-01-01

    Full Text Available Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. Melica transsilvanica is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP DNA profiling method was applied to measure genetic diversity among and within populations of M. transsilvanica. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of M. transsilvanica and 24 plants from 2 populations of M. ciliata, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with M. ciliata and M. transsilvanica, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the M. transsilvanica group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p < 0.001. The obtained results showed that the most genetic diversity resided between the populations of M. transsilvanica (86.03% while considerably lower genetic variation was found within the populations (13.97%, which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of M. transsilvanica can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of M. transsilvanica are characterized by isolated gene pools differing by a small number of loci.

  14. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

    KAUST Repository

    Kanji, Akbar

    2015-03-01

    Background: Mycobacterium tuberculosis (MTB) PE_PGRS genes belong to the PE multi-gene family. Although the function of the members of the PE_PGRS multi-gene family is not yet known, it is hypothesized that the PE_PGRS genes may be associated with genetic variability. Material and methods: Whole genome sequencing analysis was performed on (n= 37) extensively drug resistant (XDR) MTB strains from Pakistan which included Central Asian (n= 23), East African Indian (n= 2), X3 (n= 1), T group (n= 3) and Orphan (n= 8) MTB strains. Results: By analyzing 42 PE_PGRS genes, 111 SNPs were identified, of which 13 were non-synonymous SNPs (nsSNPs). The nsSNPs identified in the PE_PGRS genes were as follows: 6, 9, 10 and 55 present in each of the CAS, EAI, Orphan, T1 and X3 XDR MTB strains studied. Deletions in PE_PGRS genes: 19, 21 and 23 were observed in 7 (35.0%) CAS1 and 3 (37.5%) in Orphan XDR MTB strains, while deletions in the PE_PGRS genes: 49 and 50 were observed in 36 (95.0%) CAS1 and all CAS, CAS2 and Orphan XDR MTB strains. An insertion in PE_PGRS6 gene was observed in all CAS, EAI3 and Orphan, while insertions in the PE_PGRS genes 19 and 33 were observed in 19 (95%) CAS1 and all CAS, CAS2, EAI3 and Orphan XDR MTB strains. Conclusion: Genetic diversity in PE_PGRS genes contributes to antigenic variability and may result in increased immunogenicity of strains. This is the first study identifying variations in nsSNPs, Insertions and Deletions in the PE_PGRS genes of XDR-TB strains from Pakistan. It highlights common genetic variations which may contribute to persistence.

  15. Olivine-melt relationships and syneruptive redox variations in the 1959 eruption of Kīlauea Volcano as revealed by XANES

    Science.gov (United States)

    Helz, Rosalind L.; Cottrell, Elizabeth; Brounce, Maryjo N.; Kelley, Katherine A.

    2017-01-01

    The 1959 summit eruption of Kīlauea Volcano exhibited high lava fountains of gas-rich, primitive magma, containing olivine + chromian spinel in highly vesicular brown glass. Microprobe analysis of these samples shows that euhedral rims on olivine phenocrysts, in direct contact with glass, vary significantly in forsterite (Fo) content, at constant major-element melt composition, as do unzoned groundmass olivine crystals. Ferric/total iron (Fe+ 3/FeT)ratios for matrix and interstitial glasses, plus olivine-hosted glass inclusions in eight 1959 scoria samples have been determined by micro X-ray absorption near-edge structure spectroscopy (μ-XANES). These data show that much of the variation in Fo content reflects variation in oxidation state of iron in the melt, which varies with sulfur concentration in the glass and (locally) with proximity to scoria edges in contact with air. Data for 24 olivine-melt pairs in the better-equilibrated samples from later in the eruption show KD averaging 0.280 ± 0.03 for the exchange of Fe and Mg between olivine and melt, somewhat displaced from the value of 0.30 ± 0.03 given by Roeder and Emslie (1970). This may reflect the low SiO2 content of the 1959 magmas, which is lower than that in most Kīlauea tholeiites. More broadly, we show the potential of μ-XANES and electron microprobe to revisit and refine the value of KD in natural systems.The observed variations of Fe+ 3/FeT ratios in the glasses reflect two distinct processes. The main process, sulfur degassing, produces steady decrease of the Fe+ 3/FeT ratio. Melt inclusions in olivine are high in sulfur (1060–1500 ppm S), with Fe+ 3/FeT = 0.160–0.175. Matrix glasses are degassed (mostly S eruption and (2) the melts originally had Fe+ 3/FeT ≥ 0.175, consistent with oxygen fugacity (fO2) at least 0.4 log units above the fayalite-magnetite-quartz (FMQ) buffer at 1 atm and magmatic temperature of 1200 °C.The second process is interaction between the

  16. Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic

    Directory of Open Access Journals (Sweden)

    Maria Rosimere Xavier Amaral

    2015-08-01

    Full Text Available The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA. Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97 within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.

  17. 19 CFR 10.7 - Substantial containers or holders.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Substantial containers or holders. 10.7 Section 10... Exported and Returned § 10.7 Substantial containers or holders. (a) Substantial containers or holders... domestic products exported and returned. When such containers or holders are imported not containing or...

  18. 20 CFR 604.6 - Conformity and substantial compliance.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Conformity and substantial compliance. 604.6... FOR ELIGIBILITY FOR UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a) In... for the administration of its UC program. (b) Resolving Issues of Conformity and Substantial...

  19. Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India.

    Science.gov (United States)

    Imamura, Daisuke; Morita, Masatomo; Sekizuka, Tsuyoshi; Mizuno, Tamaki; Takemura, Taichiro; Yamashiro, Tetsu; Chowdhury, Goutam; Pazhani, Gururaja P; Mukhopadhyay, Asish K; Ramamurthy, Thandavarayan; Miyoshi, Shin-Ichi; Kuroda, Makoto; Shinoda, Sumio; Ohnishi, Makoto

    2017-02-01

    Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia, Africa, and Latin America. Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic, it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata, as a representative of the Bengal region. We analyzed whole genome sequence data of V. cholerae O1 isolated from cholera patients in Kolkata, India, from 2007 to 2014 and identified the heterogeneous genomic region in these strains. In addition, we carried out a phylogenetic analysis based on the whole genome single nucleotide polymorphisms to determine the genetic lineage of strains in Kolkata. This analysis revealed the heterogeneity of the Vibrio seventh pandemic island (VSP)-II in Kolkata strains. The ctxB genotype was also heterogeneous and was highly related to VSP-II types. In addition, phylogenetic analysis revealed the shifts in predominant strains in Kolkata. Two distinct lineages, 1 and 2, were found between 2007 and 2010. However, the proportion changed markedly in 2010 and lineage 2 strains were predominant thereafter. Lineage 2 can be divided into four sublineages, I, II, III and IV. The results of this study indicate that lineages 1 and 2-I were concurrently prevalent between 2007 and 2009, and lineage 2-III observed in 2010, followed by the predominance of lineage 2-IV in 2011 and continued until 2014. Our findings demonstrate that the epidemic of cholera in Kolkata was caused by several distinct strains that have been constantly changing within the genetic lineages of V. cholerae O1 in recent years.

  20. Genotypic variation in growth and physiological response to drought stress and re-watering reveals the critical role of recovery in drought adaptation in maize seedlings

    Directory of Open Access Journals (Sweden)

    Daoqian eChen

    2016-01-01

    Full Text Available Non-irrigated crops in temperate climates and irrigated crops in arid climates are subjected to continuous cycles of water stress and re-watering. Thus, fast and efficient recovery from water stress may be among the key determinants of plant drought adaptation. The present study was designed to comparatively analyze the roles of drought resistance and drought recovery in drought adaptation and to investigate the physiological basis of genotypic variation in drought adaptation in maize (Zea mays seedlings. As the seedlings behavior in growth associate with yield under drought, it could partly reflect the potential of drought adaptability. Growth and physiological responses to progressive drought stress and recovery were observed in seedlings of ten maize lines. The results showed that drought adaptability is closely related to drought recovery (r = 0.714**, but not to drought resistance (r = 0.332. Drought induced decreases in leaf water content, water potential, osmotic potential, gas exchange parameters, chlorophyll content, Fv/Fm and nitrogen content, and increased H2O2 accumulation and lipid peroxidation. After recovery, most of these physiological parameters rapidly returned to normal levels. The physiological responses varied between lines. Further correlation analysis indicated that the physiological bases of drought resistance and drought recovery are definitely different, and that maintaining higher chlorophyll content (r = 0.874*** and Fv/Fm (r = 0.626* under drought stress contributes to drought recovery. Our results suggest that both drought resistance and recovery are key determinants of plant drought adaptation, and that drought recovery may play a more important role than previously thought. In addition, leaf water potential, chlorophyll content and Fv/Fm could be used as efficient reference indicators in the selection of drought-adaptive genotypes.

  1. Holocene moisture variations over the arid central Asia revealed by a comprehensive sand-dune record from the central Tian Shan, NW China

    Science.gov (United States)

    Long, Hao; Shen, Ji; Chen, Jianhui; Tsukamoto, Sumiko; Yang, Linhai; Cheng, Hongyi; Frechen, Manfred

    2017-10-01

    Arid central Asia (ACA) is one of the largest arid (desert) areas in the world, and its climate is dominated by the westerlies. In this study, we examined sand dune evolution from the Bayanbulak Basin in the Tian Shan (Xinjiang, NW China), aiming to infer the Holocene moisture history of the ACA. Combined with stratigraphic observation and environmental proxies analysis (grain size, magnetic susceptibility and total organic content), large numbers of luminescence ages from multiple sites (eight sections, 79 samples) were applied to reconstruct the evolution of the sand dune accumulation in the study basin. The overall results imply very dry conditions characterized by sand dune accumulation at ∼12-6.5 ka, a wet interval between ∼6.5 and 0.8 ka when soil formation occurred, and decreased moisture during the last 0.8 ka. This moisture variation pattern is generally consistent with that inferred from many lacustrine records in the core zone of ACA, suggesting a widespread dry period in the early-to-middle Holocene and relatively wet middle-to-late Holocene. Thus, the moisture history derived from the current sand dune system contrasts with that in Asian monsoon areas, which are characterized by a strong monsoon (high precipitation) in the early and mid-Holocene and a weak monsoon (low precipitation and dry climate) during the late Holocene. Our results strongly suggest that the winter solar insolation and the external boundary conditions such as atmospheric CO2 concentration, ice sheets, and meltwater fluxes, have been major influential factors triggering the Holocene moisture evolution in the core zone of ACA.

  2. Response patterns of phytoplankton growth to variations in resuspension in the German Bight revealed by daily MERIS data in 2003 and 2004

    Directory of Open Access Journals (Sweden)

    Jian Su

    2015-10-01

    Full Text Available Chlorophyll (chl a concentration in coastal seas exhibits variability on various spatial and temporal scales. Resuspension of particulate matter can somewhat limit algal growth, but can also enhance productivity because of the intrusion of nutrient-rich pore water from sediments or bottom water layers into the whole water column. This study investigates whether characteristic changes in net phytoplankton growth can be directly linked to resuspension events within the German Bight. Satellite-derived chl a were used to derive spatial patterns of net rates of chl a increase/decrease (NR in 2003 and 2004. Spatial correlations between NR and mean water column irradiance were analysed. High correlations in space and time were found in most areas of the German Bight (R2 > 0.4, suggesting a tight coupling between light availability and algal growth during spring. These correlations were reduced within a distinct zone in the transition between shallow coastal areas and deeper offshore waters. In summer and autumn, a mismatch was found between phytoplankton blooms (chl a > 6 mg m−3 and spring-tidal induced resuspension events as indicated by bottom velocity, suggesting that there is no phytoplankton resuspension during spring tides. It is instead proposed here that frequent and recurrent spring-tidal resuspension events enhance algal growth by supplying remineralized nutrients. This hypothesis is corroborated by a lag correlation analysis between resuspension events and in-situ measured nutrient concentrations. This study outlines seasonally different patterns in phytoplankton productivity in response to variations in resuspension, which can serve as a reference for modelling coastal ecosystem dynamics.

  3. Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico.

    Science.gov (United States)

    García, Norberto A Colín; Campos, Jorge E; Musi, José L Tello; Forsman, Zac H; Muñoz, Jorge L Montero; Reyes, Alejandro Monsalvo; González, Jesús E Arias

    2017-02-01

    The genus Siderastrea exhibits high levels of morphological variability. Some of its species share similar morphological characteristics with congeners, making their identification difficult. Siderastrea stellata has been reported as an intermediary of S. siderea and S. radians in the Brazilian reef ecosystem. In an earlier study conducted in Mexico, we detected Siderastrea colonies with morphological features that were not consistent with some siderastreid species previously reported in the Gulf of Mexico. Thus, we performed a combined morphological and molecular analysis to identify Siderastrea species boundaries from the Gulf of Mexico. Some colonies presented high morphologic variability, with characteristics that corresponded to Siderastrea stellata. Molecular analysis, using the nuclear ITS and ITS2 region, corroborated the morphological results, revealing low genetic variability between S. radians and S. stellata. Since the ITS sequences did not distinguish between Siderastrea species, we used the ITS2 region to differentiate S. stellata from S. radians. This is the first report of Siderastrea stellata and its variability in the Gulf of Mexico that is supported by morphological and molecular analyses.

  4. Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

    Science.gov (United States)

    Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

    2012-09-01

    The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

  5. Revealed variations of air quality in industrial development over a remote plateau of Southwest China: an application of atmospheric visibility data

    Science.gov (United States)

    Zhao, Tianliang; Liu, Di; Zheng, Xiaobo; Yang, Lexin; Gu, Xiaoping; Hu, Jun; Shu, Zhuozhi; Chang, Jiacheng; Wu, Xiasheng

    2017-12-01

    Since the 1980s, an industrial development has bloomed in China including the Yunnan-Guizhou Plateau (YGP), a remote region in Southwest China. To analyze the regional variations in air quality over YGP during the industrial development, we adopt the equivalent visibility by excluding the influence of natural factors on the observed visibility based on the meteorological data observed at 203 sites over YGP from 1980 to 2010 in this study. The YGP air quality exhibits the tremendous spatial differences in a general distribution from western good to eastern poor air quality. A similar pattern shifts seasonally in the spatial distribution with a typical seasonality of air quality over YGP between summertime low air pollution and wintertime high air pollution. The increasing and decreasing trends in visibility are mostly concentrated, respectively, in the YGP regions with high and low visibility, displaying the phenomenon of polarization in air quality change over YGP during 1980-2010. The regional mean visibility of the YGP presents a significant declining trend with change rate of -1.5 km decade-1 for air quality deterioration. The seasonal differences in visibility between summer (33.6 km) and winter (25.2 km) became obscure with the interannual change trends of visibility with stronger declines (-2.29 km decade-1) in summer and weaker decreases (-0.89 km decade-1) in winter over 1980-2010, which lead to a indistinct seasonality of air quality change over YGP. The remote YGP had experienced more frequent haze pollution, especially in the eastern plateau over 31 years. In accompany of increasing energy consumption in the industrial development, population growth is an important factor influencing the interannual change of YGP air quality. The distinct spatial distribution in the YGP terrain exerts an impact on poor air quality in lower flatlands harbored by mountainous topography with good air quality. Declined monsoon winds could meteorologically drive the air

  6. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  7. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

    Science.gov (United States)

    Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

    2017-01-01

    Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the

  8. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Xiuqing Zhang

    Full Text Available Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality

  9. High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae.

    Science.gov (United States)

    Chang, Perng-Kuang; Scharfenstein, Leslie L; Solorzano, Cesar D; Abbas, Hamed K; Hua, Sui-Sheng T; Jones, Walker A; Zablotowicz, Robert M

    2015-05-04

    Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus morphotype that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (i.e. the S genotype). Phylogenetic studies have indicated that an isolate of the nonaflatoxigenic A. flavus with the S genotype is the ancestor of A. oryzae. Genome sequence comparison between A. flavus NRRL3357, which produces large sclerotia (L strain), and S-strain A. flavus 70S identified a region (samA-rosA) that was highly variable in the two morphotypes. A third type of samA-rosA region was found in A. oryzae RIB40. The three samA-rosA types were later revealed to be commonly present in A. flavus L-strain populations. Of the 182 L-strain A. flavus field isolates examined, 46%, 15% and 39% had the samA-rosA type of NRRL3357, 70S and RIB40, respectively. The three types also were found in 18 S-strain A. flavus isolates with different proportions. For A. oryzae, however, the majority (80%) of the 16 strains examined had the RIB40 type and none had the NRRL3357 type. The results suggested that A. oryzae strains in the current culture collections were mostly derived from the samA-rosA/RIB40 lineage of the nonaflatoxigenic A. flavus with the S genotype. Published by Elsevier B.V.

  10. Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources

    Directory of Open Access Journals (Sweden)

    Xiaoqing Rong-Mullins

    2018-02-01

    . Hence, the complement to 4NQO resistance was poor growth on nonfermentable carbon sources, which in turn varied depending on the allele of Yrr1 expressed in the isogenic yeast. The oxidation state of the yeast affected the 4NQO toxicity by altering the reactive oxygen species (ROS generated by cellular metabolism. The integration of RNA-Seq and ChIP-Seq elucidated how Yrr1 regulates global gene transcription in response to 4NQO and how various Yrr1 alleles confer differential resistance to 4NQO. This study provides guidance for further investigation into how Yrr1 regulates cellular responses to 4NQO, as well as transcriptomic resources for further analysis of transcription factor variation on carbon source utilization.

  11. Substantial variation among hernia experts in the decision for treatment of patients with incisional hernia

    DEFF Research Database (Denmark)

    Kokotovic, D; Gögenur, I; Helgstrand, F

    2017-01-01

    PURPOSE: Benign elective procedures give rise to heterogeneity in indication for surgery and surgical technique among specialized surgeons in a variety of surgical fields. The objective was to analyze the extent of agreement in surgical management among expert hernia surgeons when evaluating the ...... of treatment strategy for patients with incisional hernias was very low among experienced surgeons. A standardization of surgical decision making is desirable to develop new interventions and improve clinical outcomes....... was present in 14 cases (56%). The most common reason for not performing surgery was due to comorbidities. Agreement in operation type (open vs. laparoscopic) was present in 10 cases (40%). Agreement in mesh fixation (absorbable tacks/non-absorbable tacks/suture/other) method was also present in 10 cases (40...

  12. The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids

    NARCIS (Netherlands)

    Fu, Jingyuan; Bonder, Marc Jan; Cenit, Maria Carmen; Tigchelaar-Feenstra, Ettje; Maatman, Astrid; Dekens, Jackie A. M.; Brandsma, Eelke; Marczynska, Joanna; Imhann, Floris; Weersma, Rinse K.; Franke, Lude; Poon, Tiffany W.; Xavier, Ramnik J.; Gevers, Dirk; Hofker, Marten H.; Wijmenga, Cisca; Zhernakova, Alexandra

    2015-01-01

    Rationale: Evidence suggests that the gut microbiome is involved in the development of cardiovascular disease, with the host-microbe interaction regulating immune and metabolic pathways. However, there was no firm evidence for associations between microbiota and metabolic risk factors for

  13. Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

    NARCIS (Netherlands)

    Muya, S.M.; Bruford, M.W.; Muigai, A.W.T.; Osiemo, Z.B.; Mwachiro, E.; Ouma, B.O.; Goossens, B.

    2011-01-01

    Kenya’s black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management

  14. Controlled laboratory challenge demonstrates substantial additive genetic variation in resistance to Streptococcus iniae in Nile tilapia

    Science.gov (United States)

    Streptococcus iniae is an etiologic agent of streptococcal disease in tilapia and is one of several Streptococcus spp. that negatively impact worldwide tilapia production. Methods for the prevention and control of S. iniae include vaccines, management strategies, and antibiotics. An alternative and ...

  15. Net-Zero Building Technologies Create Substantial Energy Savings -

    Science.gov (United States)

    only an estimated 1% of commercial buildings are built to net-zero energy criteria. One reason for this Continuum Magazine | NREL Net-Zero Building Technologies Create Substantial Energy Savings Net -Zero Building Technologies Create Substantial Energy Savings Researchers work to package and share step

  16. 19 CFR 134.35 - Articles substantially changed by manufacture.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Articles substantially changed by manufacture. 134... substantially changed by manufacture. (a) Articles other than goods of a NAFTA country. An article used in the United States in manufacture which results in an article having a name, character, or use differing from...

  17. Genetic variation and geographical differentiation revealed using ...

    Indian Academy of Sciences (India)

    there are a few reports on the genetic evaluation of tung tree germplasm. .... bES, Enshi in Hubei province; SN, Suining in Sichuan province. Journal of Genetics Vol. 94, Online Resources e6 ... gene diversity. Journal of Genetics Vol. 94, Online Resources e7 .... Pan Y., Pan L., Chen L., Zhang L. L., Nevo E. and Peng J. H..

  18. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

    Directory of Open Access Journals (Sweden)

    Dawn B. Goldsmith

    2015-06-01

    Full Text Available Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS site in the summer (September and winter (March of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years.

  19. Methodology for substantiation of the fast reactor fuel element serviceability

    International Nuclear Information System (INIS)

    Tsykanov, V.A.; Maershin, A.A.

    1988-01-01

    Methodological aspects of fast reactor fuel element serviceability substantiation are presented. The choice of the experimental program and strategies of its realization to solve the problem set in short time, taking into account available experimental means, are substantiated. Factors determining fuel element serviceability depending on parameters and operational conditions are considered. The methodological approach recommending separate studing of the factors, which points to the possibility of data acquisition, required for the development of calculational models and substantiation of fuel element serviceability in pilot and experimental reactors, is described. It is shown that the special-purpose data are more useful for the substantiation of fuel element serviceability and analytical method development than unsubstantial and expensive complex tests of fuel elements and fuel assemblies, which should be conducted only at final stages for the improvement of the structure on the whole

  20. Nuclear industry in a country with a substantial oil reserve

    International Nuclear Information System (INIS)

    Alvarez, R.; Castillo, H.; Costa, D.; Galan, I.; Martinez, M.

    1981-01-01

    The importance of the development of a nuclear industry in a country like Mexico, with a substantial oil reserve is analyzed, taking into account the technical, economical, political, ecological and social aspects of the problem. (author)

  1. Variational optimization algorithms for uniform matrix product states

    Science.gov (United States)

    Zauner-Stauber, V.; Vanderstraeten, L.; Fishman, M. T.; Verstraete, F.; Haegeman, J.

    2018-01-01

    We combine the density matrix renormalization group (DMRG) with matrix product state tangent space concepts to construct a variational algorithm for finding ground states of one-dimensional quantum lattices in the thermodynamic limit. A careful comparison of this variational uniform matrix product state algorithm (VUMPS) with infinite density matrix renormalization group (IDMRG) and with infinite time evolving block decimation (ITEBD) reveals substantial gains in convergence speed and precision. We also demonstrate that VUMPS works very efficiently for Hamiltonians with long-range interactions and also for the simulation of two-dimensional models on infinite cylinders. The new algorithm can be conveniently implemented as an extension of an already existing DMRG implementation.

  2. Identification of drug resistance and immune-driven variations in hepatitis C virus (HCV) NS3/4A, NS5A and NS5B regions reveals a new approach toward personalized medicine.

    Science.gov (United States)

    Ikram, Aqsa; Obaid, Ayesha; Awan, Faryal Mehwish; Hanif, Rumeza; Naz, Anam; Paracha, Rehan Zafar; Ali, Amjad; Janjua, Hussnain Ahmed

    2017-01-01

    Cellular immune responses (T cell responses) during hepatitis C virus (HCV) infection are significant factors for determining the outcome of infection. HCV adapts to host immune responses by inducing mutations in its genome at specific sites that are important for HLA processing/presentation. Moreover, HCV also adapts to resist potential drugs that are used to restrict its replication, such as direct-acting antivirals (DAAs). Although DAAs have significantly reduced disease burden, resistance to these drugs is still a challenge for the treatment of HCV infection. Recently, drug resistance mutations (DRMs) observed in HCV proteins (NS3/4A, NS5A and NS5B) have heightened concern that the emergence of drug resistance may compromise the effectiveness of DAAs. Therefore, the NS3/4A, NS5A and NS5B drug resistance variations were investigated in this study, and their prevalence was examined in a large number of protein sequences from all HCV genotypes. Furthermore, potential CD4 + and CD8 + T cell epitopes were predicted and their overlap with genetic variations was explored. The findings revealed that many reported DRMs within NS3/4A, NS5A and NS5B are not drug-induced; rather, they are already present in HCV strains, as they were also detected in HCV-naïve patients. This study highlights several hot spots in which HLA and drug selective pressure overlap. Interestingly, these overlapping mutations were frequently observed among many HCV genotypes. This study implicates that knowledge of the host HLA type and HCV subtype/genotype can provide important information in defining personalized therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. SUBSTANTIATION OF SOLUTIONS PERTAINING TO COMPLEX PRODUCTION RECONSTRUCTION

    Directory of Open Access Journals (Sweden)

    V. Y. Gurinovich

    2011-01-01

    Full Text Available While taking an example of reconstruction and modernization of OJSC «Construction and Mounting Trust No.16, Novopolotsk» the paper substantiates solutions for complex production reconstruction. The production reconstruction is divided in three start-up facilities ensuring continuous finished-product output.

  4. 26 CFR 1.528-4 - Substantiality test.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 7 2010-04-01 2010-04-01 true Substantiality test. 1.528-4 Section 1.528-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED... residence. Units which are used for purposes auxiliary to residential use (such as laundry areas, swimming...

  5. Engineering Substantially Prolonged Human Lifespans: Biotechnological Enhancement and Ethics

    NARCIS (Netherlands)

    Derkx, P.H.J.M.

    2006-01-01

    Substantial extension of the human lifespan has recently become a subject of lively debate. One reason for this is the completion in 2001 of the Human Genome Project and the experimental avenues for biogerontological research it has opened. Another is recent theoretical progress in biogerontology.

  6. 40 CFR Appendix C to Part 112 - Substantial Harm Criteria

    Science.gov (United States)

    2010-07-01

    ... to Part 112 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS OIL POLLUTION PREVENTION Pt. 112, App. C Appendix C to Part 112—Substantial Harm Criteria 1.0Introduction The..., except in the Gulf of Mexico. In the Gulf of Mexico, it means the area shoreward of the lines of...

  7. 76 FR 63846 - Substantially Underserved Trust Areas (SUTA)

    Science.gov (United States)

    2011-10-14

    ... Cost Rural Communities; 10.861, Public Television Station Digital Transition Grant Program; 10.862... rule do not impose substantial unreimbursed direct compliance costs on Indian tribal, Alaska native, or native Hawaiian governments and sovereign institutions or have tribal implications that preempt tribal...

  8. Experiencing variation

    DEFF Research Database (Denmark)

    Kobayashi, Sofie; Berge, Maria; Grout, Brian William Wilson

    2017-01-01

    This study contributes towards a better understanding of learning dynamics in doctoral supervision by analysing how learning opportunities are created in the interaction between supervisors and PhD students, using the notion of experiencing variation as a key to learning. Empirically, we have based...... the study on four video-recorded sessions, with four different PhD students and their supervisors, all from life sciences. Our analysis revealed that learning opportunities in the supervision sessions concerned either the content matter of research (for instance, understanding soil structure......), or the research methods— more specifically how to produce valid results. Our results illustrate how supervisors and PhD students create a space of learning together in their particular discipline by varying critical aspects of their research in their discussions. Situations where more openended research issues...

  9. Child protection decisions to substantiate hospital child protection teams' reports of suspected maltreatment.

    Science.gov (United States)

    Jedwab, Merav; Benbenishty, Rami; Chen, Wendy; Glasser, Saralee; Siegal, Gil; Lerner-Geva, Liat

    2015-02-01

    The present study focuses on the way child protection officers (CPOs) in Israel assess suspected abuse and neglect (SCAN) reports made by hospital child protection teams (CPTs), to determine whether the alleged maltreatment is substantiated. The study was conducted in six medical centers and included 358 reports investigated by CPOs for SCAN. A structured questionnaire was completed by hospital CPTs to capture all relevant information on each child referred to the CPTs. Structured phone interviews were conducted with each of the CPOs who received a CPT report. Bivariate associations and multivariate logistic regressions were conducted to estimate the substantiation rate of cases reported by CPTs and the types of maltreatment substantiated, as well as to identify case characteristics of the child and the family that were associated with the CPOs' substantiation decision. CPO follow-up investigations revealed a substantiation rate of 53.5%. The maltreatment type most commonly substantiated was neglect. The case characteristics associated with substantiation included socio-demographic background, parents' health and functioning, previous contact with social services, characteristics of the hospital referral, medical findings and an assessment of the parents' behaviors. The findings of the study highlighted the importance of cooperation between the health and welfare services and the policy makers. This cooperation is essential for identifying early signs of maltreatment. Enhanced cooperation and effective information transfer between various professionals would help prevent or at least reduce the recurrence of maltreatment and would ensure that the children and their families are treated appropriately. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Domestic violence, parental substance misuse and the decision to substantiate child maltreatment.

    Science.gov (United States)

    Victor, Bryan G; Grogan-Kaylor, Andrew; Ryan, Joseph P; Perron, Brian E; Gilbert, Terri Ticknor

    2018-05-01

    Families that experience domestic violence and parental substance misuse are disproportionately involved with the child welfare system. Prior research suggests that child protective services (CPS) caseworkers are more likely to substantiate maltreatment allegations when domestic violence and parental substance misuse are identified during the investigation, pointing to one possible mechanism for this disproportionate involvement. While previous studies have relied on nationally representative data sets, the current study used administrative records from a large Midwestern child welfare agency that accounts for state-level variation in child welfare policy and practice. A total of 501,060 substantiation decisions made between 2009 and 2013 were examined to assess the influence of caseworker-perceived domestic violence and parental substance misuse on the decision to substantiate reported maltreatment. Results from multilevel modeling suggest that the identification of domestic violence and parental substance misuse during an investigation significantly increased the probability that an allegation would be substantiated. The implication of these findings for child welfare practice are considered in light of the fact that many child welfare agencies do not consider exposure to domestic violence and parental substance misuse in and of themselves to constitute child maltreatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. EXPERIMENTAL SUBSTANTIATION OF ATTRIBUTIONAL STYLE IN TRAFFIC POLICE OFFICERS’ BEHAVIOR

    Directory of Open Access Journals (Sweden)

    Olga Vladimirovna Merkusheva

    2016-02-01

    Full Text Available The article prepared for the ‘Psychological and Methodological Aspects of Professional Personnel Training at Internal Affairs Bodies of the Russian Federation’ scholar tradition looks at the applied aspect of handling security issues by traffic police officers. It presents the results of empirical study of the employees’ psychological characteristics conducted to substantiate their attributional style, which determines the specific character as well as the qua-lity and reliability of traffic police officers’ performance. Traffic police officers’ attributional style of behavior is researched with the help of attributional cognitive techniques for hazard phenomena detection as well as social perception and attribution technique and is viewed as the most stable entity, which reflects the employee’s personal and professional focus.Goal: to provide empirical substantiation of attributional style in traffic police officers’ behavior as an integral personality characteristic that ensures timely detection of hazard phenomena.

  12. Substantiation of the road toll for heavy transport vehicles

    OpenAIRE

    Burmaka, N.; Chernykh, A.

    2010-01-01

    The existing and possible additional sources of developing state and local road funds of Ukraine have been considered. The formula for calculating monthly road toll for heavy transport vehicles has been proposed. This formula includes the payment rate per every kilometer of distance, the vehicle capacity utilization factor and the run with the load. The payment rate per every kilometer of distance for transport vehicles depending on the allowed total weight has been substantiated. The given r...

  13. Patients' substantialization of disease, the hybrid symptom and metaphysical care.

    Science.gov (United States)

    Pârvan, Alexandra

    2015-06-01

    In the context of current scholarship concerned with facilitating integration between the biomedical and the patient-centred models of care, the article suggests that disease brings about an ontological disruption in patients, which is not directly addressed in either model, and may interfere with treatment and therapy outcomes if not met with a type of care termed here as 'metaphysical'. The receipt of diagnosis and medical care can give patients the sense that they are ontologically diminished, or less of a human, and along with physicians' approaches to and discourses about disease, may prompt them to seek ontological restoration or security in the same way as psychologically traumatized patients sometimes do: by treating the disease and/or the experience of harm associated with it as a thing that exists per se. I call this 'substantialization' of disease (or harm) and draw on Augustine's theory of non-substantial deficiencies (physiological and moral) and on Plato's and Plotinus's different takes on such defects in order to discuss what substantialization can do for patients. Based on literature that examines patients' ways of talking about and living with their disease, I speculate that substantialization can generate a 'hybrid symptom', consisting in patterns of exercising agency which may predispose to non-adherence. Ways in which physicians could provide metaphysical care are proposed, along with an understanding of chronic patients as hybrid ontological and agentic units, which draws on theories of enactive cognition. I opine that metaphysical care may facilitate integration between the depersonalized and personalized models of care. © 2014 John Wiley & Sons, Ltd.

  14. Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

    Science.gov (United States)

    Gonzalez, P; Labarère, J

    1998-11-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The

  15. Substantial increase in acceleration potential of pyroelectric crystals

    International Nuclear Information System (INIS)

    Tornow, W.; Lynam, S. M.; Shafroth, S. M.

    2010-01-01

    We report on a substantial increase in the acceleration potential achieved with a LiTaO 3 pyroelectric crystal. With a single 2.5 cm diameter and 2.5 cm long z-cut crystal without electric field-enhancing nanotip we produced positive ion beams with maximal energies between 300 and 310 keV during the cooling phase when the crystal was exposed to 5 mTorr of deuterium gas. These values are about a factor of 2 larger than previously obtained with single pyroelectric crystals.

  16. Clozapine-induced dysphagia with secondary substantial weight loss.

    Science.gov (United States)

    Osman, Mugtaba; Devadas, Vekneswaran

    2016-08-19

    Dysphagia is listed as a 'rare' side effect following clozapine treatment. In this case report, we describe how significant clozapine-induced dysphagia has led to significant reduction of nutritional intake with subsequent substantial weight loss. An 18-year-old single man with an established diagnosis of treatment-resistant paranoid schizophrenia recovered well on a therapeutic dose of clozapine. However, he was noted to lose weight significantly (up to 20% of his original weight) as the dose was uptitrated. This was brought about by development of dysphagia, likely to be due to clozapine. Addition of nutritional supplementary liquids and initiation of a modified behavioural dietary/swallowing programme, while repeatedly mastering the Mendelsohn manoeuvre technique, alleviated the swallowing difficulties and restored his weight. 2016 BMJ Publishing Group Ltd.

  17. Monte Carlo reactor calculation with substantially reduced number of cycles

    International Nuclear Information System (INIS)

    Lee, M. J.; Joo, H. G.; Lee, D.; Smith, K.

    2012-01-01

    A new Monte Carlo (MC) eigenvalue calculation scheme that substantially reduces the number of cycles is introduced with the aid of coarse mesh finite difference (CMFD) formulation. First, it is confirmed in terms of pin power errors that using extremely many particles resulting in short active cycles is beneficial even in the conventional MC scheme although wasted operations in inactive cycles cannot be reduced with more particles. A CMFD-assisted MC scheme is introduced as an effort to reduce the number of inactive cycles and the fast convergence behavior and reduced inter-cycle effect of the CMFD assisted MC calculation is investigated in detail. As a practical means of providing a good initial fission source distribution, an assembly based few-group condensation and homogenization scheme is introduced and it is shown that efficient MC eigenvalue calculations with fewer than 20 total cycles (including inactive cycles) are possible for large power reactor problems. (authors)

  18. Heme isomers substantially affect heme's electronic structure and function

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2017-01-01

    Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as du...

  19. Complementary sex determination substantially increases extinction proneness of haplodiploid populations.

    Science.gov (United States)

    Zayed, Amro; Packer, Laurence

    2005-07-26

    The role of genetic factors in extinction is firmly established for diploid organisms, but haplodiploids have been considered immune to genetic load impacts because deleterious alleles are readily purged in haploid males. However, we show that single-locus complementary sex determination ancestral to the haplodiploid Hymenoptera (ants, bees, and wasps) imposes a substantial genetic load through homozygosity at the sex locus that results in the production of inviable or sterile diploid males. Using stochastic modeling, we have discovered that diploid male production (DMP) can initiate a rapid and previously uncharacterized extinction vortex. The extinction rate in haplodiploid populations with DMP is an order of magnitude greater than in its absence under realistic but conservative demographic parameter values. Furthermore, DMP alone can elevate the base extinction risk in haplodiploids by over an order of magnitude higher than that caused by inbreeding depression in threatened diploids. Thus, contrary to previous expectations, haplodiploids are more, rather than less, prone to extinction for genetic reasons. Our findings necessitate a fundamental shift in approaches to the conservation and population biology of these ecologically and economically crucial insects.

  20. Substantial soil organic carbon retention along floodplains of mountain streams

    Science.gov (United States)

    Sutfin, Nicholas A.; Wohl, Ellen

    2017-07-01

    Small, snowmelt-dominated mountain streams have the potential to store substantial organic carbon in floodplain sediment because of high inputs of particulate organic matter, relatively lower temperatures compared with lowland regions, and potential for increased moisture conditions. This work (i) quantifies mean soil organic carbon (OC) content along 24 study reaches in the Colorado Rocky Mountains using 660 soil samples, (ii) identifies potential controls of OC content based on soil properties and spatial position with respect to the channel, and (iii) and examines soil properties and OC across various floodplain geomorphic features in the study area. Stepwise multiple linear regression (adjusted r2 = 0.48, p sample depth, percent sand, distance from the channel, and relative elevation from the channel are significant predictors of OC content in the study area. Principle component analysis indicates limited separation between geomorphic floodplain features based on predictors of OC content. A lack of significant differences among floodplain features suggests that the systematic random sampling employed in this study can capture the variability of OC across floodplains in the study area. Mean floodplain OC (6.3 ± 0.3%) is more variable but on average greater than values in uplands (1.5 ± 0.08% to 2.2 ± 0.14%) of the Colorado Front Range and higher than published values from floodplains in other regions, particularly those of larger rivers.

  1. Substantial proportion of global streamflow less than three months old

    Science.gov (United States)

    Jasechko, Scott; Kirchner, James W.; Welker, Jeffrey M.; McDonnell, Jeffrey J.

    2016-02-01

    Biogeochemical cycles, contaminant transport and chemical weathering are regulated by the speed at which precipitation travels through landscapes and reaches streams. Streamflow is a mixture of young and old precipitation, but the global proportions of these young and old components are not known. Here we analyse seasonal cycles of oxygen isotope ratios in rain, snow and streamflow compiled from 254 watersheds around the world, and calculate the fraction of streamflow that is derived from precipitation that fell within the past two or three months. This young streamflow accounts for about a third of global river discharge, and comprises at least 5% of discharge in about 90% of the catchments we investigated. We conclude that, although typical catchments have mean transit times of years or even decades, they nonetheless can rapidly transmit substantial fractions of soluble contaminant inputs to streams. Young streamflow is less prevalent in steeper landscapes, which suggests they are characterized by deeper vertical infiltration. Because young streamflow is derived from less than 0.1% of global groundwater storage, we conclude that this thin veneer of aquifer storage will have a disproportionate influence on stream water quality.

  2. Substantially Evolutionary Theorizing in Designing Software-Intensive Systems

    Directory of Open Access Journals (Sweden)

    Petr Sosnin

    2018-04-01

    Full Text Available Useful inheritances from scientific experience open perspective ways for increasing the degree of success in designing of systems with software. One such way is a search and build applied theory that takes into account the nature of design and the specificity of software engineering. This paper presents a substantially evolutionary approach to creating the project theories, the application of which leads to positive effects that are traditionally expected from theorizing. Any implementation of the approach is based on a reflection by designers of an operational space of designing onto a semantic memory of a question-answer type. One of the results of such reflection is a system of question-answer nets, the nodes of which register facts of interactions of designers with accessible experience. A set of such facts is used by designers for creating and using the theory that belongs to the new subclass of Grounded Theories. This sub-class is oriented on organizationally behavioral features of a project’s work based on design thinking, automated mental imagination, and thought experimenting that facilitate increasing the degree of controlled intellectualization in the design process and, correspondingly, increasing the degree of success in the development of software-intensive systems.

  3. New theory of arrhythmia. Conceptual substantiation of arrhythmia mechanisms

    Directory of Open Access Journals (Sweden)

    Vladimir I. Ermoshkin

    2015-11-01

    Full Text Available Aims A new attempt is made to substantiate the concept of the mechanism of arrhythmia and sudden cardiac death. Methods The paper is based on a theoretical analysis of special literature, personal experience of participation in conferences and discussions with leading Russian cardiologists. Results We have succeeded in demonstrating the fact that researchers ignore the fact that cardiomyocytes can be excited by mechanical pulses, when considering the arrhythmia mechanisms. We have conducted trials using the Cardiocode device. Under stress in a human, opened may be large and small arteriovenous anastomoses, via which blood under high pressure is ejected into veins. It leads to pressure surges in arteries and veins. The vena cava dilates, its tonus increases. In some cases, the pulse waves travel via anastomoses along the vena cava walls to the atria and the ventricles. An above-threshold concentration of tensions from mechanical pulses may excite cardiomyocytes from different points of the myocardium, disturbing the sinus rhythm. As a result, extrasystoles, tachycardia attacks, blocking of blood circulation in the peripheral segments of the venous arterial networks, edemata, thrombosis and metabolism disorders appear. Arrhythmia, tachycardia attacks and concomitant myocardial ischemia lead to progression of heart fibrosis. Such changes increase the probability of fibrillations and sudden cardiac death. Conclusion Unhealthy lifestyle, the presence of opening and not properly closing anastomoses may provoke a number of diseases. To avoid the cardiac arrhythmia attacks and prevent SCD, it is necessary to suppress travel of the mechanical waves within the following circuitry: aorta – artery – anastomosis – vein – vena cava – atria – ventricles. The travel of the mechanical waves within the same vessel circuitry explains the fact that the fixed couplings under extrasystoles are observed, and the beat-to-beat RR intervals under tachycardia

  4. How common is substantial weight gain after pregnancy?

    Science.gov (United States)

    Sumithran, Priya; Houlihan, Christine; Shub, Alexis; Churilov, Leonid; Pritchard, Natasha; Price, Sarah; Ekinci, Elif; Proietto, Joseph; Permezel, Michael

    2017-11-20

    Although population-based studies indicate that on average, women gain 1-2kg between pregnancies, women with obesity often attribute its development to childbearing. There is little contemporary data available regarding how commonly this occurs, particularly in women of different body mass index (BMI) categories. The aim of this study was to examine inter-pregnancy weight changes among women at a tertiary obstetric hospital in Melbourne, Australia. This was a retrospective review of data from the Birthing Outcomes System electronic record of 19,617 women aged 20 years or older, who delivered at least two consecutive singleton infants at ≥37 weeks' gestation at Mercy Hospital for Women between December 1994 and December 2015. A logistic regression model was used to assess the relationship between gain of ≥4kg/m 2 between pregnancies and maternal BMI category in the first pregnancy, adjusting for covariates of maternal age, inter-pregnancy interval, and socioeconomic status. Gain of ≥4kg/m 2 between the first two pregnancies occurred in 7.5% of normal weight women, 10.5% of overweight women, and 13.4% of women with obesity. One in five women who were normal weight in their first pregnancy increased to overweight or obese BMI categories in their second pregnancy. Substantial weight gain in relation to pregnancy affects a considerable proportion of women. Since inter-pregnancy weight gain is associated with several complications in the next pregnancy and longer term, avoiding excessive weight gain during and between pregnancies may prevent adverse health consequences in mothers and offspring. Copyright © 2017 Asia Oceania Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

  5. Modelling reveals endogenous osmotic adaptation of storage tissue water potential as an important driver determining different stem diameter variation patterns in the mangrove species Avicennia marina and Rhizophora stylosa.

    Science.gov (United States)

    Vandegehuchte, Maurits W; Guyot, Adrien; Hubeau, Michiel; De Swaef, Tom; Lockington, David A; Steppe, Kathy

    2014-09-01

    Stem diameter variations are mainly determined by the radial water transport between xylem and storage tissues. This radial transport results from the water potential difference between these tissues, which is influenced by both hydraulic and carbon related processes. Measurements have shown that when subjected to the same environmental conditions, the co-occurring mangrove species Avicennia marina and Rhizophora stylosa unexpectedly show a totally different pattern in daily stem diameter variation. Using in situ measurements of stem diameter variation, stem water potential and sap flow, a mechanistic flow and storage model based on the cohesion-tension theory was applied to assess the differences in osmotic storage water potential between Avicennia marina and Rhizophora stylosa. Both species, subjected to the same environmental conditions, showed a resembling daily pattern in simulated osmotic storage water potential. However, the osmotic storage water potential of R. stylosa started to decrease slightly after that of A. marina in the morning and increased again slightly later in the evening. This small shift in osmotic storage water potential likely underlaid the marked differences in daily stem diameter variation pattern between the two species. The results show that in addition to environmental dynamics, endogenous changes in the osmotic storage water potential must be taken into account in order to accurately predict stem diameter variations, and hence growth.

  6. Plasma processing conditions substantially influence circulating microRNA biomarker levels.

    Science.gov (United States)

    Cheng, Heather H; Yi, Hye Son; Kim, Yeonju; Kroh, Evan M; Chien, Jason W; Eaton, Keith D; Goodman, Marc T; Tait, Jonathan F; Tewari, Muneesh; Pritchard, Colin C

    2013-01-01

    Circulating, cell-free microRNAs (miRNAs) are promising candidate biomarkers, but optimal conditions for processing blood specimens for miRNA measurement remain to be established. Our previous work showed that the majority of plasma miRNAs are likely blood cell-derived. In the course of profiling lung cancer cases versus healthy controls, we observed a broad increase in circulating miRNA levels in cases compared to controls and that higher miRNA expression correlated with higher platelet and particle counts. We therefore hypothesized that the quantity of residual platelets and microparticles remaining after plasma processing might impact miRNA measurements. To systematically investigate this, we subjected matched plasma from healthy individuals to stepwise processing with differential centrifugation and 0.22 µm filtration and performed miRNA profiling. We found a major effect on circulating miRNAs, with the majority (72%) of detectable miRNAs substantially affected by processing alone. Specifically, 10% of miRNAs showed 4-30x variation, 46% showed 30-1,000x variation, and 15% showed >1,000x variation in expression solely from processing. This was predominantly due to platelet contamination, which persisted despite using standard laboratory protocols. Importantly, we show that platelet contamination in archived samples could largely be eliminated by additional centrifugation, even in frozen samples stored for six years. To minimize confounding effects in microRNA biomarker studies, additional steps to limit platelet contamination for circulating miRNA biomarker studies are necessary. We provide specific practical recommendations to help minimize confounding variation attributable to plasma processing and platelet contamination.

  7. Anonymity versus privacy in the dictator game: revealing donor decisions to recipients does not substantially impact donor behavior.

    Directory of Open Access Journals (Sweden)

    Jeffrey Winking

    Full Text Available Anonymity is often offered in economic experiments in order to eliminate observer effects and induce behavior that would be exhibited under private circumstances. However, anonymity differs from privacy in that interactants are only unaware of each others' identities, while having full knowledge of each others' actions. Such situations are rare outside the laboratory and anonymity might not meet the requirements of some participants to psychologically engage as if their actions were private. In order to explore the impact of a lack of privacy on prosocial behaviors, I expand on a study reported in Dana et al. (2006 in which recipients were left unaware of the Dictator Game and given donations as "bonuses" to their show-up fees for other tasks. In the current study, I explore whether differences between a private Dictator Game (sensu Dana et al. (2006 and a standard anonymous one are due to a desire by dictators to avoid shame or to pursue prestige. Participants of a Dictator Game were randomly assigned to one of four categories-one in which the recipient knew of (1 any donation by an anonymous donor (including zero donations, (2 nothing at all, (3 only zero donations, and (4 and only non-zero donations. The results suggest that a lack of privacy increases the shame that selfish-acting participants experience, but that removing such a cost has only minimal effects on actual behavior.

  8. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato.

    Science.gov (United States)

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-04-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene-derived markers. For the first time we report on the development and mapping of 83 Petunia microsatellites. The two maps retain the same marker order, but display significant differences of recombination frequencies at orthologous mapping intervals. A complex pattern of genomic rearrangements was detected with the related genome of tomato (Solanum lycopersicum), indicating that synteny between Petunia and other Solanaceae crops has been considerably disrupted. The newly developed markers will facilitate the genetic characterization of mutants and ecological studies on genetic diversity and speciation within the genus Petunia. The maps will provide a powerful tool to link genetic and genomic information and will be useful to support sequence assembly of the Petunia genome.

  9. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato

    OpenAIRE

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-01-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene...

  10. Standardizing economic analysis in prevention will require substantial effort.

    Science.gov (United States)

    Guyll, Max

    2014-12-01

    It is exceedingly difficult to compare results of economic analyses across studies due to variations in assumptions, methodology, and outcome measures, a fact which surely decreases the impact and usefulness of prevention-related economic research. Therefore, Crowley et al. (Prevention Science, 2013) are precisely correct in their call for increased standardization and have usefully highlighted the issues that must be addressed. However, having made the need clear, the questions become what form the solution should take, and how should it be implemented. The present discussion outlines the rudiments of a comprehensive framework for promoting standardized methodology in the estimation of economic outcomes, as encouraged by Crowley et al. In short, a single, standard, reference case approach should be clearly articulated, and all economic research should be encouraged to apply that standard approach, with results from compliant analyses being reported in a central archive. Properly done, the process would increase the ability of those without specialized training to contribute to the body of economic research pertaining to prevention, and the most difficult tasks of predicting and monetizing distal outcomes would be readily completed through predetermined models. These recommendations might be viewed as somewhat forcible, insomuch as they advocate for prescribing the details of a standard methodology and establishing a means of verifying compliance. However, it is unclear that the best practices proposed by Crowley et al. will be widely adopted in the absence of a strong and determined approach.

  11. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  12. Substantial equivalence--an appropriate paradigm for the safety assessment of genetically modified foods?

    International Nuclear Information System (INIS)

    Kuiper, Harry A.; Kleter, Gijs A.; Noteborn, Hub P.J.M.; Kok, Esther J.

    2002-01-01

    Safety assessment of genetically modified food crops is based on the concept of substantial equivalence, developed by OECD and further elaborated by FAO/WHO. The concept embraces a comparative approach to identify possible differences between the genetically modified food and its traditional comparator, which is considered to be safe. The concept is not a safety assessment in itself, it identifies hazards but does not assess them. The outcome of the comparative exercise will further guide the safety assessment, which may include (immuno)toxicological and biochemical testing. Application of the concept of substantial equivalence may encounter practical difficulties: (i) the availability of near-isogenic parental lines to compare the genetically modified food with; (ii) limited availability of methods for the detection of (un)intended effects resulting from the genetic modification; and (iii) limited information on natural variations in levels of relevant crop constituents. In order to further improve the methodology for identification of unintended effects, new 'profiling' methods are recommended. Such methods will allow for the screening of potential changes in the modified host organism at different integration levels, i.e. at the genome level, during gene expression and protein translation, and at the level of cellular metabolism

  13. Genetic variation in a grapevine progeny (Vitis vinifera L. cvs Grenache×Syrah) reveals inconsistencies between maintenance of daytime leaf water potential and response of transpiration rate under drought

    Science.gov (United States)

    Coupel-Ledru, Aude; Lebon, Éric; Christophe, Angélique; Doligez, Agnès; Cabrera-Bosquet, Llorenç; Péchier, Philippe; Hamard, Philippe; This, Patrice; Simonneau, Thierry

    2014-01-01

    In the face of water stress, plants evolved with different abilities to limit the decrease in leaf water potential, notably in the daytime (ΨM). So-called isohydric species efficiently maintain high ΨM, whereas anisohydric species cannot prevent ΨM from dropping as soil water deficit develops. The genetic and physiological origins of these differences in (an)isohydric behaviours remain to be clarified. This is of particular interest within species such as Vitis vinifera L. where continuous variation in the level of isohydry has been observed among cultivars. With this objective, a 2 year experiment was conducted on the pseudo-F1 progeny from a cross between the two widespread cultivars Syrah and Grenache using a phenotyping platform coupled to a controlled-environment chamber. Potted plants of all the progeny were analysed for ΨM, transpiration rate, and soil-to-leaf hydraulic conductance, under both well-watered and water deficit conditions. A high genetic variability was found for all the above traits. Four quantitative trait loci (QTLs) were detected for ΨM under water deficit conditions, and 28 other QTLs were detected for the different traits in either condition. Genetic variation in ΨM maintenance under water deficit weakly correlated with drought-induced reduction in transpiration rate in the progeny, and QTLs for both traits did not completely co-localize. This indicates that genetic variation in the control of ΨM under water deficit was not due simply to variation in transpiration sensitivity to soil drying. Possible origins of the diversity in (an)isohydric behaviours in grapevine are discussed on the basis of concurrent variations in soil-to-leaf hydraulic conductance and stomatal control of transpiration. PMID:25381432

  14. Geographic variation in expenditures for Workers' Compensation hospitalized claims.

    Science.gov (United States)

    Miller, T R; Levy, D T

    1999-02-01

    Past literature finds considerable variation in the cost of physician care and in the utilization of medical procedures. Variation in the cost of hospitalized care has received little attention. We examine injury costs of hospitalized claims across states. Multivariate regression analysis is used to isolate state variations, while controlling for personal and injury characteristics, and state characteristics. Injuries to workers filing Workers' Compensation lost workday claims. About 35,000 randomly sampled Workers' Compensation claims from 17 states filed between 1979 and 1988. Medical payments per episode of three injury groups: upper and lower extremity fractures and dislocations, other upper extremity injuries, and back strains and sprains. Statistical analyses reveal considerable variation in expenditures for hospitalized injuries across states, even after controlling for case mix and state characteristics. A substantial portion of the variation is explained by state rate regulations; regulated states have lower costs. The large variation in costs suggests a potential to affect the costs of hospitalized care. Efforts should be directed at those areas that have higher costs without sufficient input price, quality, or case mix justification.

  15. Photoperiodic differences in a forebrain nucleus involved in vocal plasticity: enkephalin immunoreactivity reveals volumetric variation in song nucleus lMAN but not NIf in male European starlings (Sturnus vulgaris).

    Science.gov (United States)

    Stevenson, Tyler J; Ball, Gregory F

    2010-09-15

    Seasonal variation in the volume of various song control nuclei in many passerine species remains one of the best examples of naturally occurring adult neuroplasticity among vertebrates. The lateral portion of the magnocellular nucleus of the anterior nidopallium (lMAN) is a song nucleus that is important for song learning and seems to be critical for inducing variability in the song structure that is later pruned via a feedback process to produce adult crystallized song. To date, lMAN has not been shown to exhibit seasonal changes in volume, probably because it is difficult to resolve the boundaries of lMAN when employing histological methods based on Nissl staining. Here, lMAN(core) volumes were examined in intact photostimulated (i.e., breeding), castrated photostimulated and photorefractory (i.e., nonbreeding) male starlings (Sturnus vulgaris) to investigate the degree of seasonal variation in brain morphology. We present data demonstrating that the volumes of the total MAN and lMAN(core) delineated by enkephalin immunoreactivity are greater in photostimulated male starlings as compared to photorefractory males. Moreover, two other regions associated with the song system that have not been investigated previously in the context of seasonal plasticity namely (i) the medial portion of MAN (mMAN), and (ii) the nucleus interfacialis (NIf) did not display significant volumetric variation. We propose that greater lMAN(core) volumes are associated with the increase in vocal plasticity that is generally observed prior to production of stereotyped song.

  16. Substantial Research Secures the Blue Future for our Blue Plant

    Directory of Open Access Journals (Sweden)

    Moustafa Abdel Maksoud

    2016-06-01

    Full Text Available Earth, the blue planet, is our home, and seas and oceans cover more than 70% of its surface. As the earth’s population rapidly increases and available resources decrease, seas and oceans can play a key role in assuring the long-term survival of humankind. Renewable maritime energy has huge potential to provide a considerable part of the earth’s population with decarbonised electricity generation systems. Renewable maritime energy is very flexible and can be harvested above the water’s free surface by using offshore wind turbines, on the water’s surface by using wave energy converters or below the water’s surface by using current or tidal turbines. The supposed conflict between environmental protection measures and economic interests is neither viable nor reasonable. Renewable maritime energy can be the motor for considerable substantial economic growth for many maritime regions and therefore for society at large. The fastest growing sector of renewable maritime energy is offshore wind. The annual report of the European Wind Energy Association from the year 2015 confirms the growing relevance of the offshore wind industry. In 2015, the total installed and grid-connected capacity of wind power was 12,800 MW in the EU and 6,013.4 MW in Germany. 38% of the 2015 annual installation in Germany was offshore, accounting for a capacity of 2,282.4 MW. However, there are a limited number of available installation sites in shallow water, meaning that there is an urgent need to develop new offshore structures for water depths greater than 50m. The persistent trend towards deeper waters has encouraged the offshore wind industry to look for floating wind turbine structures and larger turbines. Floating wind turbine technologies are at an early stage of development and many technical and economic challenges will still need to be faced. Nonetheless, intensive research activities and the employment of advanced technologies are the key factors in

  17. Substantial interobserver variation of thyroid volume and function by visual evaluation of thyroid (99m)Tc scintigraphy

    DEFF Research Database (Denmark)

    Soelberg, Kerstin; Grupe, Peter; Boel-Jørgensen, Henrik

    2014-01-01

    (99m)Tc-pertechnetate scintigraphy is much used in the evaluation of patients with nodular goitre. We investigated the ability of experienced observers to estimate the thyroid 24-h (131)I uptake (RAIU) and the thyroid volume by visual evaluation of the scintigram.......(99m)Tc-pertechnetate scintigraphy is much used in the evaluation of patients with nodular goitre. We investigated the ability of experienced observers to estimate the thyroid 24-h (131)I uptake (RAIU) and the thyroid volume by visual evaluation of the scintigram....

  18. Controlled challenge experiment demonstrates substantial additive genetic variation in resistance of Nile tilapia (Oreochromis niloticus) to Streptococcus iniae

    Science.gov (United States)

    Streptococcus iniae is an etiologic agent of streptococcal disease in tilapia and is one of several Streptococcus spp. that negatively impact worldwide tilapia production. Methods for the prevention and control of S. iniae include vaccines, management strategies, and antibiotics. A complimentary pre...

  19. Neighborhood-level social processes and substantiated cases of child maltreatment.

    Science.gov (United States)

    Molnar, Beth E; Goerge, Robert M; Gilsanz, Paola; Hill, Andrea; Subramanian, S V; Holton, John K; Duncan, Dustin T; Beatriz, Elizabeth D; Beardslee, William R

    2016-01-01

    Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood's children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois' child protection agency, 1995-2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis-an ecological-level, repeated cross-sectional design utilizing random-intercept logit models-with a sensitivity analysis using spatial models to control for spatial autocorrelation-revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  1. 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

  2. Genetic variation in pea (Pisum sativum L.) demonstrates the importance of root but not shoot C/N ratios in the control of plant morphology and reveals a unique relationship between shoot length and nodulation intensity.

    Science.gov (United States)

    Ludidi, Ndiko N; Pellny, Till K; Kiddle, Guy; Dutilleul, Christelle; Groten, Karin; VAN Heerden, Philippus D R; Dutt, Som; Powers, Stephen J; Römer, Peter; Foyer, Christine H

    2007-10-01

    Nodule numbers are regulated through systemic auto-regulatory signals produced by shoots and roots. The relative effects of shoot and root genotype on nodule numbers together with relationships to organ biomass, carbon (C) and nitrogen (N) status, and related parameters were measured in pea (Pisum sativum) exploiting natural genetic variation in maturity and apparent nodulation intensity. Reciprocal grafting experiments between the early (Athos), intermediate (Phönix) and late (S00182) maturity phenotypes were performed and Pearson's correlation coefficients for the parameters were calculated. No significant correlations were found between shoot C/N ratios and plant morphology parameters, but the root C/N ratio showed a strong correlation with root fresh and dry weights as well as with shoot fresh weight with less significant interactions with leaf number. Hence, the root C/N ratio rather than shoot C/N had a predominant influence on plant morphology when pea plants are grown under conditions of symbiotic nitrogen supply. The only phenotypic characteristic that showed a statistically significant correlation with nodulation intensity was shoot length, which accounted for 68.5% of the variation. A strong linear relationship was demonstrated between shoot length and nodule numbers. Hence, pea nodule numbers are controlled by factors related to shoot extension, but not by shoot or root biomass accumulation, total C or total N. The relationship between shoot length and nodule numbers persisted under field conditions. These results suggest that stem height could be used as a breeding marker for the selection of pea cultivars with high nodule numbers and high seed N contents.

  3. Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment.

    Directory of Open Access Journals (Sweden)

    Miyako Kusano

    Full Text Available As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms.

  4. Substantial secondary organic aerosol formation in a coniferous forest: observations of both day- and nighttime chemistry

    Directory of Open Access Journals (Sweden)

    A. K. Y. Lee

    2016-06-01

    Full Text Available Substantial biogenic secondary organic aerosol (BSOA formation was investigated in a coniferous forest mountain region in Whistler, British Columbia. A largely biogenic aerosol growth episode was observed, providing a unique opportunity to investigate BSOA formation chemistry in a forested environment with limited influence from anthropogenic emissions. Positive matrix factorization of aerosol mass spectrometry (AMS measurement identified two types of BSOA (BSOA-1 and BSOA-2, which were primarily generated by gas-phase oxidation of monoterpenes and perhaps sesquiterpenes. The temporal variations of BSOA-1 and BSOA-2 can be explained by gas–particle partitioning in response to ambient temperature and the relative importance of different oxidation mechanisms between day and night. While BSOA-1 arises from gas-phase ozonolysis and nitrate radical chemistry at night, BSOA-2 is likely less volatile than BSOA-1 and consists of products formed via gas-phase oxidation by OH radical and ozone during the day. Organic nitrates produced through nitrate radical chemistry can account for 22–33 % of BSOA-1 mass at night. The mass spectra of BSOA-1 and BSOA-2 have higher values of the mass fraction of m/z 91 (f91 compared to the background organic aerosol. Using f91 to evaluate BSOA formation pathways in this unpolluted, forested region, heterogeneous oxidation of BSOA-1 is a minor production pathway of BSOA-2.

  5. Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

    Science.gov (United States)

    Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-01-01

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

  6. A Substantial Plume of Escaping Planetary Ions in the MSE Northern Hemisphere Observed by MAVEN

    Science.gov (United States)

    Dong, Y.; Fang, X.; Brain, D. A.; McFadden, J. P.; Halekas, J. S.; Connerney, J. E. P.; Curry, S.; Harada, Y.; Luhmann, J. G.; Jakosky, B. M.

    2015-12-01

    The Mars-solar wind interaction accelerates and transports planetary ions away from Mars through a number of processes, including pick-up by the electromagnetic fields. The Mars Atmospheric and Volatile EvolutioN (MAVEN) spacecraft has frequently detected strong escaping planetary ion fluxes in both tailward and upstream solar wind motional electric field directions since the beginning of its science phase in November 2014. Our statistical study using three-month MAVEN data from November 2014 through February 2015 illustrates a substantial plume-like escaping planetary ion population organized by the upstream electric field with strong fluxes widely distributed in the northern hemisphere of the Mars-Sun-Electric-field (MSE) coordinate system, which is generally consistent with model predictions. The plume constitutes an important planetary ion escape channel from the Martian atmosphere in addition to the tailward escape. The >25eV O+ escape rate through the plume is estimated to be ~35% of the tailward escape and ~25% of the total escape. We will compare the dynamics of the plume and tailward escaping ions based on their velocity-space distributions with respect to the electromagnetic fields. We will also discuss the variations of the plume characteristics between different ion species (O+, O2+, and CO2+) and from the effect of different solar wind and interplanetary magnetic field (IMF) conditions.

  7. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

    Science.gov (United States)

    Chang, Chia-Hao; Li, Fan; Shao, Kwang-Tsao; Lin, Yeong-Shin; Morosawa, Takahiro; Kim, Sungmin; Koo, Hyeyoung; Kim, Won; Lee, Jae-Seong; He, Shunping; Smith, Carl; Reichard, Martin; Miya, Masaki; Sado, Tetsuya; Uehara, Kazuhiko; Lavoué, Sébastien; Chen, Wei-Jen; Mayden, Richard L

    2014-12-01

    Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Variation in Phytochemical Composition Reveals Distinct Divergence of Aloe vera (L.) Burm.f. From Other Aloe Species: Rationale Behind Selective Preference of Aloe vera in Nutritional and Therapeutic Use

    Science.gov (United States)

    Dey, Priyankar; Dutta, Somit; Chowdhury, Anurag; Das, Abhaya Prasad; Chaudhuri, Tapas Kumar

    2017-01-01

    In the present study, we have phytochemically characterized 5 different abundant Aloe species, including Aloe vera (L.) Burm.f., using silylation followed by Gas Chromatography-Mass Spectrometry technique and compared the data using multivariate statistical analysis. The results demonstrated clear distinction of the overall phytochemical profile of A vera, highlighted by its divergent spatial arrangement in the component plot. Lowest correlation of the phytochemical profiles were found between A vera and A aristata Haw. (−0.626), whereas highest correlation resided between A aristata and A aspera Haw. (0.899). Among the individual phytochemicals, palmitic acid was identified in highest abundance cumulatively, and carboxylic acids were the most predominant phytochemical species in all the Aloe species. Compared to A vera, linear correlation analysis revealed highest and lowest correlation with A aspera (R 2 = 0.9162) and A aristata (R 2 = 0.6745), respectively. Therefore, A vera demonstrated distinct spatial allocation, reflecting its greater phytochemical variability. PMID:29228808

  9. 大气水汽同位素组成的短期变异特征%Short-term variations of vapor isotope ratios reveal the influence of atmospheric processes

    Institute of Scientific and Technical Information of China (English)

    张世春; 孙晓敏; 王建林; 于贵瑞; 温学发

    2011-01-01

    Stable isotopes of atmospheric water vapor reveal rich information on water movement and phase changes in the atmosphere. Here we presented two nearly continuous time-series of δD and δ18O of atmospheric water vapor (δv) measured at hourly intervals in surface air in Beijing and above a winter wheat canopy in Shijiazhuang using in-situ measurement technique. During the precipitation events, the δv values in both Beijing and Shijiazhuang were in the state of equilibrium with precipitation water, revealing the influence of precipitation processes. However, the δv departures from the equilibrium state were positively correlated with local relative humidity. Note that the δv tended to enrich in Beijing, but deplete in Shijiazhuang during the precipitation events, which mainly resulted from the influence of transpiration processes that enriched the δv in Shijiazhuang. On seasonal time-scale, the δvvalues were log-linear functions of water vapor mixing ratios in both Beijing and Shijiazhuang. The water vapor mixing ratio was an excellent predictor of the δv by the Rayleigh distillation mechanisms, indicating that air mass advection could also play an important role in determining the δv. On a diurnal time-scale, the δv reached the minimum in the early afternoon hours in Beijing which was closely related to the atmospheric processes of boundary layer entrainment. During the peak of growing season of winter wheat, however, the δv reached the minimum in the early morning, and increased gradually through the daytime, and reached the maximum in the late afternoon, which was responsible by the interaction between boundary layer entrainment and the local atmospheric processes, such as transpiration and dew formation. This study has the implications for the important role of vegetation in determining the surface δv and highlights the need to conduct δv measurement on short-term (e.g. diurnal) time scales.

  10. Grammatical Conception of Yuriy Shevel'ov: Nominative ↔ Vocative in the System of Substantial Categoriality

    Directory of Open Access Journals (Sweden)

    Anatoliy Zahnitko

    2016-08-01

    Full Text Available Background. Analysis of Yuriy Shevel'ov’s approaches to the interpretation of the morphological tier of language, as well as his examination of particular phenomena of this level – substantiality, verbality, and others – reflects not only the author's understanding itself of all the grammatical system as a whole, and morphological one in particular, but also represents the features of modification of scientific approaches in the history of linguistic thought of mid-twentieth century, its strengthening in the studies of the XX – XXI century. The researcher’s definition of nominative and vocative cases as interrelated within the categorical substantiality is of particular importance. Purpose: to determine the main components of interpretation of the status dimension of the nominative and vocative cases within morpho-substantial categoriality of Yuriy Shevel'ov with the definition of theoretical foundations and practical principles, revealing the patterns of establishing internal sentence dimension of the nominative and vocative cases. Results: In the case theory with reliance on the sequence of forms of dependencies in the internal sentence space Yuriy Shevel'ov distinguishes five cases: genitive, dative, accusative, ablative, locative. In the statement about the nominative as grammatically independent case the scientist relies on sentence. Two-dimensionality of grammatically independent case opposes to the one-dimensional grammatically dependent nominative that is traceable in syntactic positions of predicate and apposition. Yuriy Shevel'ov did not consider addressing that is not grammatically linked to the sentence with a specific expression as an individual case. The forms of vocative case show functional three-componentity, because in its functional-semantic paradigm it covers the function of the addressee – potential subject of action (primary function that is represented in formal grammar sentence structure by the main element of

  11. Nonlinear (MARS modeling of long-term variations of surface UV-B radiation as revealed from the analysis of Belsk, Poland data for the period 1976–2000

    Directory of Open Access Journals (Sweden)

    J. W. Krzyścin

    Full Text Available A new, powerful statistical technique, multivariate adaptive regression splines (MARS, is applied to reproduce monthly fractional deviations of UV-B doses over Belsk, Poland, during the snowless (May–October part of the year in the period 1976–2000. Two kinds of regressors were used: local ones (total ozone, percentage of sky covered by low-, mid-, high-level clouds or total solar radiation over Belsk and non-local ones, i.e. those describing the long-distance forcings on the surface UV-B due to changes in the global atmospheric circulation. Standard indices of the Quasi-Biennial, North Atlantic, El Niño-Southern Oscillations, and the 11-year solar activity were used as non-local regressors. The results there indicate that the MARS procedure is able to reproduce the observed year-to-year and decadal oscillations in the UV data. The MARS model yields better model-observation agreement than an ordinary least-squares fit based on the same set of regressors. It is found that MARS is capable of handling interactions between the local and non-local regressors, suggesting a possible nonlinear nature of connections between variables characterizing the atmospheric transparency over Belsk and the long-distance forcings. MARS enables a reconstruction of the surface UV-B variations over any site based on the cloud and ozone data presently stored on web pages.

    Key words. Atmospheric composition and structure (aerosols and particles; biosphere-atmosphere interactions

  12. The human cerebral cortex is neither one nor many: Neuronal distribution reveals two quantitatively different zones in the grey matter, three in the white matter, and explains local variations in cortical folding

    Directory of Open Access Journals (Sweden)

    Pedro F. M. Ribeiro

    2013-09-01

    Full Text Available The human prefrontal cortex has been considered different in several aspects and relatively enlarged compared to the rest of the cortical areas. Here we determine whether the white and gray matter of the prefrontal portion of the human cerebral cortex have similar or different cellular compositions relative to the rest of the cortical regions by applying the Isotropic Fractionator to analyze the distribution of neurons along the entire anteroposterior axis of the cortex, and its relationship with the degree of gyrification, number of neurons under the cortical surface, and other parameters. The prefrontal region shares with the remainder of the cerebral cortex (except for occipital cortex the same relationship between cortical volume and number of neurons. In contrast, both occipital and prefrontal areas vary from other cortical areas in their connectivity through the white matter, with a systematic reduction of cortical connectivity through the white matter and an increase of the mean axon caliber along the anteroposterior axis. These two parameters explain local differences in the distribution of neurons underneath the cortical surface. We also show that local variations in cortical folding are neither a function of local numbers of neurons nor of cortical thickness, but correlate with properties of the white matter, and are best explained by the folding of the white matter surface. Our results suggest that the human cerebral cortex is divided in two zones (occipital and non-occipital that differ in how neurons distributed across their grey matter volume and in three zones (prefrontal, occipital, and non-occipital that differ in how neurons are connected through the white matter. Thus, the human prefrontal cortex has the largest fraction of neuronal connectivity through the white matter and the smallest average axonal caliber in the white matter within the cortex, although its neuronal composition fits the pattern found for other, non

  13. 20 CFR 654.13 - Determination of areas of substantial unemployment.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Determination of areas of substantial unemployment. 654.13 Section 654.13 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF... 10582 § 654.13 Determination of areas of substantial unemployment. An area of substantial unemployment...

  14. Glacial survival east and west of the 'Mekong-Salween Divide' in the Himalaya-Hengduan Mountains region as revealed by AFLPs and cpDNA sequence variation in Sinopodophyllum hexandrum (Berberidaceae).

    Science.gov (United States)

    Li, Yong; Zhai, Sheng-Nan; Qiu, Ying-Xiong; Guo, Yan-Ping; Ge, Xue-Jun; Comes, Hans Peter

    2011-05-01

    Molecular phylogeographic studies have recently begun to elucidate how plant species from the Qinghai-Tibetan Plateau (QTP) and adjacent regions responded to the Quaternary climatic oscillations. In this regard, however, far less attention has been paid to the southern and south-eastern declivities of the QTP, i.e. the Himalaya-Hengduan Mountains (HHM) region. Here, we report a survey of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA (cpDNA) sequence variation in the HHM endemic Sinopodophyllum hexandrum, a highly selfing alpine perennial herb with mainly gravity-dispersed berries (105 individuals, 19 localities). We specifically aimed to test a vicariant evolutionary hypothesis across the 'Mekong-Salween Divide', a known biogeographic and phytogeographic boundary of north-to-south trending river valleys separating the East Himalayas and Hengduan Mts. Both cpDNA and AFLPs identified two divergent phylogroups largely congruent with these mountain ranges. There was no genetic depauperation in the more strongly glaciated East Himalayas (AFLPs: H(E)=0.031; cpDNA: h(S)=0.133) compared to the mainly ice-free Hengduan Mts. (AFLPs: H(E)=0.037; cpDNA: h(S)=0.082), while population differentiation was consistently higher in the former region (AFLPs: Φ(ST)=0.522 vs. 0.312; cpDNA: Φ(ST)=0.785 vs. 0.417). Our results suggest that East Himalayan and Hengduan populations of S. hexandrum were once fragmented, persisted in situ during glacials in both areas, and have not merged again, except for a major instance of inter-lineage chloroplast capture identified at the MSD boundary. Our coalescent time estimate for all cpDNA haplotypes (c. 0.37-0.48 mya), together with paleogeological evidence, strongly rejects paleo-drainage formation as a mechanism underlying allopatric fragmentation, whereas mountain glaciers following the ridges of the MSD during glacials (and possible interglacials) could have been responsible. This study thus indicates an important role

  15. Metaleptic Variations

    OpenAIRE

    Pernot, Dominique

    2014-01-01

    Les derniers romans de Gabriel Josipovici offrent beaucoup de variété, allant de la parodie, de la fiction comique légère, dans Only Joking et Making Mistakes, à des sujets plus graves, plus personnels, ontologiques. Dans un court roman, Everything Passes, et dans un roman majeur, Goldberg: Variations, le lecteur est amené à se poser des questions sur la nature mystérieuse de la réalité, qui est, trop souvent, acceptée sans conteste par de nombreux roma...

  16. Comparison of strategies for substantiating freedom from scrapie in a sheep flock.

    Science.gov (United States)

    Durand, Benoit; Martinez, Marie-José; Calavas, Didier; Ducrot, Christian

    2009-04-30

    The public health threat represented by a potential circulation of bovine spongiform encephalopathy agent in sheep population has led European animal health authorities to launch large screening and genetic selection programmes. If demonstrated, such a circulation would have dramatic economic consequences for sheep breeding sector. In this context, it is important to evaluate the feasibility of qualification procedures that would allow sheep breeders demonstrating their flock is free from scrapie. Classical approaches, based on surveys designed to detect disease presence, do not account for scrapie specificities: the genetic variations of susceptibility and the absence of live diagnostic test routinely available. Adapting these approaches leads to a paradoxical situation in which a greater amount of testing is needed to substantiate disease freedom in genetically resistant flocks than in susceptible flocks, whereas probability of disease freedom is a priori higher in the former than in the latter. The goal of this study was to propose, evaluate and compare several qualification strategies for demonstrating a flock is free from scrapie. A probabilistic framework was defined that accounts for scrapie specificities and allows solving the preceding paradox. Six qualification strategies were defined that combine genotyping data, diagnostic tests results and flock pedigree. These were compared in two types of simulated flocks: resistant and susceptible flocks. Two strategies allowed demonstrating disease freedom in several years, for the majority of simulated flocks: a strategy in which all the flock animals are genotyped, and a strategy in which only founders animals are genotyped, the flock pedigree being known. In both cases, diagnostic tests are performed on culled animals. The less costly strategy varied according to the genetic context (resistant or susceptible) and to the relative costs of a genotyping exam and of a diagnostic test. This work demonstrates that

  17. Analysis of variations in the glutamate receptor, N-methyl D-aspartate 2A (GRIN2A gene reveals their relative importance as genetic susceptibility factors for heroin addiction.

    Directory of Open Access Journals (Sweden)

    Bin Zhao

    Full Text Available The glutamate receptor, N-methyl D-aspartate 2A (GRIN2A gene that encodes the 2A subunit of the N-methyl D-aspartate (NMDA receptor was recently shown to be involved in the development of opiate addiction. Genetic polymorphisms in GRIN2A have a plausible role in modulating the risk of heroin addiction. An association of GRIN2A single-nucleotide polymorphisms (SNPs with heroin addiction was found earlier in African Americans. To identify markers that contribute to the genetic susceptibility to heroin addiction, we examined the potential association between heroin addiction and forty polymorphisms of the GRIN2A gene using the MassARRAY system and GeneScan in this study. The frequency of the (GT26 repeats (rs3219790 in the heroin addiction group was significantly higher than that in the control group (χ(2 = 5.360, P = 0.021. The allele frequencies of three polymorphisms (rs1102972, rs1650420, and rs3104703 in intron 3 were strongly associated with heroin addiction (P<0.001, 0.0002, and <0.001, after Bonferroni correction. Three additional SNPs from the same intron (rs1071502, rs6497730, and rs1070487 had nominally significant P values for association (P<0.05, but did not pass the threshold value. Haplotype analysis revealed that the G-C-T-C-C-T-A (block 6 and T-T (block 10 haplotypes of the GRIN2A gene displayed a protective effect (P = <0.001 and 0.003. These findings point to a role for GRIN2A polymorphisms in heroin addiction among the Han Chinese from Shaanxi province, and may be informative for future genetic or neurobiological studies on heroin addiction.

  18. Introductory Biology Students’ Conceptual Models and Explanations of the Origin of Variation

    Science.gov (United States)

    Shaw, Neil; Momsen, Jennifer; Reinagel, Adam; Le, Paul; Taqieddin, Ranya; Long, Tammy

    2014-01-01

    Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers’ models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students’ written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback. PMID:25185235

  19. Information Technology & Applications Corporation v. United States: An Interested Party's "Substantial Chance" at APA Standing

    National Research Council Canada - National Science Library

    Slicker, Christina

    2003-01-01

    .... Building on CICA's "interested party" definition with Information Technology's refinement of "substantial chance" rule, the Federal Circuit has effectively translated "APA standing" into the language...

  20. 20 CFR 416.972 - What we mean by substantial gainful activity.

    Science.gov (United States)

    2010-04-01

    ... INCOME FOR THE AGED, BLIND, AND DISABLED Determining Disability and Blindness Substantial Gainful... consider activities like taking care of yourself, household tasks, hobbies, therapy, school attendance...

  1. Pluck or Luck: Does Trait Variation or Chance Drive Variation in Lifetime Reproductive Success?

    Science.gov (United States)

    Snyder, Robin E; Ellner, Stephen P

    2018-04-01

    While there has been extensive interest in how intraspecific trait variation affects ecological processes, outcomes are highly variable even when individuals are identical: some are lucky, while others are not. Trait variation is therefore important only if it adds substantially to the variability produced by luck. We ask when trait variation has a substantial effect on variability in lifetime reproductive success (LRS), using two approaches: (1) we partition the variation in LRS into contributions from luck and trait variation and (2) we ask what can be inferred about an individual's traits and with what certainty, given their observed LRS. In theoretical stage- and size-structured models and two empirical case studies, we find that luck usually dominates the variance of LRS. Even when individuals differ substantially in ways that affect expected LRS, unless the effects of luck are substantially reduced (e.g., low variability in reproductive life span or annual fecundity), most variance in lifetime outcomes is due to luck, implying that departures from "null" models omitting trait variation will be hard to detect. Luck also obscures the relationship between realized LRS and individual traits. While trait variation may influence the fate of populations, luck often governs the lives of individuals.

  2. Geographic variation in sexual behavior can explain geospatial heterogeneity in the severity of the HIV epidemic in Malawi.

    Science.gov (United States)

    Palk, Laurence; Blower, Sally

    2018-02-09

    In sub-Saharan Africa, where ~ 25 million individuals are infected with HIV and transmission is predominantly heterosexual, there is substantial geographic variation in the severity of epidemics. This variation has yet to be explained. Here, we propose that it is due to geographic variation in the size of the high-risk group (HRG): the group with a high number of sex partners. We test our hypothesis by conducting a geospatial analysis of data from Malawi, where ~ 13% of women and ~ 8% of men are infected with HIV. We used georeferenced HIV testing and behavioral data from ~ 14,000 participants of a nationally representative population-level survey: the 2010 Malawi Demographic and Health Survey (MDHS). We constructed gender-stratified epidemic surface prevalence (ESP) maps by spatially smoothing and interpolating the HIV testing data. We used the behavioral data to construct gender-stratified risk maps that reveal geographic variation in the size of the HRG. We tested our hypothesis by fitting gender-stratified spatial error regression (SER) models to the MDHS data. The ESP maps show considerable geographic variation in prevalence: 1-29% (women), 1-20% (men). Risk maps reveal substantial geographic variation in the size of the HRG: 0-40% (women), 16-58% (men). Prevalence and the size of the HRG are highest in urban centers. However, the majority of HIV-infected individuals (~75% of women, ~ 80% of men) live in rural areas, as does most of the HRG (~ 80% of women, ~ 85% of men). We identify a significant (P national average in districts where > 20% of women are in the HRG. Most importantly, the SER models show that geographic variation in the size of the HRG can explain a substantial proportion (73% for women, 67% for men) of the geographic variation in epidemic severity. Taken together, our results provide substantial support for our hypothesis. They provide a potential mechanistic explanation for the geographic variation in the severity

  3. 26 CFR 1.42-7 - Substantially bond-financed buildings. [Reserved

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 1 2010-04-01 2010-04-01 true Substantially bond-financed buildings. [Reserved] 1.42-7 Section 1.42-7 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY INCOME TAX INCOME TAXES Credits Against Tax § 1.42-7 Substantially bond-financed buildings. [Reserved] ...

  4. 20 CFR 416.1080 - Notice of right to hearing on proposed finding of substantial failure.

    Science.gov (United States)

    2010-04-01

    ... agency has substantially failed to meet our standards unless the State submits a written request for a... finding of substantial failure. 416.1080 Section 416.1080 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SUPPLEMENTAL SECURITY INCOME FOR THE AGED, BLIND, AND DISABLED Determinations of Disability...

  5. 20 CFR 404.1680 - Notice of right to hearing on proposed finding of substantial failure.

    Science.gov (United States)

    2010-04-01

    ... agency has substantially failed to meet our standards unless the State submits a written request for a... finding of substantial failure. 404.1680 Section 404.1680 Employees' Benefits SOCIAL SECURITY..., following the mandatory performance support period and the 3-month adjustment period, a State agency again...

  6. Detection of Dew-Point by substantial Raman Band Frequency Jumps (A new Method)

    DEFF Research Database (Denmark)

    Hansen, Susanne Brunsgaard; Berg, Rolf W.; Stenby, Erling Halfdan

    Detection of Dew-Point by substantial Raman Band Frequency Jumps (A new Method). See poster at http://www.kemi.dtu.dk/~ajo/rolf/jumps.pdf......Detection of Dew-Point by substantial Raman Band Frequency Jumps (A new Method). See poster at http://www.kemi.dtu.dk/~ajo/rolf/jumps.pdf...

  7. Substantiation of Optimum Stoker Number in Potassium Production by Game Method

    Directory of Open Access Journals (Sweden)

    B. A. Bogatov

    2005-01-01

    Full Text Available Dump formation process of hard halite waste in potassium production has been analyzed in the paper. The paper shows high cost of a salt dump formation and an actuality to substantiate number of ОШ-1900-110/150 stokers that are operating simultaneously. A game theory method has been used to substantiate a solution of the problem.

  8. 32 CFR 48.302 - Substantiating evidence regarding dependency and age of dependents.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Substantiating evidence regarding dependency and age of dependents. 48.302 Section 48.302 National Defense Department of Defense OFFICE OF THE... Designation of Beneficiaries § 48.302 Substantiating evidence regarding dependency and age of dependents. At...

  9. Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms

    Science.gov (United States)

    Fromm, Bastian; Worren, Merete Molton; Hahn, Christoph; Hovig, Eivind; Bachmann, Lutz

    2013-01-01

    Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of miRNA complements between animal clades. However, evolution of miRNAs within such groups is poorly explored despite the availability of comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes), miRNA complements are available for some free-living flatworms and all major parasitic lineages, except for the Monogenea. We present the miRNA complement of the monogenean flatworm Gyrodactylus salaris that facilitates a comprehensive analysis of miRNA evolution in Platyhelminthes. Using the newly designed bioinformatics pipeline miRCandRef, the miRNA complement was disentangled from next-generation sequencing of small RNAs and genomic DNA without a priori genome assembly. It consists of 39 miRNA hairpin loci of conserved miRNA families, and 22 novel miRNAs. A comparison with the miRNA complements of Schmidtea mediterranea (Turbellaria), Schistosoma japonicum (Trematoda), and Echinococcus granulosus (Cestoda) reveals a substantial loss of conserved bilaterian, protostomian, and lophotrochozoan miRNAs. Eight of the 46 expected conserved miRNAs were lost in all flatworms, 16 in Neodermata and 24 conserved miRNAs could not be detected in the cestode and the trematode. Such a gradual loss of miRNAs has not been reported before for other animal phyla. Currently, little is known about miRNAs in Platyhelminthes, and for the majority of the lost miRNAs there is no prediction of function. As suggested earlier they might be related to morphological simplifications. The presence and absence of 153 conserved miRNAs was compared for platyhelminths and 32 other metazoan taxa. Phylogenetic analyses support the monophyly of Platyhelminthes (Turbellaria + Neodermata [Monogenea {Trematoda + Cestoda}]). PMID:24025793

  10. Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling.

    Directory of Open Access Journals (Sweden)

    Junha Shin

    Full Text Available Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life-Archaea, Bacteria, and Eukaryota-suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co

  11. SSR markers reveal genetic variation between improved cassava ...

    African Journals Online (AJOL)

    SERVER

    2007-12-03

    Dec 3, 2007 ... Numerical Taxonomy and Multivariate Analysis System software .... DNA extraction and polymerase chain reaction with SSR .... Primers that have PIC value falling between 0.50 to 0.70 ..... Woodman, Lee M, Porter K (2000).

  12. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates

    KAUST Repository

    Heunis, Tiaan; Dippenaar, Anzaan; Warren, Robin M.; van Helden, Paul D.; van der Merwe, Ruben G.; Gey van Pittius, Nicolaas C.; Pain, Arnab; Sampson, Samantha L.; Tabb, David L.

    2017-01-01

    Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach we identified 59 peptides containing single amino acid variants, which covered ~9% of all total coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e. large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.

  13. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates

    KAUST Repository

    Heunis, Tiaan

    2017-08-18

    Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach we identified 59 peptides containing single amino acid variants, which covered ~9% of all total coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e. large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.

  14. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.

    Science.gov (United States)

    Heunis, Tiaan; Dippenaar, Anzaan; Warren, Robin M; van Helden, Paul D; van der Merwe, Ruben G; Gey van Pittius, Nicolaas C; Pain, Arnab; Sampson, Samantha L; Tabb, David L

    2017-10-06

    Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e., large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.

  15. SUBSTANTIAL EXCEPTIONS AND (DELIMITATIONS OF THE POWERS OF THE JUDGES ON CIVIL PROCEDURAL LAW

    Directory of Open Access Journals (Sweden)

    Igor Raatz

    2017-08-01

    Full Text Available This essay aims to unveil the role of the substantial exceptions on delimiting the powers of the judges on civil procedural law, especially regarding the ex officio judicial activity. This way, under a phenomenological method and based on a vision of guarantee of rights on procedural law, the article offers a brief explanation of the question concerning the content of the object under litigation and its role of (delimiting the powers of the judges. The work hypothesis is the addition of the substantial exceptions among the content of the object under litigation, along with the claim itself and the cause of action. The results lie on the premise that, by the substantial exceptions, the defendant extends the object under litigation – which is formed dynamically on civil procedure. The conclusion points towards the idea that the substantial exceptions act in a way of limiting the ex officio judicial activity on civil procedural law

  16. Main results of substantiation of the ecological safety of the Novovoronezh NPP-2 design

    International Nuclear Information System (INIS)

    Kopytov, I.I.; Kocher'yan, V.M.; Leonov, S.V.; Chionov, V.G.; Ehrnestova, L.S.

    2005-01-01

    Paper presents the results of the efforts to determine both the actual (hydrochemical, hydrobiological, geobotanical, soil, radiological) and the predicted parameters of the region ecology derived when substantiating the ecological safety of the Novovoronezh NPP-2 design [ru

  17. Cumulative stress and substantiated maltreatment: the importance of caregiver vulnerability and adult partner violence.

    Science.gov (United States)

    Wekerle, Christine; Wall, Anne-Marie; Leung, Eman; Trocmé, Nico

    2007-04-01

    Our goal is to assess the effect of caregiver vulnerabilities, singly and in combination, on the substantiation of child abuse (physical, sexual) and neglect, while controlling for relevant background variables. We test the moderator role of adult partner violence in qualifying the relationship between caregiver vulnerabilities and maltreatment substantiation. Secondary analyses of the 1998 Canadian Incidence Study of Reported Child Maltreatment (CIS) are used to predict child protective service investigation substantiation versus non-substantiation from a range of caregiver vulnerability factors. Involvement in partner violence was examined as a moderator in the relation between caregiver vulnerabilities and maltreatment substantiation. The CIS is an epidemiological survey of first-reported cases to child protective services, using a random sample of child welfare agencies across Canada. Child welfare workers completed a research form on the child, primary caregiver, family, perpetrator, severity and type of maltreatment, as well as services and court outcomes. All maltreatment classifications were assigned according to the Canadian legal definition of child abuse and neglect. Hierarchical logistic regression analyses were used, with stepped entry of: (1) demographic factors, socioeconomic disadvantage, and caregiver's own history of maltreatment; (2) caregiver vulnerability factors; (3) involvement in partner violence; (4) the interaction between caregiver vulnerability and partner violence. Caregiver substance abuse was found to be the single most potent kind of caregiver vulnerability in predicting maltreatment substantiation. When the total number of vulnerabilities was used as the predictor, prediction across all types of maltreatment increased, especially for substantiated neglect. Analyses also showed that the presence of partner violence in the home exacerbated the effect of caregiver vulnerability on substantiation. The total number of caregiver

  18. Genetic variation in dieback resistance

    DEFF Research Database (Denmark)

    Lobo, Albin; Hansen, Jon Kehlet; McKinney, Lea Vig

    2014-01-01

    -eastern Zealand, Denmark, and confirmed the presence of substantial genetic variation in ash dieback susceptibility. The average crown damage increased in the trial from 61% in 2009 to 66% in 2012 and 72% in 2014, while the estimated heritability was 0.42 in both 2009 and 2012 but increased to 0.53 in 2014....... Genetic correlation between assessments was 0.88 between 2009 and 2012 and 0.91 between 2009 and 2014, suggesting fairly good possibilities for early selection of superior genotypes in the presence of high infection levels in the trial. The level of crown damage had strong negative effect on growth...

  19. A SUBSTANTIAL POPULATION OF MASSIVE QUIESCENT GALAXIES AT z ∼ 4 FROM ZFOURGE

    Energy Technology Data Exchange (ETDEWEB)

    Straatman, Caroline M. S.; Labbé, Ivo [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Spitler, Lee R. [Department of Physics and Astronomy, Faculty of Sciences, Macquarie University, Sydney, NSW 2109 (Australia); Allen, Rebecca; Glazebrook, Karl; Kacprzak, Glenn G. [Centre for Astrophysics and Supercomputing, Swinburne University, Hawthorn, VIC 3122 (Australia); Altieri, Bruno [European Space Astronomy Centre (ESAC)/ESA, Villanueva de la Cañada, 28691, Madrid (Spain); Brammer, Gabriel B. [European Southern Observatory, Alonso de Córdova 3107, Casilla 19001, Vitacura, Santiago (Chile); Dickinson, Mark; Inami, Hanae [National Optical Astronomy Observatory, Tucson, AZ (United States); Van Dokkum, Pieter [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Kawinwanichakij, Lalit; Mehrtens, Nicola; Papovich, Casey [George P. and Cynthia W. Mitchell Institute for Fundamental Physics and Astronomy, Department of Physics and Astronomy, Texas A and M University, College Station, TX 77843 (United States); Kelson, Daniel D.; McCarthy, Patrick J.; Monson, Andy; Murphy, David; Persson, S. Eric; Quadri, Ryan, E-mail: straatman@strw.leidenuniv.nl [Carnegie Observatories, Pasadena, CA 91101 (United States); and others

    2014-03-01

    We report the likely identification of a substantial population of massive M ∼ 10{sup 11} M {sub ☉} galaxies at z ∼ 4 with suppressed star formation rates (SFRs), selected on rest-frame optical to near-IR colors from the FourStar Galaxy Evolution Survey (ZFOURGE). The observed spectral energy distributions show pronounced breaks, sampled by a set of near-IR medium-bandwidth filters, resulting in tightly constrained photometric redshifts. Fitting stellar population models suggests large Balmer/4000 Å breaks, relatively old stellar populations, large stellar masses, and low SFRs, with a median specific SFR of 2.9 ± 1.8 × 10{sup –11} yr{sup –1}. Ultradeep Herschel/PACS 100 μm, 160 μm and Spitzer/MIPS 24 μm data reveal no dust-obscured SFR activity for 15/19(79%) galaxies. Two far-IR detected galaxies are obscured QSOs. Stacking the far-IR undetected galaxies yields no detection, consistent with the spectral energy distribution fit, indicating independently that the average specific SFR is at least 10 × smaller than that of typical star-forming galaxies at z ∼ 4. Assuming all far-IR undetected galaxies are indeed quiescent, the volume density is 1.8 ± 0.7 × 10{sup –5} Mpc{sup –3} to a limit of log{sub 10} M/M {sub ☉} ≥ 10.6, which is 10 × and 80 × lower than at z = 2 and z = 0.1. They comprise a remarkably high fraction (∼35%) of z ∼ 4 massive galaxies, suggesting that suppression of star formation was efficient even at very high redshift. Given the average stellar age of 0.8 Gyr and stellar mass of 0.8 × 10{sup 11} M {sub ☉}, the galaxies likely started forming stars before z = 5, with SFRs well in excess of 100 M {sub ☉} yr{sup –1}, far exceeding that of similarly abundant UV-bright galaxies at z ≥ 4. This suggests that most of the star formation in the progenitors of quiescent z ∼ 4 galaxies was obscured by dust.

  20. Temporal correlation in the Goldberg variations

    OpenAIRE

    Chestopal, Victor

    2010-01-01

    An interpreter of the Goldberg Variations is almost completely deprived of such utterly important guidance as the composer's tempo markings, which are as rare in the Goldberg Variations as they are in the other works of Bach. The final goal of my study is to suggest a logical foundation, upon which an interpreter of the Goldberg Variations can make his/her choice of tempi. Upon the analysis of opus's structure, which reveals an impressive panorama of symmetries, I suggest a multilevel system ...

  1. Isozyme variation in wild and cultivated pineapple

    Science.gov (United States)

    Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

  2. Pentosan-derived water-soluble carbon nano dots with substantial fluorescence: Properties and application as a photosensitizer

    Science.gov (United States)

    Wu, Qiong; Li, Wei; Wu, Yanjiao; Huang, Zhanhua; Liu, Shouxin

    2014-10-01

    The hydrothermal carbonization of monosaccharides and polysaccharides is widely used in the production of carbonaceous material with a desired structure. However, the liquid products are regarded as waste and discarded. Here, we report a facile approach for the synthesis of water-soluble carbon nano dots (CNDs) with substantial fluorescence from the liquid by-products of the hydrothermal carbonization of pentosan, thus the by-products of pulp refining. The synthesized CNDs are monodispersed spheres with abundant oxygen-containing groups and they have an average size of 30 nm. Quantum yield measurements revealed CNDs with substantial green photoluminescence (PL) without passivation. Additionally, excitation was independent, pH-sensitive and stable. The use of CNDs as a photosensitizer in the CNDs/TiO2 system for methylene blue (MB) degradation under visible light irradiation is attractive. The spectral response range of the CNDs/TiO2 system can be widened from the UV region to a part of the visible light region (400-550 nm).

  3. Quantitative microbiome profiling links gut community variation to microbial load.

    Science.gov (United States)

    Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

    2017-11-23

    Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

  4. 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

  5. Complex researches on substantiation of construction and seismic stability of large dams in seismic region

    International Nuclear Information System (INIS)

    Negmatullaev, S.Kh.; Yasunov, P.A.

    2001-01-01

    This article is devoted to complex researches on substantiation of construction and seismic stability of large dams (Nurec hydroelectric power station) in seismic region. Geological, seismological, model, and engineering investigations are discussed in this work. At construction of Nurec hydroelectric power station the rich experience is accumulated. This experience can be used in analogous seismically active regions at construction similar hydroelectric power stations.

  6. Do substantial BMI reduction episodes among Swedish schoolchildren have any impact on their final height?

    Science.gov (United States)

    Nilsen, Bente B; Yngve, Agneta; Werner, Bo

    2018-02-06

    This study investigated whether substantial body mass index (BMI) reductions in Swedish schoolchildren aged seven years to 19 years, caused by disease, healthy or unhealthy behaviour, had any impact on their final height. We used height and weight data on 6572 subjects from two nationally representative longitudinal samples of Swedish children born in 1973 and 1981. These provided information on their final height and any BMI reduction episodes. Of the 6572 subjects (50.9% boys), among individuals with information on final height, 1118 had a BMI reduction of 5% and BMI reduction of 10% or more. On a group level, there was no statistically significant difference in the final height of individuals with BMI reductions of 10% or more and those without. The findings were independent of age and the subject's BMI at the start of the reduction episode. However, there were a number of cases where a substantial BMI reduction probably had an impact on the subject's final height. Our study found no evidence that a substantial BMI reduction had any impact on final height on a group level, but further analyses of specific case studies are necessary to determine whether substantial BMI reduction might have an impact on final height. ©2018 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  7. Substantial secondary organic aerosol formation in a coniferous forest: observations of both day- and nighttime chemistry

    OpenAIRE

    A. K. Y. Lee; J. P. D. Abbatt; W. R. Leaitch; S.-M. Li; S. J. Sjostedt; S. J. Sjostedt; J. J. B. Wentzell; J. Liggio; A. M. Macdonald

    2016-01-01

    Substantial biogenic secondary organic aerosol (BSOA) formation was investigated in a coniferous forest mountain region at Whistler, British Columbia. A largely biogenic aerosol growth episode was observed, providing a unique opportunity to investigate BSOA formation chemistry in a forested environment with limited influence from anthropogenic emissions. Positive matrix factorization of aerosol mass spectrometry (AMS) measurement identifie...

  8. 76 FR 41424 - Finding of Substantial Inadequacy of Implementation Plan; Call for Iowa State Implementation Plan...

    Science.gov (United States)

    2011-07-14

    ... modeling requirement for this SIP call should allow for the use of the modeling protocol developed by Iowa... is making a finding that the Iowa State Implementation Plan (SIP) is substantially inadequate to... ) in Muscatine County, Iowa. The specific SIP deficiencies needing revision are described below. EPA is...

  9. 77 FR 65169 - Extension of Certain Timber Sale Contracts; Finding of Substantial Overriding Public Interest

    Science.gov (United States)

    2012-10-25

    ... that are in breach, or (6) contracts when the purchaser's processing facility has not operated during... DEPARTMENT OF AGRICULTURE Forest Service Extension of Certain Timber Sale Contracts; Finding of Substantial Overriding Public Interest AGENCY: Forest Service, USDA. ACTION: Notice of contract extensions...

  10. 26 CFR 1.6662-4 - Substantial understatement of income tax.

    Science.gov (United States)

    2010-04-01

    ... arrangement does not have as its principal purpose the avoidance or evasion of Federal income tax solely as a... 26 Internal Revenue 13 2010-04-01 2010-04-01 false Substantial understatement of income tax. 1... (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Additions to the Tax, Additional Amounts, and Assessable...

  11. 75 FR 69454 - Emergency Homeowners' Loan Program: Notice of Allocation of Funding for Substantially Similar...

    Science.gov (United States)

    2010-11-12

    ... assistance and provide security for such repayment by recordation of a HUD mortgage as a junior lien on the... current first lien mortgage loan payments for which the homeowner remains responsible. IV. Submission of.... Nondiscrimination and Civil Rights Requirements States operating existing programs that provide substantially...

  12. 75 FR 27504 - Substantial Product Hazard List: Hand-Held Hair Dryers

    Science.gov (United States)

    2010-05-17

    ... immersion during their use. Section 15(a) of the CPSA defines ``substantial product hazard'' to include, a....'' Hand-held hair dryers routinely contain open-coil heating elements that are, in essence, uninsulated..., bathtub, or lavatory). The proposed rule would define ``hand-held hair dryer'' as ``an electrical...

  13. 76 FR 32215 - Agency Information Collection Activities; Proposed Collection; Comment Request; Substantiation...

    Science.gov (United States)

    2011-06-03

    ... of such disease in the United States [(U.S.)], describes the role of a nutrient or dietary ingredient... substantiation for their claims in the scientific literature. The time it takes to assemble the necessary... based on emerging science, where conducting literature searches and understanding the literature takes...

  14. Theoretical-and-Methodological Substantiation of Multilingual Model Activity in Kazakhstan Higher School Education System

    Science.gov (United States)

    Ospanova, Bikesh Revovna; Azimbayeva, Zhanat Amantayevna; Timokhina, Tatyana Vladimirovna; Seydakhmetova, Zergul Koblandiyevna

    2016-01-01

    The need of implementing the model of professional development in training an expert in the conditions of multilingualism is considered. The possibility of using the multilingual approach in the context of present day education with the use of innovative technologies of training is substantiated, the definition of "multilingual…

  15. 78 FR 889 - Finding of Substantial Inadequacy of Implementation Plan; Call for California State...

    Science.gov (United States)

    2013-01-07

    ... Resources Defense Council; and Physicians for Social Responsibility--Los Angeles, (``environmental and... ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 52 [EPA-R09-OAR-2012-0721; FRL-9767-3] Finding of Substantial Inadequacy of Implementation Plan; Call for California State Implementation Plan Revision; South...

  16. 26 CFR 1.6662-5T - Substantial and gross valuation misstatements under chapter 1 (temporary).

    Science.gov (United States)

    2010-04-01

    ..., DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Additions to the Tax, Additional... persons). (iii) Property. For purposes of this section, the term property refers to both tangible and... adjustments. For rules relating to the penalty imposed with respect to a substantial or gross valuation...

  17. 26 CFR 301.6229(c)(2)-1T - Substantial omission of income (temporary).

    Science.gov (United States)

    2010-04-01

    ....6229(c)(2)-1T Substantial omission of income (temporary). (a) Partnership return—(1) General rule. (i) If any partnership omits from the gross income stated in its return an amount properly includible... omitted from gross income if information sufficient to apprise the Commissioner of the nature and amount...

  18. 26 CFR 1.162-17 - Reporting and substantiation of certain business expenses of employees.

    Science.gov (United States)

    2010-04-01

    ... Individuals and Corporations § 1.162-17 Reporting and substantiation of certain business expenses of employees.... The term “ordinary and necessary business expenses” means only those expenses which are ordinary and..., reimbursements, or otherwise, exceeds the ordinary and necessary business expenses paid or incurred by the...

  19. 34 CFR 692.41 - What standards may a State use to determine substantial financial need?

    Science.gov (United States)

    2010-07-01

    ... PARTNERSHIP PROGRAM Leveraging Educational Assistance Partnership Program How Does A State Select Students... establishes that are approved by the Secretary. A State may define substantial financial need in terms of... “independent student” as defined under section 480(d) of the HEA. However, for good cause shown, the Secretary...

  20. Variation and Mathematics Pedagogy

    Science.gov (United States)

    Leung, Allen

    2012-01-01

    This discussion paper put forwards variation as a theme to structure mathematical experience and mathematics pedagogy. Patterns of variation from Marton's Theory of Variation are understood and developed as types of variation interaction that enhance mathematical understanding. An idea of a discernment unit comprising mutually supporting variation…

  1. 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

  2. What would happen to Superstorm Sandy under the influence of a substantially warmer Atlantic Ocean?

    Science.gov (United States)

    Lau, William K. M.; Shi, J. J.; Tao, W. K.; Kim, K. M.

    2016-01-01

    Based on ensemble numerical simulations, we find that possible responses of Sandy-like superstorms under the influence of a substantially warmer Atlantic Ocean bifurcate into two groups. In the first group, storms are similar to present-day Sandy from genesis to extratropical transition, except they are much stronger, with peak Power Destructive Index (PDI) increased by 50-80%, heavy rain by 30-50%, and maximum storm size (MSS) approximately doubled. In the second group, storms amplify substantially over the interior of the Atlantic warm pool, with peak PDI increased by 100-160%, heavy rain by 70-180%, and MSS more than tripled compared to present-day Superstorm Sandy. These storms when exiting the warm pool, recurve northeastward out to sea, subsequently interact with the developing midlatitude storm by mutual counterclockwise rotation around each other and eventually amplify into a severe Northeastern coastal storm, making landfall over the extreme northeastern regions from Maine to Nova Scotia.

  3. Technique of research of severe accidents and substantiation of safety of nuclear systems

    International Nuclear Information System (INIS)

    Ivanov, E.A.; Tchenov, S.V.

    2001-01-01

    Work is devoted to development of possible ways of solution of the problems of nuclear safety substantiation. We believe that safety in severe accidents is one of significant factors, which restrict value of nuclear industry in future power production. In connection with it we can conclude followed items: -) Substantiation of safety in severe accidents in nuclear system should be built on a deterministic way of guaranteed exception of heavy consequences; -) It is easy that this aim can be achieved by modeling in functions of common type; -) Main purpose of this work is to show that it is possible to estimate physical allowed state of system in emergency and find of trajectory of heaviest scenarios by optimization procedure; and -) In this work we have developed new method and computer code purposed for study of accident conditions of water cooled un-managed nuclear systems such as cooling ponds of spent fuel, experimental facilities etc. (authors)

  4. Substantiating the Expediency of Costs on Introduction of the System of Economic Security of Enterprise

    Directory of Open Access Journals (Sweden)

    Melikhova Tetiana O.

    2018-01-01

    Full Text Available The article substantiates expediency of introduction of the system of economic security of enterprise on the basis of money flows. The methods proposed in the long-term period stipulate the use as sources of financing: accumulated conditional economic costs, accumulated conditional gross and net money flow; and as costs: cumulative advanced costs and the advanced value of fixed assets. The article suggests methods for calculation of: gross index of conditional yield; gross conditional income of project; gross conditional profitability; gross conditional profitability of money flow. The managerial decision on introduction of the system of economic security of enterprise in the short-term production period has been substantiated on the basis of calculations of the following indicators: gross profitability of annual depreciation; annual gross economic effect; index of conditional yield of the gross money flow; differences between the conditional gross cash flow and the depreciation deductions associated with the implementation of the enterprise’s economic security system.

  5. Extremely short duration high intensity interval training substantially improves insulin action in young healthy males

    DEFF Research Database (Denmark)

    Babraj, John A; Vollaard, Niels B J; Keast, Cameron

    2009-01-01

    BACKGROUND: Traditional high volume aerobic exercise training reduces cardiovascular and metabolic disease risk but involves a substantial time commitment. Extremely low volume high-intensity interval training (HIT) has recently been demonstrated to produce improvements to aerobic function...... cycle sprints per session). Aerobic performance (250-kJ self-paced cycling time trial), and glucose, insulin and NEFA responses to a 75-g oral glucose load (oral glucose tolerance test; OGTT) were determined before and after training. RESULTS: Following 2 weeks of HIT, the area under the plasma glucose......, to substantially improve insulin action in young sedentary subjects is remarkable. This novel time-efficient training paradigm can be used as a strategy to reduce metabolic risk factors in young and middle aged sedentary populations who otherwise would not adhere to time consuming traditional aerobic exercise...

  6. Substantial Churn In Health Insurance Offerings By Small Employers, 2014-15.

    Science.gov (United States)

    Vistnes, Jessica P; Rohde, Frederick; Miller, G Edward; Cooper, Philip F

    2017-09-01

    New data for 2014-15 from the Medical Expenditure Panel Survey-Insurance Component longitudinal survey show substantial churn in insurance offers by small employers (those with fifty or fewer workers), with 14.6 percent of employers that offered insurance in 2014 having dropped it in 2015 and 5.5 percent of those that did not offer it adding coverage. Project HOPE—The People-to-People Health Foundation, Inc.

  7. Substantiation for Approaches to Treatment of Latent Autoimmune Diabetes in Adults

    Directory of Open Access Journals (Sweden)

    T.M. Tykhonova

    2014-10-01

    Conclusions. Analysis of carbohydrate metabolism on the manifestation stage and over time development of latent autoimmune diabetes in adults as well as reduction of β-cells insulin-producing function associated with autoimmune insulitis and progressing while the development of this form of disease, substantiate the rational for insulin administration as this form of diabetes has been diagnosed. If patients with latent autoimmune diabetes in adults have metabolic syndrome clusters it is quite reasonable to add metformin to insulin.

  8. Principles of geological substantiation for toxic waste disposal facilities sites selection

    International Nuclear Information System (INIS)

    Khrushchov, D. P.; Matorin, Eu. M.; Shekhunova, S. B.

    2002-01-01

    Industrial, domestic and military activities result in accumulation of toxic and hazardous waste. Disposal of these waste comprises two main approaches: technological processing (utilization and destruction) and landfill. According to concepts and programs of advanced countries technological solutions are preferable, but in fact over 70 % of waste are buried in storages, prevailingly of near surface type. The target of this paper is to present principles of geological substantiation of sites selection for toxic and hazardous waste isolation facilities location. (author)

  9. Substantial improvements not seen in health behaviors following corner store conversions in two Latino food swamps

    OpenAIRE

    Ortega, Alexander N.; Albert, Stephanie L.; Chan-Golston, Alec M.; Langellier, Brent A.; Glik, Deborah C.; Belin, Thomas R.; Garcia, Rosa Elena; Brookmeyer, Ron; Sharif, Mienah Z.; Prelip, Michael L.

    2016-01-01

    Background The effectiveness of food retail interventions is largely undetermined, yet substantial investments have been made to improve access to healthy foods in food deserts and swamps via grocery and corner store interventions. This study evaluated the effects of corner store conversions in East Los Angeles and Boyle Heights, California on perceived accessibility of healthy foods, perceptions of corner stores, store patronage, food purchasing, and eating behaviors. Methods Household data ...

  10. A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes

    OpenAIRE

    Mayr, Gerald; Scofield, R. Paul; De Pietri, Vanesa L.; Tennyson, Alan J. D.

    2017-01-01

    One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the ne...

  11. Confidence Intervals: From tests of statistical significance to confidence intervals, range hypotheses and substantial effects

    Directory of Open Access Journals (Sweden)

    Dominic Beaulieu-Prévost

    2006-03-01

    Full Text Available For the last 50 years of research in quantitative social sciences, the empirical evaluation of scientific hypotheses has been based on the rejection or not of the null hypothesis. However, more than 300 articles demonstrated that this method was problematic. In summary, null hypothesis testing (NHT is unfalsifiable, its results depend directly on sample size and the null hypothesis is both improbable and not plausible. Consequently, alternatives to NHT such as confidence intervals (CI and measures of effect size are starting to be used in scientific publications. The purpose of this article is, first, to provide the conceptual tools necessary to implement an approach based on confidence intervals, and second, to briefly demonstrate why such an approach is an interesting alternative to an approach based on NHT. As demonstrated in the article, the proposed CI approach avoids most problems related to a NHT approach and can often improve the scientific and contextual relevance of the statistical interpretations by testing range hypotheses instead of a point hypothesis and by defining the minimal value of a substantial effect. The main advantage of such a CI approach is that it replaces the notion of statistical power by an easily interpretable three-value logic (probable presence of a substantial effect, probable absence of a substantial effect and probabilistic undetermination. The demonstration includes a complete example.

  12. Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission.

    Directory of Open Access Journals (Sweden)

    Veerayuth Kittichai

    2017-10-01

    Full Text Available Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country.A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi and one eastern province (Ubon Ratchathani of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins.Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination.

  13. Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission.

    Science.gov (United States)

    Kittichai, Veerayuth; Koepfli, Cristian; Nguitragool, Wang; Sattabongkot, Jetsumon; Cui, Liwang

    2017-10-01

    Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins. Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination.

  14. TECHNICAL AND ECONOMIC SUBSTANTIATION OF PROJECTS OF THE AFFORDABLE HOUSING CONSTRUCTION

    Directory of Open Access Journals (Sweden)

    KRAVCHUNOVSKA T. S.

    2015-12-01

    Full Text Available Summary. Problem statement. The development of inhabitant locality of Ukraine is characterized by significant differences in levels of socio and economic development. An excessive concentration of population and industry in large cities, inefficient, slow development of most medium and small cities, towns and villages, considerable territorial disproportions of economic development of the country, considerable shortcomings in the territorial organization of society are observed. At the same time the tendency of the total area of increasing of inhabitant locality. The lands are used inefficiently. Among the most common problems of inhabitant locality is the housing problem. When making a decision on the design of affordable housing construction is one of the most important stages in the development of the technique and economic substantiation of the project is determination of the advisability and effectiveness of construction. The substantiation of advisability and effectiveness of affordable housing based on the definition of technical and economic indicators of projects, one of the most important among them is the cost, in its calculation is necessary to take into account the influence of organizational and technological factors, reflecting the features of construction in condition of compacted construction. Purpose. Development of methodical recommendations on substantiation of cost construction of affordable housing in the conditions of compacted construction. Conclusion. To provide a processing and the analysis of data is necessary development of the applied software on the basis of the developed block scheme of justification of cost construction of affordable housing.

  15. Introductory biology students' conceptual models and explanations of the origin of variation.

    Science.gov (United States)

    Speth, Elena Bray; Shaw, Neil; Momsen, Jennifer; Reinagel, Adam; Le, Paul; Taqieddin, Ranya; Long, Tammy

    2014-01-01

    Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers' models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students' written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback. © 2014 E. Bray Speth et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  16. Overestimated lead times in cancer screening has led to substantial underestimation of overdiagnosis

    DEFF Research Database (Denmark)

    Zahl, P-H; Juhl Jørgensen, Karsten; Gøtzsche, P C

    2013-01-01

    Published lead time estimates in breast cancer screening vary from 1 to 7 years and the percentages of overdiagnosis vary from 0 to 75%. The differences are usually explained as random variations. We study how much can be explained by using different definitions and methods.......Published lead time estimates in breast cancer screening vary from 1 to 7 years and the percentages of overdiagnosis vary from 0 to 75%. The differences are usually explained as random variations. We study how much can be explained by using different definitions and methods....

  17. Calculus of variations

    CERN Document Server

    Elsgolc, Lev D

    2007-01-01

    This concise text offers both professionals and students an introduction to the fundamentals and standard methods of the calculus of variations. In addition to surveys of problems with fixed and movable boundaries, it explores highly practical direct methods for the solution of variational problems.Topics include the method of variation in problems with fixed boundaries; variational problems with movable boundaries and other problems; sufficiency conditions for an extremum; variational problems of constrained extrema; and direct methods of solving variational problems. Each chapter features nu

  18. RELIGIOUS DEMOCRATIZATION IN INDONESIA: STRENGTHENING THE PRO-CEDURAL AND SUBSTANTIAL RELIGIOUS DEMOCRACY

    Directory of Open Access Journals (Sweden)

    Eka Hendry AR.

    2013-06-01

    Full Text Available Inspired by the book of Michael Mann about the dark side of democracy that discusses the paradox between the ideality of democratic values and empirical realities of violence in the name of freedom (democracy, this paper begins with the exposure of the paradox, such as the rise of the violent conflict between groups of people (both ethnic and religious-based and the high prevalence of violence between religious groups in Indonesia. Even worse, a very wrenching violence involves state actors (rulers. This paper tries to understand the roots of the paradox, with a look at how the relationship between state and religion and the religious community trend of Indonesia (especially Muslims. The author argues that the democratization of religion is a solution to the issues. To answer what kind of religious democracy lives in Indonesia, the author analyzes through a religious procedural (or constitutional democratic dimension and religious substantial democratic dimension. The phenomenon of disobedience of law and system and the euphoria of law-making that reflects “intolerance” in several places in Indonesia display the fundamental issue in the religious procedural democracy. Whereas in the context of religious substantial democracy, the prevailing trend of religion that serves as a political and economic vehicle and ignores religion as a substantial aspect of the behavior of the Indonesian society has resulted in the marginalization of religious position and function. Then, the infiltration of the model of political Islam has also led to alienation of the character of the Islamic society of Indonesia, from a democratic pattern to a revival (radical one. In this light, the author needs to present a strategy to encourage religious democracy in Indonesia, structurally through formulating the ideal relation model between state and religion and culturally through a substantial pattern of religion embedded with the character of Indonesian religious

  19. 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...

  20. Bilateral renal artery variation

    OpenAIRE

    Üçerler, Hülya; Üzüm, Yusuf; İkiz, Z. Aslı Aktan

    2014-01-01

    Each kidney is supplied by a single renal artery, although renal artery variations are common. Variations of the renal arteryhave become important with the increasing number of renal transplantations. Numerous studies describe variations in renalartery anatomy. Especially the left renal artery is among the most critical arterial variations, because it is the referred side forresecting the donor kidney. During routine dissection in a formalin fixed male cadaver, we have found a bilateral renal...

  1. Genetics and variation

    Science.gov (United States)

    John R. Jones; Norbert V. DeByle

    1985-01-01

    The broad genotypic variability in quaking aspen (Populus tremuloides Michx.), that results in equally broad phenotypic variability among clones is important to the ecology and management of this species. This chapter considers principles of aspen genetics and variation, variation in aspen over its range, and local variation among clones. For a more...

  2. Studying Variation in Tunes

    NARCIS (Netherlands)

    Janssen, B.; van Kranenburg, P.

    2014-01-01

    Variation in music can be caused by different phenomena: conscious, creative manipulation of musical ideas; but also unconscious variation during music recall. It is the latter phenomenon that we wish to study: variation which occurs in oral transmission, in which a melody is taught without the help

  3. Substantiated childhood maltreatment and young adulthood cannabis use disorders: A pre-birth cohort study.

    Science.gov (United States)

    Abajobir, Amanuel Alemu; Najman, Jake Moses; Williams, Gail; Strathearn, Lane; Clavarino, Alexandra; Kisely, Steve

    2017-10-01

    This study investigates the association between exposure to prospectively-substantiated childhood maltreatment between 0 and 14 years of age and lifetime cannabis use, abuse and dependence reported at 21 years. Data were taken from 2526 (51.6% female) participants in the Mater Hospital-University of Queensland Study of Pregnancy, a pre-birth, prospective, cohort study. Prospectively-substantiated cases of childhood maltreatment, reported to the government child protection agencies between 0 and 14 years of age, were linked to CIDI DSM-IV self-report data from the 21-year follow-up. Exposure to any childhood maltreatment, and childhood neglect in particular, predicted subsequent cannabis abuse with adjusted odds ratios (AORs) of 1.79 and 2.62, respectively. Any childhood maltreatment, physical abuse, emotional abuse and neglect predicted cannabis dependence with AORs of 2.47, 2.81, 2.44 and 2.68, respectively. The associations for an early age of onset of cannabis abuse and dependence were significant and consistent for maltreated children. In addition, frequency of maltreatment substantiations predicted cannabis abuse, dependence and an early age of onset of these disorders. The AORs for cannabis ever use without any DSM-IV cannabis disorder were 1.78 for any maltreatment and 2.15 for emotional abuse. Any childhood maltreatment and neglect predicted lifetime ever cannabis use, as well as cannabis use disorder. There was little evidence for any interaction between gender and different forms of childhood maltreatment and its association with cannabis use disorders. Physical abuse, emotional abuse and neglect, as well as multiple episodes of maltreatment independently predicted cannabis use disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

    Directory of Open Access Journals (Sweden)

    Melanie G Mayer

    2015-06-01

    Full Text Available Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as

  5. To what extent can isotopes help substantiate natural attenuation of chlorinated ethenes?

    DEFF Research Database (Denmark)

    Badin, A.; Broholm, Mette Martina; Hunkeler, D.

    to which isotopes could help substantiate natural attenuation of chlorinated ethenes at the field scale. Our work hence aims at exploring the latter based on data acquired in 2006 in a site located in Denmark which is contaminated with PCE and its end-products TCE, cDCE, and VC. Previous work on this site...... has enabled to demonstrate that PCE and TCE were undergoing reductive dechlorination while cDCE would be at least partially degraded through reductive dechlorination1. However, the magnitude of the contaminants attenuation by biodegradation was not evaluated. Based on simple modeling including...

  6. Method for the substantial reduction of quenching effects in luminescence spectrometry

    Science.gov (United States)

    Demas, J.N.; Jones, W.M.; Keller, R.A.

    1987-06-26

    Method for reducing quenching effects in analytical luminescence measurements. Two embodiments of the present invention are described which relate to a form of time resolution based on the amplitudes and phase shifts of modulated emission signals. In the first embodiment, the measured modulated emission signal is substantially independent of sample quenching at sufficiently high frequencies. In the second embodiment, the modulated amplitude and the phase shift between the emission signal and the excitation source are simultaneously measured. Using either method, the observed modulated amplitude may be reduced to its unquenched value. 3 figs.

  7. Substantiation of vibration strength of nuclear reactor and steam generator internals. Main problems

    International Nuclear Information System (INIS)

    Fyodorov, V.G.; Sinyavasky, V.F.

    1977-01-01

    The report details the scope and priority of studies necessary for substantiation of vibration strength of steam generator tube bundles and reactor fuel assemblies, and design modifications helping to reduce flow-induced vibration of the internals specified. Steam generator tube bundles are studied on the basis of a standard establishing vibration requirements at various stages of design, manufacture and operation of a steam generator at a nuclear power station. The main vibration characteristics of tubes obtained through model and full-scale tests are compared with calculation results. Results are provided concerning test-stand vibration tests of fuel elements and fuel assemblies. (author)

  8. Further substantial improvement of interventional diagnosis and treatment via portal vein system

    International Nuclear Information System (INIS)

    Yang Weizhu; Chen Yongde

    2006-01-01

    Along with the development of interventional appliances and proficiency of operational skills, the interventional diagnosis and treatment via hepatic portal vein system have achieved great progress and improvement. However, in order to further exploit the advantages of interventional diagnosis and treatment, the review of the anatomical structures, normal aberrance of portal venous system were needed. Getting familiar with pathologic condition to discover the new interventional appliances and embolic agents, and then in term of conduct the research on a very tough substantial base in a down-to-earth manner were important. (authors)

  9. Patterns of DNA barcode variation in Canadian marine molluscs.

    Science.gov (United States)

    Layton, Kara K S; Martel, André L; Hebert, Paul D N

    2014-01-01

    Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

  10. Multimodal exercise training in multiple sclerosis: A randomized controlled trial in persons with substantial mobility disability.

    Science.gov (United States)

    Sandroff, Brian M; Bollaert, Rachel E; Pilutti, Lara A; Peterson, Melissa L; Baynard, Tracy; Fernhall, Bo; McAuley, Edward; Motl, Robert W

    2017-10-01

    Mobility disability is a common, debilitating feature of multiple sclerosis (MS). Exercise training has been identified as an approach to improve MS-related mobility disability. However, exercise randomized controlled trials (RCTs) on mobility in MS have generally not selectively targeted those with the onset of irreversible mobility disability. The current multi-site RCT compared the efficacy of 6-months of supervised, multimodal exercise training with an active control condition for improving mobility, gait, physical fitness, and cognitive outcomes in persons with substantial MS-related mobility disability. 83 participants with substantial MS-related mobility disability underwent initial mobility, gait, fitness, and cognitive processing speed assessments and were randomly assigned to 6-months of supervised multimodal (progressive aerobic, resistance, and balance) exercise training (intervention condition) or stretching-and-toning activities (control condition). Participants completed the same outcome assessments halfway through and immediately following the 6-month study period. There were statistically significant improvements in six-minute walk performance (F(2158)=3.12, p=0.05, η p 2 =0.04), peak power output (F(2150)=8.16, pmobility disability. This is critical for informing the development of multi-site exercise rehabilitation programs in larger samples of persons with MS-related mobility disability. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Substantiating the Target Level of Economic Security of Transport Enterprises and the Instrumentarium for Its Provision

    Directory of Open Access Journals (Sweden)

    Lebedko Sergiy A.

    2017-10-01

    Full Text Available The article is aimed at substantiating the methodology for assessing the economic security of transport enterprises, determining the target level and the instrumentarium for its provision. The proposed methodical approach to the assessment of the level of economic security of transport enterprises includes the determination of the level of counteracting threats and is based on the principles of integral estimation. The formed integrated indicator includes both indicators of counteracting the internal (human, managerial and technological, force majeure, financial and external threats (market, stakeholder, power-based, natural, infrastructural. Each measure of counteracting threats is determined by results of assessment of dynamics of the three indicators. A practical testing of the proposed approach is carried out in the case of transport enterprises. Based on the established equation of the regression relationship between the level of economic security and the financial strength, a target level of economic security of transport enterprises has been substantiated. The instrumentarium to provide a targeted level of economic security according to the threat types, including preventive and reactive measures, has been developed.

  12. Predicting risk of substantial weight gain in German adults-a multi-center cohort approach.

    Science.gov (United States)

    Bachlechner, Ursula; Boeing, Heiner; Haftenberger, Marjolein; Schienkiewitz, Anja; Scheidt-Nave, Christa; Vogt, Susanne; Thorand, Barbara; Peters, Annette; Schipf, Sabine; Ittermann, Till; Völzke, Henry; Nöthlings, Ute; Neamat-Allah, Jasmine; Greiser, Karin-Halina; Kaaks, Rudolf; Steffen, Annika

    2017-08-01

    A risk-targeted prevention strategy may efficiently utilize limited resources available for prevention of overweight and obesity. Likewise, more efficient intervention trials could be designed if selection of subjects was based on risk. The aim of the study was to develop a risk score predicting substantial weight gain among German adults. We developed the risk score using information on 15 socio-demographic, dietary and lifestyle factors from 32 204 participants of five population-based German cohort studies. Substantial weight gain was defined as gaining ≥10% of weight between baseline and follow-up (>6 years apart). The cases were censored according to the theoretical point in time when the threshold of 10% baseline-based weight gain was crossed assuming linearity of weight gain. Beta coefficients derived from proportional hazards regression were used as weights to compute the risk score as a linear combination of the predictors. Cross-validation was used to evaluate the score's discriminatory accuracy. The cross-validated c index (95% CI) was 0.71 (0.67-0.75). A cutoff value of ≥475 score points yielded a sensitivity of 71% and a specificity of 63%. The corresponding positive and negative predictive values were 10.4% and 97.6%, respectively. The proposed risk score may support healthcare providers in decision making and referral and facilitate an efficient selection of subjects into intervention trials. © The Author 2016. Published by Oxford University Press on behalf of the European Public Health Association.

  13. Predicting risk of substantial weight gain in German adults—a multi-center cohort approach

    Science.gov (United States)

    Bachlechner, Ursula; Boeing, Heiner; Haftenberger, Marjolein; Schienkiewitz, Anja; Scheidt-Nave, Christa; Vogt, Susanne; Thorand, Barbara; Peters, Annette; Schipf, Sabine; Ittermann, Till; Völzke, Henry; Nöthlings, Ute; Neamat-Allah, Jasmine; Greiser, Karin-Halina; Kaaks, Rudolf

    2017-01-01

    Abstract Background A risk-targeted prevention strategy may efficiently utilize limited resources available for prevention of overweight and obesity. Likewise, more efficient intervention trials could be designed if selection of subjects was based on risk. The aim of the study was to develop a risk score predicting substantial weight gain among German adults. Methods We developed the risk score using information on 15 socio-demographic, dietary and lifestyle factors from 32 204 participants of five population-based German cohort studies. Substantial weight gain was defined as gaining ≥10% of weight between baseline and follow-up (>6 years apart). The cases were censored according to the theoretical point in time when the threshold of 10% baseline-based weight gain was crossed assuming linearity of weight gain. Beta coefficients derived from proportional hazards regression were used as weights to compute the risk score as a linear combination of the predictors. Cross-validation was used to evaluate the score’s discriminatory accuracy. Results The cross-validated c index (95% CI) was 0.71 (0.67–0.75). A cutoff value of ≥475 score points yielded a sensitivity of 71% and a specificity of 63%. The corresponding positive and negative predictive values were 10.4% and 97.6%, respectively. Conclusions The proposed risk score may support healthcare providers in decision making and referral and facilitate an efficient selection of subjects into intervention trials. PMID:28013243

  14. Pharmaceutical manufacturing facility discharges can substantially increase the pharmaceutical load to U.S. wastewaters

    Science.gov (United States)

    Scott, Tia-Marie; Phillips, Patrick J.; Kolpin, Dana W.; Colella, Kaitlyn M.; Furlong, Edward T.; Foreman, William T.; Gray, James L.

    2018-01-01

    Discharges from pharmaceutical manufacturing facilities (PMFs) previously have been identified as important sources of pharmaceuticals to the environment. Yet few studies are available to establish the influence of PMFs on the pharmaceutical source contribution to wastewater treatment plants (WWTPs) and waterways at the national scale. Consequently, a national network of 13 WWTPs receiving PMF discharges, six WWTPs with no PMF input, and one WWTP that transitioned through a PMF closure were selected from across the United States to assess the influence of PMF inputs on pharmaceutical loading to WWTPs. Effluent samples were analyzed for 120 pharmaceuticals and pharmaceutical degradates. Of these, 33 pharmaceuticals had concentrations substantially higher in PMF-influenced effluent (maximum 555,000 ng/L) compared to effluent from control sites (maximum 175 ng/L). Concentrations in WWTP receiving PMF input are variable, as discharges from PMFs are episodic, indicating that production activities can vary substantially over relatively short (several months) periods and have the potential to rapidly transition to other pharmaceutical products. Results show that PMFs are an important, national-scale source of pharmaceuticals to the environment.

  15. Videolaryngoscopes differ substantially in illumination of the oral cavity: A manikin study

    Directory of Open Access Journals (Sweden)

    Barbe MA Pieters

    2016-01-01

    Full Text Available Background and Aims: Insufficient illumination of the oral cavity during endotracheal intubation may result in suboptimal conditions. Consequently, suboptimal illumination and laryngoscopy may lead to potential unwanted trauma to soft tissues of the pharyngeal mucosa. We investigated illumination of the oral cavity by different videolaryngoscopes (VLS in a manikin model. Methods: We measured light intensity from the mouth opening of a Laerdal intubation trainer comparing different direct and indirect VLS at three occasions, resembling optimal to less-than-optimal intubation conditions; at the photographer′s dark room, in an operating theatre and outdoors in bright sunlight. Results: Substantial differences in luminance were detected between VLS. The use of LED light significantly improved light production. All VLS produced substantial higher luminance values in a well-luminated environment compared to the dark photographer′s room. The experiments outside-in bright sunlight-were interfered with by direct sunlight penetration through the synthetic material of the manikin, making correct measurement of luminance in the oropharynx invalid. Conclusion: Illumination of the oral cavity differs widely among direct and indirect VLS. The clinician should be aware of the possibility of suboptimal illumination of the oral cavity and the potential risk this poses for the patient.

  16. Substantial Mortality of Cabbage Looper (Lepidoptera: Noctuidae) From Predators in Urban Agriculture Is not Influenced by Scale of Production or Variation in Local and Landscape-Level Factors.

    Science.gov (United States)

    Lowenstein, David M; Gharehaghaji, Maryam; Wise, David H

    2017-02-01

    As Midwestern (United States) cities experience population decline, there is growing interest in converting underutilized vacant spaces to agricultural production. Urban agriculture varies in area and scope, yet most growers use similar cultivation practices such as avoiding chemical control of crop pests. For community gardens and farms that sell produce commercially, effective pest suppression by natural enemies is important for both societal, economic, and marketing reasons. To gauge the amount of prey suppression at 28 urban food-production sites, we measured removal of sentinel eggs and larvae of the cabbage looper Trichoplusia ni (Hubner), a caterpillar pest that defoliates Brassica. We investigated how landscape and local factors, such as scale of production, influence cabbage looper mortality caused by predators. Predators removed 50% of eggs and 25% of larvae over a 3-d period. Landscape factors did not predict mortality rates, and the amount of loss and damage to sentinel prey were similar across sites that differed in scale (residential gardens, community gardens, and farms). To confirm that removal of sentinel items was likely caused by natural enemies, we set up a laboratory assay that measured predation of cabbage looper eggs and larvae by several predators occurring in urban gardens. Lady beetles caused the highest mortality rates, suggesting their potential value for biocontrol; spiders and pirate bugs also consumed both eggs and larvae at high rates. Our results suggest that urban growers benefit from high consumption rates of cabbage looper eggs and larvae by arthropod predators. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. A substantial and confusing variation exists in handling of baseline covariates in randomized controlled trials: a review of trials published in leading medical journals.

    Science.gov (United States)

    Austin, Peter C; Manca, Andrea; Zwarenstein, Merrick; Juurlink, David N; Stanbrook, Matthew B

    2010-02-01

    Statisticians have criticized the use of significance testing to compare the distribution of baseline covariates between treatment groups in randomized controlled trials (RCTs). Furthermore, some have advocated for the use of regression adjustment to estimate the effect of treatment after adjusting for potential imbalances in prognostically important baseline covariates between treatment groups. We examined 114 RCTs published in the New England Journal of Medicine, the Journal of the American Medical Association, The Lancet, and the British Medical Journal between January 1, 2007 and June 30, 2007. Significance testing was used to compare baseline characteristics between treatment arms in 38% of the studies. The practice was very rare in British journals and more common in the U.S. journals. In 29% of the studies, the primary outcome was continuous, whereas in 65% of the studies, the primary outcome was either dichotomous or time-to-event in nature. Adjustment for baseline covariates was reported when estimating the treatment effect in 34% of the studies. Our findings suggest the need for greater editorial consistency across journals in the reporting of RCTs. Furthermore, there is a need for greater debate about the relative merits of unadjusted vs. adjusted estimates of treatment effect. Copyright 2010 Elsevier Inc. All rights reserved.

  18. Characterizations of the diurnal shapes of OI 630.0 nm dayglow intensity variations: inferences

    Directory of Open Access Journals (Sweden)

    D. Chakrabarty

    2002-11-01

    Full Text Available Measurements of OI 630.0 nm thermospheric dayglow emission by means of the Dayglow Photometer (DGP at Mt. Abu (24.6° N, 73.7° E, dip lat 19.09° N, a station under the crest of Equatorial Ionization Anomaly (EIA, reveal day-to-day changes in the shapes of the diurnal profiles of dayglow intensity variations. These shapes have been characterized using the magnetometer data from equatorial and low-latitude stations. Substantial changes have been noticed in the shapes of the dayglow intensity variations between 10:00–15:00 IST (Indian Standard Time during the days when normal and counter electrojet events are present over the equator. It is found that the width (the time span corresponding to 0.8 times the maximum dayglow intensity of the diurnal profile has a linear relationship with the integrated electrojet strength. Occasional deviation from this linear relationship is attributed to the presence of substantial mean meridional wind.Key words. Ionosphere (equatorial ionosphere; ionosphere – atmosphere interactions; ionospheric disturbances

  19. Characterizations of the diurnal shapes of OI 630.0 nm dayglow intensity variations: inferences

    Directory of Open Access Journals (Sweden)

    D. Chakrabarty

    Full Text Available Measurements of OI 630.0 nm thermospheric dayglow emission by means of the Dayglow Photometer (DGP at Mt. Abu (24.6° N, 73.7° E, dip lat 19.09° N, a station under the crest of Equatorial Ionization Anomaly (EIA, reveal day-to-day changes in the shapes of the diurnal profiles of dayglow intensity variations. These shapes have been characterized using the magnetometer data from equatorial and low-latitude stations. Substantial changes have been noticed in the shapes of the dayglow intensity variations between 10:00–15:00 IST (Indian Standard Time during the days when normal and counter electrojet events are present over the equator. It is found that the width (the time span corresponding to 0.8 times the maximum dayglow intensity of the diurnal profile has a linear relationship with the integrated electrojet strength. Occasional deviation from this linear relationship is attributed to the presence of substantial mean meridional wind.

    Key words. Ionosphere (equatorial ionosphere; ionosphere – atmosphere interactions; ionospheric disturbances

  20. Carbon-coated boron using low-cost naphthalene for substantial enhancement of Jc in MgB2 superconductor

    Energy Technology Data Exchange (ETDEWEB)

    Ranot, Mahipal; Shinde, K. P.; Oh, Y. S.; Kang, S. H.; Jang, S. H.; Hwang, D. Y.; Chung, K. C. [Korea Institute of Materials Science, Changwon (Korea, Republic of)

    2017-09-15

    Carbon coating approach is used to prepare carbon-doped MgB{sub 2} bulk samples using low-cost naphthalene (C{sub 10}H{sub 8}) as a carbon source. The coating of carbon (C) on boron (B) powders was achieved by direct pyrolysis of naphthalene at 120 degrees C and then the C-coated B powders were mixed well with appropriate amount of Mg by solid state reaction method. X-ray diffraction analysis revealed that there is a noticeable shift in (100) and (110) Bragg reflections towards higher angles, while no shift was observed in (002) reflections for MgB2 doped with carbon. As compared to un-doped MgB{sub 2}, a systematic enhancement in Jc(H) properties with increasing carbon doping level was observed for naphthalene-derived C-doped MgB{sub 2} samples. The substantial enhancement in Jc is most likely due to the incorporation of C into MgB{sub 2} lattice and the reduction in crystallite size, as evidenced by the increase in the FWHM values for doped samples.

  1. Solar cycle variations in IMF intensity

    International Nuclear Information System (INIS)

    King, J.H.

    1979-01-01

    Annual averages of logarithms of hourly interplanetary magnetic field (IMF) intensities, obtained from geocentric spacecraft between November 1963 and December 1977, reveal the following solar cycle variation. For 2--3 years at each solar minimum period, the IMF intensity is depressed by 10--15% relative to its mean value realized during a broad 9-year period contered at solar maximum. No systematic variations occur during this 9-year period. The solar minimum decrease, although small in relation to variations in some other solar wind parameters, is both statistically and physically significant

  2. On polar daily geomagnetic variation

    Directory of Open Access Journals (Sweden)

    Paola De Michelis

    2015-11-01

    Full Text Available The aim of this work is to investigate the nature of the daily magnetic field perturbations produced by ionospheric and magnetospheric currents at high latitudes. We analyse the hourly means of the X and Y geomagnetic field components recorded by a meridian chain of permanent geomagnetic observatories in the polar region of the Northern Hemisphere during a period of four years (1995-1998 around the solar minimum. We apply a mathematical method, known as natural orthogonal component (NOC, which is capable of characterizing the dominant modes of the geomagnetic field daily variability through a set of empirical orthogonal functions (EOFs. Using the first two modes we reconstruct a two-dimensional equivalent current representation of the ionospheric electric currents, which contribute substantially to the geomagnetic daily variations. The obtained current structures resemble the equivalent current patterns of DP2 and DP1. We characterize these currents by studying their evolution with the geomagnetic activity level and by analysing their dependence on the interplanetary magnetic field. The obtained results support the idea of a coexistence of two main processes during all analysed period although one of them, the directly driven process, represents the dominant component of the geomagnetic daily variation.

  3. Substantial variability in postoperative treatment, and convalescence recommendations following vaginal repair. A nationwide questionnaire study

    DEFF Research Database (Denmark)

    Ottesen, Marianne; Møller, Charlotte; Kehlet, H

    2001-01-01

    -employed gynecologists, and gynecologists in private practice, to patients undergoing vaginal repair. METHOD: In 1999 all Danish gynecologists (n=433) received a tested questionnaire about postoperative treatment and convalescence recommendations following vaginal repair. Non-responders received one reminder. OUTCOME...... MEASURES: Pre and postoperative treatment, and expected hospital stay. Furthermore, lifting restrictions, sick leave, and convalescence before resumption of defined activities. RESULTS: The overall response rate was 82%. The expected postoperative hospital stay was median 3 days (range, 1-7) following...... anterior repair, and 2 days (range, 1-7) following posterior repair. The recommended sick leave was median 6 weeks (range, 2-12) for patients with work with heavy lifts. There were substantial differences in recommendations. Recommended lifting restrictions were median 3 kg (range, 0-20) for median 4 weeks...

  4. Recommendations for successful substantiation of new health claims in the European Union

    DEFF Research Database (Denmark)

    Pravst, Igor; Kušar, Anita; Žmitek, Katja

    2018-01-01

    Background While functional foods offer promise for public health and innovation in the food industry, the efficiency of such foods should be assured to protect consumers from misleading claims. Globally, many countries regulate the communication of the health effects of such foods to final...... consumers. Scope and approach In the European Union (EU), the use of health claims was harmonized in 2006. All claims need to be scientifically assessed by the European Food Safety Authority (EFSA) and pre-approved. Implementing the regulation has involved a steep learning curve for stakeholders, resulting...... recommendations should be seen as a starting point for researchers in the area of nutrition and food technology, and for those dealing with functional foods, including the food industry. Keywords Functional foods; Health claims; Food labelling; Substantiation; Regulation; European Union...

  5. Challenges in Archiving and Sharing Video Data: Considering Moral, Pragmatic, and Substantial Arguments

    Directory of Open Access Journals (Sweden)

    Terhi Kirsi Korkiakangas

    2014-05-01

    Full Text Available Social science researchers are facing new challenges in data archiving and sharing. The challenges encountered for video data are different from those encountered for other types of qualitative data. I will consider these challenges with respect to the moral, pragmatic, and substantial arguments with which funding bodies justify data archiving and sharing. Throughout the article, I will draw on a recent Economic and Social Research Council funded project, “Transient Teams in the Operating Theatre,” in which our research team video recorded work activities in the operating theatre of a UK hospital, thereby dealing with highly sensitive footage. I will consider how video data, on most occasions, cannot be archived for re-use by the wider research community, but how new avenues could be developed so as to benefit from further research on such “unarchivable” datasets.

  6. Experimental and calculating substantiation of reactivity balance and energy-release distribution in BN-600 core

    International Nuclear Information System (INIS)

    Moiseev, A.V.; Khomyakov, Yu.S.; Surov, S.V.

    2013-01-01

    This paper presents the results of experimental and theoretical work done in 2003-2010 years on substantiation of neutron-physical characteristics of the BN-600 core. 1. Transition to the new core 01M2 with high burnup 11.2% h.a. (the 4-th upgrade of the BN-600 core). Transfer was made without changing the constructive of the core almost by reducing conservatism of design decisions. 2. The end of BN-600 design life cycle and extending it to 10-15 years. Need for analysis and comprehension of the BN-600 experience. 3. Development and introduction of new methods of analysis (precision method of Monte Carlo). 4. In the experiments was a change of equipment and measurement techniques

  7. Substantially Enhancing Quantum Coherence of Electrons in Graphene via Electron-Plasmon Coupling.

    Science.gov (United States)

    Cheng, Guanghui; Qin, Wei; Lin, Meng-Hsien; Wei, Laiming; Fan, Xiaodong; Zhang, Huayang; Gwo, Shangjr; Zeng, Changgan; Hou, J G; Zhang, Zhenyu

    2017-10-13

    The interplays between different quasiparticles in solids lay the foundation for a wide spectrum of intriguing quantum effects, yet how the collective plasmon excitations affect the quantum transport of electrons remains largely unexplored. Here we provide the first demonstration that when the electron-plasmon coupling is introduced, the quantum coherence of electrons in graphene is substantially enhanced with the quantum coherence length almost tripled. We further develop a microscopic model to interpret the striking observations, emphasizing the vital role of the graphene plasmons in suppressing electron-electron dephasing. The novel and transformative concept of plasmon-enhanced quantum coherence sheds new insight into interquasiparticle interactions, and further extends a new dimension to exploit nontrivial quantum phenomena and devices in solid systems.

  8. An unknown oxidative metabolism substantially contributes to soil CO2 emissions

    Directory of Open Access Journals (Sweden)

    T. Shahzad

    2013-02-01

    Full Text Available The respiratory release of CO2 from soils is a major determinant of the global carbon cycle. It is traditionally considered that this respiration is an intracellular metabolism consisting of complex biochemical reactions carried out by numerous enzymes and co-factors. Here we show that the endoenzymes released from dead organisms are stabilised in soils and have access to suitable substrates and co-factors to permit function. These enzymes reconstitute an extracellular oxidative metabolism (EXOMET that may substantially contribute to soil respiration (16 to 48% of CO2 released from soils in the present study. EXOMET and respiration from living organisms should be considered separately when studying effects of environmental factors on the C cycle because EXOMET shows specific properties such as resistance to high temperature and toxic compounds.

  9. Substantiation of basic scheme of grain cleaning machine for preparation of agricultural crops seeds

    Science.gov (United States)

    Giyevskiy, A. M.; Orobinsky, V. I.; Tarasenko, A. P.; Chernyshov, A. V.; Kurilov, D. O.

    2018-03-01

    The article presents data on the feasibility of the concept of a high-efficiency seed cleaner with the consistent use of the air flow in aspiration and the multi-tier placement of the sorting grids in grating mills. As a result of modeling, the directions for further improvement of air-screen seed cleaning machines have been identified: an increase in the proportion of sorting grids in the mills up to 70 ... 80% and an increase in the speed of the air flow in the channel of the pre-filter cleaning up to 8.0 m / s. Experiments have established the competence of using mathematical modeling of airflow in the pneumatic system with the use of a finite-volume method for solving hydrodynamic equations for substantiating the basic parameters of the pneumatic system.

  10. Substantial and sustained seizure reduction with ketogenic diet in a patient with Ohtahara syndrome

    Directory of Open Access Journals (Sweden)

    Adithya Sivaraju

    2015-01-01

    Full Text Available Ketogenic diet has been shown to be efficacious in some epileptic encephalopathies but rarely reported as being useful in children with Ohtahara syndrome. This could possibly be attributed to the rarity of the disease and associated short survival period. We report on a 5-year-old child with Ohtahara syndrome, whose seizures failed to improve with all known medications, continued to show persistent suppression-burst pattern on the electroencephalography (EEG and had substantial reduction in seizure frequency for one year post-initiation of ketogenic diet. He has not had a single visit to the emergency room because of seizures in the last one year, and more importantly, there has been a clear improvement noted in his level of interaction and temperament. Patients with Ohtahara syndrome invariably have medically intractable seizures and catastrophic neurodevelopmental outcome. Ketogenic diet is a treatment modality that might be worth considering even in this group of patients.

  11. Experimental substantiation of methodic of 11-13 years old boxers’ coordination development

    Directory of Open Access Journals (Sweden)

    Yong Qiang Liu

    2015-06-01

    Full Text Available Purpose: experimental substantiation of methodic of junior boxers’ coordination training. Material: in the research 18 boxers of 11-13 year old age participated. In total, during 4 months 42 trainings were conducted. Total time of coordination load’s fulfillment at each training was 15-45 minutes. Results: dynamic of results in control tests was statistically confident in the tested parameters of movements. It proves effectiveness of usage the tasks with complex-coordination orientation, accented on impact on sensor-informational and motor systems of movements in junior boxers’ trainings. Conclusions: coordination training in boxing at initial stage shall include specialized varied means and methods, which would facilitate formation of motor condition and skills’ basis. Motor condition and skills are a reserve for further rising of coordination abilities’ level of junior sportsmen.

  12. Technique of Substantiating Requirements for the Vision Systems of Industrial Robotic Complexes

    Directory of Open Access Journals (Sweden)

    V. Ya. Kolyuchkin

    2015-01-01

    Full Text Available In references, there is a lack of approaches to describe the justified technical requirements for the vision systems (VS of industrial robotics complexes (IRC. Therefore, an objective of the work is to develop a technique that allows substantiating requirements for the main quality indicators of VS, functioning as a part of the IRC.The proposed technique uses a model representation of VS, which, as a part of the IRC information system, sorts the objects in the work area, as well as measures their linear and angular coordinates. To solve the problem of statement there is a proposal to define the target function of a designed IRC as a dependence of the IRC indicator efficiency on the VS quality indicators. The paper proposes to use, as an indicator of the IRC efficiency, the probability of a lack of fault products when manufacturing. Based on the functions the VS perform as a part of the IRC information system, the accepted indicators of VS quality are as follows: a probability of the proper recognition of objects in the working IRC area, and confidential probabilities of measuring linear and angular orientation coordinates of objects with the specified values of permissible error. Specific values of these errors depend on the orientation errors of working bodies of manipulators that are a part of the IRC. The paper presents mathematical expressions that determine the functional dependence of the probability of a lack of fault products when manufacturing on the VS quality indicators and the probability of failures of IRC technological equipment.The offered technique for substantiating engineering requirements for the VS of IRC has novelty. The results obtained in this work can be useful for professionals involved in IRC VS development, and, in particular, in development of VS algorithms and software.

  13. Lack of Substantial Post-Cessation Weight Increase in Electronic Cigarettes Users

    Directory of Open Access Journals (Sweden)

    Cristina Russo

    2018-03-01

    Full Text Available Minimization of post-cessation weight gain in quitters is important, but existing approaches (e.g., antismoking medications shows only limited success. We investigated changes in body weight in smokers who quit or reduced substantially their cigarette consumption by switching to electronic cigarettes (ECs use. Body weight and smoking/vaping history were extracted from medical records of smokers and ex-smokers to match three study groups: (1 regular EC users on at least two consecutive follow-up visits; (2 regular smokers (and not using ECs; (3 subjects who reported sustained smoking abstinence after completing a cessation program. Review of their medical records was conducted at two follow-up visits at 6- (F/U 6m and 12-months (F/U 12m. A total of 86 EC users, 93 regular smokers, and 44 quitters were studied. In the EC users study group, cigarettes/day use decreased from 21.1 at baseline to 1.8 at F/U 12m (p < 0.0001. Dual usage was reported by approximately 50% of EC users. Both within factor (time, p < 0.0001 and between factor (study groups, p < 0.0001 produced significant effect on weight (% change from baseline, with a significant 4.8% weight gain from baseline in the quitters study group at F/U 12m. For the EC users, weight gain at F/U 12m was only 1.5% of baseline. There was no evidence of post-cessation weight increase in those who reduced substantially cigarette consumption by switching to ECs (i.e., dual users and only modest post-cessation weight increase was reported in exclusive EC users at F/U 12m. By reducing weight gain and tobacco consumption, EC-based interventions may promote an overall improvement in quality of life.

  14. Substantial Differences between Organ and Muscle Specific Tracer Incorporation Rates in a Lactating Dairy Cow.

    Directory of Open Access Journals (Sweden)

    Nicholas A Burd

    Full Text Available We aimed to produce intrinsically L-[1-(13C]phenylalanine labeled milk and beef for subsequent use in human nutrition research. The collection of the various organ tissues after slaughter allowed for us to gain insight into the dynamics of tissue protein turnover in vivo in a lactating dairy cow. One lactating dairy cow received a constant infusion of L-[1-(13C]phenylalanine (450 µmol/min for 96 h. Plasma and milk were collected prior to, during, and after the stable isotope infusion. Twenty-four hours after cessation of the infusion the cow was slaughtered. The meat and samples of the various organ tissues (liver, heart, lung, udder, kidney, rumen, small intestine, and colon were collected and stored. Approximately 210 kg of intrinsically labeled beef (bone and fat free with an average L-[1-(13C]phenylalanine enrichment of 1.8±0.1 mole percent excess (MPE was obtained. The various organ tissues differed substantially in L-[1-(13C]phenylalanine enrichments in the tissue protein bound pool, the highest enrichment levels were achieved in the kidney (11.7 MPE and the lowest enrichment levels in the skeletal muscle tissue protein of the cow (between 1.5-2.4 MPE. The estimated protein synthesis rates of the various organ tissues should be regarded as underestimates, particularly for the organs with the higher turnover rates and high secretory activity, due to the lengthened (96 h measurement period necessary for the production of the intrinsically labeled beef. Our data demonstrates that there are relatively small differences in L-[1-(13C]phenylalanine enrichments between the various meat cuts, but substantial higher enrichment values are observed in the various organ tissues. We conclude that protein turnover rates of various organs are much higher when compared to skeletal muscle protein turnover rates in large lactating ruminants.

  15. Elimination of feedwater heaters in steam turbines: Prospects for substantial energy savings

    International Nuclear Information System (INIS)

    Lorenzoni, G.

    1992-01-01

    This paper re-proposes the theory that thermal regeneration (RT) in steam turbine plants decreases thermodynamic efficiency. This theory is supported by the criterion of maximization of variation of exergy in the steam generator (CMVEG) and by an mathematical argumentation based on the first law of thermodynamics. Consequences of great importance are deduced: plant operating costs reductions and a new possibility for cogeneration, that indicates exceptional advantages for the whole power industry, since steam turbine plants are responsible for the greater part of global electric power production

  16. Pulmonary toxicity screening studies in male rats with TiO2 particulates substantially encapsulated with pyrogenically deposited, amorphous silica

    Directory of Open Access Journals (Sweden)

    Webb TR

    2006-01-01

    Full Text Available Abstract The aim of this study was to evaluate the acute lung toxicity in rats of intratracheally instilled TiO2 particles that have been substantially encapsulated with pyrogenically deposited, amorphous silica. Groups of rats were intratracheally instilled either with doses of 1 or 5 mg/kg of hydrophilic Pigment A TiO2 particles or doses of 1 or 5 mg/kg of the following control or particle-types: 1 R-100 TiO2 particles (hydrophilic in nature; 2 quartz particles, 3 carbonyl iron particles. Phosphate-buffered saline (PBS instilled rats served as additional controls. Following exposures, the lungs of PBS and particle-exposed rats were evaluated for bronchoalveolar lavage (BAL fluid inflammatory markers, cell proliferation, and by histopathology at post-instillation time points of 24 hrs, 1 week, 1 month and 3 months. The bronchoalveolar lavage results demonstrated that lung exposures to quartz particles, at both concentrations but particularly at the higher dose, produced significant increases vs. controls in pulmonary inflammation and cytotoxicity indices. Exposures to Pigment A or R-100 TiO2 particles produced transient inflammatory and cell injury effects at 24 hours postexposure (pe, but these effects were not sustained when compared to quartz-related effects. Exposures to carbonyl iron particles or PBS resulted only in minor, short-term and reversible lung inflammation, likely related to the effects of the instillation procedure. Histopathological analyses of lung tissues revealed that pulmonary exposures to Pigment A TiO2 particles produced minor inflammation at 24 hours postexposure and these effects were not significantly different from exposures to R-100 or carbonyl iron particles. Pigment A-exposed lung tissue sections appeared normal at 1 and 3 months postexposure. In contrast, pulmonary exposures to quartz particles in rats produced a dose-dependent lung inflammatory response characterized by neutrophils and foamy (lipid

  17. Integration Policies of European Cities in Comparative Perspective: Structural Convergence and Substantial Differentiation

    Directory of Open Access Journals (Sweden)

    Rinus Penninx

    2016-08-01

    Full Text Available This article aims to review the comparative study of integration policies of European cities. The first two sections present an analytical framework for the study of immigrants’ integration processes and the policies that intend to steer such processes. The third section outlines how local integration policies have developed in relation to national policies and EU integration policies, particularly after 2003. The fourth and main section analyses the framing and content of integration policies of European cities, looking at their diversity in the legal/political dimension, the socio-economic dimension – including the domains of work, housing, education and health – and the cultural, religious and ethnic dimension. It is concluded that there is a structural convergence, in the sense that in the complex structure of multilevel governance of migration and integration, cities do take a similar position, developing horizontal relations of cooperation and exchange. Cities that develop explicit integration policies tend to do this from a more inclusive and pragmatic framing than national and EU-policies. At the same time, there is great variation in what cities actually do: in the legal/political and in the cultural/religious dimensions, framing, intentions and measures do vary greatly; in the socio-economic dimension this variation is less when it comes to the domains of activity, but more in the intensity of policy intervention.

  18. Methodological substantiation of the professional functions of Responsible persons of pharmaceutical and hospital institutions

    Directory of Open Access Journals (Sweden)

    N. O. Vetiutneva

    2018-03-01

    Full Text Available The aim of the work is the content analysis and methodological justification of the professional functions of the Responsible persons for quality assurance of medicines in pharmaceutical and hospital institutions. Materials and methods. The following research methods were used: system and comparative analysis, generalization, systematization, graphic modeling, observation. Research materials: normative legal acts, normative documents, recommendations of international organizations, information of wholesale and retail pharmaceutical companies, pharmaceutical and hospital institutions, professional non-governmental organizations, placed on official web-sites and collected in the process of direct observation. Results. The personnel and qualification aspects of professional activity of Responsible persons of pharmaceutical and hospital institutions were discussed. On the basis of analysis of the modern legal and regulatory framework, a general list of professional functions of the Responsible persons of health care institutions had been formed. The content analysis and comparison of the number of the functions of Responsible persons performed in health care institutions of different types is carried out. The new functions of the Responsible persons of health care institutions are considered. The managerial nature of the professional functions of the Responsible persons and the expediency of their complementing with the leadership functions are substantiated. On the basis of international management standards, requirements of GPP and GPEP, systematization of the functions of the Responsible persons of health care institutions in the groups and subgroups was performed. Conclusions. The generalization and systematization of the professional functions of the Responsible persons of health care institutions had been carried out for five classification groups of functions, namely: leadership, planning, organizational, control and information, of which the

  19. Global and regional ocean carbon uptake and climate change: sensitivity to a substantial mitigation scenario

    Energy Technology Data Exchange (ETDEWEB)

    Vichi, Marcello; Masina, Simona; Navarra, Antonio [Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Bologna (Italy); Istituto Nazionale di Geofisica e Vulcanologia, Bologna (Italy); Manzini, Elisa [Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Bologna (Italy); Istituto Nazionale di Geofisica e Vulcanologia, Bologna (Italy); Max Planck Institute for Meteorology, Hamburg (Germany); Fogli, Pier Giuseppe [Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Bologna (Italy); Alessandri, Andrea [Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Bologna (Italy); ENEA, Rome (Italy); Patara, Lavinia [Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Bologna (Italy); Leibniz Institute of Marine Sciences (IFM-GEOMAR), Kiel (Germany); Scoccimarro, Enrico [Istituto Nazionale di Geofisica e Vulcanologia, Bologna (Italy)

    2011-11-15

    Under future scenarios of business-as-usual emissions, the ocean storage of anthropogenic carbon is anticipated to decrease because of ocean chemistry constraints and positive feedbacks in the carbon-climate dynamics, whereas it is still unknown how the oceanic carbon cycle will respond to more substantial mitigation scenarios. To evaluate the natural system response to prescribed atmospheric ''target'' concentrations and assess the response of the ocean carbon pool to these values, 2 centennial projection simulations have been performed with an Earth System Model that includes a fully coupled carbon cycle, forced in one case with a mitigation scenario and the other with the SRES A1B scenario. End of century ocean uptake with the mitigation scenario is projected to return to the same magnitude of carbon fluxes as simulated in 1960 in the Pacific Ocean and to lower values in the Atlantic. With A1B, the major ocean basins are instead projected to decrease the capacity for carbon uptake globally as found with simpler carbon cycle models, while at the regional level the response is contrasting. The model indicates that the equatorial Pacific may increase the carbon uptake rates in both scenarios, owing to enhancement of the biological carbon pump evidenced by an increase in Net Community Production (NCP) following changes in the subsurface equatorial circulation and enhanced iron availability from extratropical regions. NCP is a proxy of the bulk organic carbon made available to the higher trophic levels and potentially exportable from the surface layers. The model results indicate that, besides the localized increase in the equatorial Pacific, the NCP of lower trophic levels in the northern Pacific and Atlantic oceans is projected to be halved with respect to the current climate under a substantial mitigation scenario at the end of the twenty-first century. It is thus suggested that changes due to cumulative carbon emissions up to present and the

  20. The association between substantiated childhood maltreatment, asthma and lung function: A prospective investigation.

    Science.gov (United States)

    Abajobir, Amanuel Alemu; Kisely, Steve; Williams, Gail; Strathearn, Lane; Suresh, Sadasivam; Najman, Jake Moses

    2017-10-01

    Asthma reflects multiple and likely complex causal pathways. We investigate the possibility that childhood maltreatment is one such causal pathway. Childhood maltreatment can be interpreted as a form of early life adversity and like other life adversities may predict a range of negative health outcomes, including asthma. A total of 3762 young adults (52.63% female) from the Mater Hospital-University of Queensland Study of Pregnancy (MUSP) participated in this study. MUSP is a prospective Australian birth cohort study of mothers consecutively recruited during their first antenatal clinic visit at Brisbane's Mater Hospital from 1981 to 1983. The study followed both mother-child dyads to the age of 21years after birth. Participants reported whether they had been diagnosed by a physician with asthma by the 21-year follow-up. Trained research assistants also performed gender- and height-standardized lung function tests using a Spirobank G spirometer system attached to a laptop computer. We linked this dataset with data obtained from the child protection services and which comprised all substantiated cases of childhood maltreatment in the MUSP cohort. Substantiations of childhood maltreatment included children in an age range of 0-14years. The experience of any childhood maltreatment, particularly emotional abuse, was independently associated with self-reported physician-diagnosed asthma by the 21-year follow-up. The association was no longer significant after adjustment for a range of confounders and covariates in neglected children. Childhood maltreatment, including multiple events, was not associated with lung function in adjusted models. Childhood maltreatment, including emotional abuse, was associated with lifetime ever asthma. This was in contrast to the absence of an association with objective measures of lung function. More research is indicated on the effect of childhood maltreatment on lung function using objective measures. In the meantime, there should be a

  1. Large rainfall changes consistently projected over substantial areas of tropical land

    Science.gov (United States)

    Chadwick, Robin; Good, Peter; Martin, Gill; Rowell, David P.

    2016-02-01

    Many tropical countries are exceptionally vulnerable to changes in rainfall patterns, with floods or droughts often severely affecting human life and health, food and water supplies, ecosystems and infrastructure. There is widespread disagreement among climate model projections of how and where rainfall will change over tropical land at the regional scales relevant to impacts, with different models predicting the position of current tropical wet and dry regions to shift in different ways. Here we show that despite uncertainty in the location of future rainfall shifts, climate models consistently project that large rainfall changes will occur for a considerable proportion of tropical land over the twenty-first century. The area of semi-arid land affected by large changes under a higher emissions scenario is likely to be greater than during even the most extreme regional wet or dry periods of the twentieth century, such as the Sahel drought of the late 1960s to 1990s. Substantial changes are projected to occur by mid-century--earlier than previously expected--and to intensify in line with global temperature rise. Therefore, current climate projections contain quantitative, decision-relevant information on future regional rainfall changes, particularly with regard to climate change mitigation policy.

  2. Substantiation of health related power lifting training methodic for univeristies students with muscular skeletal apparatuse affections.

    Directory of Open Access Journals (Sweden)

    San. Zhen Qiang

    2015-11-01

    Full Text Available Purpose: substantiation of health related power lifting training methodic for universities students, who have disorders of muscular skeletal apparatus. Material: in experimental researches 126 students of 18-24 years’ age, having disorders of muscular skeletal apparatus, participated. With the help of testing we registered changes of students’ functional, physical and psycho-physiological fitness indicators. Results: optimal correlation of specific and non specific loads was found: 60% of specific and 40% of non specific. It is recommended to follow certain correlation of exercises in easy and complicated conditions: for first year students - 3:2; for second year students - 3:2; for third year - 2:3; for forth year - 2:3; for fifth year students - 1:3. Specific only for power lifting conditions and temps of students’ (with muscular skeletal apparatus affections functional, physical and psycho-physiological fitness improvement were determined. Conclusions: The requirements of the training methodic envisage correction of loads for bringing every indicator on proper level.

  3. Substantial variability in postoperative treatment, and convalescence recommendations following vaginal repair. A nationwide questionnaire study

    DEFF Research Database (Denmark)

    Ottesen, Marianne; Møller, Charlotte; Kehlet, H

    2001-01-01

    BACKGROUND: Postoperative care and convalescence recommendations following vaginal surgery are generally not evidence based. The aim of this study was to describe pre and postoperative treatment, and advice and restrictions for the convalescence period, given by Danish hospital-employed gynecolog......BACKGROUND: Postoperative care and convalescence recommendations following vaginal surgery are generally not evidence based. The aim of this study was to describe pre and postoperative treatment, and advice and restrictions for the convalescence period, given by Danish hospital......-employed gynecologists, and gynecologists in private practice, to patients undergoing vaginal repair. METHOD: In 1999 all Danish gynecologists (n=433) received a tested questionnaire about postoperative treatment and convalescence recommendations following vaginal repair. Non-responders received one reminder. OUTCOME...... anterior repair, and 2 days (range, 1-7) following posterior repair. The recommended sick leave was median 6 weeks (range, 2-12) for patients with work with heavy lifts. There were substantial differences in recommendations. Recommended lifting restrictions were median 3 kg (range, 0-20) for median 4 weeks...

  4. Substantial Physician Turnover And Beneficiary 'Churn' In A Large Medicare Pioneer ACO.

    Science.gov (United States)

    Hsu, John; Vogeli, Christine; Price, Mary; Brand, Richard; Chernew, Michael E; Mohta, Namita; Chaguturu, Sreekanth K; Weil, Eric; Ferris, Timothy G

    2017-04-01

    Alternative payment models, such as accountable care organizations (ACOs), attempt to stimulate improvements in care delivery by better alignment of payer and provider incentives. However, limited attention has been paid to the physicians who actually deliver the care. In a large Medicare Pioneer ACO, we found that the number of beneficiaries per physician was low (median of seventy beneficiaries per physician, or less than 5 percent of a typical panel). We also found substantial physician turnover: More than half of physicians either joined (41 percent) or left (18 percent) the ACO during the 2012-14 contract period studied. When physicians left the ACO, most of their attributed beneficiaries also left the ACO. Conversely, about half of the growth in the beneficiary population was because of new physicians affiliating with the ACO; the remainder joined after switching physicians. These findings may help explain the muted financial impact ACOs have had overall, and they raise the possibility of future gaming on the part of ACOs to artificially control spending. Policy refinements include coordinated and standardized risk-sharing parameters across payers to prevent any dilution of the payment incentives or confusion from a cacophony of incentives across payers. Project HOPE—The People-to-People Health Foundation, Inc.

  5. ECOLOGICAL AND ECONOMIC SUBSTANTIATION OF SELECTION OF THE METHOD FOR PLASTIC WASTE MANAGEMENT

    Directory of Open Access Journals (Sweden)

    T. P. Shanina

    2015-11-01

    Full Text Available Analysis of the classifications of plastic waste from production and consumption is made by various criteria. Distinctive features of the specifi ed waste behavior under various treatment methods (deposition at landfill, incineration and recycling are discussed. Clustering of the polymeric waste by hazard categories of the combustion products is performed. The polyvinyl-chlorides and polycarbonates which generate the most hazardous products under  the combustion are singled out in a particular cluster. The qualitative and quantitative descrip- The qualitative and quantitative description of the plastic waste generated in Ukraine from 2011 to 2013 is provided. Grossemissions of the polyvinylchloride and polystyrene waste incineration products are calculated. Evaluation of the environmental damage resulting from implementation of various methods for plastic waste management is based on an environmental tax rate having a compensatory nature. Potential profit from selling the secondary raw materials, produced from plastic waste, is analysed. Ranking of the potential methods for plastic waste management is presented in the context of ecological and economic substantiation: the most preferable method is production of secondary raw materials (recycled resources; the least preferable one is incineration of the specified wastes.

  6. Safety Design Criteria and Approaches to Safety Substantiation of the BN-1200

    International Nuclear Information System (INIS)

    Ashurko, I.

    2013-01-01

    Russian experience in SFR area: Activities on development of safety design criteria for SFRs of the 4th generation is carried out within the GIF framework. Although this reactor technology is considered as innovative that is relevant to the 4th generation, however, it has already a certain history. In this relation, it seems to be useful to analyze the corresponding experience that is available in various countries. 4 SFRs have been successfully operated in the USSR and in the Russian Federation: • Experimental reactor BR-5/10; • Research reactor BOR-60; • Prototype BN-350 power reactor; • Commercial BN-600 power unit at the Beloyarsk NPP. Thus, Russia gained a considerable experience of design, construction and operation of SFRs. In particular, a certain experience has been acquired on safety substantiation of reactors of this type and their licensing. Now BOR-60 and BN-600 continue their operation, BN-800 power unit is under construction, development of the commercial BN-1200 power unit, that is considered as the 4th generation reactor, has been started. Due to limited number of operating SFRs in the world, successful Russian experience in this area should be taken into account for further development and improvement of SFR SDC developed by the GIF Task Force. In particular, participation of SFR designers in this activities would be fruitful and useful

  7. Substantial improvements not seen in health behaviors following corner store conversions in two Latino food swamps

    Directory of Open Access Journals (Sweden)

    Alexander N. Ortega

    2016-05-01

    Full Text Available Abstract Background The effectiveness of food retail interventions is largely undetermined, yet substantial investments have been made to improve access to healthy foods in food deserts and swamps via grocery and corner store interventions. This study evaluated the effects of corner store conversions in East Los Angeles and Boyle Heights, California on perceived accessibility of healthy foods, perceptions of corner stores, store patronage, food purchasing, and eating behaviors. Methods Household data (n = 1686 were collected at baseline and 12- to 24-months post-intervention among residents surrounding eight stores, three of which implemented a multi-faceted intervention and five of which were comparisons. Bivariate analyses and logistic and linear regressions were employed to assess differences in time, treatment, and the interaction between time and treatment to determine the effectiveness of this intervention. Results Improvements were found in perceived healthy food accessibility and perceptions of corner stores. No changes were found, however, in store patronage, purchasing, or consumption of fruits and vegetables. Conclusions Results suggest limited effectiveness of food retail interventions on improving health behaviors. Future research should focus on other strategies to reduce community-level obesity.

  8. Technical considerations for evaluating substantially complete containment of high-level waste within the waste package

    International Nuclear Information System (INIS)

    Manaktala, H.K.; Interrante, C.G.

    1990-12-01

    This report deals with technical information that is considered essential for demonstrating the ability of the high-level radioactive waste package to provide ''substantially complete containment'' of its contents (vitrified waste form or spent light-water reactor fuel) for a period of 300 to 1000 years in a geological repository environment. The discussion is centered around technical considerations of the repository environment, materials and fabrication processes for the waste package components, various degradation modes of the materials of construction of the waste packages, and inspection and monitoring of the waste package during the preclosure and retrievability period, which could begin up to 50 years after initiation of waste emplacement. The emphasis in this report is on metallic materials. However, brief references have been made to other materials such as ceramics, graphite, bonded ceramic-metal systems, and other types of composites. The content of this report was presented to an external peer review panel of nine members at a workshop held at the Center for Nuclear Waste Regulatory Analyses (CNWRA), Southwest Research Institute, San Antonio, Texas, April 2--4, 1990. The recommendations of the peer review panel have been incorporated in this report. There are two companion reports; the second report in the series provides state-of-the-art techniques for uncertainty evaluations. 97 refs., 1 fig

  9. Substantiation of the safety in the technical project of Belene NPP

    International Nuclear Information System (INIS)

    Boyadzhiev, A.

    1990-01-01

    The chapter contains an evaluation of the safety of Belene NPP project, based on an experts study of the corresponding volume of the Technical Project documentation of the main contractor and also on other related documents. The authors state that most of the remarks are constitutive, part of them requiring additional information or research. The general explicit conclusion is that the materials on the safety substantiation provided in the project are insufficient for making final statements on the safety of the NPP and there is a need for a detailed analysis and expertise. There are 12 topical conclusion paragraphs and each of them comprises a number of remarks. Among the remarks there are some related to the reactivity coefficient values in certain modes of operation, the problem of the mechanical safety and control system efficiency, the unacceptable operation at nominal power in case of stringent safety rules enforcement, the insufficiency of the PSA, the automatic control systems and the software codes not standing up to the contemporary requirements. (R.Ts.)

  10. Technical considerations for evaluating substantially complete containment of high-level waste within the waste package

    Energy Technology Data Exchange (ETDEWEB)

    Manaktala, H.K. (Southwest Research Inst., San Antonio, TX (USA). Center for Nuclear Waste Regulatory Analyses); Interrante, C.G. (Nuclear Regulatory Commission, Washington, DC (USA). Div. of High-Level Waste Management)

    1990-12-01

    This report deals with technical information that is considered essential for demonstrating the ability of the high-level radioactive waste package to provide substantially complete containment'' of its contents (vitrified waste form or spent light-water reactor fuel) for a period of 300 to 1000 years in a geological repository environment. The discussion is centered around technical considerations of the repository environment, materials and fabrication processes for the waste package components, various degradation modes of the materials of construction of the waste packages, and inspection and monitoring of the waste package during the preclosure and retrievability period, which could begin up to 50 years after initiation of waste emplacement. The emphasis in this report is on metallic materials. However, brief references have been made to other materials such as ceramics, graphite, bonded ceramic-metal systems, and other types of composites. The content of this report was presented to an external peer review panel of nine members at a workshop held at the Center for Nuclear Waste Regulatory Analyses (CNWRA), Southwest Research Institute, San Antonio, Texas, April 2--4, 1990. The recommendations of the peer review panel have been incorporated in this report. There are two companion reports; the second report in the series provides state-of-the-art techniques for uncertainty evaluations. 97 refs., 1 fig.

  11. SUBSTANTIATION OF THE COST OF HOUSING CONSTRUCTION INCLUDING THE FACTOR OF INVESTMENT ATTRACTIVENESS OF TERRITORIES

    Directory of Open Access Journals (Sweden)

    ZAIATS Yi. I.

    2015-11-01

    Full Text Available Problem statement. For planning and organization of urban construction is necessary to analyze the use of areas. Territorial resources of the city, being used for construction and other urban purposes, consists of plots of land: disposable, reserved and undeveloped in previous years of construction in progress; residential districts and blocks of obsolete housing fund; industrial and municipal and warehouse enterprises being used irrationally or stopped to work; the defence department, where the amortized warehouses and other main funds are that are not used by purpose; agricultural enterprises where the obsolete industrial funds, haying, nurseries, greenhouses. The number of free areas suitable for future urban development is extremely limited. However a considerable part of the territories of almost all functional zones is used inefficiently. Purpose. Formalization of a factor of investment attractiveness of territories for the further identification and research of the connection between it and the cost of housing construction is necessary. Conclusion. The identification of regularities of influence of the factor of investment attractiveness of territories on the cost of construction of high-rise buildings allow to obtain a quantitative estimate of this effect and can be used in the development of the methodology of substantiation of the expediency and effectiveness of the implementation of highrise construction projects, based on organizational and technological aspects.

  12. Substantial Humic Acid Adsorption to Activated Carbon Air Cathodes Produces a Small Reduction in Catalytic Activity.

    Science.gov (United States)

    Yang, Wulin; Watson, Valerie J; Logan, Bruce E

    2016-08-16

    Long-term operation of microbial fuel cells (MFCs) can result in substantial degradation of activated carbon (AC) air-cathode performance. To examine a possible role in fouling from organic matter in water, cathodes were exposed to high concentrations of humic acids (HA). Cathodes treated with 100 mg L(-1) HA exhibited no significant change in performance. Exposure to 1000 mg L(-1) HA decreased the maximum power density by 14% (from 1310 ± 30 mW m(-2) to 1130 ± 30 mW m(-2)). Pore blocking was the main mechanism as the total surface area of the AC decreased by 12%. Minimization of external mass transfer resistances using a rotating disk electrode exhibited only a 5% reduction in current, indicating about half the impact of HA adsorption was associated with external mass transfer resistance and the remainder was due to internal resistances. Rinsing the cathodes with deionized water did not restore cathode performance. These results demonstrated that HA could contribute to cathode fouling, but the extent of power reduction was relatively small in comparison to large mass of humics adsorbed. Other factors, such as biopolymer attachment, or salt precipitation, are therefore likely more important contributors to long-term fouling of MFC cathodes.

  13. Intraoperative crystalloid overload leads to substantial inflammatory infiltration of intestinal anastomoses-a histomorphological analysis.

    Science.gov (United States)

    Kulemann, Birte; Timme, Sylvia; Seifert, Gabriel; Holzner, Philipp A; Glatz, Torben; Sick, Olivia; Chikhladze, Sophia; Bronsert, Peter; Hoeppner, Jens; Werner, Martin; Hopt, Ulrich T; Marjanovic, Goran

    2013-09-01

    It has been shown that crystalloid fluid-overload promotes anastomotic instability. As physiologic anastomotic healing requires the sequential infiltration of different cells, we hypothesized this to be altered by liberal fluid regimes and performed a histomorphological analysis. 36 Wistar rats were randomized into 4 groups (n=8-10 rats/group) and treated with either liberal (+) or restrictive (-) perioperative crystalline (Jonosteril = Cry) or colloidal fluid (Voluven = Col). Anastomotic samples were obtained on postoperative day 4, routinely stained and histophathologically reviewed. Anastomotic healing was assessed using a semiquantitative score, assessing inflammatory cells, anastomotic repair and collagenase activity. Overall, the crystalloid overload group (Cry (+)) showed the worst healing score (P < 0.01). A substantial increase of lymphocytes and macrophages was found in this group compared to the other three (P < 0.01). Both groups that received colloidal fluid (Col (+) and Col (-)) as well as the group that received restricted crystalloid fluid resuscitation (Cry (-)) had better intestinal healing. Collagenase activity was significantly higher in the Cry (+) group. Intraoperative infusion of high-volume crystalloid fluid leads to a pathological anastomotic inflammatory response with a marked infiltration of leukocytes and macrophages resulting in accelerated collagenolysis. Copyright © 2013 Mosby, Inc. All rights reserved.

  14. Six-Month Market Exclusivity Extensions To Promote Research Offer Substantial Returns For Many Drug Makers.

    Science.gov (United States)

    Kesselheim, Aaron S; Rome, Benjamin N; Sarpatwari, Ameet; Avorn, Jerry

    2017-02-01

    To incentivize pharmaceutical manufacturers to invest in areas of unmet medical need, policy makers frequently propose extending the market exclusivity period of desired drugs. Some such proposals are modeled after the pediatric exclusivity patent extension program, which since 1997 has provided six additional months of market exclusivity for drugs studied in children. The most recent proposal would encourage rare disease research by providing six months of extended exclusivity for any existing drug that is granted subsequent FDA approval for a new rare disease indication. Yet the economic impact of such proposals is rarely addressed. We found that for the thirteen FDA-approved drugs that gained supplemental approval for a rare disease indication from 2005 through 2010, the median projected cost of clinical trials leading to approval was $29.8 million. If the exclusivity extension had been in place, the median discounted financial gain to manufacturers would have been $94.6 million. Median net returns would have been $82.4 million, with higher returns for drugs with higher annual sales. Extending market exclusivity would provide substantial compensation to many manufacturers, particularly for top-selling products, far in excess of the cost of conducting these trials. Alternative strategies to incentivize the study of approved drugs for rare diseases may offer similar benefits at a lower cost. Project HOPE—The People-to-People Health Foundation, Inc.

  15. Monitoring failure rates of commercial implant brands; substantial equivalence in question?

    Science.gov (United States)

    Hujoel, Philippe; Becker, William; Becker, Burton

    2013-07-01

    The aim of this study was to report on the failure rates of two distinct dental implant systems in a clinical practice setting. Date of implant placement and loss were entered prospectively in a data registry system. Failure rates of two commercially pure titanium implants, one with a porous oxydized surface (POS) and the other with a chemically altered surface (CAS), were assessed using a quality control chart and survival analyses. A total of 860 POS and 759 CAS implants were placed. A warning of an increased failure rate of the CAS implant was identified by means of the quality control chart. Survival analyses indicated that the CAS implant failure rate was twice that of the POS implant (Hazard Ratio: 2.08; 95% CI: 1.33-3.28, P-value POS implant was associated with a non-significant 64% drop in the implant failure rate within less than a year (HR: 0.36; 95% CI: 0.12-1.14; P-value POS implant and an 8% failure with the CAS implant appears inconsistent with the assumption of substantial equivalence. © 2012 John Wiley & Sons A/S.

  16. A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes.

    Science.gov (United States)

    Mayr, Gerald; Scofield, R Paul; De Pietri, Vanesa L; Tennyson, Alan J D

    2017-12-12

    One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals.

  17. Grammar Clinical Marker Yields Substantial Heritability for Language Impairments in 16-Year-Old Twins.

    Science.gov (United States)

    Dale, Philip S; Rice, Mabel L; Rimfeld, Kaili; Hayiou-Thomas, Marianna E

    2018-01-22

    There is a need for well-defined language phenotypes suitable for adolescents in twin studies and other large-scale research projects. Rice, Hoffman, and Wexler (2009) have developed a grammatical judgment measure as a clinical marker of language impairment, which has an extended developmental range to adolescence. We conducted the first twin analysis, along with associated phenotypic analyses of validity, of an abridged, 20-item version of this grammatical judgment measure (GJ-20), based on telephone administration using prerecorded stimuli to 405 pairs of 16-year-olds (148 monozygotic and 257 dizygotic) drawn from the Twins Early Development Study (Haworth, Davis, & Plomin, 2012). The distribution of scores is markedly skewed negatively, as expected for a potential clinical marker. Low performance on GJ-20 is associated with lower maternal education, reported learning disability (age 7 years), and low scores on language tests administered via the Twins Early Development Study (age 16 years) as well as General Certificate of Secondary Education English and Math examination performance (age 16 years). Liability threshold estimates for the genetic influence on low performance on GJ-20 are substantial, ranging from 36% with a lowest 10% criterion to 74% for a lowest 5% criterion. The heritability of GJ-20 scores, especially at more extreme cutoffs, along with the score distribution and association with other indicators of language impairments, provides additional evidence for the potential value of this measure as a clinical marker of specific language impairment.

  18. Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities.

    Science.gov (United States)

    Dini-Andreote, Francisco; Pylro, Victor Satler; Baldrian, Petr; van Elsas, Jan Dirk; Salles, Joana Falcão

    2016-08-01

    Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem.

  19. 21 CFR 101.43 - Substantial compliance of food retailers with the guidelines for the voluntary nutrition labeling...

    Science.gov (United States)

    2010-04-01

    ... FOR HUMAN CONSUMPTION FOOD LABELING Specific Nutrition Labeling Requirements and Guidelines § 101.43 Substantial compliance of food retailers with the guidelines for the voluntary nutrition labeling of raw fruit... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Substantial compliance of food retailers with the...

  20. 75 FR 64683 - Liability for Termination of Single-Employer Plans; Treatment of Substantial Cessation of Operations

    Science.gov (United States)

    2010-10-20

    ... Termination of Single-Employer Plans; Treatment of Substantial Cessation of Operations AGENCY: Pension Benefit... cessations of operations by employers that maintain single-employer plans. DATES: Comments must be submitted... 4062(e), which provides for reporting of and liability for certain substantial cessations of operations...

  1. SUBSTANTIATION OF THE NEED AND POSSIBILITIES FOR OPTIMIZATION ON PHARMACEUTICAL SUPPORT FOR WOMEN WITH THYTOID GLAND PATHOLOGY

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    G. T. Glembotskaya

    2015-01-01

    Full Text Available Last decades the amount of people with thynoid gland diseases has increased significantly all over the globe. This disease has more negative consequences for women organism during all aging hormonal changes. Similarity of symptoms of thynoid glands diseases and a range of aging hormonal changes complicates the problem. At that the question of pharmaceutical assistance for women with this pathology was not the object of organizational and economical researches in the Russian Federation, despite their relevance. The purpose is the study of a degree of scientific development of the mentioned problem and representation of the elements of problem situation in the chosen segment of medical and pharmaceutical assistance consumers. Based on the analysis of literature and statistic data, content analysis of rules and regulations, concerning procedures and the relations in the pharmaceutical assistance system, and the results of the conducted sociological survey, we have formed the elements of a problem situation in the chosen segment of medical and pharmaceutical support consumers. Sociological, graphic, logic, contentanalysis were used as methods of the study. We have substantiated a scientific and practice need in development of methodological principals of pharmaceutical support optimization for women with thynoid gland pathology; we have reasoned the opportunities and principal directions of specialized pharmaceutical assistance to the given segment of drug consumers. We have proved the timeliness of the study for organization of pharmaceutical assistance for women with thynoid gland pathology due to its specifically negative consequences during all aging hormonal changes in an organism. We have revealed the presence of risk factors and exceptionally low awareness of women in thynoid gland pathology against the background of excessive occupation of women in active working ages. We have determined a niche in formation of informational mass with

  2. Hypertension: New perspective on its definition and clinical management by bedtime therapy substantially reduces cardiovascular disease risk.

    Science.gov (United States)

    Hermida, Ramón C; Ayala, Diana E; Fernández, José R; Mojón, Artemio; Smolensky, Michael H

    2018-05-01

    Diagnosis of hypertension-elevated blood pressure (BP) associated with increased cardiovascular disease (CVD) risk-and its management for decades have been based primarily on single time-of-day office BP measurements (OBPM) assumed representative of systolic (SBP) and diastolic BP (DBP) during the entire 24-hours span. Around-the-clock ambulatory blood pressure monitoring (ABPM), however, reveals BP undergoes 24-hours patterning characterized in normotensives and uncomplicated hypertensives by striking morning-time rise, 2 daytime peaks-one ~2-3 hours after awakening and the other early evening, small midafternoon nadir and 10-20% decline (BP dipping) in the asleep BP mean relative to the wake-time BP mean. A growing number of outcome trials substantiate correlation between BP and target organ damage, vascular and other risks is greater for the ABPM-derived asleep BP mean, independent and stronger predictor of CVD risk, than daytime OBPM or ABPM-derived awake BP. Additionally, bedtime hypertension chronotherapy, that is, ingestion of ≥1 conventional hypertension medications at bedtime to achieve efficient attenuation of asleep BP, better reduces total CVD events by 61% and major events (CVD death, myocardial infarction, ischaemic and haemorrhagic stroke) by 67%-even in more vulnerable chronic kidney disease, diabetes and resistant hypertension patients-than customary on-awaking therapy that targets wake-time BP. Such findings of around-the-clock ABPM and bedtime hypertension outcome trials, consistently indicating greater importance of asleep BP than daytime OBPM or ambulatory awake BP, call for a new definition of true arterial hypertension plus modern approaches for its diagnosis and management. © 2018 Stichting European Society for Clinical Investigation Journal Foundation.

  3. The ecological importance of intraspecific variation.

    Science.gov (United States)

    Des Roches, Simone; Post, David M; Turley, Nash E; Bailey, Joseph K; Hendry, Andrew P; Kinnison, Michael T; Schweitzer, Jennifer A; Palkovacs, Eric P

    2018-01-01

    Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.

  4. Experimental substantiation and clinical use of functional pneumoepidurography in the diagnosis of lumbar osteochondrosis i

    Energy Technology Data Exchange (ETDEWEB)

    Sharov, B.K.; Plekhanov, L.G. (Chelyabinskij Meditsinskij Inst. (USSR))

    Anatomic and X-ray correlations in 31 postmortem unfixed specimens of the vertebral lumbar region have shown that in the diagnosis of disk prolapse and commissural processes in the anterior epidural space roentgenopositive contrast substances are not much superior to roentgenonegative ones. Functional pneumoepidurogaphy used in 102 patients with lumbar osteochondrosis helped to reveal intervertebral disk prolapse at all the stages of degenerative affection, to evaluate function of the disk-ligamentous apparatus and to specify the nature of a pathological process in the epidural space.

  5. The influence of population characteristics on variation in general practice based morbidity estimations

    Directory of Open Access Journals (Sweden)

    van den Dungen C

    2011-11-01

    Full Text Available Abstract Background General practice based registration networks (GPRNs provide information on morbidity rates in the population. Morbidity rate estimates from different GPRNs, however, reveal considerable, unexplained differences. We studied the range and variation in morbidity estimates, as well as the extent to which the differences in morbidity rates between general practices and networks change if socio-demographic characteristics of the listed patient populations are taken into account. Methods The variation in incidence and prevalence rates of thirteen diseases among six Dutch GPRNs and the influence of age, gender, socio economic status (SES, urbanization level, and ethnicity are analyzed using multilevel logistic regression analysis. Results are expressed in median odds ratios (MOR. Results We observed large differences in morbidity rate estimates both on the level of general practices as on the level of networks. The differences in SES, urbanization level and ethnicity distribution among the networks' practice populations are substantial. The variation in morbidity rate estimates among networks did not decrease after adjusting for these socio-demographic characteristics. Conclusion Socio-demographic characteristics of populations do not explain the differences in morbidity estimations among GPRNs.

  6. Morphometric variations of the 7th cervical vertebrae of Zulu, White, and Colored South Africans.

    Science.gov (United States)

    Kibii, Job M; Pan, Rualing; Tobias, Phillip V

    2010-05-01

    The 7th cervical vertebrae of 240 cadavers of South African Zulu, White, and Colored population groups were examined to determine morphometric variation. White and Colored females had statistically significant narrower cervical anteroposterior diameters than their male counterparts, whereas no statistically significant difference between sexes of the Zulu population group was observed in this variable. In addition, although Zulu and Colored females had statistically significant narrower cervical transverse diameters than their male counterparts, there was no statistically significant variation between South African white males and females in this respect. The findings indicate that sexual dimorphism is more apparent in the vertebral centrum, across the three population groups, where males had significantly larger dimensions in centrum anteroposterior diameter, height, and width than their female counterparts. The study further reveals that sexual dimorphism is more apparent when one compares aspects of the 7th cervical vertebra between sexes within the same population group. Overall, the dimensions of the various variates of the vertebra are substantially smaller in women than in men. The smaller dimensions, particularly of the centrum, may be the result of lower skeletal mass in women and render them more vulnerable to fractures resulting from compression forces. 2010 Wiley-Liss, Inc.

  7. Female adolescents with severe substance and conduct problems have substantially less brain gray matter volume.

    Directory of Open Access Journals (Sweden)

    Manish S Dalwani

    Full Text Available Structural neuroimaging studies have demonstrated lower regional gray matter volume in adolescents with severe substance and conduct problems. These research studies, including ours, have generally focused on male-only or mixed-sex samples of adolescents with conduct and/or substance problems. Here we compare gray matter volume between female adolescents with severe substance and conduct problems and female healthy controls of similar ages.Female adolescents with severe substance and conduct problems will show significantly less gray matter volume in frontal regions critical to inhibition (i.e. dorsolateral prefrontal cortex and ventrolateral prefrontal cortex, conflict processing (i.e., anterior cingulate, valuation of expected outcomes (i.e., medial orbitofrontal cortex and the dopamine reward system (i.e. striatum.We conducted whole-brain voxel-based morphometric comparison of structural MR images of 22 patients (14-18 years with severe substance and conduct problems and 21 controls of similar age using statistical parametric mapping (SPM and voxel-based morphometric (VBM8 toolbox. We tested group differences in regional gray matter volume with analyses of covariance, adjusting for age and IQ at p<0.05, corrected for multiple comparisons at whole-brain cluster-level threshold.Female adolescents with severe substance and conduct problems compared to controls showed significantly less gray matter volume in right dorsolateral prefrontal cortex, left ventrolateral prefrontal cortex, medial orbitofrontal cortex, anterior cingulate, bilateral somatosensory cortex, left supramarginal gyrus, and bilateral angular gyrus. Considering the entire brain, patients had 9.5% less overall gray matter volume compared to controls.Female adolescents with severe substance and conduct problems in comparison to similarly aged female healthy controls showed substantially lower gray matter volume in brain regions involved in inhibition, conflict processing, valuation

  8. Agroecological Substantiation for the Use of Treated Wastewater for Irrigation of Agricultural Land

    Directory of Open Access Journals (Sweden)

    Yulia Domashenko

    2018-01-01

    Full Text Available The objective of this work is the agroecological substantiation of the use of treated wastewater for irrigation of agricultural land. As the result of the experimental research, it was established that the soil microfloraplays an essential role in strengthening or weakening the biological activity of soil. Therefore, with an irrigation rate of 250 m 3 /ha of wastewater, a 1.5 times increase in the number of microbiota colonies is observed on average both in hog farms and cattle breeding complexes; with a rate of 350 m 3 /ha – a 2-fold increase; with a rate of 450 m 3 /ha – a 3.5–4-fold increase. An increase in nitrifying soil features has also been observed. Thus, if the value on the control in the soil layer from 0 cm to 60 cm is 27.2 mg of nitrate per 1 kg of arid soil, in the version with wastewater irrigation it reaches 46.7 mg. According to the research results, the use of defecate, the waste of sugar production, in the treatment of wastewater of livestock farms does not have a negative agroecological impact on the soil. Therefore, the method of wastewater treatment of pig-breeding complexes and farms can be recommended for use in irrigation reclamation, which includes treatment of wastewater with burnt defecate in the dose of 50–200 mg/dm 3 , with the pH value varying in the range of 7.5–8.5. After settling-out of the obtained mixture in settlers, it is divided into a transparent liquid fraction and the sediment, i.e. an organomineral fertilizer. Afterwards, the fluidbody is fed to irrigation of agricultural land, and its excess is discharged into waterways and reservoirs. The sediment is fed to the vortex layer equipment with mobile ferromagnetic particles or thermolized, where their complete disinfection takes place.

  9. Results of a "GWAS plus:" general cognitive ability is substantially heritable and massively polygenic.

    Directory of Open Access Journals (Sweden)

    Robert M Kirkpatrick

    Full Text Available We carried out a genome-wide association study (GWAS for general cognitive ability (GCA plus three other analyses of GWAS data that aggregate the effects of multiple single-nucleotide polymorphisms (SNPs in various ways. Our multigenerational sample comprised 7,100 Caucasian participants, drawn from two longitudinal family studies, who had been assessed with an age-appropriate IQ test and had provided DNA samples passing quality screens. We conducted the GWAS across ∼ 2.5 million SNPs (both typed and imputed, using a generalized least-squares method appropriate for the different family structures present in our sample, and subsequently conducted gene-based association tests. We also conducted polygenic prediction analyses under five-fold cross-validation, using two different schemes of weighting SNPs. Using parametric bootstrapping, we assessed the performance of this prediction procedure under the null. Finally, we estimated the proportion of variance attributable to all genotyped SNPs as random effects with software GCTA. The study is limited chiefly by its power to detect realistic single-SNP or single-gene effects, none of which reached genome-wide significance, though some genomic inflation was evident from the GWAS. Unit SNP weights performed about as well as least-squares regression weights under cross-validation, but the performance of both increased as more SNPs were included in calculating the polygenic score. Estimates from GCTA were 35% of phenotypic variance at the recommended biological-relatedness ceiling. Taken together, our results concur with other recent studies: they support a substantial heritability of GCA, arising from a very large number of causal SNPs, each of very small effect. We place our study in the context of the literature-both contemporary and historical-and provide accessible explication of our statistical methods.

  10. Pediatric chronic pancreatitis is associated with genetic risk factors and substantial disease burden.

    Science.gov (United States)

    Schwarzenberg, Sarah Jane; Bellin, Melena; Husain, Sohail Z; Ahuja, Monika; Barth, Bradley; Davis, Heather; Durie, Peter R; Fishman, Douglas S; Freedman, Steven D; Gariepy, Cheryl E; Giefer, Matthew J; Gonska, Tanja; Heyman, Melvin B; Himes, Ryan; Kumar, Soma; Morinville, Veronique D; Lowe, Mark E; Nuehring, Neil E; Ooi, Chee Y; Pohl, John F; Troendle, David; Werlin, Steven L; Wilschanski, Michael; Yen, Elizabeth; Uc, Aliye

    2015-04-01

    To determine the clinical presentation, diagnostic variables, risk factors, and disease burden in children with chronic pancreatitis. We performed a cross-sectional study of data from the International Study Group of Pediatric Pancreatitis: In Search for a Cure, a registry of children with acute recurrent pancreatitis and chronic pancreatitis. Between-group differences were compared using Wilcoxon rank-sum test. Among 170 subjects in the registry, 76 (45%) had chronic pancreatitis; 57% were female, 80% were white; median age at diagnosis was 9.9 years. Pancreatitis-predisposing genetic mutations were identified in 51 (67%) and obstructive risk factors in 25 (33%). Toxic/metabolic and autoimmune factors were uncommon. Imaging demonstrated ductal abnormalities and pancreatic atrophy more commonly than calcifications. Fifty-nine (77%) reported abdominal pain within the past year; pain was reported as constant and receiving narcotics in 28%. Children with chronic pancreatitis reported a median of 3 emergency department visits and 2 hospitalizations in the last year. Forty-seven subjects (70%) missed 1 day of school in the past month as the result of chronic pancreatitis; 26 (34%) missed 3 or more days. Children reporting constant pain were more likely to miss school (P = .002), visit the emergency department (P = .01), and experience hospitalizations (P = .03) compared with children with episodic pain. Thirty-three children (43%) underwent therapeutic endoscopic retrograde pancreatography; one or more pancreatic surgeries were performed in 30 (39%). Chronic pancreatitis occurs at a young age with distinct clinical features. Genetic and obstructive risk factors are common, and disease burden is substantial. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Orange juice substantially reduces the bioavailability of the beta-adrenergic-blocking agent celiprolol.

    Science.gov (United States)

    Lilja, Jari J; Juntti-Patinen, Laura; Neuvonen, Pertti J

    2004-03-01

    Grapefruit juice was recently found to decrease plasma concentrations of the beta-adrenergic receptor-blocking agent celiprolol. Our objective was to investigate the effect of orange juice on the pharmacokinetics of celiprolol in healthy subjects. In a randomized crossover study with 2 phases and a washout of 2 weeks, 10 healthy volunteers ingested either 200 mL normal-strength orange juice or water 3 times a day for 2 days. On the morning of day 3, 1 hour after ingestion of 200 mL orange juice or water, each subject ingested 100 mg celiprolol with either 200 mL orange juice or water. In addition, 200 mL orange juice or water was ingested at 4, 10, 22, and 27 hours after celiprolol intake. The concentrations of celiprolol in plasma and its excretion into urine were measured up to 33 hours after its dosing. Systolic and diastolic blood pressures and heart rate were recorded up to 10 hours. Orange juice reduced the mean peak plasma concentration of celiprolol by 89% (P orange juice. Orange juice reduced the urinary excretion of celiprolol by 77% (P Orange juice substantially reduces the bioavailability of celiprolol, but the mechanism of this interaction remains to be resolved. For example, modulation of intestinal pH and of function of transporters implicated in the absorption of celiprolol may be involved. Because of the great extent of the orange juice-celiprolol interaction and a wide use of orange juice, this interaction is likely to have clinical importance in some patients, although hemodynamic consequences were not seen in young healthy subjects.

  12. USING SPLINE FUNCTIONS FOR THE SUBSTANTIATION OF TAX POLICIES BY LOCAL AUTHORITIES

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    Otgon Cristian

    2011-07-01

    Full Text Available The paper aims to approach innovative financial instruments for the management of public resources. In the category of these innovative tools have been included polynomial spline functions used for budgetary sizing in the substantiating of fiscal and budgetary policies. In order to use polynomial spline functions there have been made a number of steps consisted in the establishment of nodes, the calculation of specific coefficients corresponding to the spline functions, development and determination of errors of approximation. Also in this paper was done extrapolation of series of property tax data using polynomial spline functions of order I. For spline impelementation were taken two series of data, one reffering to property tax as a resultative variable and the second one reffering to building tax, resulting a correlation indicator R=0,95. Moreover the calculation of spline functions are easy to solve and due to small errors of approximation have a great power of predictibility, much better than using ordinary least squares method. In order to realise the research there have been used as methods of research several steps, namely observation, series of data construction and processing the data with spline functions. The data construction is a daily series gathered from the budget account, reffering to building tax and property tax. The added value of this paper is given by the possibility of avoiding deficits by using spline functions as innovative instruments in the publlic finance, the original contribution is made by the average of splines resulted from the series of data. The research results lead to conclusion that the polynomial spline functions are recommended to form the elaboration of fiscal and budgetary policies, due to relatively small errors obtained in the extrapolation of economic processes and phenomena. Future research directions are taking in consideration to study the polynomial spline functions of second-order, third

  13. One Minute of Marijuana Secondhand Smoke Exposure Substantially Impairs Vascular Endothelial Function.

    Science.gov (United States)

    Wang, Xiaoyin; Derakhshandeh, Ronak; Liu, Jiangtao; Narayan, Shilpa; Nabavizadeh, Pooneh; Le, Stephenie; Danforth, Olivia M; Pinnamaneni, Kranthi; Rodriguez, Hilda J; Luu, Emmy; Sievers, Richard E; Schick, Suzaynn F; Glantz, Stanton A; Springer, Matthew L

    2016-07-27

    Despite public awareness that tobacco secondhand smoke (SHS) is harmful, many people still assume that marijuana SHS is benign. Debates about whether smoke-free laws should include marijuana are becoming increasingly widespread as marijuana is legalized and the cannabis industry grows. Lack of evidence for marijuana SHS causing acute cardiovascular harm is frequently mistaken for evidence that it is harmless, despite chemical and physical similarity between marijuana and tobacco smoke. We investigated whether brief exposure to marijuana SHS causes acute vascular endothelial dysfunction. We measured endothelial function as femoral artery flow-mediated dilation (FMD) in rats before and after exposure to marijuana SHS at levels similar to real-world tobacco SHS conditions. One minute of exposure to marijuana SHS impaired FMD to a comparable extent as impairment from equal concentrations of tobacco SHS, but recovery was considerably slower for marijuana. Exposure to marijuana SHS directly caused cannabinoid-independent vasodilation that subsided within 25 minutes, whereas FMD remained impaired for at least 90 minutes. Impairment occurred even when marijuana lacked cannabinoids and rolling paper was omitted. Endothelium-independent vasodilation by nitroglycerin administration was not impaired. FMD was not impaired by exposure to chamber air. One minute of exposure to marijuana SHS substantially impairs endothelial function in rats for at least 90 minutes, considerably longer than comparable impairment by tobacco SHS. Impairment of FMD does not require cannabinoids, nicotine, or rolling paper smoke. Our findings in rats suggest that SHS can exert similar adverse cardiovascular effects regardless of whether it is from tobacco or marijuana. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  14. Psilocybin can occasion mystical-type experiences having substantial and sustained personal meaning and spiritual significance.

    Science.gov (United States)

    Griffiths, R R; Richards, W A; McCann, U; Jesse, R

    2006-08-01

    Although psilocybin has been used for centuries for religious purposes, little is known scientifically about its acute and persisting effects. This double-blind study evaluated the acute and longer-term psychological effects of a high dose of psilocybin relative to a comparison compound administered under comfortable, supportive conditions. The participants were hallucinogen-naïve adults reporting regular participation in religious or spiritual activities. Two or three sessions were conducted at 2-month intervals. Thirty volunteers received orally administered psilocybin (30 mg/70 kg) and methylphenidate hydrochloride (40 mg/70 kg) in counterbalanced order. To obscure the study design, six additional volunteers received methylphenidate in the first two sessions and unblinded psilocybin in a third session. The 8-h sessions were conducted individually. Volunteers were encouraged to close their eyes and direct their attention inward. Study monitors rated volunteers' behavior during sessions. Volunteers completed questionnaires assessing drug effects and mystical experience immediately after and 2 months after sessions. Community observers rated changes in the volunteer's attitudes and behavior. Psilocybin produced a range of acute perceptual changes, subjective experiences, and labile moods including anxiety. Psilocybin also increased measures of mystical experience. At 2 months, the volunteers rated the psilocybin experience as having substantial personal meaning and spiritual significance and attributed to the experience sustained positive changes in attitudes and behavior consistent with changes rated by community observers. When administered under supportive conditions, psilocybin occasioned experiences similar to spontaneously occurring mystical experiences. The ability to occasion such experiences prospectively will allow rigorous scientific investigations of their causes and consequences.

  15. Biological substantiation of antipsychotic-associated pneumonia: Systematic literature review and computational analyses.

    Science.gov (United States)

    Sultana, Janet; Calabró, Marco; Garcia-Serna, Ricard; Ferrajolo, Carmen; Crisafulli, Concetta; Mestres, Jordi; Trifirò', Gianluca

    2017-01-01

    Antipsychotic (AP) safety has been widely investigated. However, mechanisms underlying AP-associated pneumonia are not well-defined. The aim of this study was to investigate the known mechanisms of AP-associated pneumonia through a systematic literature review, confirm these mechanisms using an independent data source on drug targets and attempt to identify novel AP drug targets potentially linked to pneumonia. A search was conducted in Medline and Web of Science to identify studies exploring the association between pneumonia and antipsychotic use, from which information on hypothesized mechanism of action was extracted. All studies had to be in English and had to concern AP use as an intervention in persons of any age and for any indication, provided that the outcome was pneumonia. Information on the study design, population, exposure, outcome, risk estimate and mechanism of action was tabulated. Public repositories of pharmacology and drug safety data were used to identify the receptor binding profile and AP safety events. Cytoscape was then used to map biological pathways that could link AP targets and off-targets to pneumonia. The literature search yielded 200 articles; 41 were included in the review. Thirty studies reported a hypothesized mechanism of action, most commonly activation/inhibition of cholinergic, histaminergic and dopaminergic receptors. In vitro pharmacology data confirmed receptor affinities identified in the literature review. Two targets, thromboxane A2 receptor (TBXA2R) and platelet activating factor receptor (PTAFR) were found to be novel AP target receptors potentially associated with pneumonia. Biological pathways constructed using Cytoscape identified plausible biological links potentially leading to pneumonia downstream of TBXA2R and PTAFR. Innovative approaches for biological substantiation of drug-adverse event associations may strengthen evidence on drug safety profiles and help to tailor pharmacological therapies to patient risk

  16. National South African HIV prevalence estimates robust despite substantial test non-participation

    Directory of Open Access Journals (Sweden)

    Guy Harling

    2017-07-01

    Full Text Available Background. South African (SA national HIV seroprevalence estimates are of crucial policy relevance in the country, and for the worldwide HIV response. However, the most recent nationally representative HIV test survey in 2012 had 22% test non-participation, leaving the potential for substantial bias in current seroprevalence estimates, even after controlling for selection on observed factors. Objective. To re-estimate national HIV prevalence in SA, controlling for bias due to selection on both observed and unobserved factors in the 2012 SA National HIV Prevalence, Incidence and Behaviour Survey. Methods. We jointly estimated regression models for consent to test and HIV status in a Heckman-type bivariate probit framework. As selection variable, we used assigned interviewer identity, a variable known to predict consent but highly unlikely to be associated with interviewees’ HIV status. From these models, we estimated the HIV status of interviewed participants who did not test. Results. Of 26 710 interviewed participants who were invited to test for HIV, 21.3% of females and 24.3% of males declined. Interviewer identity was strongly correlated with consent to test for HIV; declining a test was weakly associated with HIV serostatus. Our HIV prevalence estimates were not significantly different from those using standard methods to control for bias due to selection on observed factors: 15.1% (95% confidence interval (CI 12.1 - 18.6 v. 14.5% (95% CI 12.8 - 16.3 for 15 - 49-year-old males; 23.3% (95% CI 21.7 - 25.8 v. 23.2% (95% CI 21.3 - 25.1 for 15 - 49-year-old females. Conclusion. The most recent SA HIV prevalence estimates are robust under the strongest available test for selection bias due to missing data. Our findings support the reliability of inferences drawn from such data.

  17. Expansion of a globally pervasive grass occurs without substantial trait differences between home and away populations.

    Science.gov (United States)

    Leifso, A; MacDougall, A S; Husband, B; Hierro, J L; Köchy, M; Pärtel, M; Peltzer, D A

    2012-12-01

    The global expansion of species beyond their ancestral ranges can derive from mechanisms that are trait-based (e.g., post-establishment evolved differences compared to home populations) or circumstantial (e.g., propagule pressure, with no trait-based differences). These mechanisms can be difficult to distinguish following establishment, but each makes unique predictions regarding trait similarity between ancestral ('home') and introduced ('away') populations. Here, we tested for trait-based population differences across four continents for the globally distributed grass Dactylis glomerata, to assess the possible role of trait evolution in its worldwide expansion. We used a common-environment glasshouse experiment to quantify trait differences among home and away populations, and the potential relevance of these differences for competitive interactions. Few significant trait differences were found among continents, suggesting minimal change during global expansion. All populations were polyploids, with similar foliar carbon:nitrogen ratios (a proxy for defense), chlorophyll content, and biomass. Emergence time and growth rate favored home populations, resulting in their competitive superiority over away populations. Small but significant trait differences among away populations suggest different introductory histories or local adaptive responses following establishment. In summary, the worldwide distribution of this species appears to have arisen from its pre-adapted traits promoting growth, and its repeated introduction with cultivation and intense propagule pressure. Global expansion can thus occur without substantial shifts in growth, reproduction, or defense. Rather than focusing strictly on the invader, invasion success may also derive from the traits found (or lacking) in the recipient community and from environmental context including human disturbance.

  18. NSRD-06. Computational Capability to Substantiate DOE-HDBK-3010 Data

    Energy Technology Data Exchange (ETDEWEB)

    Louie, David L.Y. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Brown, Alexander L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-12-01

    Safety basis analysts throughout the U.S. Department of Energy (DOE) complex rely heavily on the information provided in the DOE Hand book, DOE-HDBK-3010, Airborne Release Fractions/Rates and Resp irable Fractions for Nonreactor Nuclear Facilities , to determine source terms. In calcula ting source terms, analysts tend to use the DOE Handbook's bounding values on airbor ne release fractions (ARFs) and respirable fractions (RFs) for various cat egories of insults (representing potential accident release categories). This is typica lly due to both time constraints and the avoidance of regulatory critique. Unfort unately, these bounding ARFs/RFs represent extremely conservative values. Moreover, th ey were derived from very limited small- scale table-top and bench/labo ratory experiments and/or fr om engineered judgment. Thus the basis for the data may not be re presentative to the actual unique accident conditions and configura tions being evaluated. The goal of this res earch is to develop a more ac curate method to identify bounding values for the DOE Handbook using the st ate-of-art multi-physics-based high performance computer codes. This enable s us to better understand the fundamental physics and phenomena associated with the ty pes of accidents for the data described in it. This research has examined two of the DOE Handbook's liquid fire experiments to substantiate the airborne release frac tion data. We found th at additional physical phenomena (i.e., resuspension) need to be included to derive bounding values. For the specific cases of solid powder under pre ssurized condition and mechanical insult conditions the codes demonstrated that we can simulate the phenomena. This work thus provides a low-cost method to establis h physics-justified sa fety bounds by taking into account specific geometri es and conditions that may not have been previously measured and/or are too costly to do so.

  19. Gait biomechanics of skipping are substantially different than those of running.

    Science.gov (United States)

    McDonnell, Jessica; Willson, John D; Zwetsloot, Kevin A; Houmard, Joseph; DeVita, Paul

    2017-11-07

    The inherit injury risk associated with high-impact exercises calls for alternative ways to achieve the benefits of aerobic exercise while minimizing excessive stresses to body tissues. Skipping presents such an alternative, incorporating double support, flight, and single support phases. We used ground reaction forces (GRFs), lower extremity joint torques and powers to compare skipping and running in 20 healthy adults. The two consecutive skipping steps on each limb differed significantly from each other, and from running. Running had the longest step length, the highest peak vertical GRF, peak knee extensor torque, and peak knee negative and positive power and negative and positive work. Skipping had the greater cadence, peak horizontal GRF, peak hip and ankle extensor torques, peak ankle negative power and work, and peak ankle positive power. The second vs first skipping step had the shorter step length, higher cadence, peak horizontal GRF, peak ankle extensor torque, and peak ankle negative power, negative work, and positive power and positive work. The first skipping step utilized predominately net negative joint work (eccentric muscle action) while the second utilized predominately net positive joint work (concentric muscle action). The skipping data further highlight the persistence of net negative work performed at the knee and net positive work performed at the ankle across locomotion gaits. Evidence of step segregation was seen in distribution of the braking and propelling impulses and net work produced across the hip, knee, and ankle joints. Skipping was substantially different than running and was temporally and spatially asymmetrical with successive foot falls partitioned into a dominant function, either braking or propelling whereas running had a single, repeated step in which both braking and propelling actions were performed equally. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Substantiation of strength of TVSA-ALPHA fuel assembly under dynamic seismic loads

    International Nuclear Information System (INIS)

    Tutnov, A.; Kiselev, A.; Kiselev, A.; Krutko, E.; Kiselev, I.; Samoilov, O.; Kaydalov, V.

    2009-01-01

    A special place in the substantiation of the safe operation of fuel assemblies is the assessment their operating capability under seismic loads, leading to short-term (several seconds or tens of seconds) the dynamic effects on the reactor core. The level of acceleration of various elements of the reactor installation can be higher than 1,5 g (g - acceleration of gravity) and depends on the height of these elements relatively the ground, which movement causes an earthquake. This dynamic load cause significant deformation of the active zones design element, in particular of the fuel assemblies (FA), which could lead to a contact (or impact) interaction between them. The report presents the results of studies of stress-strain state of FA of TVSA-ALPHA type under the influence of seismic loads of the 8th level on Richter scale using standard approach. According to a normative approach the natural frequencies and modes of FA are calculated in the preliminary stage. The obtained results are conservative from the point of view that in the real FA design the most loaded SG in the middle of the fuel assemblies are made in a combined with mixing grid variant, which are joint by a common rim. This increases the overall carrying capacity of SG as compared with the calculation SG model. It is also necessary to bear in mind that the dynamic (impact) loading the basic mechanical properties of the material may have a significant difference from static (standard) values. This refers in particular to the yield limit, the value of which can be several times higher than specified in the calculation

  1. Morphological substantiation for acute immobilization stress-related disorders of adaptation mechanisms.

    Science.gov (United States)

    Koptev, Mykhailo M; Vynnyk, Nataliia I

    Nowadays, an individual is being constantly accompanied by stresses in his/her everyday life. Stress reactions, produced in the process of evolution, have become the organisms' response to emergency action or pathological factors and are the important link in adaptation process. However, the adverse course of stress reaction can lead to derangement of the adaptation mechanisms in the body and become the element of the pathogenesis of various diseases. The study was aimed at morphological substantiation of derangement of adaptation mechanisms in white Wistar rats caused by the acute immobilization stress. 40 Wistar white male rats of 240-260 g body weight aged 8-10 months were involved into study. 20 laboratory animals were assigned to the main group and the rest 20 rats formed the control (II) group. Experimental stress model was simulated by immobilization of rats, lying supine, for 6 hours. Morphological examination of heart, lungs and kidneys was carried out after animals' decapitation, which proved the derangement of rats' adaptation mechanisms caused by the acute immobilization stress. It has been established that six-hour immobility of rats, lying in the supine position, led to the development of destructive phenomena, hemorrhagic lesions and impaired hemomicrocirculation. Microscopically, the acute immobilization stress causes significant subendocardial hemorrhages, plethora of vessels of hemomicrocirculatory flow with dysdiemorrhysis, myocardial intersticium edema in the heart. Histologically, immobilization-induced trauma causes significant hemodynamic disorders, spasm of arterioles and considerable venous hyperemia, concomitant with microthrombosis in kidneys; at the same time dystrophic lesions and desquamation of epithelium of renal tubules has been observed in renal corpuscles. The abovementioned structural changes can contribute to origination and development of multiple lesions, demonstrating the morphologically grounded role of the acute

  2. 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.

  3. Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [Univ. of Minnesota, Minneapolis, MN (United States)

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  4. Variation in Recommendation for Surgical Treatment for Compressive Neuropathy

    NARCIS (Netherlands)

    Hageman, Michiel G. H.; Becker, Stephanie J. E.; Bot, Arjan G. J.; Guitton, Thierry; Ring, David; Wahegaonkar, Abhijeet L.; Garcia, Aida E.; Schefer, Alan; Castillo, Alberto Perez; Terrono, Andrew L.; Gurman, Andrew W.; Apard, T.; Watkins, Barry; Ilyas, Asif; Hearon, Bernard F.; Wills, Brian P. D.; Wintman, Bruce I.; Swigart, Carrie; Spath, Catherine; Dario, Cesar; Miranda, Oliveira; Goldfarb, Charles A.; Cassidy, Charles; Metzger, Charles; Eaton, Charles; Wilson, Chris; Walsh, Christopher J.; Wilson, Christopher J.; Jones, Christopher M.; Young, Colby; Bottke, Craig A.; Osei, Daniel A.; Kirkpatrick, D. Kay; Tate, David; Polatsch, Daniel; Nelson, David L.; Kalainov, David M.; Lamey, David M.; Hanel, Doug; Ostrowski, David M.; Miller, David R.; McKee, Desirae M.; Shin, Eon K.; Ruchelsman, David; Bonatz, Ekkehard; Hofmeister, Eric P.; Fischer, Evan S.; Kaplan, F. Thomas D.; Fernandes, C. H.; Forigua, Jamie E.; Cayon Cayon, Fidel Ernesto; Raia, Frank J.; Walter, Frank L.; Frykman, Gary K.; Pess, Gary M.; Kuzma, Gary R.; Huemer, Georg M.; Byrd, Gregory Dee; Balfour, George W.; Caro, Gladys Cecilia Zambrano; Hernandez, German Ricardo; DeSilva, Gregory; Bamberger, H. Brent; Grunwald, H. W.; MccUtchan, Hal; Solomon, Harrison; Kimball, Hervey L.; Stuart, J. E. B.; Lin, Ines C.; Choueka, Jack; Reid, James G.; Boler, James M.; Pomerance, Jay; Johnson, Jeff W.; Yao, Jeffrey; Calandruccio, Jim; Green, Jennifer B.; Wolf, Jennifer Moriatis; Frankenhoff, Jessica A.; Oakey, Jerome W.; Fischer, Jochen; Howlett, John; Jiuliano, John; Erickson, John M.; McAuliffe, John; Evans, John P.; Taras, John; Boretto, Jorge G.; Isaacs, Jonathan; Di Giovanni, Jose Fernando; Nolla, Jose; Abzug, Joshua M.; Adams, Julie; Chivers, Karel; Prommersberger, Karl-Josef; Malone, Kevin J.; Lee, Kendrick; Halperin, Lawrence S.; Weiss, Lawrence; Benson, Leon; Lane, Lewis B.; Paz, Lior; Lattanza, Lisa; Palmer, M. Jason; Catalano, Louis; Richard, Marc J.; Rizzo, Marco; Boyer, Martin; Calcagni, Maurizio; Wood, Megan M.; Baskies, Michael; Grafe, Michael W.; Behrman, Michael; Jones, Michael; Quinn, Michael; Nancollas, Michael; Kessler, Michael W.; Pirela-Cruz, Miguel A.; Patel, Milan M.; Felipe, Naquira Escobar Luis; Harness, Neil G.; Akabudike, Ngozi M.; Horangic, Nicholas J.; Semenkin, Oleg M.; Leung, Nicky L.; McCulloch, Patrick T.; Owens, Patrick W.; Martineau, Paul A.; Bettinger, Paul; Guidera, Paul; Hoepfner, Peter E.; Sitaram, Prasad; DeNoble, Peter H.; Jebson, Peter; Coogan, Philip; Dantuluri, Phani; Gaston, R. Glenn; Nyszkiewicz, Ralf; Costanzo, Ralph M.; de Bedout, Ramon; Hauck, Randy; Fricker, Renato M.; GIlbert, Richard S.; Hutchison, Richard L.; Barth, Richard W.; Papandrea, Rick; Szabo, Robert M.; Gray, Robert R. L.; Nathan, Ross; Spruijt, Sander; Shatford, Russell; Klinefelter, Ryan; Sodha, Samir; Calfee, Ryan P.; Kakar, Sanjeev; Kaplan, Saul; Duncan, Scott F.; Mitchell, Scott; Dodds, Seth; Jacoby, Sidney M.; Kennedy, Stephen A.; Marczyk, Stanley Casimir; Dailey, Stephen W.; Kronlage, Steve; Alter, Steven; Beldner, Steven; McCabe, Steven J.; Hilliard, Stuart M.; Fischer, Thomas J.; Baxamusa, Taizoon; Taleb, C.; Varecka, Thomas F.; Wyrick, Theresa; Havenhill, Timothy G.; Siff, Todd; Knoll, Victoria D.; Patel, Vipul P.; Batson, W. Arnnold; Hammert, Warren C.; van Wyk, William J.

    2013-01-01

    Purpose It is our impression that there is substantial, unexplained variation in hand surgeon recommendations for treatment of peripheral mononeuropathy. We tested the null hypothesis that specific patient and provider factors do not influence recommendations for surgery. Methods Using a web-based

  5. Debate over Islamic Symbolism and Substantialism in the Formulation of Local Regulation in Tasikmalaya Municipality

    Directory of Open Access Journals (Sweden)

    Fitriyani Yuliawati

    2018-01-01

    Full Text Available This study aims to reveal debate over the formulation of local regulation. Particularly, it seeks to know political dynamics at the grassroot level in policy-making. Theoretical assumption mentions that policy-making is not only a process of government technocracy, but it can also a debate over current discourse among citizens. The qualitative study discloses that the political debate over this discourse occurs due to contradictory perspectives on the aspirations of Shari’a law as a part of formal institutions in the state. The first camp argued that Islam should exist in the public as an effort to build an ideal society. Islam must be included as part of the state, at least in local regulation. In contrast, the second camp argued that in building the ideal society, state does not need to include Islam as part of the state in the regulation.

  6. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions

    Energy Technology Data Exchange (ETDEWEB)

    Angle, Jordan C.; Morin, Timothy H.; Solden, Lindsey M.; Narrowe, Adrienne B.; Smith, Garrett J.; Borton, Mikayla A.; Rey-Sanchez, Camilo; Daly, Rebecca A.; Mirfenderesgi, Golnazalsdat; Hoyt, David W.; Riley, William J.; Miller, Christopher S.; Bohrer, Gil; Wrighton, Kelly C.

    2017-11-16

    The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats1-4. In contrast, here porewater and greenhouse-gas flux measurements show clear evidence for methane production in well-oxygenated soils from a freshwater wetland. A comparison of oxic to anoxic soils revealed up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recovered the first near complete genomes for a novel methanogen species, and showed acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanosaeta oxydurans, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimated that a dominant fraction of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together our findings challenge a widely-held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.

  7. Quantum variational calculus

    CERN Document Server

    Malinowska, Agnieszka B

    2014-01-01

    This Brief puts together two subjects, quantum and variational calculi by considering variational problems involving Hahn quantum operators. The main advantage of its results is that they are able to deal with nondifferentiable (even discontinuous) functions, which are important in applications. Possible applications in economics are discussed. Economists model time as continuous or discrete. Although individual economic decisions are generally made at discrete time intervals, they may well be less than perfectly synchronized in ways discrete models postulate. On the other hand, the usual assumption that economic activity takes place continuously, is nothing else than a convenient abstraction that in many applications is far from reality. The Hahn quantum calculus helps to bridge the gap between the two families of models: continuous and discrete. Quantum Variational Calculus is self-contained and unified in presentation. It provides an opportunity for an introduction to the quantum calculus of variations fo...

  8. Variational Monte Carlo Technique

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 8. Variational Monte Carlo Technique: Ground State Energies of Quantum Mechanical Systems. Sukanta Deb. General Article Volume 19 Issue 8 August 2014 pp 713-739 ...

  9. Variational principles in physics

    CERN Document Server

    Basdevant, Jean-Louis

    2007-01-01

    Optimization under constraints is an essential part of everyday life. Indeed, we routinely solve problems by striking a balance between contradictory interests, individual desires and material contingencies. This notion of equilibrium was dear to thinkers of the enlightenment, as illustrated by Montesquieu’s famous formulation: "In all magistracies, the greatness of the power must be compensated by the brevity of the duration." Astonishingly, natural laws are guided by a similar principle. Variational principles have proven to be surprisingly fertile. For example, Fermat used variational methods to demonstrate that light follows the fastest route from one point to another, an idea which came to be known as Fermat’s principle, a cornerstone of geometrical optics. Variational Principles in Physics explains variational principles and charts their use throughout modern physics. The heart of the book is devoted to the analytical mechanics of Lagrange and Hamilton, the basic tools of any physicist. Prof. Basdev...

  10. Cigarette smoking substantially alters plasma microRNA profiles in healthy subjects

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Kei; Yokota, Shin-ichi; Tatsumi, Naoyuki; Fukami, Tatsuki; Yokoi, Tsuyoshi; Nakajima, Miki, E-mail: nmiki@p.kanazawa-u.ac.jp

    2013-10-01

    Circulating microRNAs (miRNAs) are receiving attention as potential biomarkers of various diseases, including cancers, chronic obstructive pulmonary disease, and cardiovascular disease. However, it is unknown whether the levels of circulating miRNAs in a healthy subject might vary with external factors in daily life. In this study, we investigated whether cigarette smoking, a habit that has spread throughout the world and is a risk factor for various diseases, affects plasma miRNA profiles. We determined the profiles of 11 smokers and 7 non-smokers by TaqMan MicroRNA array analysis. A larger number of miRNAs were detected in smokers than in non-smokers, and the plasma levels of two-thirds of the detected miRNAs (43 miRNAs) were significantly higher in smokers than in non-smokers. A principal component analysis of the plasma miRNA profiles clearly separated smokers and non-smokers. Twenty-four of the miRNAs were previously reported to be potential biomarkers of disease, suggesting the possibility that smoking status might interfere with the diagnosis of disease. Interestingly, we found that quitting smoking altered the plasma miRNA profiles to resemble those of non-smokers. These results suggested that the differences in the plasma miRNA profiles between smokers and non-smokers could be attributed to cigarette smoking. In addition, we found that an acute exposure of ex-smokers to cigarette smoke (smoking one cigarette) did not cause a dramatic change in the plasma miRNA profile. In conclusion, we found that repeated cigarette smoking substantially alters the plasma miRNA profile, interfering with the diagnosis of disease or signaling potential smoking-related diseases. - Highlights: • Plasma miRNA profiles were unambiguously different between smokers and non-smokers. • Smoking status might interfere with the diagnosis of disease using plasma miRNAs. • Changes of plasma miRNA profiles may be a signal of smoking-related diseases.

  11. Wnt5a signaling is a substantial constituent in bone morphogenetic protein-2-mediated osteoblastogenesis

    International Nuclear Information System (INIS)

    Nemoto, Eiji; Ebe, Yukari; Kanaya, Sousuke; Tsuchiya, Masahiro; Nakamura, Takashi; Tamura, Masato; Shimauchi, Hidetoshi

    2012-01-01

    Highlights: ► Wnt5a is identified in osteoblasts in tibial growth plate and bone marrow. ► Osteoblastic differentiation is associated with increased expression of Wnt5a/Ror2. ► Wnt5a/Ror2 signaling is important for BMP-2-mediated osteoblastic differentiation. ► Wnt5a/Ror2 operates independently of BMP-Smad pathway. -- Abstract: Wnts are secreted glycoproteins that mediate developmental and post-developmental physiology by regulating cellular processes including proliferation, differentiation, and apoptosis through β-catenin-dependent canonical and β-catenin-independent noncanonical pathway. It has been reported that Wnt5a activates noncanonical Wnt signaling through receptor tyrosine kinase-like orphan receptor 2 (Ror2). Although it appears that Wnt5a/Ror2 signaling supports normal bone physiology, the biological significance of noncanonical Wnts in osteogenesis is essentially unknown. In this study, we identified expression of Wnt5a in osteoblasts in the ossification zone of the tibial growth plate as well as bone marrow of the rat tibia as assessed by immunohistochemistry. In addition, we show that osteoblastic differentiation mediated by BMP-2 is associated with increased expression of Wnt5a and Ror2 using cultured pre-osteoblasts, MC3T3-E1 cells. Silencing gene expression of Wnt5a and Ror2 in MC3T3-E1 cells results in suppression of BMP-2-mediated osteoblastic differentiation, suggesting that Wnt5a and Ror2 signaling are of substantial importance for BMP-2-mediated osteoblastic differentiation. BMP-2 stimulation induced phosphorylation of Smad1/5/8 in a similar fashion in both siWnt5a-treated cells and control cells, suggesting that Wnt5a was dispensable for the phosphorylation of Smads by BMP-2. Taken together, our results suggest that Wnt5a/Ror2 signaling appears to be involved in BMP-2-mediated osteoblast differentiation in a Smad independent pathway.

  12. Imatinib treatment causes substantial transcriptional changes in adult Schistosoma mansoni in vitro exhibiting pleiotropic effects.

    Directory of Open Access Journals (Sweden)

    Christin Buro

    2014-06-01

    Imatinib on worm physiology substantiating the role of PKs as interesting targets.

  13. Evidence that global evapotranspiration makes a substantial contribution to the global atmospheric temperature slowdown

    Science.gov (United States)

    Leggett, L. Mark W.; Ball, David A.

    2018-02-01

    The difference between the time series trend for temperature expected from the increasing level of atmospheric CO2 and that for the (more slowly rising) observed temperature has been termed the global surface temperature slowdown. In this paper, we characterise the single time series made from the subtraction of these two time series as the `global surface temperature gap'. We also develop an analogous atmospheric CO2 gap series from the difference between the level of CO2 and first-difference CO2 (that is, the change in CO2 from one period to the next). This paper provides three further pieces of evidence concerning the global surface temperature slowdown. First, we find that the present size of both the global surface temperature gap and the CO2 gap is unprecedented over a period starting at least as far back as the 1860s. Second, ARDL and Granger causality analyses involving the global surface temperature gap against the major candidate physical drivers of the ocean heat sink and biosphere evapotranspiration are conducted. In each case where ocean heat data was available, it was significant in the models: however, evapotranspiration, or its argued surrogate precipitation, also remained significant in the models alongside ocean heat. In terms of relative scale, the standardised regression coefficient for evapotranspiration was repeatedly of the same order of magnitude as—typically as much as half that for—ocean heat. The foregoing is evidence that, alongside the ocean heat sink, evapotranspiration is also likely to be making a substantial contribution to the global atmospheric temperature outcome. Third, there is evidence that both the ocean heat sink and the evapotranspiration process might be able to continue into the future to keep the temperature lower than the level-of-CO2 models would suggest. It is shown that this means there can be benefit in using the first-difference CO2 to temperature relationship shown in Leggett and Ball (Atmos Chem Phys 15

  14. Cigarette smoking substantially alters plasma microRNA profiles in healthy subjects

    International Nuclear Information System (INIS)

    Takahashi, Kei; Yokota, Shin-ichi; Tatsumi, Naoyuki; Fukami, Tatsuki; Yokoi, Tsuyoshi; Nakajima, Miki

    2013-01-01

    Circulating microRNAs (miRNAs) are receiving attention as potential biomarkers of various diseases, including cancers, chronic obstructive pulmonary disease, and cardiovascular disease. However, it is unknown whether the levels of circulating miRNAs in a healthy subject might vary with external factors in daily life. In this study, we investigated whether cigarette smoking, a habit that has spread throughout the world and is a risk factor for various diseases, affects plasma miRNA profiles. We determined the profiles of 11 smokers and 7 non-smokers by TaqMan MicroRNA array analysis. A larger number of miRNAs were detected in smokers than in non-smokers, and the plasma levels of two-thirds of the detected miRNAs (43 miRNAs) were significantly higher in smokers than in non-smokers. A principal component analysis of the plasma miRNA profiles clearly separated smokers and non-smokers. Twenty-four of the miRNAs were previously reported to be potential biomarkers of disease, suggesting the possibility that smoking status might interfere with the diagnosis of disease. Interestingly, we found that quitting smoking altered the plasma miRNA profiles to resemble those of non-smokers. These results suggested that the differences in the plasma miRNA profiles between smokers and non-smokers could be attributed to cigarette smoking. In addition, we found that an acute exposure of ex-smokers to cigarette smoke (smoking one cigarette) did not cause a dramatic change in the plasma miRNA profile. In conclusion, we found that repeated cigarette smoking substantially alters the plasma miRNA profile, interfering with the diagnosis of disease or signaling potential smoking-related diseases. - Highlights: • Plasma miRNA profiles were unambiguously different between smokers and non-smokers. • Smoking status might interfere with the diagnosis of disease using plasma miRNAs. • Changes of plasma miRNA profiles may be a signal of smoking-related diseases

  15. Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.

    Science.gov (United States)

    Thielen, Alexander; Lengauer, Thomas; Swenson, Luke C; Dong, Winnie W Y; McGovern, Rachel A; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

    2011-01-01

    The main determinants of HIV-1 coreceptor usage are located in the V3-loop of gp120, although mutations in V2 and gp41 are also known. Incorporation of V2 is known to improve prediction algorithms; however, this has not been confirmed for gp41 mutations. Samples with V3 and gp41 genotypes and Trofile assay (Monogram Biosciences, South San Francisco, CA, USA) results were taken from the HOMER cohort (n=444) and from patients screened for the MOTIVATE studies (n=1,916; 859 with maraviroc outcome data). Correlations of mutations with tropism were assessed using Fisher's exact test and prediction models trained using support vector machines. Models were validated by cross-validation, by testing models from one dataset on the other, and by analysing virological outcome. Several mutations within gp41 were highly significant for CXCR4 usage; most strikingly an insertion occurring in 7.7% of HOMER-R5 and 46.3% of HOMER-X4 samples (MOTIVATE 5.7% and 25.2%, respectively). Models trained on gp41 sequence alone achieved relatively high areas under the receiver-operating characteristic curve (AUCs; HOMER 0.713 and MOTIVATE 0.736) that were almost as good as V3 models (0.773 and 0.884, respectively). However, combining the two regions improved predictions only marginally (0.813 and 0.902, respectively). Similar results were found when models were trained on HOMER and validated on MOTIVATE or vice versa. The difference in median log viral load decrease at week 24 between patients with R5 and X4 virus was 1.65 (HOMER 2.45 and MOTIVATE 0.79) for V3 models, 1.59 for gp41-models (2.42 and 0.83, respectively) and 1.58 for the combined predictor (2.44 and 0.86, respectively). Several mutations within gp41 showed strong correlation with tropism in two independent datasets. However, incorporating gp41 mutations into prediction models is not mandatory because they do not improve substantially on models trained on V3 sequences alone.

  16. Seventy years of continuous encroachment substantially increases 'blue carbon' capacity as mangroves replace intertidal salt marshes.

    Science.gov (United States)

    Kelleway, Jeffrey J; Saintilan, Neil; Macreadie, Peter I; Skilbeck, Charles G; Zawadzki, Atun; Ralph, Peter J

    2016-03-01

    Shifts in ecosystem structure have been observed over recent decades as woody plants encroach upon grasslands and wetlands globally. The migration of mangrove forests into salt marsh ecosystems is one such shift which could have important implications for global 'blue carbon' stocks. To date, attempts to quantify changes in ecosystem function are essentially constrained to climate-mediated pulses (30 years or less) of encroachment occurring at the thermal limits of mangroves. In this study, we track the continuous, lateral encroachment of mangroves into two south-eastern Australian salt marshes over a period of 70 years and quantify corresponding changes in biomass and belowground C stores. Substantial increases in biomass and belowground C stores have resulted as mangroves replaced salt marsh at both marine and estuarine sites. After 30 years, aboveground biomass was significantly higher than salt marsh, with biomass continuing to increase with mangrove age. Biomass increased at the mesohaline river site by 130 ± 18 Mg biomass km(-2)  yr(-1) (mean ± SE), a 2.5 times higher rate than the marine embayment site (52 ± 10 Mg biomass km(-2) yr(-1) ), suggesting local constraints on biomass production. At both sites, and across all vegetation categories, belowground C considerably outweighed aboveground biomass stocks, with belowground C stocks increasing at up to 230 ± 62 Mg C km(-2) yr(-1) (± SE) as mangrove forests developed. Over the past 70 years, we estimate mangrove encroachment may have already enhanced intertidal biomass by up to 283 097 Mg and belowground C stocks by over 500 000 Mg in the state of New South Wales alone. Under changing climatic conditions and rising sea levels, global blue carbon storage may be enhanced as mangrove encroachment becomes more widespread, thereby countering global warming. © 2015 John Wiley & Sons Ltd.

  17. Substantial decline in sugar-sweetened beverage consumption among California’s children and adolescents

    Directory of Open Access Journals (Sweden)

    Lu Shi

    2010-08-01

    Full Text Available Lu Shi, Jeroen van MeijgaardUCLA Health Forecasting, UCLA School of Public Health, Los Angeles, CA, USAIntroduction: Few studies have looked at changes among risk factors that might help explain why childhood obesity prevalence in the US has leveled off in recent years. We present an analysis of the California Health Interview Survey (CHIS that examines trends in childhood and adolescent obesity as well as trends in sugar-sweetened beverage (SSB consumption.Method: We compared 3 separate cross-sectional samples (2003, 2005, and 2007 from biennial CHIS for 3 age groups, age 2–5, age 6–11 and age 12–17. We calculated the prevalence of high SSB consumption (defined as having more than one SSB during the previous day. 2 measures of obesity were used – weight-for-age at or above the 95th percentile on national growth charts for children aged 2–11, and body mass index for age at or above the 95th percentile on national growth charts for adolescents aged 12–17. Logistic regression analysis is used to estimate adjusted odds ratios of high SSB consumption in 2005 and 2007 compared with the baseline year of 2003.Results: From 2003 to 2007, each age group experienced a substantial decline in high SSB consumption (16.4%–5.0% for age 2–5, P < 0.001; 22.5%–9.9% for age 6–11, P < 0.001; 35.7%–25.7% for age 12–17, P < 0.001. Declines in the prevalence of children’s obesity were significant among children age 2–5 (P < 0.001 and age 6–11 (P < 0.05 but not among adolescents (P = 0.42. Children and teenagers in 2005 and 2007 were significantly less likely than those surveyed in 2003 to have high SSB consumption after adjusting for gender, age, race/ethnicity, poverty level, and parental education (P < 0.001.Conclusion: Policy actions may have impacted the prevalence of SSB consumption in the population. Further research is needed to examine the contribution of declining SSB consumption on the leveling off of obesity trends and the

  18. General quantum variational calculus

    Directory of Open Access Journals (Sweden)

    Artur M. C. Brito da Cruz

    2018-02-01

    Full Text Available We develop a new variational calculus based in the general quantum difference operator recently introduced by Hamza et al. In particular, we obtain optimality conditions for generalized variational problems where the Lagrangian may depend on the endpoints conditions and a real parameter, for the basic and isoperimetric problems, with and without fixed boundary conditions. Our results provide a generalization to previous results obtained for the $q$- and Hahn-calculus.

  19. Generalized quasi variational inequalities

    Energy Technology Data Exchange (ETDEWEB)

    Noor, M.A. [King Saud Univ., Riyadh (Saudi Arabia)

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  20. Mitigating component performance variation

    Science.gov (United States)

    Gara, Alan G.; Sylvester, Steve S.; Eastep, Jonathan M.; Nagappan, Ramkumar; Cantalupo, Christopher M.

    2018-01-09

    Apparatus and methods may provide for characterizing a plurality of similar components of a distributed computing system based on a maximum safe operation level associated with each component and storing characterization data in a database and allocating non-uniform power to each similar component based at least in part on the characterization data in the database to substantially equalize performance of the components.

  1. Assessment of genetic variation of selected spiderplant (Cleome ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... matrix calculated on the basis of UPGMA clustering algorithm revealed that the 4 morphotypes formed ... Key words: Cleome gynandra, genetic variation, morphotypes, .... Research Foundation of Kenya, Kericho, Kenya.

  2. Seasonal variation in heavy metal concentration in mangrove foliage

    Digital Repository Service at National Institute of Oceanography (India)

    Untawale, A.G.; Wafar, S.; Bhosle, N.B.

    Seasonal variation in the concentration of some heavy metals in the leaves of seven species of mangrove vegetation from Goa, revealed that maximum concentration of iron and manganese occurs during the monsoon season without any significant toxic...

  3. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  4. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  5. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Brunak, Søren; Olsen, JV

    2010-01-01

    and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global...

  6. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  7. GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Johanna A Bac-Molenaar

    Full Text Available Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature.

  8. Substantial Effect of Melanin Influencing Factors on Melanogenesis in Muzzle Melanocytes of Differently Colored Hanwoo

    Directory of Open Access Journals (Sweden)

    Touseef Amna

    2012-07-01

    Full Text Available The present study was designed to investigate the effect of α-melanocyte-stimulating hormone (α-MSH, nitric oxide (NO and L-cysteine on melanin production and expression of related genes MC1R, Tyr, Tyrp-1 and Tyrp-2 in muzzle melanocytes of differently colored three native Hanwoo cattle. Muzzle samples were taken from black, brindle and brown Hanwoo and purified melanocytes were cultured with α-MSH, nitric oxide and L-cysteine at 100 nM, 50 µM and 0.07 mg/ml of media respectively. The amounts of total melanin, eumelanin and mRNA expression at Tyr, Tyrp-1, Tyrp-2 and MC1R levels were quantified. α-MSH and nitric oxide significantly increased (p<0.05 the amount of total melanin in black and brindle whereas eumelanin production in brown Hanwoo muzzle melanocytes. On the contrary, L-cysteine greatly (p<0.05 depressed the eumelanin production in black color but increased in brown. Simultaneously, up regulation of Tyr by nitric oxide and α-MSH and down regulation of Tyr, Tyrp-2 and MC1R genes by L-cysteine were observed in muzzle melanocytes of all three phenotypes. The results of this study revealed nitric oxide and α-MSH contribute hyper-pigmentation by enhancing eumelanogenesis whereas L-cysteine contributes to pheomelanin production in different colored Hanwoo muzzle melanocytes.

  9. Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

    Science.gov (United States)

    Schneider, Nadine; Hindle, Sally; Lange, Gudrun; Klein, Robert; Albrecht, Jürgen; Briem, Hans; Beyer, Kristin; Claußen, Holger; Gastreich, Marcus; Lemmen, Christian; Rarey, Matthias

    2012-06-01

    The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.

  10. [Hygienic substantiation of the permissible levels for tetracycline-group antibiotics in food].

    Science.gov (United States)

    Onishchenko, G G; Sheveleva, S A; Khotimchenko, S A

    2012-01-01

    For the purpose of justification of the hygienic standard for tetracycline-group antibiotics in the food production established in the Russian Federation at more rigid level, than maximum and admissible levels (MAL) of the Codex Alimentarius Commission, the analysis of data of literature on negative nature of impact of low concentration of these antibiotics on an organism and the environmental conditions and risk for health has been performed. Inadequacy of the accepted admissible daily dose (ADD) accepted by The Joint FAO/WHO Expert Committee on Food Additives (JECFA) on action on selection of resistant E. coli in intestines, for the wide contingent of consumers in connection with ignoring of obvious factors of uncertainty (gastrointestinal dysbiosis, age and individual variations in the microbiota of people synergy with other antibiotics residues in food and indirect impact on an organism through microflora from the natural habitat (resistance genes, modified causative organisms with altered properties).. By the analysis of information received with the use of modern molecular and genetic methods, the role of Subinhibitory concentrations (sub-MICs) of tetracyclines as biologically active substances, signaling molecules which, without causing obvious negative consequences in a macroorganism, serve as a major factor of regulation of a transcription in microorganisms and activation of a horizontal gene transfer coding resistance, transferred on conjugative transposons of Tn916-Tn1545 family. Reasonable scientific data on a dominating contribution of minor levels of tetracyclines in globalization in the nature of the most adverse transmissive type of the antibiotic resistance interfaced to formation new bacterial pathotypes, as consequences of irrationally high scales of application in agriculture and strengthened impact on microbic ecosystems of live organisms and objects of habitat are presented. For minimization of this mediated risk for health the need of

  11. Allozyme variation in spineless Pejibaye (Bactris gasipaes Kunth)

    Science.gov (United States)

    Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

  12. Regional variation in electroconvulsive therapy use.

    LENUS (Irish Health Repository)

    Dunne, R

    2011-03-01

    Although electroconvulsive therapy (ECT) is the most powerful treatment for depression, substantial variability in use has been described in Ireland. The Mental Health Commission collects usage data from approved centres but does not include home addresses or independent sector patients. Therefore, estimates of regional variation cannot be accurate, e.g. 145 (35% of total) independent sector patients were omitted from their 2008 analysis. When public and independent sector patients are combined inter-regional variation for 2008 is more than halved (chi-squared decreased from 83 to 30), with Western region contributing most to variation (chi-squared = 43). Ratio of ECT programmes to depressed admissions correlated negatively with rate for depressed admissions (r = -0.53, p = 0.01), while depressed admission numbers correlated with acute beds per area (r = 0.68, p = 0.001). Regional variation in ECT is less than previously reported; service factors probably account for much of this with smaller centres admitting severely ill patients more likely to require ECT.

  13. Chemistry of plutonium revealed

    International Nuclear Information System (INIS)

    Connick, R.E.

    1992-01-01

    In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. In this paper the work carried out at Berkeley from the spring of 1942 to the summer of 1945 is described briefly. The aqueous chemistry of plutonium is quite remarkable. Important insights were obtained from tracer experiments, but the full complexity was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were based on aqueous solutions, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, an equilibrium was rapidly established among the four aqueous oxidation states, while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element are reported

  14. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    This work presents a method for designing facial interfaces for sociable android robots with respect to the fundamental rules of human affect expression. Extending the work of Paul Ekman towards a robotic direction, we follow the judgment-based approach for evaluating facial expressions to test...... findings are based on the results derived from a number of judgments, and suggest that before programming the facial expressions of a Geminoid, the Original should pass through the proposed procedure. According to our recommendations, the facial expressions of an android should be tested by judges, even...... in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  15. Hawaii's volcanoes revealed

    Science.gov (United States)

    Eakins, Barry W.; Robinson, Joel E.; Kanamatsu, Toshiya; Naka, Jiro; Smith, John R.; Takahashi, Eiichi; Clague, David A.

    2003-01-01

    Hawaiian volcanoes typically evolve in four stages as volcanism waxes and wanes: (1) early alkalic, when volcanism originates on the deep sea floor; (2) shield, when roughly 95 percent of a volcano's volume is emplaced; (3) post-shield alkalic, when small-volume eruptions build scattered cones that thinly cap the shield-stage lavas; and (4) rejuvenated, when lavas of distinct chemistry erupt following a lengthy period of erosion and volcanic quiescence. During the early alkalic and shield stages, two or more elongate rift zones may develop as flanks of the volcano separate. Mantle-derived magma rises through a vertical conduit and is temporarily stored in a shallow summit reservoir from which magma may erupt within the summit region or be injected laterally into the rift zones. The ongoing activity at Kilauea's Pu?u ?O?o cone that began in January 1983 is one such rift-zone eruption. The rift zones commonly extend deep underwater, producing submarine eruptions of bulbous pillow lava. Once a volcano has grown above sea level, subaerial eruptions produce lava flows of jagged, clinkery ?a?a or smooth, ropy pahoehoe. If the flows reach the ocean they are rapidly quenched by seawater and shatter, producing a steep blanket of unstable volcanic sediment that mantles the upper submarine slopes. Above sea level then, the volcanoes develop the classic shield profile of gentle lava-flow slopes, whereas below sea level slopes are substantially steeper. While the volcanoes grow rapidly during the shield stage, they may also collapse catastrophically, generating giant landslides and tsunami, or fail more gradually, forming slumps. Deformation and seismicity along Kilauea's south flank indicate that slumping is occurring there today. Loading of the underlying Pacific Plate by the growing volcanic edifices causes subsidence, forming deep basins at the base of the volcanoes. Once volcanism wanes and lava flows no longer reach the ocean, the volcano continues to submerge, while

  16. Fimbrial phase variation

    DEFF Research Database (Denmark)

    Khandige, Surabhi; Møller-Jensen, Jakob

    2016-01-01

    Surface fimbriae of pathogenic Escherichia coli facilitate sensing, adhesion and even invasion of host epithelial cells. While it is known that the pathogen has the potential to express a plethora of fimbrial variants susceptible to rapid phase ON/OFF variation, it is an open question if the fimb......Surface fimbriae of pathogenic Escherichia coli facilitate sensing, adhesion and even invasion of host epithelial cells. While it is known that the pathogen has the potential to express a plethora of fimbrial variants susceptible to rapid phase ON/OFF variation, it is an open question...... if the fimbrial diversity seen at the population level is the product of random stochasticity or a concerted effort based on active communication. Here we discuss the possibility of a mechanism alternative to a stochastic fimbrial phase variation model affecting the dynamics of a heterogeneous population....

  17. Variation, structure and norms

    DEFF Research Database (Denmark)

    Harder, Peter

    2014-01-01

    in linguistics: those that see linguistic norms as antithetical to a descriptive and variational linguistics. Once such a re-evaluation has taken place, however, the social recontextualization of cognition will enable linguistics (including sociolinguistics as an integral part), to eliminate the cracks...... that an evolutionary account can reintegrate the opposed fragments into a whole picture that puts each of them in their ‘ecological position’ with respect to each other. Empirical usage facts should be seen in the context of operational norms in relation to which actual linguistic choices represent adaptations....... Variational patterns should be seen in the context of structural categories without which there would be only ‘differences’ rather than variation. And emergence, individual choice, and flux should be seen in the context of the individual’s dependence on lineages of community practice sustained by collective...

  18. Plasma creatinine in dogs: intra- and inter-laboratory variation in 10 European veterinary laborat

    NARCIS (Netherlands)

    Mrs. Ulleberg, T.; Robben, J.H.; Nordahl, K.; Mr. Ulleberg, T.; Heiene, R.

    2011-01-01

    Abstract BACKGROUND: There is substantial variation in reported reference intervals for canine plasma creatinine among veterinary laboratories, thereby influencing the clinical assessment of analytical results. The aims of the study was to determine the inter- and intra-laboratory variation in

  19. Variations in Financial Performance among Peer Groups of Critical Access Hospitals

    Science.gov (United States)

    Pink, George H.; Holmes, George M.; Thompson, Roger E.; Slifkin, Rebecca T.

    2007-01-01

    Context: Among the large number of hospitals with critical access hospital (CAH) designation, there is substantial variation in facility revenue as well as the number and types of services provided. If these variations have material effects on financial indicators, then performance comparisons among all CAHs are problematic. Purpose: To…

  20. Spatial variation in the relationship between performance and metabolic rate in wild juvenile Atlantic salmon

    Science.gov (United States)

    Grethe Robertsen; John D. Armstrong; Keith H. Nislow; Ivar Herfindal; Simon McKelvey; Sigurd Einum; Martin. Genner

    2014-01-01

    Maintenance of metabolic rate (MR, the energy cost of self-maintenance) is linked to behavioural traits and fitness and varies substantially within populations. Despite having received much attention, the causes and consequences of this variation remain obscure. Theoretically, such within-population variation in fitness-related traits can be maintained by environmental...

  1. BIOCHEMICAL SUBSTANTIATION OF COMBINED THERAPY APPLICATION IN THE ACUTE PHASE OF EXPERIMENTAL HELMINTHIASIS OF ANIMALS

    Directory of Open Access Journals (Sweden)

    E. A. Grishina

    2017-01-01

    Full Text Available The purpose of this study was to investigate the influence of the invasion process and different strategies of treatment on some biochemical blood indices of mice infested with Syphacia obvelata and Trichocephalus muris of gastrointestinal tract, in order to optimize etiotropic therapy and improve its efficiency. Materials and methods. In the experiment were used albino mice, divided into the following groups: intact animals (control group; animals infected with Syphacia obvelata; animals infected with Trichocephalus muris; infected animals, who received a single dose of albendazole (7 mg/kg; infected animals, who received a single dose of albendazole (7 mg/kg and gamavit dose intramuscularly (0.3 cm3/kg simultaneously. Blood for the studies was taken from the animals at 1, 3, 7, 10, 14, 17, 21 days after the infection and after drug administration. From biochemical parameters were determined activities of next enzymes: alanine aminotransferase (ALT, aspartate aminotransferase (AST, gamma-glutamyl transferase (γ-GTP and alkaline phosphatase (AP – with kinetic method IFCC. Results. Infecting animals with helminthes caused a noticeable increase in AP and gamma-GTP levels and cytolytic activity of enzymes: ALT and AST compared with intact group. The above-mentioned complex of metabolic changes clearly reveals a disturbance in hepatocyte metabolism that leads to the decrease in detoxifying function of the liver. This can be apparently explained with toxic effects of helminthes waste products. Albendazole mono-therapy in the therapeutic dose (7 mg/kg of mice infected with both Syphacia and Trichocephalus caused an even greater increase in ALT and AST levels and also increased serum levels of alkaline phosphatase and γ-GTP, compared with the control and infected animals, that clearly shows an additional toxic effect from the antihelmintic drug. The use of albendazole in combination with a complex antioxidant “Gamavit” in animals infected with

  2. 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...

  3. 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...

  4. Splines and variational methods

    CERN Document Server

    Prenter, P M

    2008-01-01

    One of the clearest available introductions to variational methods, this text requires only a minimal background in calculus and linear algebra. Its self-contained treatment explains the application of theoretic notions to the kinds of physical problems that engineers regularly encounter. The text's first half concerns approximation theoretic notions, exploring the theory and computation of one- and two-dimensional polynomial and other spline functions. Later chapters examine variational methods in the solution of operator equations, focusing on boundary value problems in one and two dimension

  5. 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

  6. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    Science.gov (United States)

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  7. Length of FMR1 repeat alleles within the normal range does not substantially affect the risk of early menopause

    Science.gov (United States)

    Ruth, Katherine S.; Bennett, Claire E.; Schoemaker, Minouk J.; Weedon, Michael N.; Swerdlow, Anthony J.; Murray, Anna

    2016-01-01

    STUDY QUESTION Is the length of FMR1 repeat alleles within the normal range associated with the risk of early menopause? SUMMARY ANSWER The length of repeat alleles within the normal range does not substantially affect risk of early menopause. WHAT IS KNOWN ALREADY There is a strong, well-established relationship between length of premutation FMR1 alleles and age at menopause, suggesting that this relationship could continue into the normal range. Within the normal range, there is conflicting evidence; differences in ovarian reserve have been identified with FMR1 repeat allele length, but a recent population-based study did not find any association with age at menopause as a quantitative trait. STUDY DESIGN, SIZE, DURATION We analysed cross-sectional baseline survey data collected at recruitment from 2004 to 2010 from a population-based, prospective epidemiological cohort study of >110 000 women to investigate whether repeat allele length was associated with early menopause. PARTICIPANTS/MATERIALS, SETTING, METHOD We included 4333 women from the Breakthrough Generations Study (BGS), of whom 2118 were early menopause cases (menopause under 46 years) and 2215 were controls. We analysed the relationship between length of FMR1 alleles and early menopause using logistic regression with allele length as continuous and categorical variables. We also conducted analyses with the outcome age at menopause as a quantitative trait as well as appropriate sensitivity and exploratory analyses. MAIN RESULTS AND THE ROLE OF CHANCE There was no association of the shorter or longer FMR1 allele or their combined genotype with the clinically relevant end point of early menopause in our main analysis. Likewise, there were no associations with age at menopause as a quantitative trait in our secondary analysis. LIMITATIONS, REASONS FOR CAUTION Women with homozygous alleles in the normal range may have undetected FMR1 premutation alleles, although there was no evidence to suggest this. We

  8. Worldwide Weather Radar Imagery May Allow Substantial Increase in Meteorite Fall Recovery

    Science.gov (United States)

    Fries, Marc; Matson, Robert; Schaefer, Jacob; Fries, Jeffery; Hankey, Mike; Anderson, Lindsay

    2014-01-01

    Weather radar imagery is a valuable new technique for the rapid recovery of meteorite falls, to include falls which would not otherwise be recovered (e.g. Battle Mountain). Weather radar imagery reveals about one new meteorite fall per year (18 falls since 1998), using weather radars in the United States alone. However, an additional 75 other nations operate weather radar networks according to the UN World Meteorological Organization (WMO). If the imagery of those radars were analyzed, the current rate of meteorite falls could be improved considerably, to as much as 3.6 times the current recovery rate based on comparison of total radar areal coverage. Recently, the addition of weather radar imagery, seismometry and internet-based aggregation of eyewitness reports has improved the speed and accuracy of fresh meteorite fall recovery [e.g. 1,2]. This was demonstrated recently with the radar-enabled recovery of the Sutter's Mill fall [3]. Arguably, the meteorites recovered via these methods are of special scientific value as they are relatively unweathered, fresh falls. To illustrate this, a recent SAO/NASA ADS search using the keyword "meteorite" shows that all 50 of the top search results included at least one named meteorite recovered from a meteorite fall. This is true even though only 1260 named meteorite falls are recorded among the >49,000 individual falls recorded in the Meteoritical Society online database. The US NEXRAD system used thus far to locate meteorite falls covers most of the United States' surface area. Using a WMO map of the world's weather radars, we estimate that the total coverage of the other 75 national weather radar networks equals about 3.6x NEXRAD's coverage area. There are two findings to draw from this calculation: 1) For the past 16 years during which 18 falls are seen in US radar data, there should be an additional 65 meteorite falls recorded in worldwide radar imagery. Also: 2) if all of the world's radar data could be analyzed, the

  9. Global variations in health: evaluating Wilkinson's income inequality hypothesis using the World Values Survey.

    Science.gov (United States)

    Jen, Min Hua; Jones, Kelvyn; Johnston, Ron

    2009-02-01

    This international comparative study analyses individual-level data derived from the World Values Survey to evaluate Wilkinson's [(1996). Unhealthy societies: The afflictions of inequality. London: Routledge; (1998). Mortality and distribution of income. Low relative income affects mortality [letter; comment]. British Medical Journal, 316, 1611-1612] income inequality hypothesis regarding variations in health status. Random-coefficient, multilevel modelling provides a direct test of Wilkinson's hypothesis using micro-data on individuals and macro-data on income inequalities analysed simultaneously. This overcomes the ecological fallacy that has troubled previous research into links between individual self-rated health, individual income, country income and income inequality data. Logic regression analysis reveals that there are substantial differences between countries in self-rated health after taking account of age and gender, and individual income has a clear effect in that poorer people report experiencing worse health. The Wilkinson hypothesis is not supported, however, since there is no significant relationship between health and income inequality when individual factors are taken into account. Substantial differences between countries remain even after taking account of micro- and macro-variables; in particular the former communist countries report high levels of poor health.

  10. Variations in government contract in Malaysia

    Directory of Open Access Journals (Sweden)

    Jaspal Singh Nachatar

    2010-12-01

    Full Text Available The complexity of construction works means that it is hardly possible to complete a project without changes to the plans or the construction process itself. There can only be a minority of contracts of any size in which the subject matter when completed is identical in every respect with what was contemplated at the outset. As such, variations are inevitable in even the best-planned contracts. This study is attempted to examine the ways a variation was formed in law and project, in finding out whether the Standard Form of Contract used in Malaysia particularly the government Public Works Department (PWD form has been utilized to the best level in variation cases. Additionally, this study examined the benefits of variations to parties in contract and also provides suggestions and assumptions in an effort to contribute solutions to issues and problem detected. The research methodology used in this study was an extensive review of relevant literature, case study, empirical questionnaires and structured interviews and general observations based on experience and surroundings. The academic study approach incorporated stages such as initial understanding, data and information gathering, analysis of data, findings and conclusion and general suggestions in the study. The major findings of this study, among others, revealed that the existences of variations are common in projects. The main cause of variations was due to client request because of inadequate project objectives for the designer to develop comprehensive design. Besides, the analysis pointed out that the government form of contract the Public Works Department (PWD 203/203A can help in overcoming projects with variation because of the clear defined procedure. This study also found that proper planning and coordination at tender stage can minimize the risk of ‘unwanted’ variations. In conclusion, this study recommended that future research should be done in design and build based contract

  11. Variation and Linguistic Theory.

    Science.gov (United States)

    Bailey, Charles-James N.

    This volume presents principles and models for describing language variation, and introduces a time-based, dynamic framework for linguistic description. The book first summarizes some of the problems of grammatical description encountered from Saussure through the present and then outlines possibilities for new descriptions of language which take…

  12. On exterior variational calculus

    International Nuclear Information System (INIS)

    Aldrovandi, R.; Kraenkel, R.A.

    1987-01-01

    Exterior variational calculus is introduced through examples in field theory. It provides a very simple technique to decide on the existence of Lagrangians for given equations of motions and, in the case, to find them. Only local aspects are discussed but the analogy to exterior calculus on finite dimensional manifolds is complete, strongly suggesting its suitability to the study of topological aspects. (Author) [pt

  13. Variational transition state theory

    International Nuclear Information System (INIS)

    Truhlar, D.G.

    1986-01-01

    This project is concerned with the development and applications of generalized transition state theory and multidimensional tunneling approximations to chemical reaction rates. They have developed and implemented several practical versions of variational transition state theory (VTST), namely canonical variational theory (CVT), improved canonical variational theory (ICVT), and microcanonical variational theory (μVT). They have also developed and implemented several accurate multidimensional semiclassical tunneling approximations, the most accurate of which are the small-curvature semiclassical adiabatic (SCSA), large-curvature version-3 (LC3), and least-action (LA) approximations. They have applied the methods to thermal rate constants, using transmission coefficients based on ground-state tunneling, and they have also presented and applied adiabatic and diabatic extensions to calculated rate constants for vibrationally excited reactants. Their general goal is to develop accurate methods for calculating chemical reaction rate constants that remain practical even for reasonably complicated molecules. The approximations mentioned above yield rate constants for systems whose potential energy surface is known or assumed. Thus a second, equally important aspect of their work is the determination or modeling, semi-empirically and/or from electronic structure calculations, of potential energy surfaces

  14. Variation in decision making

    NARCIS (Netherlands)

    Dall, Sasha R. X.; Gosling, Samuel; Gordon D.A., Brown,; Dingemanse, Niels; Ido, Erev,; Martin, Kocher,; Laura, Schulz,; Todd, Peter M; Weissing, Franz; Wolf, Max; Hammerstein, Peter; Stevens, Jeffrey R.

    2012-01-01

    Variation in how organisms allocate their behavior over their lifetimes is key to determining Darwinian fitness., and thus the evolution of human and nonhuman decision making. This chapter explores how decision making varies across biologically and societally significant scales and what role such

  15. Seasonal Variation in Epidemiology

    Science.gov (United States)

    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…

  16. The variational spiked oscillator

    International Nuclear Information System (INIS)

    Aguilera-Navarro, V.C.; Ullah, N.

    1992-08-01

    A variational analysis of the spiked harmonic oscillator Hamiltonian -d 2 / d x 2 + x 2 + δ/ x 5/2 , δ > 0, is reported in this work. A trial function satisfying Dirichlet boundary conditions is suggested. The results are excellent for a large range of values of the coupling parameter. (author)

  17. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  18. Decadal atmosphere-ocean variations in the Pacific

    Science.gov (United States)

    Trenberth, Kevin E.; Hurrell, James W.

    1994-03-01

    Considerable evidence has emerged of a substantial decade-long change in the north Pacific atmosphere and ocean lasting from about 1976 to 1988. Observed significant changes in the atmospheric circulation throughout the troposphere revealed a deeper and eastward shifted Aleutian low pressure system in the winter half year which advected warmer and moister air along the west coast of North America and into Alaska and colder air over the north Pacific. Consequently, there were increases in temperatures and sea surface temperatures (SSTs) along the west coast of North America and Alaska but decreases in SSTs over the central north Pacific, as well as changes in coastal rainfall and streamflow, and decreases in sea ice in the Bering Sea. Associated changes occurred in the surface wind stress, and, by inference, in the Sverdrup transport in the north Pacific Ocean. Changes in the monthly mean flow were accompanied by a southward shift in the storm tracks and associated synoptic eddy activity and in the surface ocean sensible and latent heat fluxes. In addition to the changes in the physical environment, the deeper Aleutian low increased the nutrient supply as seen through increases in total chlorophyll in the water column, phytoplankton and zooplankton. These changes, along with the altered ocean currents and temperatures, changed the migration patterns and increased the stock of many fish species. A north Pacific (NP) index is defined to measure the decadal variations, and the temporal variability of the index is explored on daily, annual, interannual and decadal time scales. The dominant atmosphere-ocean relation in the north Pacific is one where atmospheric changes lead SSTs by one to two months. However, strong ties are revealed with events in the tropical Pacific, with changes in tropical Pacific SSTs leading SSTs in the north Pacific by three months. Changes in the storm tracks in the north Pacific help to reinforce and maintain the anomalous circulation in the

  19. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    Directory of Open Access Journals (Sweden)

    Ruth Barral-Arca

    Full Text Available The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM, prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype

  20. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    Science.gov (United States)

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies.

  1. Consistency of Estimated Global Water Cycle Variations Over the Satellite Era

    Science.gov (United States)

    Robertson, F. R.; Bosilovich, M. G.; Roberts, J. B.; Reichle, R. H.; Adler, R.; Ricciardulli, L.; Berg, W.; Huffman, G. J.

    2013-01-01

    Motivated by the question of whether recent indications of decadal climate variability and a possible "climate shift" may have affected the global water balance, we examine evaporation minus precipitation (E-P) variability integrated over the global oceans and global land from three points of view-remotely sensed retrievals / objective analyses over the oceans, reanalysis vertically-integrated moisture convergence (MFC) over land, and land surface models forced with observations-based precipitation, radiation and near-surface meteorology. Because monthly variations in area-averaged atmospheric moisture storage are small and the global integral of moisture convergence must approach zero, area-integrated E-P over ocean should essentially equal precipitation minus evapotranspiration (P-ET) over land (after adjusting for ocean and land areas). Our analysis reveals considerable uncertainty in the decadal variations of ocean evaporation when integrated to global scales. This is due to differences among datasets in 10m wind speed and near-surface atmospheric specific humidity (2m qa) used in bulk aerodynamic retrievals. Precipitation variations, all relying substantially on passive microwave retrievals over ocean, still have uncertainties in decadal variability, but not to the degree present with ocean evaporation estimates. Reanalysis MFC and P-ET over land from several observationally forced diagnostic and land surface models agree best on interannual variations. However, upward MFC (i.e. P-ET) reanalysis trends are likely related in part to observing system changes affecting atmospheric assimilation models. While some evidence for a low-frequency E-P maximum near 2000 is found, consistent with a recent apparent pause in sea-surface temperature (SST) rise, uncertainties in the datasets used here remain significant. Prospects for further reducing uncertainties are discussed. The results are interpreted in the context of recent climate variability (Pacific Decadal

  2. The nonholonomic variational principle

    Energy Technology Data Exchange (ETDEWEB)

    Krupkova, Olga [Department of Algebra and Geometry, Faculty of Science, Palacky University, Tomkova 40, 779 00 Olomouc (Czech Republic); Department of Mathematics, La Trobe University, Bundoora, Victoria 3086 (Australia)], E-mail: krupkova@inf.upol.cz

    2009-05-08

    A variational principle for mechanical systems and fields subject to nonholonomic constraints is found, providing Chetaev-reduced equations as equations for extremals. Investigating nonholonomic variations of the Chetaev type and their properties, we develop foundations of the calculus of variations on constraint manifolds, modelled as fibred submanifolds in jet bundles. This setting is appropriate to study general first-order 'nonlinear nonitegrable constraints' that locally are given by a system of first-order ordinary or partial differential equations. We obtain an invariant constrained first variation formula and constrained Euler-Lagrange equations both in intrinsic and coordinate forms, and show that the equations are the same as Chetaev equations 'without Lagrange multipliers', introduced recently by other methods. We pay attention to two possible settings: first, when the constrained system arises from an unconstrained Lagrangian system defined in a neighbourhood of the constraint, and second, more generally, when an 'internal' constrained system on the constraint manifold is given. In the latter case a corresponding unconstrained system need not be a Lagrangian, nor even exist. We also study in detail an important particular case: nonholonomic constraints that can be alternatively modelled by means of (co)distributions in the total space of the fibred manifold; in nonholonomic mechanics this happens whenever constraints affine in velocities are considered. It becomes clear that (and why) if the distribution is completely integrable (= the constraints are semiholonomic), the principle of virtual displacements holds and can be used to obtain the constrained first variational formula by a more or less standard procedure, traditionally used when unconstrained or holonomic systems are concerned. If, however, the constraint is nonintegrable, no significant simplifications are available. Among others, some properties of nonholonomic

  3. Diurnal variations of Titan

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  4. Within-Individual Variation in Preferences Equity Effects of Congestion Charges

    DEFF Research Database (Denmark)

    Borjesson, Maria; Cherchi, Elisabetta; Bierlaire, Michel

    2013-01-01

    in VTT arising from income differences was found to be substantially smaller than the variation in VTT between trips. Moreover, the variability in VTT averaged over all trips within each individual was considerably smaller than the variability in VTT for all observed trips. Therefore, the assumption...... that variation in VTT between observed trips reflects the variation in the average VTT between individuals, which is usually made in equity analyses, will over-state the between-individual variation. The results suggest that if intraindividual variation in preferences is not taken into account, the negative...

  5. Lexical variations in the Bible translations

    Directory of Open Access Journals (Sweden)

    Barashkova Daria Sergeyevna

    2018-04-01

    Full Text Available The paper contains the comparative analysis of the Ostromir Gospels (1056-1057 and the Synodal translation of the Bible in order to identify lexical variations (alternatives. A source of the analysis are identic contexts from the Bible. Besides the author examines the materials of the others Old Slavonic written manuscripts. As a result of the comparative analysis some lexical options reflecting both synonymic and hyper-hyponymic relations and derivational variability were revealed.

  6. Causal Genetic Variation Underlying Metabolome Differences.

    Science.gov (United States)

    Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye; Sudarsanam, Priya; Nayler, Darcy; Staller, Max V; Cohen, Barak A

    2017-08-01

    An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81 , cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype. Copyright © 2017 by the Genetics Society of America.

  7. People attending pulmonary rehabilitation demonstrate a substantial engagement with technology and willingness to use telerehabilitation: a survey

    Directory of Open Access Journals (Sweden)

    Zachariah Seidman

    2017-07-01

    Conclusion: People attending metropolitan pulmonary rehabilitation, maintenance exercise classes and support groups had substantial technology engagement, with high device access and use, and good self-rated technology competence. The majority of participants were willing to use telerehabilitation, especially if they were regular users of technology devices. [Seidman Z, McNamara R, Wootton S, Leung R, Spencer L, Dale M, Dennis S, McKeough Z (2017 People attending pulmonary rehabilitation demonstrate a substantial engagement with technology and willingness to use telerehabilitation: a survey. Journal of Physiotherapy 63: 175–181

  8. Prediction of seasonal climate-induced variations in global food production

    Science.gov (United States)

    Iizumi, Toshichika; Sakuma, Hirofumi; Yokozawa, Masayuki; Luo, Jing-Jia; Challinor, Andrew J.; Brown, Molly E.; Sakurai, Gen; Yamagata, Toshio

    2013-10-01

    Consumers, including the poor in many countries, are increasingly dependent on food imports and are thus exposed to variations in yields, production and export prices in the major food-producing regions of the world. National governments and commercial entities are therefore paying increased attention to the cropping forecasts of important food-exporting countries as well as to their own domestic food production. Given the increased volatility of food markets and the rising incidence of climatic extremes affecting food production, food price spikes may increase in prevalence in future years. Here we present a global assessment of the reliability of crop failure hindcasts for major crops at two lead times derived by linking ensemble seasonal climatic forecasts with statistical crop models. We found that moderate-to-marked yield loss over a substantial percentage (26-33%) of the harvested area of these crops is reliably predictable if climatic forecasts are near perfect. However, only rice and wheat production are reliably predictable at three months before the harvest using within-season hindcasts. The reliabilities of estimates varied substantially by crop--rice and wheat yields were the most predictable, followed by soybean and maize. The reasons for variation in the reliability of the estimates included the differences in crop sensitivity to the climate and the technology used by the crop-producing regions. Our findings reveal that the use of seasonal climatic forecasts to predict crop failures will be useful for monitoring global food production and will encourage the adaptation of food systems toclimatic extremes.

  9. Genetic variation in social influence on mate preferences

    Science.gov (United States)

    Rebar, Darren; Rodríguez, Rafael L.

    2013-01-01

    Patterns of phenotypic variation arise in part from plasticity owing to social interactions, and these patterns contribute, in turn, to the form of selection that shapes the variation we observe in natural populations. This proximate–ultimate dynamic brings genetic variation in social environments to the forefront of evolutionary theory. However, the extent of this variation remains largely unknown. Here, we use a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess how mate preferences are influenced by genetic variation in the social environment. We used full-sibling split-families as ‘treatment’ social environments, and reared focal females alongside each treatment family, describing the mate preferences of the focal females. With this method, we detected substantial genetic variation in social influence on mate preferences. The mate preferences of focal females varied according to the treatment families along with which they grew up. We discuss the evolutionary implications of the presence of such genetic variation in social influence on mate preferences, including potential contributions to the maintenance of genetic variation, the promotion of divergence, and the adaptive evolution of social effects on fitness-related traits. PMID:23698010

  10. Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

    Directory of Open Access Journals (Sweden)

    Cook James M

    2009-03-01

    Full Text Available Abstract Background Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306 of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may

  11. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

    Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

  12. 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)

  13. Canonical variate regression.

    Science.gov (United States)

    Luo, Chongliang; Liu, Jin; Dey, Dipak K; Chen, Kun

    2016-07-01

    In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Lidar observed seasonal variation of vertical canopy structure in the Amazon evergreen forests

    Science.gov (United States)

    Tang, H.; Dubayah, R.

    2017-12-01

    Both light and water are important environmental factors governing tree growth. Responses of tropical forests to their changes are complicated and can vary substantially across different spatial and temporal scales. Of particular interest is the dry-season greening-up of Amazon forests, a phenomenon undergoing considerable debates whether it is real or a "light illusion" caused by artifacts of passive optical remote sensing techniques. Here we analyze seasonal dynamic patterns of vertical canopy structure in the Amazon forests using lidar observations from NASA's Ice, Cloud, and and land Elevation Satellite (ICESat). We found that the net greening of canopy layer coincides with the wet-to-dry transition period, and its net browning occurs mostly at the late dry season. The understory also shows a seasonal cycle, but with an opposite variation to canopy and minimal correlation to seasonal variations in rainfall or radiation. Our results further suggest a potential interaction between canopy layers in the light regime that can optimize the growth of Amazon forests during the dry season. This light regime variability that exists in both spatial and temporal domains can better reveal the dry-season greening-up phenomenon, which appears less obvious when treating the Amazon forests as a whole.

  15. 36 CFR 51.55 - What must a concessioner do after substantial completion of the capital improvement?

    Science.gov (United States)

    2010-07-01

    ... together with, if requested by the Director, a written certification from a certified public accountant... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false What must a concessioner do after substantial completion of the capital improvement? 51.55 Section 51.55 Parks, Forests, and Public...

  16. 26 CFR 301.6621-2T - Questions and answers relating to the increased rate of interest on substantial underpayments...

    Science.gov (United States)

    2010-04-01

    ...) the expenditure was prepaid for tax avoidance purposes and not for a business purpose, or (iii) the... rate of interest on substantial underpayments attributable to certain tax motivated transactions... underpayments attributable to certain tax motivated transactions (temporary). The following questions and...

  17. Substantial Fatigue Similarity of a New Small-Scale Test Rig to Actual Wheel-Rail System

    NARCIS (Netherlands)

    Naeimi, M.; Li, Z.; Petrov, R.H.; Dollevoet, R.P.B.J.; Sietsma, J.; Wu, J.

    2014-01-01

    The substantial similarity of fatigue mechanism in a new test rig for rolling contact fatigue (RCF) has been investigated. A new reduced-scale test rig is designed to perform controlled RCF tests in wheel-rail materials. The fatigue mechanism of the rig is evaluated in this study using a combined

  18. 21 CFR 740.10 - Labeling of cosmetic products for which adequate substantiation of safety has not been obtained.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Labeling of cosmetic products for which adequate..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) COSMETICS COSMETIC PRODUCT WARNING STATEMENTS Warning Statements § 740.10 Labeling of cosmetic products for which adequate substantiation of safety has not been...

  19. The Impact of Family Engagement and Child Welfare Services on Maltreatment Re-reports and Substantiated Re-reports.

    Science.gov (United States)

    Fuller, Tamara; Zhang, Saijun

    2017-08-01

    Despite decades of debate about the most effective ways to intervene with families reported to child protective services (CPS), little evidence exists regarding the types of services or approach that reduce children's risk of additional maltreatment. The current study used data collected during a statewide experimental evaluation of CPS to examine the impact of numerous service variables, family engagement, and family characteristics on the risk of maltreatment re-reports and substantiated re-reports among families initially reported for neglect and risk of harm. The sample included 4,868 families with screened-in reports that were randomly assigned to receive either an investigation or an assessment. The results of the Cox regression analyses found that service duration, intensity, and breadth were unrelated to maltreatment re-report or substantiated re-reports, but caseworker ratings of the service-need match were associated with both. The provision of domestic violence services was related to decreased risk of maltreatment re-reports. Increased levels of family engagement were associated with lowered risk of both maltreatment re-reports and substantiated re-reports. Once the effects of services, engagement, and family characteristics were taken into account, CPS response pathway (investigation or assessment) had no relationship to maltreatment re-reports or substantiated re-reports.

  20. Structural genomic variations and Parkinson's disease.

    Science.gov (United States)

    Bandrés-Ciga, Sara; Ruz, Clara; Barrero, Francisco J; Escamilla-Sevilla, Francisco; Pelegrina, Javier; Vives, Francisco; Duran, Raquel

    2017-10-01

    Parkinson's disease (PD) is the second most common neurodegenerative disease, whose prevalence is projected to be between 8.7 and 9.3 million by 2030. Until about 20 years ago, PD was considered to be the textbook example of a "non-genetic" disorder. Nowadays, PD is generally considered a multifactorial disorder that arises from the combination and complex interaction of genes and environmental factors. To date, a total of 7 genes including SNCA, LRRK2, PARK2, DJ-1, PINK 1, VPS35 and ATP13A2 have been seen to cause unequivocally Mendelian PD. Also, variants with incomplete penetrance in the genes LRRK2 and GBA are considered to be strong risk factors for PD worldwide. Although genetic studies have provided valuable insights into the pathogenic mechanisms underlying PD, the role of structural variation in PD has been understudied in comparison with other genomic variations. Structural genomic variations might substantially account for such genetic substrates yet to be discovered. The present review aims to provide an overview of the structural genomic variants implicated in the pathogenesis of PD.

  1. Titan Casts Revealing Shadow

    Science.gov (United States)

    2004-05-01

    A rare celestial event was captured by NASA's Chandra X-ray Observatory as Titan -- Saturn's largest moon and the only moon in the Solar System with a thick atmosphere -- crossed in front of the X-ray bright Crab Nebula. The X-ray shadow cast by Titan allowed astronomers to make the first X-ray measurement of the extent of its atmosphere. On January 5, 2003, Titan transited the Crab Nebula, the remnant of a supernova explosion that was observed to occur in the year 1054. Although Saturn and Titan pass within a few degrees of the Crab Nebula every 30 years, they rarely pass directly in front of it. "This may have been the first transit of the Crab Nebula by Titan since the birth of the Crab Nebula," said Koji Mori of Pennsylvania State University in University Park, and lead author on an Astrophysical Journal paper describing these results. "The next similar conjunction will take place in the year 2267, so this was truly a once in a lifetime event." Animation of Titan's Shadow on Crab Nebula Animation of Titan's Shadow on Crab Nebula Chandra's observation revealed that the diameter of the X-ray shadow cast by Titan was larger than the diameter of its solid surface. The difference in diameters gives a measurement of about 550 miles (880 kilometers) for the height of the X-ray absorbing region of Titan's atmosphere. The extent of the upper atmosphere is consistent with, or slightly (10-15%) larger, than that implied by Voyager I observations made at radio, infrared, and ultraviolet wavelengths in 1980. "Saturn was about 5% closer to the Sun in 2003, so increased solar heating of Titan may account for some of this atmospheric expansion," said Hiroshi Tsunemi of Osaka University in Japan, one of the coauthors on the paper. The X-ray brightness and extent of the Crab Nebula made it possible to study the tiny X-ray shadow cast by Titan during its transit. By using Chandra to precisely track Titan's position, astronomers were able to measure a shadow one arcsecond in

  2. Genetic regulation of the variation of circulating insulin-like growth factors and leptin in human pedigrees.

    Science.gov (United States)

    Pantsulaia, Ia; Pantsulaia, I; Trofimov, Svetlana; Kobyliansky, Eugene; Livshits, Gregory

    2005-07-01

    Recent literature has shown that circulating levels of insulin-like growth factor I (IGF-I) and/or IGF binding proteins (IGF-BPs) may be of importance in the risk assessment of several chronic diseases including cancer, cardiovascular disease, diabetes mellitus and so on. The present study examined the extent of genetic and environmental influences on the populational variation of circulating IGF-I and IGF-BP-1 in apparently healthy and ethnically homogeneous white families. The plasma levels of each of the studied biochemical indices were determined by enzyme-linked immunoassay in 563 individuals aged 18 to 80 years. Quantitative genetic analysis showed that the IGF-I variation was appreciably attributable to genetic effects (47.1% +/- 9.0%), whereas for IGF-BP-1, only 23.3% +/- 7.8% of the interindividual variation was explained by genetic determinants. Common familial environment factors contributed significantly only to IGF-BP-1 variation (23.3% +/- 7.8%). In addition, we examined the covariations between these molecules and between them and IGF-BP-3 and leptin that were previously studied in the same sample. The analysis revealed that the pleiotropic genetic effects were significant for 2 pairs of traits, namely for IGF-I and IGF-BP-3, and for IGF-BP-1 and leptin. The bivariate heritability estimates were 0.21 +/- 0.04 and 0.15 +/- 0.05. The common environmental factors were consistently a significant source of correlation between all pairs (barring IGF-I and leptin) of the studied molecules; they were the sole predictors of correlation between IGF-I and IGF-BP-1, and between IGF-BP-1 and IGF-BP-3. Our results affirm the existence of specific and common genetic pathways that in combination determine a substantial proportion of the circulating variation of these molecules.

  3. Substantial injuries influence ranking position in young elite athletes of athletics, cross-country skiing and orienteering.

    Science.gov (United States)

    von Rosen, P; Heijne, A

    2018-04-01

    The relationship between injury and performance in young athletes is scarcely studied. The aim of this study was therefore to explore the association between injury prevalence and ranking position among adolescent elite athletes. One hundred and sixty-two male and female adolescent elite athletes (age range 15-19), competing in athletics (n = 59), cross-country skiing (n = 66), and orienteering (n = 37), were monitored weekly over 22-47 weeks using a web-based injury questionnaire. Ranking lists were collected. A significant (P = .003) difference was found in the seasonal substantial injury prevalence across the ranked athletes over the season, where the top-ranked (median 3.6%, 25-75th percentiles 0%-14.3%) and middle-ranked athletes (median 2.3%, 25-75th percentiles 0%-10.0%) had a lower substantial injury prevalence compared to the low-ranked athletes (median 11.3%, 25-75th percentiles 2.5%-27.1%), during both preseason (P = .002) and competitive season (P = .031). Athletes who improved their ranking position (51%, n = 51) reported a lower substantial injury prevalence (median 0%, 25-75th percentiles 0%-10.0%) compared to those who decreased (49%, n = 49) their ranking position (md 6.7%, 25-75th percentiles 0%-22.5%). In the top-ranked group, no athlete reported substantial injury more than 40% of all data collection time points compared to 9.6% (n = 5) in the middle-ranked, and 17.3% (n = 9) in the low-ranked group. Our results provide supporting evidence that substantial injuries, such as acute and overuse injuries leading to moderate or severe reductions in training or sports performance, influence ranking position in adolescent elite athletes. The findings are crucial to stakeholders involved in adolescent elite sports and support the value of designing effective preventive interventions for substantial injuries. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Compositional variations revealed by ASTER image analysis of the Viedma Volcano, southern Andes Volcanic Zone Variaciones composicionales reveladas mediante análisis de imágenes ASTER del volcán Viedma, Zona Volcánica Andina Austral

    Directory of Open Access Journals (Sweden)

    Chiaki Kobayashi

    2010-07-01

    Full Text Available We conducted a lithological mapping of the Viedma volcano, one of five volcanoes in the Andean Austral Volcanic Zone (AVZ, using remote sensing techniques. We used data of the Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER sensor which is highly effective in geological research, to understand build-up processes and to deduce compositional variation of the Viedma volcano emerging from the South Patagonian ice field. The volcanic edifice was divided into bright parts that mainly compose the eastern flank of the volcano and dark parts at the central crater area based on the observation in visible and near infrared ranges. The SiO2 concentration was cal-culated using the bands in the visible and thermal infrared regions. The dark part and the bright part have approximately 51 wt% and 63 wt% average SiO2 content respectively, indicating that the exposures of the Viedma volcano have a wide variation in SiO2 concentration. Although, according to other authors, ejecta from the Viedma volcano have 64-66 wt% SiO2 and other AV Z volcanoes are essentially monolithologic dacite/andesite volcanoes, the edifice of the Viedma volcano appears to be composed mostly of basalts or older rocks/basement with low silica contents.Mediante el uso de técnica de sensoría remota se ha desarrollado un mapeo litológico del volcán Viedma, uno de los cinco volcanes de la Zona Volcánica Andina Austral (ZVA. Para este efecto, se ha utilizado el radiómetro ‘Advanced Spaceborne Thermal Emission and Reflection’ (ASTER que es muy efectivo en investigación geológica, para entender los procesos que han controlado la estructura y deducir las variaciones composi-cionales del volcán Viedma, que sobresale levemente de la superficie del campo de hielo Patagónico Sur. Sobre la base de la observación en el intervalo del espectro visible e infrarrojo cercano, en el edificio se distinguen partes brillantes que corresponden al flanco oriental del volcán y

  5. 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.

  6. Family-Based Benchmarking of Copy Number Variation Detection Software.

    Science.gov (United States)

    Nutsua, Marcel Elie; Fischer, Annegret; Nebel, Almut; Hofmann, Sylvia; Schreiber, Stefan; Krawczak, Michael; Nothnagel, Michael

    2015-01-01

    The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection software tools, namely Affymetrix Power Tools (APT), QuantiSNP, PennCNV, GLAD, R-gada and VEGA, and assessed their level of pair-wise prediction concordance. The tool-specific CNV prediction accuracy was assessed in silico by way of intra-familial validation. Software tools differed greatly in terms of the number and length of the CNVs predicted as well as the number of markers included in a CNV. All software tools predicted substantially more deletions than duplications. Intra-familial validation revealed consistently low levels of prediction accuracy as measured by the proportion of validated CNVs (34-60%). Moreover, up to 20% of apparent family-based validations were found to be due to chance alone. Software using Hidden Markov models (HMM) showed a trend to predict fewer CNVs than segmentation-based algorithms albeit with greater validity. PennCNV yielded the highest prediction accuracy (60.9%). Finally, the pairwise concordance of CNV prediction was found to vary widely with the software tools involved. We recommend HMM-based software, in particular PennCNV, rather than segmentation-based algorithms when validity is the primary concern of CNV detection. QuantiSNP may be used as an additional tool to detect sets of CNVs not detectable by the other tools. Our study also reemphasizes the need for laboratory-based validation, such as qPCR, of CNVs predicted in silico.

  7. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

    Science.gov (United States)

    Greenblum, Sharon; Turnbaugh, Peter J; Borenstein, Elhanan

    2012-01-10

    The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short of providing a comprehensive understanding of the impact of this variation on the community and on the host. Here, we introduce a metagenomic systems biology computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic networks. Focusing on the gut microbiome, we analyze fecal metagenomic data from 124 unrelated individuals, as well as six monozygotic twin pairs and their mothers, and generate community-level metabolic networks of the microbiome. Placing variations in gene abundance in the context of these networks, we identify both gene-level and network-level topological differences associated with obesity and inflammatory bowel disease (IBD). We show that genes associated with either of these host states tend to be located at the periphery of the metabolic network and are enriched for topologically derived metabolic "inputs." These findings may indicate that lean and obese microbiomes differ primarily in their interface with the host and in the way they interact with host metabolism. We further demonstrate that obese microbiomes are less modular, a hallmark of adaptation to low-diversity environments. We additionally link these topological variations to community species composition. The system-level approach presented here lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health.

  8. 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.

  9. Wisdom, Uncertainty, and Ambiguity in Management Decisions Based on Experiences and the Trustworthiness of Research Methods to Substantiate Them

    Directory of Open Access Journals (Sweden)

    Ronald Jean Degen

    2017-12-01

    Full Text Available Wisdom, uncertainty, and ambiguity will always exist in management decisions. One danger for firms lies in managers making decisions based on faulty theories acquired through personal experiences or learned from the experiences of others. Often, these decisions don’t generate the expected outcome and may even put the future of the firm at risk. Managers, to avoid this risk, are required to become wiser, more discerning, and more appropriately skeptical toward personal theories or theories learned from management gurus that propose simplistic formulas and quick-fix remedies. In this paper, the author discusses the risk of decisions based on personal theories or theories learned from others, the business research methods used to substantiate these theories, the philosophical assumptions of business research, the strength and weaknesses of qualitative and quantitative research methods, the benefits of combining both methods, and the trustworthiness of research methods in general for substantiating the theories used by managers in their decision-making. 

  10. Coarse Grained Exponential Variational Autoencoders

    KAUST Repository

    Sun, Ke; Zhang, Xiangliang

    2017-01-01

    Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually

  11. Variational submanifolds of Euclidean spaces

    Science.gov (United States)

    Krupka, D.; Urban, Z.; Volná, J.

    2018-03-01

    Systems of ordinary differential equations (or dynamical forms in Lagrangian mechanics), induced by embeddings of smooth fibered manifolds over one-dimensional basis, are considered in the class of variational equations. For a given non-variational system, conditions assuring variationality (the Helmholtz conditions) of the induced system with respect to a submanifold of a Euclidean space are studied, and the problem of existence of these "variational submanifolds" is formulated in general and solved for second-order systems. The variational sequence theory on sheaves of differential forms is employed as a main tool for the analysis of local and global aspects (variationality and variational triviality). The theory is illustrated by examples of holonomic constraints (submanifolds of a configuration Euclidean space) which are variational submanifolds in geometry and mechanics.

  12. Introduction to global variational geometry

    CERN Document Server

    Krupka, Demeter

    2015-01-01

    The book is devoted to recent research in the global variational theory on smooth manifolds. Its main objective is an extension of the classical variational calculus on Euclidean spaces to (topologically nontrivial) finite-dimensional smooth manifolds; to this purpose the methods of global analysis of differential forms are used. Emphasis is placed on the foundations of the theory of variational functionals on fibered manifolds - relevant geometric structures for variational principles in geometry, physical field theory and higher-order fibered mechanics. The book chapters include: - foundations of jet bundles and analysis of differential forms and vector fields on jet bundles, - the theory of higher-order integral variational functionals for sections of a fibred space, the (global) first variational formula in infinitesimal and integral forms- extremal conditions and the discussion of Noether symmetries and generalizations,- the inverse problems of the calculus of variations of Helmholtz type- variational se...

  13. Gauging Variational Inference

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ahn, Sungsoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of); Shin, Jinwoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of)

    2017-05-25

    Computing partition function is the most important statistical inference task arising in applications of Graphical Models (GM). Since it is computationally intractable, approximate methods have been used to resolve the issue in practice, where meanfield (MF) and belief propagation (BP) are arguably the most popular and successful approaches of a variational type. In this paper, we propose two new variational schemes, coined Gauged-MF (G-MF) and Gauged-BP (G-BP), improving MF and BP, respectively. Both provide lower bounds for the partition function by utilizing the so-called gauge transformation which modifies factors of GM while keeping the partition function invariant. Moreover, we prove that both G-MF and G-BP are exact for GMs with a single loop of a special structure, even though the bare MF and BP perform badly in this case. Our extensive experiments, on complete GMs of relatively small size and on large GM (up-to 300 variables) confirm that the newly proposed algorithms outperform and generalize MF and BP.

  14. 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.

  15. Harmonically excited orbital variations

    International Nuclear Information System (INIS)

    Morgan, T.

    1985-01-01

    Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable ex