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Sample records for analysis suggests overlapping

  1. Comprehensive Analysis Suggests Overlapping Expression of Rice ONAC Transcription Factors in Abiotic and Biotic Stress Responses

    Directory of Open Access Journals (Sweden)

    Lijun Sun

    2015-02-01

    Full Text Available NAC (NAM/ATAF/CUC transcription factors comprise a large plant-specific gene family that contains more than 149 members in rice. Extensive studies have revealed that NAC transcription factors not only play important roles in plant growth and development, but also have functions in regulation of responses to biotic and abiotic stresses. However, biological functions for most of the members in the NAC family remain unknown. In this study, microarray data analyses revealed that a total of 63 ONAC genes exhibited overlapping expression patterns in rice under various abiotic (salt, drought, and cold and biotic (infection by fungal, bacterial, viral pathogens, and parasitic plants stresses. Thirty-eight ONAC genes exhibited overlapping expression in response to any two abiotic stresses, among which 16 of 30 selected ONAC genes were upregulated in response to exogenous ABA. Sixty-five ONAC genes showed overlapping expression patterns in response to any two biotic stresses. Results from the present study suggested that members of the ONAC genes with overlapping expression pattern may have pleiotropic biological functions in regulation of defense response against different abiotic and biotic stresses, which provide clues for further functional analysis of the ONAC genes in stress tolerance and pathogen resistance.

  2. Comprehensive analysis suggests overlapping expression of rice ONAC transcription factors in abiotic and biotic stress responses.

    Science.gov (United States)

    Sun, Lijun; Huang, Lei; Hong, Yongbo; Zhang, Huijuan; Song, Fengming; Li, Dayong

    2015-01-01

    NAC (NAM/ATAF/CUC) transcription factors comprise a large plant-specific gene family that contains more than 149 members in rice. Extensive studies have revealed that NAC transcription factors not only play important roles in plant growth and development, but also have functions in regulation of responses to biotic and abiotic stresses. However, biological functions for most of the members in the NAC family remain unknown. In this study, microarray data analyses revealed that a total of 63 ONAC genes exhibited overlapping expression patterns in rice under various abiotic (salt, drought, and cold) and biotic (infection by fungal, bacterial, viral pathogens, and parasitic plants) stresses. Thirty-eight ONAC genes exhibited overlapping expression in response to any two abiotic stresses, among which 16 of 30 selected ONAC genes were upregulated in response to exogenous ABA. Sixty-five ONAC genes showed overlapping expression patterns in response to any two biotic stresses. Results from the present study suggested that members of the ONAC genes with overlapping expression pattern may have pleiotropic biological functions in regulation of defense response against different abiotic and biotic stresses, which provide clues for further functional analysis of the ONAC genes in stress tolerance and pathogen resistance. PMID:25690040

  3. Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses

    Directory of Open Access Journals (Sweden)

    Bhattacharjee Annapurna

    2010-01-01

    Full Text Available Abstract Background Glutathione S-transferases (GSTs are the ubiquitous enzymes that play a key role in cellular detoxification. Although several GSTs have been identified and characterized in various plant species, the knowledge about their role in developmental processes and response to various stimuli is still very limited. In this study, we report genome-wide identification, characterization and comprehensive expression analysis of members of GST gene family in crop plant rice, to reveal their function(s. Results A systematic analysis revealed the presence of at least 79 GST genes in the rice genome. Phylogenetic analysis grouped GST proteins into seven classes. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of GST gene family members in rice. The tandem gene duplications have contributed a major role in expansion of this gene family. Microarray data analysis revealed tissue-/organ- and developmental stage-specific expression patterns of several rice GST genes. At least 31 GST genes showed response to plant hormones auxin and cytokinin. Furthermore, expression analysis showed the differential expression of quite a large number of GST genes during various abiotic stress (20, arsenate stress (32 and biotic stress (48 conditions. Many of the GST genes were commonly regulated by developmental processes, hormones, abiotic and biotic stresses. Conclusion The transcript profiling suggests overlapping and specific role(s of GSTs during various stages of development in rice. Further, the study provides evidence for the role of GSTs in mediating crosstalk between various stress and hormone response pathways and represents a very useful resource for functional analysis of selected members of this family in rice.

  4. Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons.

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    Dominique Garmyn

    Full Text Available Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

  5. The genotypic structure of a multi-host bumblebee parasite suggests a role for ecological niche overlap.

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    Rahel M Salathé

    Full Text Available The genotypic structure of parasite populations is an important determinant of ecological and evolutionary dynamics of host-parasite interactions with consequences for pest management and disease control. Genotypic structure is especially interesting where multiple hosts co-exist and share parasites. We here analyze the natural genotypic distribution of Crithidia bombi, a trypanosomatid parasite of bumblebees (Bombus spp., in two ecologically different habitats over a time period of three years. Using an algorithm to reconstruct genotypes in cases of multiple infections, and combining these with directly identified genotypes from single infections, we find a striking diversity of infection for both data sets, with almost all multi-locus genotypes being unique, and are inferring that around half of the total infections are resulting from multiple strains. Our analyses further suggest a mixture of clonality and sexuality in natural populations of this parasite species. Finally, we ask whether parasite genotypes are associated with host species (the phylogenetic hypothesis or whether ecological factors (niche overlap in flower choice shape the distribution of parasite genotypes (the ecological hypothesis. Redundancy analysis demonstrates that in the region with relatively high parasite prevalence, both host species identity and niche overlap are equally important factors shaping the distribution of parasite strains, whereas in the region with lower parasite prevalence, niche overlap more strongly contributes to the distribution observed. Overall, our study underlines the importance of ecological factors in shaping the natural dynamics of host-parasite systems.

  6. EVOG: a database for evolutionary analysis of overlapping genes.

    Science.gov (United States)

    Kim, Dae-Soo; Cho, Chi-Young; Huh, Jae-Won; Kim, Heui-Soo; Cho, Hwan-Gue

    2009-01-01

    Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. In this study, we implemented evolutionary visualizer for overlapping genes (EVOG), a Web-based DB with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish and Drosophila. This integrated database provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG DB components included a number of overlapping genes (10074 in human, 10,009 in chimpanzee, 67,039 in orangutan, 51,001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10,700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation to disease by comparing the expression profiles of overlapping genes. EVOG is available at http://neobio.cs.pusan.ac.kr/evog/. PMID:18986995

  7. Experience moderates overlap between object and face recognition, suggesting a common ability

    Science.gov (United States)

    Gauthier, Isabel; McGugin, Rankin W.; Richler, Jennifer J.; Herzmann, Grit; Speegle, Magen; Van Gulick, Ana E.

    2014-01-01

    Some research finds that face recognition is largely independent from the recognition of other objects; a specialized and innate ability to recognize faces could therefore have little or nothing to do with our ability to recognize objects. We propose a new framework in which recognition performance for any category is the product of domain-general ability and category-specific experience. In Experiment 1, we show that the overlap between face and object recognition depends on experience with objects. In 256 subjects we measured face recognition, object recognition for eight categories, and self-reported experience with these categories. Experience predicted neither face recognition nor object recognition but moderated their relationship: Face recognition performance is increasingly similar to object recognition performance with increasing object experience. If a subject has a lot of experience with objects and is found to perform poorly, they also prove to have a low ability with faces. In a follow-up survey, we explored the dimensions of experience with objects that may have contributed to self-reported experience in Experiment 1. Different dimensions of experience appear to be more salient for different categories, with general self-reports of expertise reflecting judgments of verbal knowledge about a category more than judgments of visual performance. The complexity of experience and current limitations in its measurement support the importance of aggregating across multiple categories. Our findings imply that both face and object recognition are supported by a common, domain-general ability expressed through experience with a category and best measured when accounting for experience. PMID:24993021

  8. Analysis of Surface Roughness at Overlapping Laser Shock Peening

    Science.gov (United States)

    Dai, F. Z.; Zhang, Z. D.; Zhou, J. Z.; Lu, J. Z.; Zhang, Y. K.

    2016-02-01

    The overlapping effects on surface roughness are studied when samples are treated by laser shock peening (LSP). Surface roughness of overlapped circular laser spot is calculated by ISO 25178 height parameters. The usually used overlapping styles namely isosceles-right-triangle-style (AAP) and equilateral-triangle-style (AAA) are carefully investigated when the overlapping degree in x-axis (ηx) is below 50%. Surface roughness of isosceles-right-triangle-style attains its minimum value at ηx of 29.3%, and attains its maximum value at ηx of 43.6%. Surface roughness of equilateral-triangle-style attains its minimum value at ηx of 42.3%, and attains its maximum value at ηx of 32%. Experimental results are well consistent with theoretical analysis.

  9. EVOG: a database for evolutionary analysis of overlapping genes

    OpenAIRE

    Kim, Dae-Soo; Cho, Chi-Young; Huh, Jae-Won; Kim, Heui-Soo; Cho, Hwan-Gue

    2008-01-01

    Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. In this study, we implemented evolutionary visualizer for overlapping genes (EVOG), a Web-based DB with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Using this ...

  10. Long memory analysis by using maximal overlapping discrete wavelet transform

    Science.gov (United States)

    Shafie, Nur Amalina binti; Ismail, Mohd Tahir; Isa, Zaidi

    2015-05-01

    Long memory process is the asymptotic decay of the autocorrelation or spectral density around zero. The main objective of this paper is to do a long memory analysis by using the Maximal Overlapping Discrete Wavelet Transform (MODWT) based on wavelet variance. In doing so, stock market of Malaysia, China, Singapore, Japan and United States of America are used. The risk of long term and short term investment are also being looked into. MODWT can be analyzed with time domain and frequency domain simultaneously and decomposing wavelet variance to different scales without loss any information. All countries under studied show that they have long memory. Subprime mortgage crisis in 2007 is occurred in the United States of America are possible affect to the major trading countries. Short term investment is more risky than long term investment.

  11. Modeling Overlapping Laminations in Magnetic Core Materials Using 2-D Finite-Element Analysis

    DEFF Research Database (Denmark)

    Jensen, Bogi Bech; Guest, Emerson David; Mecrow, Barrie C.

    2015-01-01

    This paper describes a technique for modeling overlapping laminations in magnetic core materials using two-dimensional finite-element (2-D FE) analysis. The magnetizing characteristic of the overlapping region is captured using a simple 2-D FE model of the periodic overlapping geometry and a comp...

  12. Rheumatoid Arthritis-Associated Interstitial Lung Disease and Idiopathic Pulmonary Fibrosis: Shared Mechanistic and Phenotypic Traits Suggest Overlapping Disease Mechanisms.

    Science.gov (United States)

    Paulin, Francisco; Doyle, Tracy J; Fletcher, Elaine A; Ascherman, Dana P; Rosas, Ivan O

    2015-01-01

    The prevalence of clinically evident interstitial lung disease in patients with rheumatoid arthritis is approximately 10%. An additional 33% of undiagnosed patients have interstitial lung abnormalities that can be detected with high-resolution computed tomography. Rheumatoid arthritis-interstitial lung disease patients have three times the risk of death compared to those with rheumatoid arthritis occurring in the absence of interstitial lung disease, and the mortality related to interstitial lung disease is rising. Rheumatoid arthritis-interstitial lung disease is most commonly classified as the usual interstitial pneumonia pattern, overlapping mechanistically and phenotypically with idiopathic pulmonary fibrosis, but can occur in a non-usual interstitial pneumonia pattern, mainly nonspecific interstitial pneumonia. Based on this, we propose two possible pathways to explain the coexistence of rheumatoid arthritis and interstitial lung disease: (i) Rheumatoid arthritis-interstitial lung disease with a non-usual interstitial pneumonia pattern may come about when an immune response against citrullinated peptides taking place in another site (e.g. the joints) subsequently affects the lungs; (ii) Rheumatoid arthritis-interstitial lung disease with a usual interstitial pneumonia pattern may represent a disease process in which idiopathic pulmonary fibrosis-like pathology triggers an immune response against citrullinated proteins that promotes articular disease indicative of rheumatoid arthritis. More studies focused on elucidating the basic mechanisms leading to different sub-phenotypes of rheumatoid arthritis-interstitial lung disease and the overlap with idiopathic pulmonary fibrosis are necessary to improve our understanding of the disease process and to define new therapeutic targets.

  13. Association of variants at 1q32 and STAT3 with ankylosing spondylitis suggests genetic overlap with Crohn's disease.

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    Patrick Danoy

    Full Text Available Ankylosing spondylitis (AS is a common inflammatory arthritic condition. Overt inflammatory bowel disease (IBD occurs in about 10% of AS patients, and in addition 70% of AS cases may have subclinical terminal ileitis. Spondyloarthritis is also common in IBD patients. We therefore tested Crohn's disease susceptibility genes for association with AS, aiming to identify pleiotropic genetic associations with both diseases. Genotyping was carried out using Sequenom and Applied Biosystems TaqMan and OpenArray technologies on 53 markers selected from 30 Crohn's disease associated genomic regions. We tested genotypes in a population of unrelated individual cases (n = 2,773 and controls (n = 2,215 of white European ancestry for association with AS. Statistical analysis was carried out using a Cochran-Armitage test for trend in PLINK. Strong association was detected at chr1q32 near KIF21B (rs11584383, P = 1.6 × 10(-10, odds ratio (OR = 0.74, 95% CI:0.68-0.82. Association with disease was also detected for 2 variants within STAT3 (rs6503695, P = 4.6 × 10(-4. OR = 0.86 (95% CI:0.79-0.93; rs744166, P = 2.6 × 10(-5, OR = 0.84 (95% CI:0.77-0.91. Association was confirmed for IL23R (rs11465804, P = 1.2 × 10(-5, OR = 0.65 (95% CI:0.54-0.79, and further associations were detected for IL12B (rs10045431, P = 5.2 × 10(-5, OR = 0.83 (95% CI:0.76-0.91, CDKAL1 (rs6908425, P = 1.1 × 10(-4, OR = 0.82 (95% CI:0.74-0.91, LRRK2/MUC19 (rs11175593, P = 9.9 × 10(-5, OR = 1.92 (95% CI: 1.38-2.67, and chr13q14 (rs3764147, P = 5.9 × 10(-4, OR = 1.19 (95% CI: 1.08-1.31. Excluding cases with clinical IBD did not significantly affect these findings. This study identifies chr1q32 and STAT3 as ankylosing spondylitis susceptibility loci. It also further confirms association for IL23R and detects suggestive association with another 4 loci. STAT3 is a key signaling molecule within the Th17 lymphocyte differentiation pathway and further enhances the case for a major role of

  14. Analysis of amplitude spectra with overlapping peaks from scintillation detectors

    International Nuclear Information System (INIS)

    A technique is proposed for resolution of overlapping peaks in amplitude spectra obtained by scintillation detectors. Based on the technique, a program was developed and is being used in practical measurements at Kozloduy NPP. The program works in environment of MathCAD, version 2, of the firm MathSoft, Inc. As regards the handling of amplitude spectra, a software emulation on an multichannel analyzer with a personal computer was developed. The language used for program emulation is QuickBASIC, version 4.0 of the firm Microsoft Corp. (author)

  15. Genomic analysis suggests higher susceptibility of children to air pollution

    DEFF Research Database (Denmark)

    van Leeuwen, Danitsja M; Pedersen, Marie; Hendriksen, Peter J M;

    2008-01-01

    between parents. Very little overlap was observed between children and adults. The two most important biological processes or molecular functions significantly modulated in children, but not in adults, are nucleosome and immune response related. Our study suggests differences between children and adults...

  16. Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis.

    Science.gov (United States)

    Laub, Brian G; Budy, Phaedra

    2015-08-01

    A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans. PMID:25627117

  17. Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis

    Science.gov (United States)

    Laub, P; Budy, Phaedra

    2015-01-01

    A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.

  18. [Application of the racial algorithm in energy dispersive X-ray fluorescence overlapped spectrum analysis].

    Science.gov (United States)

    Zeng, Guo-Qiang; Luo, Yao-Yao; Ge, Liang-Quan; Zhang, Qing-Xian; Gu, Yi; Cheng, Feng

    2014-02-01

    In the energy dispersive X-ray fluorescence spectrum analysis, scintillation detector such as NaI (Tl) detector usually has a low energy resolution at around 8%. The low energy resolution causes problems in spectral data analysis especially in the high background and low counts condition, it is very limited to strip the overlapped spectrum, and the more overlapping the peaks are, the more difficult to peel the peaks, and the qualitative and quantitative analysis can't be carried out because we can't recognize the peak address and peak area. Based on genetic algorithm and immune algorithm, we build a new racial algorithm which uses the Euclidean distance as the judgment of evolution, the maximum relative error as the iterative criterion to be put into overlapped spectrum analysis, then we use the Gaussian function to simulate different overlapping degrees of the spectrum, and the racial algorithm is used in overlapped peak separation and full spectrum simulation, the peak address deviation is in +/- 3 channels, the peak area deviation is no more than 5%, and it is proven that this method has a good effect in energy dispersive X-ray fluorescence overlapped spectrum analysis.

  19. Parametric analysis and design equation of ultimate capacity for unstiffened overlapped CHS K-joints

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A finite element model simulating an experiment on unstiffened,overlapped circular hollow structure (CHS)K-joints was generated and validated by comparing the ultimate capacities,deformation processes and failure modes of the experimental results.Using this model,the stress distribution,propagation of plasticity and the failure modes of overlapped joints with through-brace-in-compression and welded hidden seams were analyzed.The effect of geometric parameters,with or without hidden welds,and the loading hierarchy reversal of braces on the ultimate capacity of the joints were also studied.The results of finite element parametric analysis indicate that the brace-tochord thickness ratio has relatively large effects on the failure mechanism and ultimate capacity of overlapped joints.It was also found that the absence of hidden welds has less significance on the ultimate capacity of through-brace-incompression joints than through-brace-in tension joints.Finally,based on the design equation of gap joints,a formula predicting the ultimate capacity of overlapped CHS K-joints was derived by applying multivariate regression analysis.Results from the proposed design equation are consistent with experimental results.

  20. Analysis of transcript and protein overlap in a human osteosarcoma cell line

    Directory of Open Access Journals (Sweden)

    Emanuelsson Olof

    2010-12-01

    Full Text Available Abstract Background An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC and immunofluorescence microscopy (IF. Results A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2% were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies. Conclusion This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.

  1. Nonlinear structure analysis of carbon and energy markets with MFDCCA based on maximum overlap wavelet transform

    Science.gov (United States)

    Cao, Guangxi; Xu, Wei

    2016-02-01

    This paper investigates the nonlinear structure between carbon and energy markets by employing the maximum overlap wavelet transform (MODWT) as well as the multifractal detrended cross-correlation analysis based on maximum overlap wavelet transform (MFDCCA-MODWT). Based on the MODWT multiresolution analysis and the statistic Qcc(m) significance, relatively significant cross-correlations are obtained between carbon and energy future markets either on different time scales or on the whole. The result of the Granger causality test indicates bidirectional Granger causality between carbon and electricity future markets, although the Granger causality relationship between the carbon and oil price is not evident. The existence of multifractality for the returns between carbon and energy markets is proven with the MFDCCA-MODWT algorithm. In addition, results of investigating the origin of multifractality demonstrate that both long-range correlations and fat-tailed distributions play important roles in the contributions of multifractality.

  2. Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

    OpenAIRE

    Guttman, Miklos; Weis, David D.; John R Engen; Lee, Kelly K.

    2013-01-01

    Noisy and overlapped mass spectrometry data hinders the sequence coverage that can be obtained from Hydrogen Deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are reencountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regressio...

  3. Overlap in diet and distribution of two goose species suggests potential for competition at a common moulting area in West Greenland

    DEFF Research Database (Denmark)

    Raundrup, Katrine; Levermann, Nette; Poulsen, Michael

    2012-01-01

    decreased over the last 15-20 years, while the Canada Goose, a species new to the area, has increased. This study explores the overlap in diet and space use of these species in Mudderbugten and Kvandalen, together with factors that could influence the degree of competition between the two species. Data......Inter-specific competition can occur where two or more species overlap in diet and/or spatial distribution. Such interactions might be most prevalent where a species invades areas previously occupied by another species. In West Greenland, the number of native Greenland White-fronted Geese has...... on activity budgets and spatial distribution were obtained from observations of behaviour, and diet selection was determined through analyses of plant epidermal fragments in faecal samples that were subsequently genotyped to goose species. No differences in diet or spatial distribution of the two species were...

  4. Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape.

    Directory of Open Access Journals (Sweden)

    Dustin C Hancks

    2015-05-01

    Full Text Available A diverse subset of pattern recognition receptors (PRRs detects pathogen-associated nucleic acids to initiate crucial innate immune responses in host organisms. Reflecting their importance for host defense, pathogens encode various countermeasures to evade or inhibit these immune effectors. PRRs directly engaged by pathogen inhibitors often evolve under recurrent bouts of positive selection that have been described as molecular 'arms races.' Cyclic GMP-AMP synthase (cGAS was recently identified as a key PRR. Upon binding cytoplasmic double-stranded DNA (dsDNA from various viruses, cGAS generates the small nucleotide secondary messenger cGAMP to signal activation of innate defenses. Here we report an evolutionary history of cGAS with recurrent positive selection in the primate lineage. Recent studies indicate a high degree of structural similarity between cGAS and 2'-5'-oligoadenylate synthase 1 (OAS1, a PRR that detects double-stranded RNA (dsRNA, despite low sequence identity between the respective genes. We present comprehensive comparative evolutionary analysis of cGAS and OAS1 primate sequences and observe positive selection at nucleic acid binding interfaces and distributed throughout both genes. Our data revealed homologous regions with strong signatures of positive selection, suggesting common mechanisms employed by unknown pathogen encoded inhibitors and similar modes of evasion from antagonism. Our analysis of cGAS diversification also identified alternately spliced forms missing multiple sites under positive selection. Further analysis of selection on the OAS family in primates, which comprises OAS1, OAS2, OAS3 and OASL, suggests a hypothesis where gene duplications and domain fusion events result in paralogs that provide another means of escaping pathogen inhibitors. Together our comparative evolutionary analysis of cGAS and OAS provides new insights into distinct mechanisms by which key molecular sentinels of the innate immune system

  5. Cladistic biogeographic analysis suggests an early Caribbean diversification in Mexico

    Science.gov (United States)

    Escalante, Tania; Rodríguez, Gerardo; Cao, Nathanaël; Ebach, Malte C.; Morrone, Juan J.

    2007-07-01

    The Great American Biotic Interchange has been the predominant paradigm for explaining biotic diversification in the Nearctic/Neotropical overlap or Mexican Transition Zone, which is commonly explained by the collision of the North and South American continental plates, which began in the Oligocene and fused both landmasses. In the most far-reaching cladistic biogeographical analysis of the area to date, evidence has been found supporting the existence of a remnant Caribbean region extending from eastern Mexico to southeastern USA, a hypothesis that challenges current views of the Great American Biotic Interchange and the Mexican Transition Zone. We show herein that an older terrane, which has drifted to the present day positions of Yucatan and Cuba, may be biogeographically linked to an early ‘Gondwanan’ biota of the Paleocene (ca. 60 Ma). The evidence indicates an east west biotic divide in Mexico, existing before the collision and formation of Central America. The south north division of the country, previously recognized by several authors as associated with the Great American Biotic Interchange and the Mexican Transition Zone, is of a younger age.

  6. Finite Element Analysis of Composite Joint Configurations with Gaps and Overlaps

    Science.gov (United States)

    Krueger, Ronald

    2014-01-01

    The goal of the current study is to identify scenarios for which thermal and moisture effects become significant in the loading of a composite structure. In the current work, a simple configuration was defined, and material properties were selected. A Fortran routine was created to automate the mesh generation process. The routine was used to create the models for the initial mesh refinement study. A combination of element length and width suitable for further studies was identified. Also, the effect of the overlap length and gap length on computed shear and through-thickness stresses along the bondline of the joints was studied for the mechanical load case. Further, the influence of neighboring gaps and overlaps on these joint stresses was studied and was found to be negligible. The results suggest that for an initial study it is sufficient to focus on one configuration with fixed overlap and gap lengths to study the effects of mechanical, thermal and moisture loading and combinations thereof on computed joint stresses

  7. Analysis of topological structure of the QCD vacuum with overlap-Dirac operator eigenmode

    CERN Document Server

    Iritani, Takumi; Hashimoto, Shoji

    2013-01-01

    Using the eigenmodes of the overlap-Dirac operator, we study the topological structure of the QCD vacuum. We investigate the space-time profile of the low-lying eigenmodes and their contribution to the vacuum action density and chiral condensate under the existence of static color sources. We demonstrate that the low-lying Dirac eigenmode shows the flux-tube structure, which suggests the relevance to confinement. We also analyze the chiral condensate in the flux-tube. Chiral symmetry is partially restored inside the flux, and the reduction of the condensate is about 20% at the center of the tube.

  8. Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

    DEFF Research Database (Denmark)

    Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia;

    2014-01-01

    these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach......, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large...

  9. Anti-proteinase 3 antibodies in diffuse systemic sclerosis (SSc with normotensive renal impairment: is it suggestive for an overlapping between SSc and idiopathic vasculitis?

    Directory of Open Access Journals (Sweden)

    V. Campanella

    2011-09-01

    Full Text Available Objective. To test the prevalence of anti-neutrophil cytoplasmic antibodies (ANCA in systemic sclerosis (SSc and to verify a possible association of ANCA with normotensive renal involvement in SSc. Patients and methods: 51 patients affected by SSc, 35 with diffuse scleroderma (dSSc and 16 with limited scleroderma (lSSc, were tested for ANCA by indirect immunofluorescence (IIF on human ethanol and formalin-acetone-fixed granulocytes (before and after DNase treatment, by conventional enzyme linked immuno-sorbent assay (ELISA and by capture-ELISA. Results. Six out of 51 selected SSc patients had ANCA by IIF (11.7% and five presented a perinuclear/nuclear atypical ANCA pattern. In all cases we only found anti-proteinase3 (aPR3 antibodies. All ANCA positive patients had diffuse form of SSc (17.1%, all were anti-Scl70 positive (aScl70, five patients had proteinuria, three had microscopic haematuria. All ANCA positive patients were normotensive with normal renin plasma levels, the mean erythrocyte sedimentation rate (ESR was higher in this group compared to the other SSc patients. Conclusions. Our study shows that aPR3 is not rare in dSSc. According to the clinical and serological findings and to the recent literature, we can hypothesise that when ANCA are found in SSc, an overlapping of scleroderma with systemic necrotizing vasculitis should be suspected.

  10. Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

    Science.gov (United States)

    Guttman, Miklos; Weis, David D.; Engen, John R.; Lee, Kelly K.

    2013-12-01

    Noisy and overlapped mass spectrometry data hinder the sequence coverage that can be obtained from hydrogen deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are re-encountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11 %. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2.

  11. User Suggestions Extraction from customer Reviews A Sentiment Analysis approach

    Directory of Open Access Journals (Sweden)

    Vishwanath.J,

    2011-03-01

    Full Text Available Customer review is a major criterion for the improvement of the quality of services rendered and enhancement of the deliverables. Blogs, articles and discussion forums, provide manufacturers or sellers with a good understanding of the reception level of their products in the competitive market. An interesting area from the business analysis perspective, this paper discusses an opinion based mining technique for the extraction of the relevant data using Natural Language Processing and text analysis, and comprehends suggestions from an actionable feedback.

  12. SCAM analysis of Panx1 suggests a peculiar pore structure.

    Science.gov (United States)

    Wang, Junjie; Dahl, Gerhard

    2010-11-01

    Vertebrates express two families of gap junction proteins: the well-characterized connexins and the pannexins. In contrast to connexins, pannexins do not appear to form gap junction channels but instead function as unpaired membrane channels. Pannexins have no sequence homology to connexins but are distantly related to the invertebrate gap junction proteins, innexins. Despite the sequence diversity, pannexins and connexins form channels with similar permeability properties and exhibit similar membrane topology, with two extracellular loops, four transmembrane (TM) segments, and cytoplasmic localization of amino and carboxy termini. To test whether the similarities extend to the pore structure of the channels, pannexin 1 (Panx1) was subjected to analysis with the substituted cysteine accessibility method (SCAM). The thiol reagents maleimidobutyryl-biocytin and 2-trimethylammonioethyl-methanethiosulfonate reacted with several cysteines positioned in the external portion of the first TM segment (TM1) and the first extracellular loop. These data suggest that portions of TM1 and the first extracellular loop line the outer part of the pore of Panx1 channels. In this aspect, the pore structures of Panx1 and connexin channels are similar. However, although the inner part of the pore is lined by amino-terminal amino acids in connexin channels, thiol modification was detected in carboxyterminal amino acids in Panx1 channels by SCAM analysis. Thus, it appears that the inner portion of the pores of Panx1 and connexin channels may be distinct. PMID:20937692

  13. Analysis and correction of track overlapping on nuclear track detectors (SSNTD)

    Energy Technology Data Exchange (ETDEWEB)

    Palacios, D.; Sajo B, L.; Barros, H.; Avila, Y. [Universidad Simon Bolivar, P. O. 89000 Caracas (Venezuela, Bolivarian Republic of); Fusella, E. [Instituto de Estudios Avanzados, Apartado 17606, Caracas 1015-A (Venezuela, Bolivarian Republic of)

    2011-02-15

    The problem of nuclear track overlapping is addressed assuming the stochastic character of charged particle registry and the fact that even monoenergetic beam perpendicularly impacting on detector surface will show a distribution for track radius values. Asymmetric distributions of overlapping tracks were obtained for very low or very high simulated track quantities, while for intermediate values the distributions were well described by Gaussian s. A model for the track overlapping process was developed, considering the dependence of the quantity of non overlapping tracks on the number of simulated tracks by a second order homogeneous differential lineal equation. Its solution contains only one free parameter that is related to track geometry and field view area. By successive approximation, the number of total induced tracks (which is proportional to particle fluence) is determined from the knowledge of the amount of non overlapping tracks, dimensions of the field view and average track radius. (Author)

  14. Low Self-Control and the Victim-Offender Overlap: A Gendered Analysis.

    Science.gov (United States)

    Flexon, Jamie L; Meldrum, Ryan C; Piquero, Alex R

    2016-07-01

    The overlap between victimization and offending is well documented. Yet, there have been fewer investigations of the reasons underlying this relationship. One possible, but understudied, explanation lies with Gottfredson and Hirschi's arguments regarding self-control. The current study adds to this line of inquiry by assessing whether low self-control accounts for the victim-offender overlap in a sample of young adults and whether self-control accounts for the observed overlap similarly across gender. Results from a series of bivariate probit regression models indicate that low self-control is positively related to both victimization and offending. However, only among males does low self-control account for a substantive portion of the victim-offender overlap. Limitations of the study and implications and directions for future research are discussed. PMID:25711616

  15. A More Accurate Measure of Local Public Goods: Overlapping Government Combinations as Units of Analysis

    Directory of Open Access Journals (Sweden)

    Samuel B. Stone

    2014-01-01

    Full Text Available This study posits and tests the viability of a new unit of analysis for local public goods in metropolitan areas: overlapping government combinations (OGCs. Counties, municipalities, school districts, and other special districts operate simultaneously within the same space, each providing their own set of local public goods. Residents of the same city can live within the boundaries of different counties, school districts and other special districts and thus receive (and pay for very different quantities and qualities of public goods. Though there is a great deal of literature devoted to the variation of local public goods in a fragmented metropolitan region, there is none that cumulates the different local government types into units that represent the true bundles of local public goods that are provided to citizens and property owners. This study tackles this problem through the application of geographic information systems (GIS to stack counties, municipalities, and school districts in the Dallas-Fort Worth-Arlington CMSA into unique OGCs. The unique OGCs are compared to their underlying component governments with respect to property tax rates and school performance and are found to be statistically distinct.

  16. Vacuum structure revealed by over-improved stout-link smearing compared with the overlap analysis for quenched QCD

    International Nuclear Information System (INIS)

    A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff λcut. The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeVcut<600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)

  17. Vacuum structure revealed by over-improved stout-link smearing compared with the overlap analysis for quenched QCD

    Energy Technology Data Exchange (ETDEWEB)

    Ilgenfritz, E.M.; Leinweber, D.; Moran, P. [Adelaide Univ., SA (AU). Special Research Centre for the Subatomic Structure of Matter (CSSM); Koller, K. [Muenchen Univ. (Germany). Sektion Physik; Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Weinberg, V. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Freie Univ. Berlin (Germany). Inst. fuer Theoretische Physik

    2008-01-11

    A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff {lambda}{sub cut}. The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeV<{lambda}{sub cut}<600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)

  18. Genomic analysis suggests higher susceptibility of children to air pollution

    NARCIS (Netherlands)

    Leeuwen, D.M. van; Pedersen, M.; Hendriksen, P.J.M.; Boorsma, A.; Herwijnen, M.H.M. van; Gottschalk, R.W.H.; Kirsch-Volders, M.; Knudsen, L.E.; Šrám, R.J.; Bajak, E.; Delft, J.H.M. van; Kleinjans, J.C.S.

    2008-01-01

    Differences in biological responses to exposure to hazardous airborne substances between children and adults have been reported, suggesting children to be more susceptible. Aim of this study was to improve our understanding of differences in susceptibility in cancer risk associated with air pollutio

  19. Analysis of existing risk assessments, and list of suggestions

    CERN Document Server

    Heimsch, Laura

    2016-01-01

    The scope of this project was to analyse risk assessments made at CERN and extracting some crucial information about the different methodologies used, profiles of people who make the risk assessments, and gathering information of whether the risk matrix was used and if the acceptable level of risk was defined. Second step of the project was to trigger discussion inside HSE about risk assessment by suggesting a risk matrix and a risk assessment template.

  20. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions

    DEFF Research Database (Denmark)

    Pendle, Alison F; Clark, Gillian P; Boon, Reinier;

    2005-01-01

    The eukaryotic nucleolus is involved in ribosome biogenesis and a wide range of other RNA metabolism and cellular functions. An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. Here, we describe the first proteomic...

  1. Infants' brain responses to speech suggest analysis by synthesis.

    Science.gov (United States)

    Kuhl, Patricia K; Ramírez, Rey R; Bosseler, Alexis; Lin, Jo-Fu Lotus; Imada, Toshiaki

    2014-08-01

    Historic theories of speech perception (Motor Theory and Analysis by Synthesis) invoked listeners' knowledge of speech production to explain speech perception. Neuroimaging data show that adult listeners activate motor brain areas during speech perception. In two experiments using magnetoencephalography (MEG), we investigated motor brain activation, as well as auditory brain activation, during discrimination of native and nonnative syllables in infants at two ages that straddle the developmental transition from language-universal to language-specific speech perception. Adults are also tested in Exp. 1. MEG data revealed that 7-mo-old infants activate auditory (superior temporal) as well as motor brain areas (Broca's area, cerebellum) in response to speech, and equivalently for native and nonnative syllables. However, in 11- and 12-mo-old infants, native speech activates auditory brain areas to a greater degree than nonnative, whereas nonnative speech activates motor brain areas to a greater degree than native speech. This double dissociation in 11- to 12-mo-old infants matches the pattern of results obtained in adult listeners. Our infant data are consistent with Analysis by Synthesis: auditory analysis of speech is coupled with synthesis of the motor plans necessary to produce the speech signal. The findings have implications for: (i) perception-action theories of speech perception, (ii) the impact of "motherese" on early language learning, and (iii) the "social-gating" hypothesis and humans' development of social understanding.

  2. Pan-atlantic analysis of the overlap of a highly migratory species, the leatherback turtle, with pelagic longline fisheries.

    Science.gov (United States)

    Fossette, S; Witt, M J; Miller, P; Nalovic, M A; Albareda, D; Almeida, A P; Broderick, A C; Chacón-Chaverri, D; Coyne, M S; Domingo, A; Eckert, S; Evans, D; Fallabrino, A; Ferraroli, S; Formia, A; Giffoni, B; Hays, G C; Hughes, G; Kelle, L; Leslie, A; López-Mendilaharsu, M; Luschi, P; Prosdocimi, L; Rodriguez-Heredia, S; Turny, A; Verhage, S; Godley, B J

    2014-04-01

    Large oceanic migrants play important roles in ecosystems, yet many species are of conservation concern as a result of anthropogenic threats, of which incidental capture by fisheries is frequently identified. The last large populations of the leatherback turtle, Dermochelys coriacea, occur in the Atlantic Ocean, but interactions with industrial fisheries could jeopardize recent positive population trends, making bycatch mitigation a priority. Here, we perform the first pan-Atlantic analysis of spatio-temporal distribution of the leatherback turtle and ascertain overlap with longline fishing effort. Data suggest that the Atlantic probably consists of two regional management units: northern and southern (the latter including turtles breeding in South Africa). Although turtles and fisheries show highly diverse distributions, we highlight nine areas of high susceptibility to potential bycatch (four in the northern Atlantic and five in the southern/equatorial Atlantic) that are worthy of further targeted investigation and mitigation. These are reinforced by reports of leatherback bycatch at eight of these sites. International collaborative efforts are needed, especially from nations hosting regions where susceptibility to bycatch is likely to be high within their exclusive economic zone (northern Atlantic: Cape Verde, Gambia, Guinea Bissau, Mauritania, Senegal, Spain, USA and Western Sahara; southern Atlantic: Angola, Brazil, Namibia and UK) and from nations fishing in these high-susceptibility areas, including those located in international waters.

  3. Expression analysis of Arabidopsis XH/XS-domain proteins indicates overlapping and distinct functions for members of this gene family.

    Science.gov (United States)

    Butt, Haroon; Graner, Sonja; Luschnig, Christian

    2014-03-01

    RNA-directed DNA methylation (RdDM) is essential for de novo DNA methylation in higher plants, and recent reports established novel elements of this silencing pathway in the model organism Arabidopsis thaliana. Involved in de novo DNA methylation 2 (IDN2) and the closely related factor of DNA methylation (FDM) are members of a plant-specific family of dsRNA-binding proteins characterized by conserved XH/XS domains and implicated in the regulation of RdDM at chromatin targets. Genetic analyses have suggested redundant as well as non-overlapping activities for different members of the gene family. However, detailed insights into the function of XH/XS-domain proteins are still elusive. By the generation and analysis of higher-order mutant combinations affected in IDN2 and further members of the gene family, we have provided additional evidence for their redundant activity. Distinct roles for members of the XH/XS-domain gene family were indicated by differences in their expression and subcellular localization. Fluorescent protein-tagged FDM genes were expressed either in nuclei or in the cytoplasm, suggestive of activities of XH/XS-domain proteins in association with chromatin as well as outside the nuclear compartment. In addition, we observed altered location of a functional FDM1-VENUS reporter from the nucleus into the cytoplasm under conditions when availability of further FDM proteins was limited. This is suggestive of a mechanism by which redistribution of XH/XS-domain proteins could compensate for the loss of closely related proteins.

  4. Deformation analysis of a film-overlapped micro-pump membrane structure

    International Nuclear Information System (INIS)

    A novel approach is developed to study a film-overlapped membrane structure. Meanwhile, the established model is employed to design the micro-pump membrane structure and to evaluate its pumping efficiency. Two-dimensional coupling effects between the overlapping actuator films and the deformable membrane are thoroughly investigated, including the influences on the membrane from the overlapping films' elongation effects, Poisson's ratio effects and shear strain effects. Overall deformations and interactions for the three-layer membrane structures are accurately calculated through exercising the developed model, in contrast to what difficulties are usually encountered in carrying out FEM methods with very thin elements meshed for the actuator films. Furthermore, this study demonstrates that the high stiffness of the actuating metal films needs to be reflected in the equivalent stiffness of the membrane structures, especially when the sizes of the actuator films become compatible with the sizes of the membranes. Hence, the optimal micro-pumping efficiency of a membrane structure is acquired upon exercising the developed model, and larger sizes of the actuating films do not definitely obtain larger pumping efficiencies for the electromagnetically actuated micro-pumps

  5. SPARK: Sparsity-based analysis of reliable k-hubness and overlapping network structure in brain functional connectivity.

    Science.gov (United States)

    Lee, Kangjoo; Lina, Jean-Marc; Gotman, Jean; Grova, Christophe

    2016-07-01

    Functional hubs are defined as the specific brain regions with dense connections to other regions in a functional brain network. Among them, connector hubs are of great interests, as they are assumed to promote global and hierarchical communications between functionally specialized networks. Damage to connector hubs may have a more crucial effect on the system than does damage to other hubs. Hubs in graph theory are often identified from a correlation matrix, and classified as connector hubs when the hubs are more connected to regions in other networks than within the networks to which they belong. However, the identification of hubs from functional data is more complex than that from structural data, notably because of the inherent problem of multicollinearity between temporal dynamics within a functional network. In this context, we developed and validated a method to reliably identify connectors and corresponding overlapping network structure from resting-state fMRI. This new method is actually handling the multicollinearity issue, since it does not rely on counting the number of connections from a thresholded correlation matrix. The novelty of the proposed method is that besides counting the number of networks involved in each voxel, it allows us to identify which networks are actually involved in each voxel, using a data-driven sparse general linear model in order to identify brain regions involved in more than one network. Moreover, we added a bootstrap resampling strategy to assess statistically the reproducibility of our results at the single subject level. The unified framework is called SPARK, i.e. SParsity-based Analysis of Reliable k-hubness, where k-hubness denotes the number of networks overlapping in each voxel. The accuracy and robustness of SPARK were evaluated using two dimensional box simulations and realistic simulations that examined detection of artificial hubs generated on real data. Then, test/retest reliability of the method was assessed

  6. SPARK: Sparsity-based analysis of reliable k-hubness and overlapping network structure in brain functional connectivity.

    Science.gov (United States)

    Lee, Kangjoo; Lina, Jean-Marc; Gotman, Jean; Grova, Christophe

    2016-07-01

    Functional hubs are defined as the specific brain regions with dense connections to other regions in a functional brain network. Among them, connector hubs are of great interests, as they are assumed to promote global and hierarchical communications between functionally specialized networks. Damage to connector hubs may have a more crucial effect on the system than does damage to other hubs. Hubs in graph theory are often identified from a correlation matrix, and classified as connector hubs when the hubs are more connected to regions in other networks than within the networks to which they belong. However, the identification of hubs from functional data is more complex than that from structural data, notably because of the inherent problem of multicollinearity between temporal dynamics within a functional network. In this context, we developed and validated a method to reliably identify connectors and corresponding overlapping network structure from resting-state fMRI. This new method is actually handling the multicollinearity issue, since it does not rely on counting the number of connections from a thresholded correlation matrix. The novelty of the proposed method is that besides counting the number of networks involved in each voxel, it allows us to identify which networks are actually involved in each voxel, using a data-driven sparse general linear model in order to identify brain regions involved in more than one network. Moreover, we added a bootstrap resampling strategy to assess statistically the reproducibility of our results at the single subject level. The unified framework is called SPARK, i.e. SParsity-based Analysis of Reliable k-hubness, where k-hubness denotes the number of networks overlapping in each voxel. The accuracy and robustness of SPARK were evaluated using two dimensional box simulations and realistic simulations that examined detection of artificial hubs generated on real data. Then, test/retest reliability of the method was assessed

  7. Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network.

    Directory of Open Access Journals (Sweden)

    Aartjan J W te Velthuis

    Full Text Available Binding selectivity and cross-reactivity within one of the largest and most abundant interaction domain families, the PDZ family, has long been enigmatic. The complete human PDZ domain complement (the PDZome consists of 267 domains and we applied here a Bayesian selectivity model to predict hundreds of human PDZ domain interactions, using target sequences of 22,997 non-redundant proteins. Subsequent analysis of these binding scores shows that PDZs can be divided into two genome-wide clusters that coincide well with the division between canonical class 1 and 2 PDZs. Within the class 1 PDZs we observed binding overlap at unprecedented levels, mediated by two residues at positions 1 and 5 of the second α-helix of the binding pocket. Eight PDZ domains were subsequently selected for experimental binding studies and to verify the basics of our predictions. Overall, the PDZ domain class 1 cross-reactivity identified here implies that auxiliary mechanisms must be in place to overcome this inherent functional overlap and to minimize cross-selectivity within the living cell. Indeed, when we superimpose PDZ domain binding affinities with gene ontologies, network topology data and the domain position within a PDZ superfamily protein, functional overlap is minimized and PDZ domains position optimally in the binding space. We therefore propose that PDZ domain selectivity is achieved through cellular context rather than inherent binding specificity.

  8. Exploring forest infrastructures equipment through multivariate analysis: complementarities, gaps and overlaps in the Mediterranean basin

    Directory of Open Access Journals (Sweden)

    Sofia Bajocco

    2013-12-01

    Full Text Available The countries of the Mediterranean basin face several challenges regarding the sustainability of forest ecosystems and the delivery of crucial goods and services that they provide in a context of rapid global changes. Advancing scientific knowledge and foresting innovation is essential to ensure the sustainable management of Mediterranean forests and maximize the potential role of their unique goods and services in building a knowledge-based bioeconomy in the region. In this context, the European project FORESTERRA ("Enhancing FOrest RESearch in the MediTERRAnean through improved coordination and integration” aims at reinforcing the scientific cooperation on Mediterranean forests through an ambitious transnational framework in order to reduce the existing research fragmentation and maximize the effectiveness of forest research activities. Within the FORESTERRA project framework, this work analyzed the infrastructures equipment of the Mediterranean countries belonging to the project Consortium. According to the European Commission, research infrastructures are facilities, resources and services that are used by the scientific communities to conduct research and foster innovation. To the best of our knowledge, the equipment and availability of infrastructures, in terms of experimental sites, research facilities and databases, have only rarely been explored. The aim of this paper was hence to identify complementarities, gaps and overlaps among the different forest research institutes in order to create a scientific network, optimize the resources and trigger collaborations.

  9. Destabilization analysis of overlapping underground chambers induced by blasting vibration with catastrophe theory

    Institute of Scientific and Technical Information of China (English)

    YAN Chang-bin; XU Guo-yuan; ZUO Yu-jun

    2006-01-01

    According to the main characters of overlapping underground chambers, the roof (floor) of two adjacent underground chambers is simplified to the mechanical model that is the beam with build-in ends. And vibration load due to blasting is simplified to harmonic wave. The catastrophic model of double cusp for underground chambers destabilization induced by blasting vibration has been established under the circumstances of considering deadweight of the beam, and the condition of destabilization has been worked out. The critical safety thickness of the roof (floor) of underground chambers has been confirmed according to the destabilization condition. The influence of amplitude and frequency of blasting vibration load on the critical safety thickness has been analyzed, and the quantitative relation between velocity, frequency of blasting vibration and critical safety thickness has been determined. Research results show that the destabilization of underground chambers is not only dependent on the amplitude and frequency of blasting vibration load, but also related to deadweight load and intrinsic attribute. It is accordant to testing results and some related latest research results of blasting seismic effect. With increasing amplitude, the critical safety thickness of underground chambers decreases gradually. And the possibility of underground chambers destabilization increases. When the frequency of blasting vibration is equal to or very close to the frequency of beam, resonance effect will take place in the system. Then the critical safety thickness will turn to zero, underground chambers will be damaged severely, and its loading capacity will lose on the whole.

  10. Predicting 3D pose in partially overlapped X-ray images of knee prostheses using model-based Roentgen stereophotogrammetric analysis (RSA).

    Science.gov (United States)

    Hsu, Chi-Pin; Lin, Shang-Chih; Shih, Kao-Shang; Huang, Chang-Hung; Lee, Chian-Her

    2014-12-01

    After total knee replacement, the model-based Roentgen stereophotogrammetric analysis (RSA) technique has been used to monitor the status of prosthetic wear, misalignment, and even failure. However, the overlap of the prosthetic outlines inevitably increases errors in the estimation of prosthetic poses due to the limited amount of available outlines. In the literature, quite a few studies have investigated the problems induced by the overlapped outlines, and manual adjustment is still the mainstream. This study proposes two methods to automate the image processing of overlapped outlines prior to the pose registration of prosthetic models. The outline-separated method defines the intersected points and segments the overlapped outlines. The feature-recognized method uses the point and line features of the remaining outlines to initiate registration. Overlap percentage is defined as the ratio of overlapped to non-overlapped outlines. The simulated images with five overlapping percentages are used to evaluate the robustness and accuracy of the proposed methods. Compared with non-overlapped images, overlapped images reduce the number of outlines available for model-based RSA calculation. The maximum and root mean square errors for a prosthetic outline are 0.35 and 0.04 mm, respectively. The mean translation and rotation errors are 0.11 mm and 0.18°, respectively. The errors of the model-based RSA results are increased when the overlap percentage is beyond about 9%. In conclusion, both outline-separated and feature-recognized methods can be seamlessly integrated to automate the calculation of rough registration. This can significantly increase the clinical practicability of the model-based RSA technique.

  11. Bond overlap population analysis on through-space electron transfer in [3n]cyclophanes (n = 2 – 5)

    International Nuclear Information System (INIS)

    Through-space electron transfer between the benzene rings of [3n]cyclophanes, n = 2 – 5, was investigated using density functional theory calculations, CAM-B3LYP/6-311++G**. An external point charge, q, was placed on the axis perpendicular to a benzene ring of the cyclophane molecule. The dependence of the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap and bond overlap population (BOP) of cyclophanes on the values of q and n are discussed. The HOMO–LUMO gap generally decreases as q decreases and n increases. It is found from the BOP analysis that electron transfer occurs mainly through LUMO + 2 for n = 2, LUMO for n = 3 and n = 4, and LUMO + 4 for n = 5. The result that the values of the BOP for n = 2 and 5 increase as q decreases means that the through-space electron transfer is enhanced by the negative charge on the neighboring molecule in the solid. - Highlights: • Bond overlap population (BOP) analysis for electron transfer in [3n]cyclophanes. • Specification of the first excited states and orbital component of cyclophanes. • Change of BOP and electron path by external point charge and methylene bridge

  12. Intra-articular Hyaluronic Acid in Treating Knee Osteoarthritis: a PRISMA-Compliant Systematic Review of Overlapping Meta-analysis.

    Science.gov (United States)

    Xing, Dan; Wang, Bin; Liu, Qiang; Ke, Yan; Xu, Yuankun; Li, Zhichang; Lin, Jianhao

    2016-01-01

    Numerous meta-analyses have been conducted aiming to compare hyaluronic acid (HA) and placebo in treating knee osteoarthritis (OA). Nevertheless, the conclusions of these meta-analyses are not in consistency. The purpose of the present study was to perform a systematic review of overlapping meta-analyses investigating the efficacy and safety of HA for Knee OA and to provide treatment recommendations through the best evidence. A systematic review was conducted based on the PRISMA guidelines. The meta-analyses and/or systematic reviews that compared HA and placebo for knee OA were identified. AMSTAR instrument was used to evaluate the methodological quality of individual study. The information of heterogeneity within each variable was fetched for the individual studies. Which meta-analyses can provide best evidence was determined according to Jadad algorithm. Twelve meta-analyses met the eligibility requirements. The Jadad decision making tool suggests that the highest quality review should be selected. As a result, a high-quality Cochrane review was included. The present systematic review of overlapping meta-analyses demonstrates that HA is an effective intervention in treating knee OA without increased risk of adverse events. Therefore, the present conclusions may help decision makers interpret and choose among discordant meta-analyses. PMID:27616273

  13. Intra-articular Hyaluronic Acid in Treating Knee Osteoarthritis: a PRISMA-Compliant Systematic Review of Overlapping Meta-analysis.

    Science.gov (United States)

    Xing, Dan; Wang, Bin; Liu, Qiang; Ke, Yan; Xu, Yuankun; Li, Zhichang; Lin, Jianhao

    2016-09-12

    Numerous meta-analyses have been conducted aiming to compare hyaluronic acid (HA) and placebo in treating knee osteoarthritis (OA). Nevertheless, the conclusions of these meta-analyses are not in consistency. The purpose of the present study was to perform a systematic review of overlapping meta-analyses investigating the efficacy and safety of HA for Knee OA and to provide treatment recommendations through the best evidence. A systematic review was conducted based on the PRISMA guidelines. The meta-analyses and/or systematic reviews that compared HA and placebo for knee OA were identified. AMSTAR instrument was used to evaluate the methodological quality of individual study. The information of heterogeneity within each variable was fetched for the individual studies. Which meta-analyses can provide best evidence was determined according to Jadad algorithm. Twelve meta-analyses met the eligibility requirements. The Jadad decision making tool suggests that the highest quality review should be selected. As a result, a high-quality Cochrane review was included. The present systematic review of overlapping meta-analyses demonstrates that HA is an effective intervention in treating knee OA without increased risk of adverse events. Therefore, the present conclusions may help decision makers interpret and choose among discordant meta-analyses.

  14. A habitat overlap analysis derived from Maxent for Tamarisk and the South-western Willow Flycatcher

    Institute of Scientific and Technical Information of China (English)

    Patricia YORK; Paul EVANGELISTA; Sunil KUMAR; James GRAHAM; Curtis FLATHER; Thomas STOHLGREN

    2011-01-01

    Biologic control of the introduced and invasive,woody plant tamarisk (Tamarix spp,saltcedar) in south-western states is controversial because it affects habitat of the federally endangered South-western Willow Flycatcher (Empidonax traillii extimus).These songbirds sometimes nest in tamarisk where floodplain-level invasion replaces native habitats.Biologic control,with the saltcedar leaf beetle (Diorhabda elongate),began along the Virgin River,Utah,in 2006,enhancing the need for comprehensive understanding of the tamarisk-flycatcherrelationship.We used maximum entropy (Maxent) modeling to separately quantify the current extent of dense tamarisk habitat ( > 50% cover) and the potential extent of habitat available for E.traillii extimus within the studied watersheds.We used transformations of 2008 Landsat Thematic Mapper images and a digital elevation model as environmental input variables.Maxent models performed well for the flycatcher and tamarisk with Area Under the ROC Curve (AUC) values of 0.960 and 0.982,respectively.Classification of thresholds and comparison of the two Maxent outputs indicated moderate spatial overlap between predicted suitable habitat for E.traillii extimus and predicted locations with dense tamarisk stands,where flycatcher habitat will potentially change flycatcher habitats.Dense tamarisk habitat comprised 500 km2 within the study area,of which 11.4% was also modeled as potential habitat for E.traillii extimus.Potential habitat modeled for the flycatcher constituted 190 km2,of which 30.7% also contained dense tamarisk habitat.Results showed that both native vegetation and dense tamarisk habitats exist in the study area and that most tamarisk infestations do not contain characteristics that satisfy the habitat requirements of E.traillii extimus.Based on this study,effective biologic control of Tamarix spp.may,in the short term,reduce suitable habitat available to E.traillii extimus,but also has the potential in the long term to increase

  15. Overlapping Consensus in Malaysia

    OpenAIRE

    Monsen, Mats

    2007-01-01

    An empirical study of how Malaysian pluralism is understood through Islam Hadhari, Article 11 and the Inter-faith Commission against the backdrop of current Malaysian political and social history, coupled with a theoretical analysis through John Rawls' Political Liberalism, with particular emphasis on the idea of Overlapping Consensus. The thesis is an attempt at applying Rawls' theory on the practical case of Malaysia, as a plural society, while at the same time using the practical case of M...

  16. Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice

    OpenAIRE

    Garg, Rohini; Tyagi, Akhilesh K.; Jain, Mukesh

    2012-01-01

    Hormones exert pleiotropic effects on plant growth and development throughout the life cycle. Many of these effects are mediated at molecular level via altering gene expression. In this study, we investigated the exogenous effect of plant hormones, including auxin, cytokinin, abscisic acid, ethylene, salicylic acid and jasmonic acid, on the transcription of rice genes at whole genome level using microarray. Our analysis identified a total of 4171 genes involved in several biological processes...

  17. Overlap of food addiction and substance use disorders definitions: analysis of animal and human studies.

    Science.gov (United States)

    Hone-Blanchet, Antoine; Fecteau, Shirley

    2014-10-01

    Food has both homeostatic and hedonic components, which makes it a potent natural reward. Food related reward could therefore promote an escalation of intake and trigger symptoms associated to withdrawal, suggesting a behavioral parallel with substance abuse. Animal and human theoretical models of food reward and addiction have emerged, raising further interrogations on the validity of a bond between Substance Use Disorders, as clinically categorized in the DSM 5, and food reward. These models propose that highly palatable food items, rich in sugar and/or fat, are overly stimulating to the brain's reward pathways. Moreover, studies have also investigated the possibility of causal link between food reward and the contemporary obesity epidemic, with obesity being potentiated and maintained due to this overwhelming food reward. Although natural rewards are a hot topic in the definition and categorization of Substance Use Disorders, proofs of concept and definite evidence are still inconclusive. This review focuses on available results from experimental studies in animal and human models exploring the concept of food addiction, in an effort to determine if it depicts a specific phenotype and if there is truly a neurobiological similarity between food addiction and Substance Use Disorders. It describes results from sugar, fat and sweet-fat bingeing in rodent models, and behavioral and neurobiological assessments in different human populations. Although pieces of behavioral and neurobiological evidence supporting a food addiction phenotype in animals and humans are interesting, it seems premature to conclude on its validity.

  18. Non-random retention of protein-coding overlapping genes in Metazoa

    Directory of Open Access Journals (Sweden)

    Bork Peer

    2008-04-01

    Full Text Available Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm. Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.

  19. The impact of overlapping processes on rockfall hazard analysis - the Bolonia Bay study (southern Spain)

    Science.gov (United States)

    Fernandez-Steeger, T.; Grützner, C.; Reicherter, K.; Braun, A.; Höbig, N.

    2009-04-01

    For rockfall simulations, competitive case studies and data sets are important to develop and evaluate the models or software. Especially for empirical or data driven stochastic modelling the quality of the reference data sets has a major impact on model skills and knowledge discovery. Therefore, rockfalls in the Bolonia Bay close to Tarifa (Spain) were mapped. Here, the siliciclastic Miocene rocks (megaturbidites) are intensively joined and disaggregated by a perpendicular joint system. Although bedding supports stability as the dip is not directed towards the rock face, the deposits indicate a continuous process of material loss from the 80 m high cliff of the San Bartolome mountain front by single large rock falls. For more than 300 blocks data on size, shape, type of rock, and location were collected. The work concentrated on rockfall blocks with a volume of more than 2 m³ and up to 350 m³. Occasionally very long "runout" distances of up to 2 km have been observed. For all major source areas and deposits, runout analysis using empirical models and a numerical trajectorian model has been performed. The most empirical models are principally based on the relation between fall height and travel distance. Beside the "Fahrböschung" from Heim (1932) the "shadow angle" introduced by Evans and Hungr (1993) is most common today. However, studies from different sites show a wide variance of the angle relations (Dorren 2003, Corominas 1996). The reasons for that might be different environments and trigger mechanisms, or varying secondary effects such as post-depositional movement. Today, "semi" numerical approaches based on trajectorian models are quite common to evaluate the rockfall energy and the runout distance for protection measures and risk evaluations. The results of the models highly depend on the quality of the input parameters. One problem here might be that some of the parameters, especially the dynamic ones, are not easy to determine and the quality of the

  20. A post-modification approach to independent component analysis for resolution of overlapping GC/MS signals: from independent components to chemical components

    Institute of Scientific and Technical Information of China (English)

    WANG Wei; CAI WenSheng; SHAO XueGuang

    2007-01-01

    Independent component analysis (ICA) has demonstrated its power to extract mass spectra from overlapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is proposed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively.

  1. Whole genome sequence analysis suggests intratumoral heterogeneity in dissemination of breast cancer to lymph nodes.

    Directory of Open Access Journals (Sweden)

    Kevin Blighe

    Full Text Available BACKGROUND: Intratumoral heterogeneity may help drive resistance to targeted therapies in cancer. In breast cancer, the presence of nodal metastases is a key indicator of poorer overall survival. The aim of this study was to identify somatic genetic alterations in early dissemination of breast cancer by whole genome next generation sequencing (NGS of a primary breast tumor, a matched locally-involved axillary lymph node and healthy normal DNA from blood. METHODS: Whole genome NGS was performed on 12 µg (range 11.1-13.3 µg of DNA isolated from fresh-frozen primary breast tumor, axillary lymph node and peripheral blood following the DNA nanoball sequencing protocol. Single nucleotide variants, insertions, deletions, and substitutions were identified through a bioinformatic pipeline and compared to CIN25, a key set of genes associated with tumor metastasis. RESULTS: Whole genome sequencing revealed overlapping variants between the tumor and node, but also variants that were unique to each. Novel mutations unique to the node included those found in two CIN25 targets, TGIF2 and CCNB2, which are related to transcription cyclin activity and chromosomal stability, respectively, and a unique frameshift in PDS5B, which is required for accurate sister chromatid segregation during cell division. We also identified dominant clonal variants that progressed from tumor to node, including SNVs in TP53 and ARAP3, which mediates rearrangements to the cytoskeleton and cell shape, and an insertion in TOP2A, the expression of which is significantly associated with tumor proliferation and can segregate breast cancers by outcome. CONCLUSION: This case study provides preliminary evidence that primary tumor and early nodal metastasis have largely overlapping somatic genetic alterations. There were very few mutations unique to the involved node. However, significant conclusions regarding early dissemination needs analysis of a larger number of patient samples.

  2. OVERLAPPING VIRTUAL CADASTRAL DOCUMENTATION

    Directory of Open Access Journals (Sweden)

    Madalina - Cristina Marian

    2013-12-01

    Full Text Available Two cadastrale plans of buildings, can overlap virtual. Overlap is highlighted when digital reception. According to Law no. 7/1996 as amended and supplemented, to solve these problems is by updating the database graphs, the repositioning. This paper addresses the issue of overlapping virtual cadastre in the history of the period 1999-2012.

  3. Fast Overlapping Group Lasso

    CERN Document Server

    Liu, Jun

    2010-01-01

    The group Lasso is an extension of the Lasso for feature selection on (predefined) non-overlapping groups of features. The non-overlapping group structure limits its applicability in practice. There have been several recent attempts to study a more general formulation, where groups of features are given, potentially with overlaps between the groups. The resulting optimization is, however, much more challenging to solve due to the group overlaps. In this paper, we consider the efficient optimization of the overlapping group Lasso penalized problem. We reveal several key properties of the proximal operator associated with the overlapping group Lasso, and compute the proximal operator by solving the smooth and convex dual problem, which allows the use of the gradient descent type of algorithms for the optimization. We have performed empirical evaluations using the breast cancer gene expression data set, which consists of 8,141 genes organized into (overlapping) gene sets. Experimental results demonstrate the eff...

  4. Analysis of Thermal and Chemical Effets on Negative Valve Overlap Period Energy Recovery for Low-Temperature Gasoline Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Ekoto, Dr Isaac [Sandia National Laboratories (SNL); Peterson, Dr. Brian [University of Edinburgh; Szybist, James P [ORNL; Northrop, Dr. William [University of Minnesota

    2015-01-01

    A central challenge for efficient auto-ignition controlled low-temperature gasoline combustion (LTGC) engines has been achieving the combustion phasing needed to reach stable performance over a wide operating regime. The negative valve overlap (NVO) strategy has been explored as a way to improve combustion stability through a combination of charge heating and altered reactivity via a recompression stroke with a pilot fuel injection. The study objective was to analyze the thermal and chemical effects on NVO-period energy recovery. The analysis leveraged experimental gas sampling results obtained from a single-cylinder LTGC engine along with cylinder pressure measurements and custom data reduction methods used to estimate period thermodynamic properties. The engine was fueled by either iso-octane or ethanol, and operated under sweeps of NVO-period oxygen concentration, injection timing, and fueling rate. Gas sampling at the end of the NVO period was performed via a custom dump-valve apparatus, with detailed sample speciation by in-house gas chromatography. The balance of NVO-period input and output energy flows was calculated in terms of fuel energy, work, heat loss, and change in sensible energy. Experiment results were complemented by detailed chemistry single-zone reactor simulations performed at relevant mixing and thermodynamic conditions, with results used to evaluate ignition behavior and expected energy recovery yields. For the intermediate bulk-gas temperatures present during the NVO period (900-1100 K), weak negative temperature coefficient behavior with iso-octane fueling significantly lengthened ignition delays relative to similar ethanol fueled conditions. Faster ethanol ignition chemistry led to lower recovered fuel intermediate yields relative to similar iso-octane fueled conditions due to more complete fuel oxidation. From the energy analysis it was found that increased NVO-period global equivalence ratio, either from lower NVOperiod oxygen

  5. Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-03-01

    Full Text Available Abstract The plant-infecting members of the genus Fijivirus (family Reoviridae have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons that overlaps the 3' end of the major ORF (~920–940 codons in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.

  6. A post-modification approach to independent compo-nent analysis for resolution of overlapping GC/MS signals:from independent components to chemical components

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Independent component analysis (ICA) has demonstrated its power to extract mass spectra from over-lapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is pro-posed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively.

  7. Business Communication in Less Commonly Taught Languages: Teaching Suggestions through Discourse Analysis:

    Directory of Open Access Journals (Sweden)

    Glaucia V. Silva

    2010-01-01

    Full Text Available The knowledge generated by studies in discourse analysis is rarely brought into the teaching of business communication in a foreign language. Instead of presenting learners with "samples" of language after which they will pattern their production, foreign language instructors may invite learners to analyze the interplay between text and context in their own and in others' discourses. Therefore, the teaching of communicative functions (such as requesting, apologizing, suggesting, etc. in foreign languages should go beyond the presentation, production and practice of textual forms: learners should be actively involved in doing discourse analysis in order to be able to make principled decisions when formulating suggestions in the workplace. In the case of less commonly taught languages, this approach is especially important, since textbooks and other teaching materials are not likely to include analysis and/ or focused applications of communicative functions. The recommendations included in this article contribute to fulfill this need in the teaching of LCTLs.

  8. Comparative analysis on overlap welding properties of fiber laser and CO2 laser for body-in-white sheets

    International Nuclear Information System (INIS)

    Highlights: ► The welding property of fiber laser is systematically studied on galvanized steel. ► The welding property of and CO2 laser is systematically studied on galvanized steel. ► The welding properties of the two kinds of laser sources are compared. ► The configuration of overlap joints by using the two kinds of lasers is different. ► The mechanical properties of joints by using the two kinds of lasers are different. - Abstract: A systematic study on overlap welding properties of autobody galvanized steel is conducted by using the late-model fiber laser and CO2 laser respectively. The welding joints surface formation, cross-sectional weld shape and mechanical properties of the two types of lasers are compared, and it is analyzed whether dissimilar laser sources would impact the welding quality, so as to control and optimize the craft quality of laser welding automobile body. The results show that under the test conditions, the weld fusion width presents wide at the top and narrow at the bottom and the cross-sections of overlap joints take a “Y” shape by using CO2 laser welding, while those by using fiber laser welding have a shape like “I” which was mean the fusion widths of the upper and lower surface are almost the same. And the anti-shearing force of fiber laser welding joints was stronger due to its larger inter-sheet joint connection width. In addition, under certain conditions, the fiber laser welding could result in more uniform and finer joints, higher strength and hardness, and better mechanical properties

  9. Contribution to automatic image recognition. Application to analysis of plain scenes of overlapping parts in robot technology

    International Nuclear Information System (INIS)

    A method for object modeling and overlapped object automatic recognition is presented. Our work is composed of three essential parts: image processing, object modeling, and evaluation of the implementation of the stated concepts. In the first part, we present a method of edge encoding which is based on a re-sampling of the data encoded according to Freeman, this method generates an isotropic, homogenous and very precise representation. The second part relates to object modeling. This important step makes much easier the recognition work. The new method proposed characterizes a model with two groups of information: the description group containing the primitives, the discrimination group containing data packs, called 'transition vectors'. Based on this original method of information organization, a 'relative learning' is able to select, to ignore and to update the information concerning the objects already learned, according to the new information to be included into the data base. The recognition is a two-pass process: the first pass determines very efficiently the presence of objects by making use of each object's particularities, and this hypothesis is either confirmed or rejected by the following fine verification pass. The last part describes in detail the experimentation results. We demonstrate the robustness of the algorithms with images in both poor lighting and overlapping objects conditions. The system, named SOFIA, has been installed into an industrial vision system series and works in real time. (author)

  10. Analysis on User Network Influence Under Micro-blog Overlapping Topic%微博交叠主题下用户网络影响力分析

    Institute of Scientific and Technical Information of China (English)

    刘继; 李磊

    2015-01-01

    网络舆情管理是社会创新管理的重要内容之一,网络舆情主题演化分析是网络舆情态势预测的重要环节。本文将用户参与不同主题的交叠度和用户的关注关系网络的交叠度结合起来,构建了舆情主题交叠网络影响度模型,对“城管”“腐败”主题中微博用户的交叠影响进行挖掘。发现少量微博用户对主题交叠演化产生了重大影响,利用该模型可提高网络主题交叠演化中网民影响的挖掘效率,对这些影响力高的网民进行监控和引导将有助于预控网络舆情演化。%Network public opinion management is an import part of innovative society management, and analysis of subject evolution of network public opinion is a critical clue to the tendency prediction of public opinion. This paper takes into consideration the influence of the content of opinion information and netizen's social network, combining the overlapping degree of participating subject and following re-lation network, to construct an overlapping influence model of network public opinion subjects, and mines the overlapping influence of two subjects such as"city inspector" and "corruption". The results indicate that certain netizens have an important influence on the overlap-ping evolution of blog subjects, the efficiency of mining important netizens’ influence in opinion overlapping evolution can be enhanced with this model, and supervising and guiding those influential netizens can contribute to the pre-controlling effort of the network public o-pinion evolution.

  11. Overlap in Facebook Profiles Reflects Relationship Closeness.

    Science.gov (United States)

    Castañeda, Araceli M; Wendel, Markie L; Crockett, Erin E

    2015-01-01

    We assessed the association between self-reported Inclusion of Other in the Self (IOS) and Facebook overlap. Ninety-two participants completed online measures of IOS and investment model constructs. Researchers then recorded Facebook data from participants' profile pages. Results from multilevel models revealed that IOS predicted Facebook overlap. Furthermore, Facebook overlap was associated with commitment and investment in ways comparable to self-reported IOS. These findings suggest that overlap in Facebook profiles can be used to measure relationship closeness. PMID:25635533

  12. Stable isotope analysis of energy dynamics in aquatic ecosystems suggests trophic shifts following severe wildfire

    Science.gov (United States)

    Martens, A. M.; Silins, U.; Bladon, K. D.; Williams, C.; Wagner, M. J.; Luchkow, E.

    2015-12-01

    Wildfire alters landscapes and can have significant impacts on stream ecosystems. The 2003 Lost Creek wildfire was one of the most severe on Alberta's eastern rocky mountain slopes, resulting in elevated sediment production and nutrient (phosphorus, nitrogen, and carbon) export in impacted streams. These resulted in increased algal productivity and macroinvertebrate abundance and diversity, and as a result, fish in watersheds draining wildfire affected catchments were larger than those in the same age class from reference (unburned) watersheds. In the present investigation, stable isotope analysis of C and N was utilized to evaluate ecosystem energy dynamics and describe trophic relationships in those watersheds. Aquatic invertebrates from burned catchments showed enrichment in δ13C and δ15N relative to algae suggesting a reliance on algae (autochthony) as a primary source of energy. Invertebrates from unburned systems were depleted in δ13C relative to algae indicating reliance on allochthonous or terrestrial primary energy sources. Preliminary analysis of δ15N in macroinvertebrates showed slight enrichment in burned catchments suggesting a trophic shift. More comprehensive macroinvertebrate sampling and identification has been conducted; isotopic analysis will provide greater resolution of how specific families within feeding guilds have been affected by wildfire. This will provide more robust insights into how wildfires may impact stream ecology in mountain environments.

  13. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

    Directory of Open Access Journals (Sweden)

    Claudia Gonzaga-Jauregui

    2015-08-01

    Full Text Available Charcot-Marie-Tooth (CMT disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼45% (17/37 of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

  14. Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

    Directory of Open Access Journals (Sweden)

    Lundberg Cathryn

    2008-01-01

    Full Text Available Abstract Background Gene expression measurements from breast cancer (BrCa tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic clinical arrays show little overlap in the sets of genes identified. One approach to identify a set of consistently dysregulated candidate genes in these tumors is to employ meta-analysis of multiple independent microarray datasets. This allows one to compare expression data from a diverse collection of breast tumor array datasets generated on either cDNA or oligonucleotide arrays. Results We gathered expression data from 9 published microarray studies examining estrogen receptor positive (ER+ and estrogen receptor negative (ER- BrCa tumor cases from the Oncomine database. We performed a meta-analysis and identified genes that were universally up or down regulated with respect to ER+ versus ER- tumor status. We surveyed both the proximal promoter and 3' untranslated regions (3'UTR of our top-ranking genes in each expression group to test whether common sequence elements may contribute to the observed expression patterns. Utilizing a combination of known transcription factor binding sites (TFBS, evolutionarily conserved mammalian promoter and 3'UTR motifs, and microRNA (miRNA seed sequences, we identified numerous motifs that were disproportionately represented between the two gene classes suggesting a common regulatory network for the observed gene expression patterns. Conclusion Some of the genes we identified distinguish key transcripts previously seen in array studies, while others are newly defined. Many of the genes identified as overexpressed in ER- tumors were previously identified as expression markers for neoplastic transformation in multiple human cancers. Moreover, our motif analysis identified a collection of

  15. Analysis on Characteristics of the High Pressure Jet Grouting Overlap Pile%高压旋喷桩体搭接处成桩特点分析

    Institute of Scientific and Technical Information of China (English)

    张彬; 任立侠; 黄建喜; 曹佳艺; 宋志彬

    2012-01-01

    The high pressure jet grouting overlap pile body is a pile of weak link, to improve the quality of the high pressure jet grouting overlap pile body is one of an important aspects to ensure a good project construction. So the combination of the theory and experiment methods was taken to analyze the characteristics and laws of the forma-tion of the overlap pile body. Through the method of numerical simulation, an analysis was carried out on the high pressure jet grouting with face to face spraying in the sandy stratum, the flow field distribution features of the flow is concluded from it. By the test on cores of the overlap pile from the soil stratum and the sandy stratum, the conclu-sions are also obtained that part of the construction parameters and the high pressure jet grouting formation can impact the regulation of the pile characteristics. Eventually, the rules of spray flow field at each phase in the strata, the over-lap pile body features and the corresponding relationship between them are get, all of them have important significance to conducting the project in the future.%高压旋喷所形成桩体间的搭接部位是成桩中的薄弱环节,提高搭接桩体的成桩质量是保证工程施工质量的重要因素之一.因此分别采取理论和试验相结合的方法来分析桩体搭接处成桩特点及规律.通过数值模拟的方法将在砂质地层中进行的高压旋喷对喷试验进行了模拟分析,得出流向流场分布特点.并通过对土质及砂质地层中桩体间搭接处的开挖心样进行试验分析,得出部分施工参数、喷射地层对桩体搭接处成桩特点的影响规律.最终得出地层中各相的对喷流场规律和桩体搭接处成桩特点规律以及两者间一定的对应关系,这将对进一步在工程施工中保证工程质量起到指导意义.

  16. Problems in wavelet analysis of hydrologic series and some suggestions on improvement

    Institute of Scientific and Technical Information of China (English)

    WANG Hongrui; YE Letian; LIU Changming; YANG Chi; LIU Peng

    2007-01-01

    Applying the wavelet theory and methods to investigate the hydrologic processes such as precipitation and runoff is a hot field. However, several aspects in research are usually ignored: the effect of admissible condition of wavelet functions and the disturbance of noises for the detection of periods, the effect of the length of a hydrologic time-series on the final result, and the choice between the anomaly and the original time series for wavelet analysis. In this paper, these issues are fully discussed. Precipitation data from Lanzhou Precipitation Station are taken for case study. The result indicates that in the wavelet analysis of hydrologic series, denoise methods should be used to eliminate the influence of noises. The MexHat wavelet function satisfies the admissible condition, which ensures that the periodic properties of hydrologic processes can be well represented by using the MexHat wavelet for decomposition. The affected range of hydrologic series which should be discarded before analysis is given. It is also suggested that the anomaly series should be used to highlight the actual undulation of the hydrologic series.

  17. Illusion induced overlapped optics.

    Science.gov (United States)

    Zang, XiaoFei; Shi, Cheng; Li, Zhou; Chen, Lin; Cai, Bin; Zhu, YiMing; Zhu, HaiBin

    2014-01-13

    The traditional transformation-based cloak seems like it can only hide objects by bending the incident electromagnetic waves around the hidden region. In this paper, we prove that invisible cloaks can be applied to realize the overlapped optics. No matter how many in-phase point sources are located in the hidden region, all of them can overlap each other (this can be considered as illusion effect), leading to the perfect optical interference effect. In addition, a singular parameter-independent cloak is also designed to obtain quasi-overlapped optics. Even more amazing of overlapped optics is that if N identical separated in-phase point sources covered with the illusion media, the total power outside the transformation region is N2I0 (not NI0) (I0 is the power of just one point source, and N is the number point sources), which seems violating the law of conservation of energy. A theoretical model based on interference effect is proposed to interpret the total power of these two kinds of overlapped optics effects. Our investigation may have wide applications in high power coherent laser beams, and multiple laser diodes, and so on.

  18. Illusion induced overlapped optics.

    Science.gov (United States)

    Zang, XiaoFei; Shi, Cheng; Li, Zhou; Chen, Lin; Cai, Bin; Zhu, YiMing; Zhu, HaiBin

    2014-01-13

    The traditional transformation-based cloak seems like it can only hide objects by bending the incident electromagnetic waves around the hidden region. In this paper, we prove that invisible cloaks can be applied to realize the overlapped optics. No matter how many in-phase point sources are located in the hidden region, all of them can overlap each other (this can be considered as illusion effect), leading to the perfect optical interference effect. In addition, a singular parameter-independent cloak is also designed to obtain quasi-overlapped optics. Even more amazing of overlapped optics is that if N identical separated in-phase point sources covered with the illusion media, the total power outside the transformation region is N2I0 (not NI0) (I0 is the power of just one point source, and N is the number point sources), which seems violating the law of conservation of energy. A theoretical model based on interference effect is proposed to interpret the total power of these two kinds of overlapped optics effects. Our investigation may have wide applications in high power coherent laser beams, and multiple laser diodes, and so on. PMID:24515019

  19. Double-wavelength overlapping resonance Rayleigh scattering technique for the simultaneous quantitative analysis of three β-adrenergic blockade

    Science.gov (United States)

    Tan, Xuanping; Yang, Jidong; Li, Qin; Yang, Qiong; Shen, Yizhong

    2016-05-01

    Four simple and accurate spectrophotometric methods were proposed for the simultaneous determination of three β-adrenergic blockade, e.g. atenolol, metoprolol and propranolol. The methods were based on the reaction of the three drugs with erythrosine B (EB) in a Britton-Robinson buffer solution at pH 4.6. EB could combine with the drugs to form three ion-association complexes, which resulted in the resonance Rayleigh scattering (RRS) intensity that is enhanced significantly with new RRS peaks that appeared at 337 nm and 370 nm, respectively. In addition, the fluorescence intensity of EB was also quenched. The enhanced scattering intensities of the two peaks and the fluorescence quenched intensity of EB were proportional to the concentrations of the drugs, respectively. What is more, the RRS intensity overlapped with the double-wavelength of 337 nm and 370 nm (so short for DW-RRS) was also proportional to the drugs concentrations. So, a new method with highly sensitive for simultaneous determination of three bisoprolol drugs was established. Finally, the optimum reaction conditions, influencing factors and spectral enhanced mechanism were investigated. The new DW-RRS method has been applied to simultaneously detect the three β-blockers in fresh serum with satisfactory results.

  20. Fractal analysis reveals subclasses of neurons and suggests an explanation of their spontaneous activity.

    Science.gov (United States)

    Favela, Luis H; Coey, Charles A; Griff, Edwin R; Richardson, Michael J

    2016-07-28

    The present work used fractal time series analysis (detrended fluctuation analysis; DFA) to examine the spontaneous activity of single neurons in an anesthetized animal model, specifically, the mitral cells in the rat main olfactory bulb. DFA bolstered previous research in suggesting two subclasses of mitral cells. Although there was no difference in the fractal scaling of the interspike interval series at the shorter timescales, there was a significant difference at longer timescales. Neurons in Group B exhibited fractal, power-law scaled interspike intervals, whereas neurons in Group A exhibited random variation. These results raise questions about the role of these different cells within the olfactory bulb and potential explanations of their dynamics. Specifically, self-organized criticality has been proposed as an explanation of fractal scaling in many natural systems, including neural systems. However, this theory is based on certain assumptions that do not clearly hold in the case of spontaneous neural activity, which likely reflects intrinsic cell dynamics rather than activity driven by external stimulation. Moreover, it is unclear how self-organized criticality might account for the random dynamics observed in Group A, and how these random dynamics might serve some functional role when embedded in the typical activity of the olfactory bulb. These theoretical considerations provide direction for additional experimental work. PMID:27189719

  1. Frequency analysis of amyloplast movement in Arabidopsis suggests dynamic gravity sensing

    Science.gov (United States)

    Hasenstein, K.; Gilroy, S.

    We investigated the motility of amyloplasts in root caps of Arabidopsis thaliana to analyze the interaction between the acto-myosin system and plastids In addition to sedimentation cytoskeletal activity appears to lift amyloplasts and may cause impinging of sedimenting amyloplasts onto the membrane system This activity may represent graviperception We analyzed the frequency of amyloplast motion by Fourier analysis based upon the position of amyloplasts in image sequences taken at 6 second intervals The frequency analysis showed a maximum at an average cycle of about 16 seconds 0 06 Hz for vertical and lateral displacement However amyloplast velocity was frequency independent Application of the actin-depolymerizing agent Latrunculin B 0 1 mu M reduced the maximum displacement but did not change the frequency DMSO-treated roots showed a similar reduction The frequency dependency was similar for cell from different positions within the root cap The data suggest that the saltatory motion of amyloplasts is a continuous process that is mediated by cytoskeletal events and is an integral part of gravisensing Therefore gravisensing may depend on the dynamic motion of statoliths rather than simple aggregation onto the lower cell membrane Supported by NASA grants NAG2-1423 NAG10-0190 KHH and NAG2-1594 NSF MCB 02-12099 SG

  2. Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes.

    Science.gov (United States)

    Tuberosa, Roberto; Sanguineti, Maria Corinna; Landi, Pierangelo; Giuliani, Marcella Michela; Salvi, Silvio; Conti, Sergio

    2002-01-01

    We investigated the overlap among quantitative trait loci (QTLs) in maize for seminal root traits measured in hydroponics with QTLs for grain yield under well-watered (GY-WW) and water-stressed (GY-WS) field conditions as well as for a drought tolerance index (DTI) computed as GY-WS/GY-WW. In hydroponics, 11, 7, 9, and 10 QTLs were identified for primary root length (R1L), primary root diameter (R1D), primary root weight (R1W), and for the weight of the adventitious seminal roots (R2W), respectively. In the field, 7, 8, and 9 QTLs were identified for GY-WW, GY-WS, and DTI, respectively. Despite the weak correlation of root traits in hydroponics with GY-WW, GY-WS, and DTI, a noticeable overlap between the corresponding QTLs was observed. QTLs for R2W most frequently and consistently overlapped with QTLs for GY-WW, GY-WS, and/or DTI. At four QTL regions, an increase in R2W was positively associated with GY-WW, GY-WS, and/or DTI. A 10 cM interval on chromosome 1 between PGAMCTA205 and php20644 showed the strongest effect on R1L, R1D, R2W, GY-WW, GY-WS, and DTI. These results indicate the feasibility of using hydroponics in maize to identify QTL regions controlling root traits at an early growth stage and also influencing GY in the field. A comparative analysis of the QTL regions herein identified with those described in previous studies investigating root traits in different maize populations revealed a number of QTLs in common.

  3. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Jin Hailing

    2009-04-01

    Full Text Available Abstract Background Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. Results In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs generated with the 454 technology and the massively parallel signature sequencing (MPSS method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM, which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G, upstream of the D arm (from G to C, U, or A, and downstream of the D arm (from G to U. The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A, N2-methylguanosine (m2G, and N2-N2-methylguanosine (m22G. Conclusion These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.

  4. Meta-analysis suggests choosy females get sexy sons more than "good genes".

    Science.gov (United States)

    Prokop, Zofia M; Michalczyk, Łukasz; Drobniak, Szymon M; Herdegen, Magdalena; Radwan, Jacek

    2012-09-01

    Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice. PMID:22946794

  5. Preventing lodging in bioenergy crops: a biomechanical analysis of maize stalks suggests a new approach.

    Science.gov (United States)

    Von Forell, Greg; Robertson, Daniel; Lee, Shien Yang; Cook, Douglas D

    2015-07-01

    The hypothetical ideal for maize (Zea mays) bioenergy production would be a no-waste plant: high-yielding, with silage that is easily digestible for conversion to biofuel. However, increased digestibility is typically associated with low structural strength and a propensity for lodging. The solution to this dilemma may lie in our ability to optimize maize morphology using tools from structural engineering. To investigate how material (tissue) and geometric (morphological) factors influence stalk strength, detailed structural models of the maize stalk were created using finite-element software. Model geometry was obtained from high-resolution x-ray computed tomography (CT) scans, and scan intensity information was integrated into the models to infer inhomogeneous material properties. A sensitivity analysis was performed by systematically varying material properties over broad ranges, and by modifying stalk geometry. Computational models exhibited realistic stress and deformation patterns. In agreement with natural failure patterns, maximum stresses were predicted near the node. Maximum stresses were observed to be much more sensitive to changes in dimensions of the stalk cross section than they were to changes in material properties of stalk components. The average sensitivity to geometry was found to be more than 10-fold higher than the average sensitivity to material properties. These results suggest a new strategy for the breeding and development of bioenergy maize varieties in which tissue weaknesses are counterbalanced by relatively small increases (e.g. 5%) in stalk diameter that reduce structural stresses.

  6. Preventing lodging in bioenergy crops: a biomechanical analysis of maize stalks suggests a new approach.

    Science.gov (United States)

    Von Forell, Greg; Robertson, Daniel; Lee, Shien Yang; Cook, Douglas D

    2015-07-01

    The hypothetical ideal for maize (Zea mays) bioenergy production would be a no-waste plant: high-yielding, with silage that is easily digestible for conversion to biofuel. However, increased digestibility is typically associated with low structural strength and a propensity for lodging. The solution to this dilemma may lie in our ability to optimize maize morphology using tools from structural engineering. To investigate how material (tissue) and geometric (morphological) factors influence stalk strength, detailed structural models of the maize stalk were created using finite-element software. Model geometry was obtained from high-resolution x-ray computed tomography (CT) scans, and scan intensity information was integrated into the models to infer inhomogeneous material properties. A sensitivity analysis was performed by systematically varying material properties over broad ranges, and by modifying stalk geometry. Computational models exhibited realistic stress and deformation patterns. In agreement with natural failure patterns, maximum stresses were predicted near the node. Maximum stresses were observed to be much more sensitive to changes in dimensions of the stalk cross section than they were to changes in material properties of stalk components. The average sensitivity to geometry was found to be more than 10-fold higher than the average sensitivity to material properties. These results suggest a new strategy for the breeding and development of bioenergy maize varieties in which tissue weaknesses are counterbalanced by relatively small increases (e.g. 5%) in stalk diameter that reduce structural stresses. PMID:25873674

  7. Analytical Problems and Suggestions in the Analysis of Behavioral Economic Demand Curves.

    Science.gov (United States)

    Yu, Jihnhee; Liu, Liu; Collins, R Lorraine; Vincent, Paula C; Epstein, Leonard H

    2014-01-01

    Behavioral economic demand curves (Hursh, Raslear, Shurtleff, Bauman, & Simmons, 1988) are innovative approaches to characterize the relationships between consumption of a substance and its price. In this article, we investigate common analytical issues in the use of behavioral economic demand curves, which can cause inconsistent interpretations of demand curves, and then we provide methodological suggestions to address those analytical issues. We first demonstrate that log transformation with different added values for handling zeros changes model parameter estimates dramatically. Second, demand curves are often analyzed using an overparameterized model that results in an inefficient use of the available data and a lack of assessment of the variability among individuals. To address these issues, we apply a nonlinear mixed effects model based on multivariate error structures that has not been used previously to analyze behavioral economic demand curves in the literature. We also propose analytical formulas for the relevant standard errors of derived values such as P max, O max, and elasticity. The proposed model stabilizes the derived values regardless of using different added increments and provides substantially smaller standard errors. We illustrate the data analysis procedure using data from a relative reinforcement efficacy study of simulated marijuana purchasing. PMID:26741176

  8. Extensive Molecular Analysis Suggested the Strong Genetic Heterogeneity of Idiopathic Chronic Pancreatitis

    Science.gov (United States)

    Sofia, Valentina Maria; Da Sacco, Letizia; Surace, Cecilia; Tomaiuolo, Anna Cristina; Genovese, Silvia; Grotta, Simona; Gnazzo, Maria; Petrocchi, Stefano; Ciocca, Laura; Alghisi, Federico; Montemitro, Enza; Martemucci, Luigi; Elce, Ausilia; Lucidi, Vincenzina; Castaldo, Giuseppe; Angioni, Adriano

    2016-01-01

    Genetic features of chronic pancreatitis (CP) have been investigated extensively, mainly by testing genes associated to the trypsinogen activation pathway. However, different molecular pathways involving other genes may be implicated in CP pathogenesis. A total of 80 patients with idiopathic chronic pancreatitis (ICP) were investigated using a Next-Generation Sequencing (NGS) approach with a panel of 70 genes related to six different pancreatic pathways: premature activation of trypsinogen, modifier genes of cystic fibrosis phenotype, pancreatic secretion and ion homeostasis, calcium signaling and zymogen granules (ZG) exocytosis, autophagy and autoimmune pancreatitis-related genes. We detected mutations in 34 out of 70 genes examined; of the 80 patients, 64 (80.0%) were positive for mutations in one or more genes and 16 (20.0%) had no mutations. Mutations in CFTR were detected in 32 of the 80 patients (40.0%) and 22 of them exhibited at least one mutation in genes of other pancreatic pathways. Of the remaining 48 patients, 13/80 (16.3%) had mutations in genes involved in premature activation of trypsinogen and 19/80 (23.8%) had mutations only in genes of the other pathways: 38 (59.3%) of the 64 patients positive for mutations showed variants in two or more genes. Our data, although to be extended with functional analysis of novel mutations, suggest a high rate of genetic heterogeneity in CP and that trans-heterozygosity may predispose to the ICP phenotype. PMID:27264265

  9. Burden Analysis of Rare Microdeletions Suggests a Strong Impact of Neurodevelopmental Genes in Genetic Generalised Epilepsies

    Science.gov (United States)

    Trucks, Holger; Schulz, Herbert; de Kovel, Carolien G.; Kasteleijn-Nolst Trenité, Dorothée; Sonsma, Anja C. M.; Koeleman, Bobby P.; Lindhout, Dick; Weber, Yvonne G.; Lerche, Holger; Kapser, Claudia; Schankin, Christoph J.; Kunz, Wolfram S.; Surges, Rainer; Elger, Christian E.; Gaus, Verena; Schmitz, Bettina; Helbig, Ingo; Muhle, Hiltrud; Stephani, Ulrich; Klein, Karl M.; Rosenow, Felix; Neubauer, Bernd A.; Reinthaler, Eva M.; Zimprich, Fritz; Feucht, Martha; Møller, Rikke S.; Hjalgrim, Helle; De Jonghe, Peter; Suls, Arvid; Lieb, Wolfgang; Franke, Andre; Strauch, Konstantin; Gieger, Christian; Schurmann, Claudia; Schminke, Ulf; Nürnberg, Peter; Sander, Thomas

    2015-01-01

    Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes. PMID:25950944

  10. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies.

    Directory of Open Access Journals (Sweden)

    Dennis Lal

    2015-05-01

    Full Text Available Genetic generalised epilepsy (GGE is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb and rare (< 1% autosomal microdeletions with high calling confidence (≥ 200 markers were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1 assess the microdeletion burden in common GGE syndromes, 2 estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3 identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9. Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17 relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6 or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1 were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1. Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.

  11. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies.

    Science.gov (United States)

    Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger; Schulz, Herbert; de Kovel, Carolien G; Kasteleijn-Nolst Trenité, Dorothée; Sonsma, Anja C M; Koeleman, Bobby P; Lindhout, Dick; Weber, Yvonne G; Lerche, Holger; Kapser, Claudia; Schankin, Christoph J; Kunz, Wolfram S; Surges, Rainer; Elger, Christian E; Gaus, Verena; Schmitz, Bettina; Helbig, Ingo; Muhle, Hiltrud; Stephani, Ulrich; Klein, Karl M; Rosenow, Felix; Neubauer, Bernd A; Reinthaler, Eva M; Zimprich, Fritz; Feucht, Martha; Møller, Rikke S; Hjalgrim, Helle; De Jonghe, Peter; Suls, Arvid; Lieb, Wolfgang; Franke, Andre; Strauch, Konstantin; Gieger, Christian; Schurmann, Claudia; Schminke, Ulf; Nürnberg, Peter; Sander, Thomas

    2015-05-01

    Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes. PMID:25950944

  12. Analysis of pea HMG-I/Y expression suggests a role in defence gene regulation.

    Science.gov (United States)

    Klosterman, Steven J; Choi, Jane J; Hadwiger, Lee A

    2003-07-01

    SUMMARY HMG-I/Y proteins are characterized by the presence of AT-hook motifs, DNA binding domains that recognize AT-rich tracts of DNA. By facilitating protein:protein and protein:DNA interactions in the vicinity of these AT-rich binding sites, HMG-I/Y positively or negatively regulates gene expression. Several pea defence gene promoters have AT-rich tracts of DNA that are potential targets for modulation via HMG-I/Y. In this study, a comparison of the expression of a pea defence gene (DRR206) mRNA relative to the expression of HMG-I/Y mRNA was monitored by Northern analysis following the inoculation of a fungal pathogen, Fusarium solani or treatment with chitosan and a F. solani DNase (Fsph DNase). In pea pod endocarp tissue, HMG-I/Y expression was observed at high levels in untreated tissue and at lower levels 6 h following inoculation or wounding of the tissue. Western blots with an antipea HMG-I/Y polyclonal antibody also revealed that pea HMG-I/Y is expressed at decreased levels 6 h following inoculation or elicitor treatment. HMG-I/Y extracted from pea caused alterations in the gel migration of radio-labelled AT-rich sequences from the pea DRR206 promoter, suggesting that similar interactions could exist in vivo. Agroinfiltration was utilized to express the pea HMG-I/Y gene in tobacco containing a chimeric gene fusion of a promoter from the PR gene, DRR206, and the beta-glucuronidase (GUS) reporter gene. Transient expression of pea HMG-I/Y led to a decrease in GUS reporter gene activity in the heterologous tobacco system. These data implicate pea HMG-I/Y abundance in the down-regulation of DRR206 gene expression, and possibly HMG-I/Y depletion in the expression of defence genes in pea.

  13. Statistical analysis of iron geochemical data suggests limited late Proterozoic oxygenation

    Science.gov (United States)

    Sperling, Erik A.; Wolock, Charles J.; Morgan, Alex S.; Gill, Benjamin C.; Kunzmann, Marcus; Halverson, Galen P.; MacDonald, Francis A.; Knoll, Andrew H.; Johnston, David T.

    2015-07-01

    Sedimentary rocks deposited across the Proterozoic-Phanerozoic transition record extreme climate fluctuations, a potential rise in atmospheric oxygen or re-organization of the seafloor redox landscape, and the initial diversification of animals. It is widely assumed that the inferred redox change facilitated the observed trends in biodiversity. Establishing this palaeoenvironmental context, however, requires that changes in marine redox structure be tracked by means of geochemical proxies and translated into estimates of atmospheric oxygen. Iron-based proxies are among the most effective tools for tracking the redox chemistry of ancient oceans. These proxies are inherently local, but have global implications when analysed collectively and statistically. Here we analyse about 4,700 iron-speciation measurements from shales 2,300 to 360 million years old. Our statistical analyses suggest that subsurface water masses in mid-Proterozoic oceans were predominantly anoxic and ferruginous (depleted in dissolved oxygen and iron-bearing), but with a tendency towards euxinia (sulfide-bearing) that is not observed in the Neoproterozoic era. Analyses further indicate that early animals did not experience appreciable benthic sulfide stress. Finally, unlike proxies based on redox-sensitive trace-metal abundances, iron geochemical data do not show a statistically significant change in oxygen content through the Ediacaran and Cambrian periods, sharply constraining the magnitude of the end-Proterozoic oxygen increase. Indeed, this re-analysis of trace-metal data is consistent with oxygenation continuing well into the Palaeozoic era. Therefore, if changing redox conditions facilitated animal diversification, it did so through a limited rise in oxygen past critical functional and ecological thresholds, as is seen in modern oxygen minimum zone benthic animal communities.

  14. First in-depth analysis of the novel Th2-type cytokines in salmonid fish reveals distinct patterns of expression and modulation but overlapping bioactivities

    Science.gov (United States)

    Wang, Tiehui; Johansson, Petronella; Abós, Beatriz; Holt, Amy; Tafalla, Carolina; Jiang, Youshen; Wang, Alex; Xu, Qiaoqing; Qi, Zhitao; Huang, Wenshu; Costa, Maria M.; Diaz-Rosales, Patricia; Holland, Jason W.; Secombes, Christopher J.

    2016-01-01

    IL-4 and IL-13 are closely related canonical type-2 cytokines in mammals and have overlapping bioactivities via shared receptors. They are frequently activated together as part of the same immune response and are the signature cytokines produced by T-helper (Th)2 cells and type-2 innate lymphoid cells (ILC2), mediating immunity against extracellular pathogens. Little is known about the origin of type-2 responses, and whether they were an essential component of the early adaptive immune system that gave a fitness advantage by limiting collateral damage caused by metazoan parasites. Two evolutionary related type-2 cytokines, IL-4/13A and IL-4/13B, have been identified recently in several teleost fish that likely arose by duplication of an ancestral IL-4/13 gene as a consequence of a whole genome duplication event that occurred at the base of this lineage. However, studies of their comparative expression levels are largely missing and bioactivity analysis has been limited to IL-4/13A in zebrafish. Through interrogation of the recently released salmonid genomes, species in which an additional whole genome duplication event has occurred, four genomic IL-4/13 loci have been identified leading to the cloning of three active genes, IL-4/13A, IL-4/13B1 and IL-4/13B2, in both rainbow trout and Atlantic salmon. Comparative expression analysis by real-time PCR in rainbow trout revealed that the IL-4/13A expression is broad and high constitutively but less responsive to pathogen-associated molecular patterns (PAMPs) and pathogen challenge. In contrast, the expression of IL-4/13B1 and IL-4/13B2 is low constitutively but is highly induced by viral haemorrhagic septicaemia virus (VHSH) infection and during proliferative kidney disease (PKD) in vivo, and by formalin-killed bacteria, PAMPs, the T cell mitogen PHA, and the T-cell cytokines IL-2 and IL-21 in vitro. Moreover, bioactive recombinant cytokines of both IL-4/13A and B were produced and found to have shared but also distinct

  15. Status Quo, Analysis and Suggestions for Public Awareness on Wetland Conservation in China

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiaoyun; XU Jiliang; YUAN Jun

    2011-01-01

    To understand the status of public awareness on wetland conservation in China, 1 237 people from 8 provinces or municipality were interviewed by questionnaire. After analysis of the results, 88.5% of the interviewees know the word ‘wetland'. TV and radio is the main tool for them to get information. More than two thirds of the respondents mainly learn the information on wetland conservation through TV and radio. There are still big gaps among different people in understanding wetland. Only 13.3% of the respondents give a completely right answer on question ‘ which areas are wetlands'. Most of the respondents cited lakes, marshes and rivers as wetlands, but more than half of them do not regard beaches, reservoirs, paddy fields and fish ponds as wetlands. Most of the people cited wetlands can provide such functions as water conservation, climate regulation, protecting wildlife, removing pollution, but know little about other functions such as flood control, provisioning of aquatic products, and soil retention, and much less about the cultural functions such as recreation, and inherited folk culture. Except for wastewater discharge, nearly half of the general public knows little about other threats of the wetland, while most of the people do not believe that artificial aquaculture will cause threats to the wetland areas. Public awareness on wetland conservation in China needs to be improved. Most of the respondents cited that TV, radio and internet are the most effective ways to publicize information on wetland conservation. More than two thirds of the respondents mainly learn the information on wetland conservation through TV and radio, while 38.0% of the respondents mainly through internet.Specifically, for farmers/fishermen, posters/picture albums can benefit them more than the internet; the undergraduates also expect to learn wetland mainly through posters/picture albums; while for the primary and middle school students, the school education is another

  16. Symptom overlap in anxiety and multiple sclerosis.

    LENUS (Irish Health Repository)

    O Donnchadha, Seán

    2013-02-14

    BACKGROUND: The validity of self-rated anxiety inventories in people with multiple sclerosis (pwMS) is unclear. However, the appropriateness of self-reported depression scales has been widely examined. Given somatic symptom overlap between depression and MS, research emphasises caution when using such scales. OBJECTIVE: This study evaluates symptom overlap between anxiety and MS in a group of 33 individuals with MS, using the Beck Anxiety Inventory (BAI). METHODS: Participants underwent a neurological examination and completed the BAI. RESULTS: A novel procedure using hierarchical cluster analysis revealed three distinct symptom clusters. Cluster one (\\'wobbliness\\' and \\'unsteady\\') grouped separately from all other BAI items. These symptoms are well-recognised MS-related symptoms and we question whether their endorsement in pwMS can be considered to reflect anxiety. A modified 19-item BAI (mBAI) was created which excludes cluster one items. This removal reduced the number of MS participants considered \\'anxious\\' by 21.21% (low threshold) and altered the level of anxiety severity for a further 27.27%. CONCLUSION: Based on these data, it is suggested that, as with depression measures, researchers and clinicians should exercise caution when using brief screening measures for anxiety in pwMS.

  17. Packing ellipsoids with overlap

    CERN Document Server

    Uhler, Caroline

    2012-01-01

    The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application - chromosome organization in the human cell nucleus - is discussed briefly, and some illustrative results are presented.

  18. Data-Mining Analysis Suggests an Epigenetic Pathogenesis for Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Jonathan D. Wren

    2005-01-01

    the T2DM literature. The goal of this analysis was to conduct a comprehensive survey to identify novel factors implicated in the pathology of T2DM by statistically evaluating mutually shared associations. Surprisingly, epigenetic factors were among the highest statistical scores in this analysis, strongly implicating epigenetic changes within the body as causal factors in the pathogenesis of T2DM. Further analysis implicates adipocytes as the potential tissue of origin, and cytokines or cytokine-like genes as the dysregulated factor(s responsible for the T2DM phenotype. The analysis provides a wealth of literature supporting this hypothesis, which—if true—represents an important paradigm shift for researchers studying the pathogenesis of T2DM.

  19. Analysis and Suggestions on Management Strategies in Eco-industrial Parks in China

    Institute of Scientific and Technical Information of China (English)

    Yanfang ZHOU; Zhonghong YANG

    2012-01-01

    Abstract In the research, management strategies and problems of eco-industrial parks were mainly analyzed and some suggestions were proposed based on eco-in- dustrial park, circular economy and ecologization of industrial park in China, providing references for ecologica~ization policy design of industrial parks in China.

  20. Linkage analysis suggests a locus of ichthyosis vulgaris on 1q22.

    Science.gov (United States)

    Zhong, Wei; Cui, Bin; Zhang, Yizhi; Jiang, Haisong; Wei, Shengcai; Bu, Lei; Zhao, Guoping; Hu, Landian; Kong, Xiangyin

    2003-01-01

    Ichthyosis vulgaris (IV) is an inherited scaling skin disorder with a prevalence estimated at 2.29% in China. The gene responsible for this disorder has not been elucidated. To find the disease gene, we ascertained two Chinese IV families. Linkage analysis identified an IV locus on chromosome 1q22 with a maximum two-point Lod score of 2.47 at D1S1653 (theta=0.00). Haplotype analysis placed the critical region in a 7-cM interval defined by D1S1653 and D1S2675. These results provide the basis for further identifying the gene responsible for IV disorder.

  1. Analysis on Protection of GI Product Liupao Tea and Suggestions of its Industrial Supervision

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    From humanistic characteristics,historical origin,fame,quality,and the correlation between quality and production region,we analyze key factors of protection for Geographic Indication product Liupao Tea.We also analyze industrial development of Liupao Tea from processing threshold,scale of processing enterprises,standard and index,planting base,research and development and technology popularization,and pesticide control.In line with these situations,we put forward following suggestions.First,it is proposed to raise standard index and formulate national standard for Liupao Tea.Second,we should popularize the industrial mode of "market + association(enterprise) + base" and establish demonstration area for protection of Geographic Indication product Liupao Tea.Third,it is recommended to raise the production and processing threshold.Fourth,we should establish special production inspection and research and development institution.Fifth,it is suggested to set up independent supervision organization.

  2. The Disgust Scale: Item Analysis, Factor Structure, and Suggestions for Refinement

    Science.gov (United States)

    Olatunji, Bunmi O.; Williams, Nathan L.; Tolin, David F.; Abramowitz, Jonathan S.; Sawchuk, Craig N.; Lohr, Jeffrey M.; Elwood, Lisa S.

    2007-01-01

    In the 4 studies presented (N = 1,939), a converging set of analyses was conducted to evaluate the item adequacy, factor structure, reliability, and validity of the Disgust Scale (DS; J. Haidt, C. McCauley, & P. Rozin, 1994). The results suggest that 7 items (i.e., Items 2, 7, 8, 21, 23, 24, and 25) should be considered for removal from the DS.…

  3. A Suggested Approach for a Cost Analysis of Alternative IMS Configurations.

    Science.gov (United States)

    Besel, Ronald

    An approach to a cost analysis of pilot, prototype, model and operational versions of the Southwest Regional Laboratory's (SWRL) Instructional Management System (IMS) is described. Five classes of systems (conceptual, pilot, prototype, model and operational) are defined, and a system development process relating classes of systems in presented.…

  4. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

    DEFF Research Database (Denmark)

    Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger;

    2015-01-01

    Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1...... a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes....

  5. Communicating Comparative Findings from Meta-Analysis in Educational Research: Some Examples and Suggestions

    Science.gov (United States)

    Higgins, Steve; Katsipataki, Maria

    2016-01-01

    This article reviews some of the strengths and limitations of the comparative use of meta-analysis findings, using examples from the Sutton Trust-Education Endowment Foundation Teaching and Learning "Toolkit" which summarizes a range of educational approaches to improve pupil attainment in schools. This comparative use of quantitative…

  6. Niche Overlap and Network Specialization of Flower-Visiting Bees in an Agricultural System.

    Science.gov (United States)

    Carvalho, D M; Presley, S J; Santos, G M M

    2014-12-01

    Different resource use strategies manifest as differences in the realized niches of species. Niche segregation may involve several dimensions of the niche, such as diet, space, and time. We measured the level of redundancy and complementarity of a bee-plant interaction network in an agricultural system. Because flower resource diversity is high and resource abundance associated with flowering phenology varies throughout the year, we hypothesized that trophic overlap in the community would be low (i.e., high niche complementarity). In contrast, we expected a combination of physiological constraints and exploitation competition to create high temporal overlap, leading to high redundancy in the time of use of floral resources. Dietary overlap was low (NOih = 0.18): niches of 88% of species pairs had less than 30% overlap. In contrast, temporal overlap was intermediate (NOih = 0.49): niches of 65% of species pairs had 30% to 60% overlap. Network analysis showed that bees separated their dietary niches and had intermediate complementary specialization (H2' = 0.46). In terms of their temporal niches (H2' = 0.12), bees were generalists, with high temporal redundancy. Temperature was not a key factor in the determination of niche overlap, suggesting that environmental factors do not likely have a primary role in determining high redundancy in the temporal use of floral resources. Rather, temporal overlap is likely associated with the timing of nectar production by flowers. Our results suggest that bees partition a wide variety of available floral resources, resulting in low dietary overlap and intermediate temporal overlap. PMID:27194056

  7. Analysis on Protection of GI Product Xiangshan Spirit and Suggestions of Its Industrial Supervision

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    From name, historic stories, reputation, traffic and location factors, and natural factors as production and processing, water, raw material and yeast, this paper firstly analyzes key factors for protection of GI product Xiangshan Spirit. Then, it discusses differences in quality characteristics between Xiangshan Spirit and other rice flavor type spirits. Besides, industrial development of Xiangshan Spirit is analyzed from residues of pesticides, quality of water for making wine, and exclusive use of geographical indication Xiangshan Spirit. Finally, it puts forward following suggestions, including formulating and implementing local standard GI Product Xiangshan Spirit, strengthening quality control over rice raw material, implementing "enterprise + base" industrial model, and support group enterprises with government as leader.

  8. Business Communication in Less Commonly Taught Languages: Teaching Suggestions through Discourse Analysis:

    OpenAIRE

    Glaucia V. Silva; Denise Santos

    2010-01-01

    The knowledge generated by studies in discourse analysis is rarely brought into the teaching of business communication in a foreign language. Instead of presenting learners with "samples" of language after which they will pattern their production, foreign language instructors may invite learners to analyze the interplay between text and context in their own and in others' discourses. Therefore, the teaching of communicative functions (such as requesting, apologizing, sugg...

  9. Analysis of Random Metric Spaces Explains Emergence Phenomenon and Suggests Discreteness of Physical Space

    OpenAIRE

    Kosheleva, O.; V. Kreinovieh

    2015-01-01

    In many practical situations, systems follow the pattern set by the second law of thermodynamics: they evolve from an organized inhomogeneous state into a homogeneous structure-free state. In many other practical situations, however, we observe the opposite emergence phenomenon: in an originally homogeneous structure-free state, an inhomogeneous structure spontaneously appears. In this paper, we show that the analysis of random metric spaces provides a possible explanation for this phenomenon...

  10. Striatal proteomic analysis suggests that first L-dopa dose equates to chronic exposure.

    Directory of Open Access Journals (Sweden)

    Birger Scholz

    Full Text Available L-3,4-dihydroxypheylalanine (L-dopa-induced dyskinesia represent a debilitating complication of therapy for Parkinson's disease (PD that result from a progressive sensitization through repeated L-dopa exposures. The MPTP macaque model was used to study the proteome in dopamine-depleted striatum with and without subsequent acute and chronic L-dopa treatment using two-dimensional difference in-gel electrophoresis (2D-DIGE and mass spectrometry. The present data suggest that the dopamine-depleted striatum is so sensitive to de novo L-dopa treatment that the first ever administration alone would be able (i to induce rapid post-translational modification-based proteomic changes that are specific to this first exposure and (ii, possibly, lead to irreversible protein level changes that would be not further modified by chronic L-dopa treatment. The apparent equivalence between first and chronic L-dopa administration suggests that priming would be the direct consequence of dopamine loss, the first L-dopa administrations only exacerbating the sensitization process but not inducing it.

  11. Three suggestions on the definition of terms for the safety and reliability analysis of digital systems

    International Nuclear Information System (INIS)

    As digital instrumentation and control systems are being progressively introduced into nuclear power plants, a growing number of related technical issues are coming to light needing to be resolved. As a result, an understanding of relevant terms and basic concepts becomes increasingly important. Under the framework of the OECD/NEA WGRISK DIGREL Task Group, the authors were involved in reviewing definitions of terms forming the supporting vocabulary for addressing issues related to the safety and reliability analysis of digital instrumentation and control (SRA of DI and C). These definitions were extracted from various standards regulating the disciplines that form the technical and scientific basis of SRA DI and C. The authors discovered that different definitions are provided by different standards within a common discipline and used differently across various disciplines. This paper raises the concern that a common understanding of terms and basic concepts has not yet been established to address the very specific technical issues facing SRA DI and C. Based on the lessons learned from the review of the definitions of interest and the analysis of dependency relationships existing between these definitions, this paper establishes a set of recommendations for the development of a consistent terminology for SRA DI and C. - Highlights: ●We reviewed definitions of terms used in reliability analysis of digital systems. ●Different definitions are provided by different standards within a common discipline. ●Acyclic and cyclic structures of dependency in defining terms are compared. ●Three recommendations for the development of a consistent terminology provided

  12. Small-scale wood combustion. Analysis and suggestions by the Energy Agency

    International Nuclear Information System (INIS)

    Through the R and D program Biofuel - Health - Environment (BHM) it has been confirmed that emissions from old equipment for wood combustion represent an important problem. At present there are about 180,000 old wood boilers in use for space heating in Sweden. A simple modification as installing an hot water accumulator tank could reduce the emissions considerably, and even better results could be achieved by replacing the boilers with new equipment. Wood combustion in old installations cause large emissions of particles and volatile matter, and measurements and modelling show that problems will arise to meet new emission limits in certain areas with high concentration of wood firing. Installation of boilers using old technology makes the problem worse. In the BHM program, it has been suggested that new regulation should be adopted where permits would be obligatory for wood fueled boilers, and/or that the local government would have the authority the issue local regulations depending on local conditions

  13. Overlap extension PCR cloning.

    Science.gov (United States)

    Bryksin, Anton; Matsumura, Ichiro

    2013-01-01

    Rising demand for recombinant proteins has motivated the development of efficient and reliable cloning methods. Here we show how a beginner can clone virtually any DNA insert into a plasmid of choice without the use of restriction endonucleases or T4 DNA ligase. Chimeric primers encoding plasmid sequence at the 5' ends and insert sequence at the 3' ends are designed and synthesized. Phusion(®) DNA polymerase is utilized to amplify the desired insert by PCR. The double-stranded product is subsequently employed as a pair of mega-primers in a PCR-like reaction with circular plasmids. The original plasmids are then destroyed in restriction digests with Dpn I. The product of the overlap extension PCR is used to transform competent Escherichia coli cells. Phusion(®) DNA polymerase is used for both the amplification and fusion reactions, so both steps can be monitored and optimized in the same way. PMID:23996437

  14. Genome wide expression analysis suggests perturbation of vascular homeostasis during high altitude pulmonary edema.

    Directory of Open Access Journals (Sweden)

    Manish Sharma

    Full Text Available BACKGROUND: High altitude pulmonary edema (HAPE is a life-threatening form of non-cardiogenic edema which occurs in unacclimatized but otherwise normal individuals within two to four days after rapid ascent to altitude beyond 3000 m. The precise pathoetiology and inciting mechanisms regulating HAPE remain unclear. METHODOLOGY/PRINCIPLE FINDINGS: We performed global gene expression profiling in individuals with established HAPE compared to acclimatized individuals. Our data suggests concurrent modulation of multiple pathways which regulate vascular homeostasis and consequently lung fluid dynamics. These pathways included those which regulate vasoconstriction through smooth muscle contraction, cellular actin cytoskeleton rearrangements and endothelial permeability/dysfunction. Some notable genes within these pathways included MYLK; rho family members ARGEF11, ARHGAP24; cell adhesion molecules such as CLDN6, CLDN23, PXN and VCAM1 besides other signaling intermediates. Further, several important regulators of systemic/pulmonary hypertension including ADRA1D, ECE1, and EDNRA were upregulated in HAPE. We also observed significant upregulation of genes involved in paracrine signaling through chemokines and lymphocyte activation pathways during HAPE represented by transcripts of TNF, JAK2, MAP2K2, MAP2K7, MAPK10, PLCB1, ARAF, SOS1, PAK3 and RELA amongst others. Perturbation of such pathways can potentially skew vascular homeostatic equilibrium towards altered vascular permeability. Additionally, differential regulation of hypoxia-sensing, hypoxia-response and OXPHOS pathway genes in individuals with HAPE were also observed. CONCLUSIONS/SIGNIFICANCE: Our data reveals specific components of the complex molecular circuitry underlying HAPE. We show concurrent perturbation of multiple pathways regulating vascular homeostasis and suggest multi-genic nature of regulation of HAPE.

  15. Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community

    Directory of Open Access Journals (Sweden)

    Richard Allen White III

    2016-01-01

    Full Text Available Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g alpha and delta classes were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic

  16. Genome-wide analysis of HIF-2α chromatin binding sites under normoxia in human bronchial epithelial cells (BEAS-2B) suggests its diverse functions.

    Science.gov (United States)

    Lee, Meng-Chang; Huang, Hsin-Ju; Chang, Tzu-Hao; Huang, Hsieh-Chou; Hsieh, Shen-Yuan; Chen, Yi-Siou; Chou, Wei-Yuan; Chiang, Chiao-Hsi; Lai, Ching-Huang; Shiau, Chia-Yang

    2016-01-01

    Constitutive functional HIF-2α was recently identified in cancer and stem cell lines under normoxia. In this study, BEAS-2B, a bronchial epithelial cell line, was shown to constitutively express active HIF-2α under normoxia and exhibit markers of pluripotency including Oct-4, Nanog, and sphere formation. Oct-4 expression was reduced after knockdown of HIF-2α under normoxia. Global enrichment analysis of HIF-2α demonstrated the diverse functions of HIF-2α under normoxia. Bioinformatics analysis of the enriched loci revealed an enhancer role of HIF-2α binding sites, involvement of HIF-2α interacting proteins, and enriched de novo motifs which suggest the diverse role of HIF-2α in pseudohypoxia. The low ratio of the discovered loci overlapping with those revealed in cancer cell lines 786-O (16.1%) and MCF-7 (15.9%) under hypoxia indicated a prevailing non-canonical mechanism. Hypoxia had positive, marginal or adverse effects on the enrichment of the selected loci in ChIP-PCR assays. Deletion of the N-terminal activation domain (N-TAD) of HIF-2α disrupted the reporting activity of two of the loci annotated to ELN and ANKRD31. Hypoxia incurring abundance variation of HIF-2α may misrepresent the N-TAD functions as canonical hypoxia inducible features via C-TAD activation. Elucidation of the pseudohypoxia functions of constitutive HIF-2α is useful for resolving its role in malignancy and pluripotency.

  17. Seismic performance analysis and design suggestion for frame buildings with cast-in-place staircases

    Science.gov (United States)

    Feng, Yuan; Wu, Xiaobin; Xiong, Yaoqing; Li, Congchun; Yang, Wen

    2013-06-01

    Many staircases in reinforced concrete (RC) frame structures suffered severe damage during the Wenchuan earthquake. Elastic analyses for 18 RC structure models with and without staircases are conducted and compared to study the influence of the staircase on the stiffness, displacements and internal forces of the structures. To capture the yielding development and damage mechanism of frame structures, elasto-plastic analysis is carried out for one of the 18 models. Based on the features observed in the analyses, a new type of staircase design i.e., isolating them from the master structure to eliminate the effect of K-type struts, is proposed and discussed. It is concluded that the proposed method of staircase isolation is effective and feasible for engineering design, and does not significantly increase the construction cost.

  18. Analysis on Protection of GI Product Hanyuan Chinese Prickly Ash and Suggestions of its Industrial Development

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Hanyuan Prickly Ash is a type of GI products with very deep cultural essence.From such humanistic factors as name origin,historical origin,fame,cultivation technology,and management measure,and such natural factors as climatic environment and soil conditions,this paper analysis key factors for protection of GI product Hanyuan Prickly Ash.Then it discusses about industrial development of Hanyuan Prickly Ash from suitable planting areas and climate.It proposes that we should gradually raise safety and hygienic indexes,revise and implement local standards,strengthen popularization of harmless production technologies and quality control of product,promote "enterprise + base" industrial model,and implement government marketing of brand and industry.

  19. Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach.

    Science.gov (United States)

    Gagen, Emma J; Denman, Stuart E; Padmanabha, Jagadish; Zadbuke, Someshwar; Al Jassim, Rafat; Morrison, Mark; McSweeney, Christopher S

    2010-12-01

    Reductive acetogenesis via the acetyl coenzyme A (acetyl-CoA) pathway is an alternative hydrogen sink to methanogenesis in the rumen. Functional gene-based analysis is the ideal approach for investigating organisms capable of this metabolism (acetogens). However, existing tools targeting the formyltetrahydrofolate synthetase gene (fhs) are compromised by lack of specificity due to the involvement of formyltetrahydrofolate synthetase (FTHFS) in other pathways. Acetyl-CoA synthase (ACS) is unique to the acetyl-CoA pathway and, in the present study, acetyl-CoA synthase genes (acsB) were recovered from a range of acetogens to facilitate the design of acsB-specific PCR primers. fhs and acsB libraries were used to examine acetogen diversity in the bovine rumen and forestomach of the tammar wallaby (Macropus eugenii), a native Australian marsupial demonstrating foregut fermentation analogous to rumen fermentation but resulting in lower methane emissions. Novel, deduced amino acid sequences of acsB and fhs affiliated with the Lachnospiraceae in both ecosystems and the Ruminococcaeae/Blautia group in the rumen. FTHFS sequences that probably originated from nonacetogens were identified by low "homoacetogen similarity" scores based on analysis of FTHFS residues, and comprised a large proportion of FTHFS sequences from the tammar wallaby forestomach. A diversity of FTHFS and ACS sequences in both ecosystems clustered between the Lachnospiraceae and Clostridiaceae acetogens but without close sequences from cultured isolates. These sequences probably originated from novel acetogens. The community structures of the acsB and fhs libraries from the rumen and the tammar wallaby forestomach were different (LIBSHUFF, P < 0.001), and these differences may have significance for overall hydrogenotrophy in both ecosystems.

  20. Phylogenetic analysis suggests that sociality is associated with reduced effectiveness of selection.

    Science.gov (United States)

    Settepani, Virginia; Bechsgaard, Jesper; Bilde, Trine

    2016-01-01

    The evolution of sociality in spiders is associated with female bias, reproductive skew and an inbreeding mating system, factors that cause a reduction in effective population size and increase effects of genetic drift. These factors act to decrease the effectiveness of selection, thereby increasing the fixation probability of deleterious mutations. Comparative studies of closely related species with contrasting social traits and mating systems provide the opportunity to test consequences of low effective population size on the effectiveness of selection empirically. We used phylogenetic analyses of three inbred social spider species and seven outcrossing subsocial species of the genus Stegodyphus, and compared dN/dS ratios and codon usage bias between social Inbreeding and subsocial outcrossing mating systems to assess the effectiveness of selection. The overall results do not differ significantly between the social inbreeding and outcrossing species, but suggest a tendency for lower codon usage bias and higher dN/dS ratios in the social inbreeding species compared with their outcrossing congeners. The differences in dN/dS ratio and codon usage bias between social and subsocial species are modest but consistent with theoretical expectations of reduced effectiveness of selection in species with relatively low effective population size. The modest differences are consistent with relatively recent evolution of social mating systems. Additionally, the short terminal branches and lack of speciation of the social lineages, together with low genetic diversity lend support for the transient state of permanent sociality in spiders. PMID:26843931

  1. Comparative skull analysis suggests species-specific captivity-related malformation in lions (Panthera leo.

    Directory of Open Access Journals (Sweden)

    Joseph Saragusty

    Full Text Available Lion (Panthera leo populations have dramatically decreased worldwide with a surviving population estimated at 32,000 across the African savannah. Lions have been kept in captivity for centuries and, although they reproduce well, high rates of stillbirths as well as morbidity and mortality of neonate and young lions are reported. Many of these cases are associated with bone malformations, including foramen magnum (FM stenosis and thickened tentorium cerebelli. The precise causes of these malformations and whether they are unique to captive lions remain unclear. To test whether captivity is associated with FM stenosis, we evaluated 575 lion skulls of wild (N = 512 and captive (N = 63 origin. Tiger skulls (N = 276; 56 captive, 220 wild were measured for comparison. While no differences were found between males and females or between subadults and adults in FM height (FMH, FMH of captive lions (17.36±3.20 mm was significantly smaller and with greater variability when compared to that in wild lions (19.77±2.11 mm. There was no difference between wild (18.47±1.26 mm and captive (18.56±1.64 mm tigers in FMH. Birth origin (wild vs. captive as a factor for FMH remained significant in lions even after controlling for age and sex. Whereas only 20/473 wild lions (4.2% had FMH equal to or smaller than the 5th percentile of the wild population (16.60 mm, this was evident in 40.4% (23/57 of captive lion skulls. Similar comparison for tigers found no differences between the captive and wild populations. Lions with FMH equal to or smaller than the 5th percentile had wider skulls with smaller cranial volume. Cranial volume remained smaller in both male and female captive lions when controlled for skull size. These findings suggest species- and captivity-related predisposition for the pathology in lions.

  2. Use of multivariate analysis to suggest a new molecular classification of colorectal cancer

    Science.gov (United States)

    Domingo, Enric; Ramamoorthy, Rajarajan; Oukrif, Dahmane; Rosmarin, Daniel; Presz, Michal; Wang, Haitao; Pulker, Hannah; Lockstone, Helen; Hveem, Tarjei; Cranston, Treena; Danielsen, Havard; Novelli, Marco; Davidson, Brian; Xu, Zheng-Zhou; Molloy, Peter; Johnstone, Elaine; Holmes, Christopher; Midgley, Rachel; Kerr, David; Sieber, Oliver; Tomlinson, Ian

    2013-01-01

    Abstract Molecular classification of colorectal cancer (CRC) is currently based on microsatellite instability (MSI), KRAS or BRAF mutation and, occasionally, chromosomal instability (CIN). Whilst useful, these categories may not fully represent the underlying molecular subgroups. We screened 906 stage II/III CRCs from the VICTOR clinical trial for somatic mutations. Multivariate analyses (logistic regression, clustering, Bayesian networks) identified the primary molecular associations. Positive associations occurred between: CIN and TP53 mutation; MSI and BRAF mutation; and KRAS and PIK3CA mutations. Negative associations occurred between: MSI and CIN; MSI and NRAS mutation; and KRAS mutation, and each of NRAS, TP53 and BRAF mutations. Some complex relationships were elucidated: KRAS and TP53 mutations had both a direct negative association and a weaker, confounding, positive association via TP53–CIN–MSI–BRAF–KRAS. Our results suggested a new molecular classification of CRCs: (1) MSI+ and/or BRAF-mutant; (2) CIN+ and/or TP53– mutant, with wild-type KRAS and PIK3CA; (3) KRAS- and/or PIK3CA-mutant, CIN+, TP53-wild-type; (4) KRAS– and/or PIK3CA-mutant, CIN–, TP53-wild-type; (5) NRAS-mutant; (6) no mutations; (7) others. As expected, group 1 cancers were mostly proximal and poorly differentiated, usually occurring in women. Unexpectedly, two different types of CIN+ CRC were found: group 2 cancers were usually distal and occurred in men, whereas group 3 showed neither of these associations but were of higher stage. CIN+ cancers have conventionally been associated with all three of these variables, because they have been tested en masse. Our classification also showed potentially improved prognostic capabilities, with group 3, and possibly group 1, independently predicting disease-free survival. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. PMID:23165447

  3. The Trends and Prospects of Health Information Standards : Standardization Analysis and Suggestions

    International Nuclear Information System (INIS)

    Ubiquitous health care system, which is one of the developing solution technologies of IT, BT and NT, could give us new medical environments in future. Implementing health information systems can be complex, expensive and frustrating. Healthcare professionals seeking to acquire or upgrade systems do not have a convenient, reliable way of specifying a level of adherence to communication standards sufficient to achieve truly efficient interoperability. Great progress has been made in establishing such standards-DICOM, IHE and HL7, notably, are now highly advanced. IHE has defined a common framework to deliver the basic interoperability needed for local and regional health information networks. It has developed a foundational set of standards-based integration profiles for information exchange with three interrelated efforts. HL7 is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. Most SDOs produce standards (protocols) for a particular healthcare domain such as pharmacy, medical devices, imaging or insurance transactions. HL7's domain is clinical and administrative data. HL7 is an international community of healthcare subject matter experts and information scientists collaborating to create standards for the exchange, management and integration of electronic healthcare information. The ASTM specification for Continuity of Care Record was developed by subcommittee E31.28 on electronic health records, which includes clinicians, provider institutions, administrators, patient advocates, vendors, and health industry. In this paper, there are suggestions that provide a test bed, demonstration and specification of how standards such a IHE, HL7, ASTM can be used to provide an integrated environment.

  4. Genome-wide analysis suggests divergent evolution of lipid phosphotases/phosphotransferase genes in plants.

    Science.gov (United States)

    Wang, Peng; Chen, Zhenxi; Kasimu, Rena; Chen, Yinhua; Zhang, Xiaoxiao; Gai, Jiangtao

    2016-08-01

    Genes of the LPPT (lipid phosphatase/phosphotransferase) family play important roles in lipid phosphorous transfer and triacylglycerol accumulation in plants. To provide overviews of the plant LPPT family and their overall relationships, here we carried out genome-wide identifications and analyses of plant LPPT family members. A total of 643 putative LPPT genes were identified from 48 sequenced plant genomes, among which 205 genes from 14 plants were chosen for further analyses. Plant LPPT genes belonged to three distinctive groups, namely the LPT (lipid phosphotransfease), LPP (lipid phosphatase), and pLPP (plastidic lipid phosphotransfease) groups. Genes of the LPT group could be further partitioned into three groups, two of which were only identified in terrestrial plants. Genes in the LPP and pLPP groups experienced duplications in early stages of plant evolution. Among 17 Zea mays LPPT genes, divergence of temporal-spatial expression patterns was revealed based on microarray data analysis. Peptide sequences of plant LPPT genes harbored different conserved motifs. A test of Branch Model versus One-ratio Model did not support significant selective pressures acting on different groups of LPPT genes, although quite different nonsynonymous evolutionary rates and selective pressures were observed. The complete picture of the plant LPPT family provided here should facilitate further investigations of plant LPPT genes and offer a better understanding of lipid biosynthesis in plants. PMID:27501416

  5. Network analysis of human fMRI data suggests modular restructuring after simulated acquired brain injury.

    Science.gov (United States)

    Ruiz Vargas, E; Mitchell, D G V; Greening, S G; Wahl, L M

    2016-01-01

    The pathophysiology underlying neurocognitive dysfunction following mild traumatic brain injury (TBI), or concussion, is poorly understood. In order to shed light on the effects of TBI at the functional network or modular level, our research groups are engaged in the acquisition and analysis of functional magnetic resonance imaging data from subjects post-TBI. Complementary to this effort, in this paper we use mathematical and computational techniques to determine how modular structure changes in response to specific mechanisms of injury. In particular, we examine in detail the potential effects of focal contusions, diffuse axonal degeneration and diffuse microlesions, illustrating the extent to which functional modules are preserved or degenerated by each type of injury. One striking prediction of our study is that the left and right hemispheres show a tendency to become functionally separated post-injury, but only in response to diffuse microlesions. We highlight other key differences among the effects of the three modelled injuries and discuss their clinical implications. These results may help delineate the functional mechanisms underlying several of the cognitive sequelae associated with TBI. PMID:26463519

  6. Main Consequences of IFRS Adoption: Analysis of Existing Literature and Suggestions for Further Research

    Directory of Open Access Journals (Sweden)

    Isabel Maria Estima Costa Lourenço

    2015-08-01

    Full Text Available This study characterizes the results of scientific research on the effect of adopting the International Financial Reporting Standards (IFRS that have been published in the most prestigious scientific journals in the field of accounting at the international level and it identifies avenues for further research. Based on the analysis of a set of 67 articles published by the accounting journals that make up the Social Sciences Citation Index (SSCI, published between 2000 and 2013, it is concluded that, as a general rule, IFRS adoption has a positive effect on information quality, the capital market, analysts' ability to predict, comparability, and information use. Nevertheless, this effect depends on some factors, such as country's characteristics (namely, the enforcement level and companies' characteristics. Sharing rules is not, by itself, enough to create a common business language, and management incentives and institutional factors play a major role in framing the characteristics of financial reporting. Finally, some gaps are identified in the literature and avenues for further research are introduced.

  7. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts

    Directory of Open Access Journals (Sweden)

    Normand Philippe

    2008-01-01

    genomes, suggesting that plant cell wall polysaccharide degradation may not be crucial to root infection, or that this degradation varies among strains. We hypothesize that the relative lack of secreted polysaccharide-degrading enzymes in Frankia reflects a strategy used by these bacteria to avoid eliciting host defense responses. The esterases, lipases, and proteases found in the core Frankia secretome might facilitate hyphal penetration through the cell wall, release carbon sources, or modify chemical signals. The core secretome also includes extracellular solute-binding proteins and Frankia-specific hypothetical proteins that may enable the actinorhizal symbiosis.

  8. Integrative analysis of transgenic alfalfa (Medicago sativa L.) suggests new metabolic control mechanisms for monolignol biosynthesis.

    Science.gov (United States)

    Lee, Yun; Chen, Fang; Gallego-Giraldo, Lina; Dixon, Richard A; Voit, Eberhard O

    2011-05-01

    The entanglement of lignin polymers with cellulose and hemicellulose in plant cell walls is a major biological barrier to the economically viable production of biofuels from woody biomass. Recent efforts of reducing this recalcitrance with transgenic techniques have been showing promise for ameliorating or even obviating the need for costly pretreatments that are otherwise required to remove lignin from cellulose and hemicelluloses. At the same time, genetic manipulations of lignin biosynthetic enzymes have sometimes yielded unforeseen consequences on lignin composition, thus raising the question of whether the current understanding of the pathway is indeed correct. To address this question systemically, we developed and applied a novel modeling approach that, instead of analyzing the pathway within a single target context, permits a comprehensive, simultaneous investigation of different datasets in wild type and transgenic plants. Specifically, the proposed approach combines static flux-based analysis with a Monte Carlo simulation in which very many randomly chosen sets of parameter values are evaluated against kinetic models of lignin biosynthesis in different stem internodes of wild type and lignin-modified alfalfa plants. In addition to four new postulates that address the reversibility of some key reactions, the modeling effort led to two novel postulates regarding the control of the lignin biosynthetic pathway. The first posits functionally independent pathways toward the synthesis of different lignin monomers, while the second postulate proposes a novel feedforward regulatory mechanism. Subsequent laboratory experiments have identified the signaling molecule salicylic acid as a potential mediator of the postulated control mechanism. Overall, the results demonstrate that mathematical modeling can be a valuable complement to conventional transgenic approaches and that it can provide biological insights that are otherwise difficult to obtain. PMID:21625579

  9. Integrative analysis of transgenic alfalfa (Medicago sativa L. suggests new metabolic control mechanisms for monolignol biosynthesis.

    Directory of Open Access Journals (Sweden)

    Yun Lee

    2011-05-01

    Full Text Available The entanglement of lignin polymers with cellulose and hemicellulose in plant cell walls is a major biological barrier to the economically viable production of biofuels from woody biomass. Recent efforts of reducing this recalcitrance with transgenic techniques have been showing promise for ameliorating or even obviating the need for costly pretreatments that are otherwise required to remove lignin from cellulose and hemicelluloses. At the same time, genetic manipulations of lignin biosynthetic enzymes have sometimes yielded unforeseen consequences on lignin composition, thus raising the question of whether the current understanding of the pathway is indeed correct. To address this question systemically, we developed and applied a novel modeling approach that, instead of analyzing the pathway within a single target context, permits a comprehensive, simultaneous investigation of different datasets in wild type and transgenic plants. Specifically, the proposed approach combines static flux-based analysis with a Monte Carlo simulation in which very many randomly chosen sets of parameter values are evaluated against kinetic models of lignin biosynthesis in different stem internodes of wild type and lignin-modified alfalfa plants. In addition to four new postulates that address the reversibility of some key reactions, the modeling effort led to two novel postulates regarding the control of the lignin biosynthetic pathway. The first posits functionally independent pathways toward the synthesis of different lignin monomers, while the second postulate proposes a novel feedforward regulatory mechanism. Subsequent laboratory experiments have identified the signaling molecule salicylic acid as a potential mediator of the postulated control mechanism. Overall, the results demonstrate that mathematical modeling can be a valuable complement to conventional transgenic approaches and that it can provide biological insights that are otherwise difficult to obtain.

  10. Analysis of Neogene deformation between Beaver, Utah, and Barstow, California: suggestions for altering the extensional paradigm

    Science.gov (United States)

    Anderson, R. Ernest; Beard, L. Sue; Mankinen, Edward A.; Hillhouse, John W.

    2013-01-01

    -scale coupling is critical to understanding major NS shortening and westerly tectonic escape in the Lake Mead area. One north-elongate uplift in the Hingeline shear zone is a positive flower structure along a strike-slip fault, and we postulate that most other large uplifts are diapiric, resulting from extension-normal inflow of ductile substrate, rather than second-order isostatic responses to tectonic unloading. We also postulate that large steep-axis rotations, and some small ones as well, result from basal tractions imparted by gradients in southerly directed subjacent ductile flow rather than by shear coupling imparted by laterally variable elongation strains. The shortening strain recorded in the rotations and related structures probably matches or exceeds the magnitude of lengthening, even for the Lake Mead area where we do not question local large (~65 km) west-directed lengthening. We assess the results of extensive recent earth-science research in the Lake Mead area and conclude that previously published models of N-S convergence, westerly tectonic rafting, and N-S occlusion are valid and record unique tectonic escape accommodation for south-directed displacement of the Great Basin sector of the Basin and Range. Genetic ties between the south-directed displacement and plate-interaction forces are elusive, and we suggest the displacement results from body forces inherent in the Basin and Range.

  11. Electron Microprobe Analysis of Hf in Zircon: Suggestions for Improved Accuracy of a Difficult Measurement

    Science.gov (United States)

    Fournelle, J.; Hanchar, J. M.

    2013-12-01

    It is not commonly recognized as such, but the accurate measurement of Hf in zircon is not a trivial analytical issue. This is important to assess because Hf is often used as an internal standard for trace element analyses of zircon by LA-ICPMS. The issues pertaining to accuracy revolve around: (1) whether the Hf Ma or the La line is used; (2) what accelerating voltage is applied if Zr La is also measured, and (3) what standard for Hf is used. Weidenbach, et al.'s (2004) study of the 91500 zircon demonstrated the spread (in accuracy) of possible EPMA values for six EPMA labs, 2 of which used Hf Ma, 3 used Hf La, and one used Hf Lb, and standards ranged from HfO2, a ZrO2-HfO2 compound, Hf metal, and hafnon. Weidenbach, et al., used the ID-TIMS values as the correct value (0.695 wt.% Hf.), for which not one of the EPMA labs came close to that value (3 were low and 3 were high). Those data suggest: (1) that there is a systematic underestimation error of the 0.695 wt% Hf (ID-TIMS Hf) value if Hf Ma is used; most likely an issue with the matrix correction, as the analytical lines and absorption edges of Zr La, Si Ka and Hf Ma are rather tightly packed in the electromagnetic spectrum. Mass absorption coefficients are easily in error (e.g., Donovan's determination of the MAC of Hf by Si Ka of 5061 differs from the typically used Henke value of 5449 (Donovan et al, 2002); and (2) For utilization of the Hf La line, however, the second order Zr Ka line interferes with Hf La if the accelerating voltage is greater than 17.99 keV. If this higher keV is used and differential mode PHA is applied, only a portion of the interference is removed (e.g., removal of escape peaks), causing an overestimation of Hf content. Unfortunately, it is virtually impossible to apply an interference correction in this case, as it is impossible to locate Hf-free Zr probe standard. We have examined many of the combinations used by those six EPMA labs and concluded that the optimal EPMA is done with Hf

  12. Correction methodology for the spectral interfering {gamma}-rays overlapping to the analytical peaks used in the analysis of {sup 232}Th

    Energy Technology Data Exchange (ETDEWEB)

    Yuecel, H., E-mail: haluk.yucel@ankara.edu.t [Institute of Nuclear Sciences, Ankara University (Australia), Besevler Yerleskesi, Tandogan, 06100 Ankara (Turkey); Koese, E. [Institute of Nuclear Sciences, Ankara University (Australia), Besevler Yerleskesi, Tandogan, 06100 Ankara (Turkey); Esen, A.N. [Energy Institute, Istanbul Technical University (ITU), Maslak, 34469 Istanbul (Turkey); Bor, D. [Institute of Nuclear Sciences, Ankara University (Australia), Besevler Yerleskesi, Tandogan, 06100 Ankara (Turkey)

    2011-06-15

    In the {gamma}-ray spectrometric analysis of the radionuclides, a correction factor is generally required for the spectral interfering {gamma}-rays in determining the net areas of the analytical peaks because some interfering {gamma}-rays often might contribute to the analytical peaks of interest. In present study, a correction methodology for the spectral interfering {gamma}-rays (CSI) is described. In particular, in the analysis of {sup 232}Th contained in samples, the interfering {gamma}-rays due to {sup 226}Ra, {sup 235}U, {sup 238}U and their decay products often overlap to the peaks of interest from {sup 232}Th decay products, and vise versa. For the validation of the proposed CSI method, several certified reference materials (CRM) containing U and Th were measured by using a 76.5% efficient n-type Ge detector. The required correction factors were quantified for spectral interference, self-absorption and true coincidence summing (TCS) effects for the relevant {gamma}-rays. The measured results indicate that if one ignores the contributions of the interfering {gamma}-rays to the analytical peaks at 583.2 keV of {sup 208}Tl and 727.3 keV of {sup 212}Bi, this leads to a significantly systematic influence on the resulted activities of {sup 232}Th. The correction factors required for spectral interference and TCS effects are estimated to be {approx}13.6% and {approx}15.4% for 583.2 keV peak. For the 727.3 keV peak, the correction factor is estimated to be {approx}15% for spectral interference, and {approx}5% for the TCS effects at the presently used detection geometry. On the other hand, the measured results also indicate that ignoring the contribution of the interfering {gamma}-rays to the areas of the analytical peaks at 860.6 keV of {sup 208}Tl, 338.3 and 911.2 keV of {sup 228}Ac does not lead to any significant systematic influence on the {sup 232}Th analysis. Because these factors are remained generally less than {approx}5%, i.e., within overall uncertainty

  13. Topological susceptibility from overlap fermion

    Institute of Scientific and Technical Information of China (English)

    应和平; 张剑波

    2003-01-01

    We numerically calculate the topological charge of the gauge configurations on a finite lattice by the fermionic method with overlap fermions. By using the lattice index theorem, we identify the index of the massless overlap fermion operator to the topological charge of the background gauge configuration. The resulting topological susceptibility X is in good agreement with the anticipation made by Witten and Veneziano.

  14. Saccade plan overlap and cancellation during free viewing.

    Science.gov (United States)

    Wu, Esther X W; Chua, Fook-Kee; Yen, Shih-Cheng

    2016-10-01

    In the current study, we examined how the saccadic system responds when visual information changes dynamically in our environment. Previous studies, using the double-step task, have shown that (a) saccade plans could overlap, such that saccade preparation to an object started even while the saccade preparation to another object was ongoing, and (b) saccade plans could be cancelled before they were completed. In these studies, saccade targets were restricted to a few, experimenter-defined locations. Here, we examined whether saccade plan overlap and cancellation mechanisms could be observed in free-viewing conditions. For each trial, we constructed sets of two images, each containing five objects. All objects have unique positions. Image 1 was presented for several fixations, before Image 2 was presented during a fixation, presumably while a saccade plan to an object in Image 1 was ongoing. There were two crucial findings: (a) First, the saccade immediately following the transition was sometimes executed towards objects in Image 2, and not an object in Image 1, suggesting that the earlier saccade plan to an Image 1 object had been cancelled. Second, analysis of the temporal data also suggested that preparation of the first post-transition saccade started before an earlier saccade plan to an Image 1 object was executed, implying that saccade plans overlapped.

  15. Literature-Informed Analysis of a Genome-Wide Association Study of Gestational Age in Norwegian Women and Children Suggests Involvement of Inflammatory Pathways

    Science.gov (United States)

    Bacelis, Jonas; Juodakis, Julius; Sengpiel, Verena; Zhang, Ge; Myhre, Ronny; Muglia, Louis J.; Nilsson, Staffan; Jacobsson, Bo

    2016-01-01

    Background Five-to-eighteen percent of pregnancies worldwide end in preterm birth, which is the major cause of neonatal death and morbidity. Approximately 30% of the variation in gestational age at birth can be attributed to genetic factors. Genome-wide association studies (GWAS) have not shown robust evidence of association with genomic loci yet. Methods We separately investigated 1921 Norwegian mothers and 1199 children from pregnancies with spontaneous onset of delivery. Individuals were further divided based on the onset of delivery: initiated by labor or prelabor rupture of membranes. Genetic association with ultrasound-dated gestational age was evaluated using three genetic models and adaptive permutations. The top-ranked loci were tested for enrichment in 12 candidate gene-sets generated by text-mining PubMed abstracts containing pregnancy-related keywords. Results The six GWAS did not reveal significant associations, with the most extreme empirical p = 5.1 × 10−7. The top loci from maternal GWAS with deliveries initiated by labor showed significant enrichment in 10 PubMed gene-sets, e.g., p = 0.001 and 0.005 for keywords "uterus" and "preterm" respectively. Enrichment signals were mainly caused by infection/inflammation-related genes TLR4, NFKB1, ABCA1, MMP9. Literature-informed analysis of top loci revealed further immunity genes: IL1A, IL1B, CAMP, TREM1, TFRC, NFKBIA, MEFV, IRF8, WNT5A. Conclusion Our analyses support the role of inflammatory pathways in determining pregnancy duration and provide a list of 32 candidate genes for a follow-up work. We observed that the top regions from GWAS in mothers with labor-initiated deliveries significantly more often overlap with pregnancy-related genes than would be expected by chance, suggesting that increased sample size would benefit similar studies. PMID:27490719

  16. Prevalence and Overlap of Childhood and Adult Physical, Sexual, and Emotional Abuse: A Descriptive Analysis of Results from the Boston Area Community Health (BACH) Survey

    OpenAIRE

    Chiu, Gretchen R.; Lutfey, Karen E.; Litman, Heather J.; Link, Carol L.; Hall, Susan A.; McKinlay, John B.

    2013-01-01

    Abuse is associated with a wide variety of health problems, yet comprehensive population-based data are scant. Existing literature focuses on a single type of abuse, population, or lifestage. Using a racially/ethnically diverse community-based sample, we document the prevalence of physical, emotional, and sexual abuse by lifestage and gender; assess variation in abuse by socio-demographics; establish overlap of abuses; and examine childhood abuse relationships with abuse in adulthood. Prevale...

  17. Direct and indirect effects in the regulation of overlapping promoters.

    Science.gov (United States)

    Bendtsen, Kristian Moss; Erdossy, János; Csiszovszki, Zsolt; Svenningsen, Sine Lo; Sneppen, Kim; Krishna, Sandeep; Semsey, Szabolcs

    2011-09-01

    Optimal response to environmental stimuli often requires activation of certain genes and repression of others. Dual function regulatory proteins play a key role in the differential regulation of gene expression. While repression can be achieved by any DNA binding protein through steric occlusion of RNA polymerase in the promoter region, activation often requires a surface on the regulatory protein to contact RNAP and thus facilitate transcription initiation. RNAP itself is also a DNA binding protein, therefore it can function as a transcriptional repressor. Searching the Escherichia coli promoter database we found that ∼14% of the identified 'forward' promoters overlap with a promoter oriented in the opposite direction. In this article we combine a mathematical model with experimental analysis of synthetic regulatory regions to investigate interference of overlapping promoters. We find that promoter interference depends on the characteristics of overlapping promoters. The model predicts that promoter strength and interference can be regulated separately, which provides unique opportunities for regulation. Our experimental data suggest that in principle any DNA binding protein can be used for both activation and repression of promoter transcription, depending on the context. These findings can be exploited in the construction of synthetic networks. PMID:21609952

  18. Path analysis suggests phytoene accumulation is the key step limiting the carotenoid pathway in white carrot roots

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2005-01-01

    Full Text Available Two F2 carrot (Daucus carota L. populations (orange rooted Brasilia x very dark orange rooted High Carotene Mass - HCM cross and the dark orange rooted cultivated variety B493 x white rooted wild carrot Queen Anne's Lace - QAL cross with very unrelated genetic backgrounds were used to investigate intrinsic factors limiting carotenoid accumulation in carrots by applying phenotypic correlation and path analysis to study the relationships between major root carotenes, root color and several other morphological traits. Most of the correlations between traits were close and agreed in sign between the two populations. Root weight had a moderate to highly significant positive correlation with leaf length, root length and top and middle root diameter. Although phenotypic correlations failed to identify the order of the substrates and products in the carotenoid pathway the correct order of substrates and products (phytoene -> zeta-carotene -> lycopene was identified in the causal diagram of beta-carotene for the Brasilia x HCM population. Path analysis of beta-carotene synthesis in the B493 x QAL population suggested that selection for root carotenes had little effect on plant morphological traits. Causal model of beta-carotene and lycopene in the B493 x QAL population suggested that phytoene synthesis is the key step limiting the carotenoid pathway in white carrots. Path analysis, first presented by Sewall Wright to study quantitative traits, appears to be a powerful statistical approach for the identification of key compounds in complex pathways.

  19. Comprehensive analysis of cystatin family genes suggests their putative functions in sexual reproduction, embryogenesis, and seed formation.

    Science.gov (United States)

    Zhao, Peng; Zhou, Xue-mei; Zou, Jie; Wang, Wei; Wang, Lu; Peng, Xiong-bo; Sun, Meng-xiang

    2014-09-01

    Cystatins are tightly bound and reversible inhibitors of cysteine proteases in C1A and C13 peptidase families, which have been identified in several species and shown to function in vegetative development and response to biotic/abiotic stresses in plants. Recent work revealed their critical role in regulating programmed cell death during embryogenesis in tobacco and suggested their more comprehensive roles in the process of sexual plant reproduction, although little is known about cystatin family genes in the processes. Here, 10 cystatin family genes in Nicotiana tabacum were identified using an expressed sequence tag (EST)-based gene clone strategy. Analysis of their biochemical properties showed that nine of them have the potency to inhibit the activities of both commercial cathepsin L-like proteases and extracted cysteine proteases from seeds, but with different K i values depending on the types of proteases and the developmental stages of the seed tested. This suggests that cystatin-dependent cathepsin L-like proteolytic pathways are probably important for early seed development. Comprehensive expression profile analysis revealed that cystatin family genes showed manifold variations in their transcription levels in different plant cell types, including the sperm, egg, and zygote, especially in the embryo and seed at different developmental stages. More interestingly, intracellular localization analysis of each cystatin revealed that most members of cystatin families are recognized as secretory proteins with signal peptides that direct them to the endoplasmic reticulum. These results suggest their widespread roles in cell fate determination and cell-cell communication in the process of sexual reproduction, especially in gamete and embryo development, as well as in seed formation.

  20. Experimental burn plot trial in the Kruger National Park: history, experimental design and suggestions for data analysis

    Directory of Open Access Journals (Sweden)

    R. Biggs

    2003-12-01

    Full Text Available The experimental burn plot (EBP trial initiated in 1954 is one of few ongoing long-termfire ecology research projects in Africa. The trial aims to assess the impacts of differentfire regimes in the Kruger National Park. Recent studies on the EBPs have raised questions as to the experimental design of the trial, and the appropriate model specificationwhen analysing data. Archival documentation reveals that the original design was modified on several occasions, related to changes in the park's fire policy. These modifications include the addition of extra plots, subdivision of plots and changes in treatmentsover time, and have resulted in a design which is only partially randomised. The representativity of the trial plots has been questioned on account of their relatively small size,the concentration of herbivores on especially the frequently burnt plots, and soil variation between plots. It is suggested that these factors be included as covariates inexplanatory models or that certain plots be excluded from data analysis based on resultsof independent studies of these factors. Suggestions are provided for the specificationof the experimental design when analysing data using Analysis of Variance. It is concluded that there is no practical alternative to treating the trial as a fully randomisedcomplete block design.

  1. Depression-Burnout Overlap in Physicians.

    Directory of Open Access Journals (Sweden)

    Walter Wurm

    Full Text Available Whether burnout is a distinct phenomenon rather than a type of depression and whether it is a syndrome, limited to three "core" components (emotional exhaustion, depersonalization and low personal accomplishment are subjects of current debate. We investigated the depression-burnout overlap, and the pertinence of these three components in a large, representative sample of physicians.In a cross-sectional study, all Austrian physicians were invited to answer a questionnaire that included the Major Depression Inventory (MDI, the Hamburg Burnout Inventory (HBI, as well as demographic and job-related parameters. Of the 40093 physicians who received an invitation, a total of 6351 (15.8% participated. The data of 5897 participants were suitable for analysis.Of the participants, 10.3% were affected by major depression. Our study results suggest that potentially 50.7% of the participants were affected by symptoms of burnout. Compared to physicians unaffected by burnout, the odds ratio of suffering from major depression was 2.99 (95% CI 2.21-4.06 for physicians with mild, 10.14 (95% CI 7.58-13.59 for physicians with moderate, 46.84 (95% CI 35.25-62.24 for physicians with severe burnout and 92.78 (95% CI 62.96-136.74 for the 3% of participants with the highest HBI_sum (sum score of all ten HBI components. The HBI components Emotional Exhaustion, Personal Accomplishment and Detachment (representing depersonalization tend to correlate more highly with the main symptoms of major depression (sadness, lack of interest and lack of energy than with each other. A combination of the HBI components Emotional Exhaustion, Helplessness, Inner Void and Tedium (adj.R2 = 0.92 explained more HBI_sum variance than the three "core" components (adj.R2 = 0.85 of burnout combined. Cronbach's alpha for Emotional Exhaustion, Helplessness, Inner Void and Tedium combined was 0.90 compared to α = 0.54 for the combination of the three "core" components.This study demonstrates the

  2. Depression-Burnout Overlap in Physicians

    Science.gov (United States)

    Wurm, Walter; Vogel, Katrin; Holl, Anna; Ebner, Christoph; Bayer, Dietmar; Mörkl, Sabrina; Szilagyi, Istvan-Szilard; Hotter, Erich; Kapfhammer, Hans-Peter; Hofmann, Peter

    2016-01-01

    Background Whether burnout is a distinct phenomenon rather than a type of depression and whether it is a syndrome, limited to three “core” components (emotional exhaustion, depersonalization and low personal accomplishment) are subjects of current debate. We investigated the depression-burnout overlap, and the pertinence of these three components in a large, representative sample of physicians. Methods In a cross-sectional study, all Austrian physicians were invited to answer a questionnaire that included the Major Depression Inventory (MDI), the Hamburg Burnout Inventory (HBI), as well as demographic and job-related parameters. Of the 40093 physicians who received an invitation, a total of 6351 (15.8%) participated. The data of 5897 participants were suitable for analysis. Results Of the participants, 10.3% were affected by major depression. Our study results suggest that potentially 50.7% of the participants were affected by symptoms of burnout. Compared to physicians unaffected by burnout, the odds ratio of suffering from major depression was 2.99 (95% CI 2.21–4.06) for physicians with mild, 10.14 (95% CI 7.58–13.59) for physicians with moderate, 46.84 (95% CI 35.25–62.24) for physicians with severe burnout and 92.78 (95% CI 62.96–136.74) for the 3% of participants with the highest HBI_sum (sum score of all ten HBI components). The HBI components Emotional Exhaustion, Personal Accomplishment and Detachment (representing depersonalization) tend to correlate more highly with the main symptoms of major depression (sadness, lack of interest and lack of energy) than with each other. A combination of the HBI components Emotional Exhaustion, Helplessness, Inner Void and Tedium (adj.R2 = 0.92) explained more HBI_sum variance than the three “core” components (adj.R2 = 0.85) of burnout combined. Cronbach’s alpha for Emotional Exhaustion, Helplessness, Inner Void and Tedium combined was 0.90 compared to α = 0.54 for the combination of the three

  3. Seeding for pervasively overlapping communities

    CERN Document Server

    Lee, Conrad; McDaid, Aaron; Hurley, Neil

    2011-01-01

    In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms that are designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes increasingly important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.

  4. Seeding for pervasively overlapping communities

    Science.gov (United States)

    Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil

    2011-06-01

    In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms specifically designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes more important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.

  5. Burnout-depression overlap: a review.

    Science.gov (United States)

    Bianchi, Renzo; Schonfeld, Irvin Sam; Laurent, Eric

    2015-03-01

    Whether burnout is a form of depression or a distinct phenomenon is an object of controversy. The aim of the present article was to provide an up-to-date review of the literature dedicated to the question of burnout-depression overlap. A systematic literature search was carried out in PubMed, PsycINFO, and IngentaConnect. A total of 92 studies were identified as informing the issue of burnout-depression overlap. The current state of the art suggests that the distinction between burnout and depression is conceptually fragile. It is notably unclear how the state of burnout (i.e., the end stage of the burnout process) is conceived to differ from clinical depression. Empirically, evidence for the distinctiveness of the burnout phenomenon has been inconsistent, with the most recent studies casting doubt on that distinctiveness. The absence of consensual diagnostic criteria for burnout and burnout research's insufficient consideration of the heterogeneity of depressive disorders constitute major obstacles to the resolution of the raised issue. In conclusion, the epistemic status of the seminal, field-dominating definition of burnout is questioned. It is suggested that systematic clinical observation should be given a central place in future research on burnout-depression overlap.

  6. Genetic analysis of threatened Australian grayling Prototroctes maraena suggests recruitment to coastal rivers from an unstructured marine larval source population.

    Science.gov (United States)

    Schmidt, D J; Crook, D A; O'Connor, J P; Hughes, J M

    2011-01-01

    Population genetic variation of Australian grayling Prototroctes maraena was examined to determine whether the dispersal strategy of this amphidromous species favours retention of larvae and juveniles in close proximity to their natal river, or mixing of populations via marine dispersal. Variation in microsatellite and mitochondrial DNA markers was unstructured and differentiation was indistinguishable from zero across four coastal rivers spanning approximately one-quarter of the continental range of the species. This result indicates that the marine larval and juvenile phase probably facilitates extensive gene flow among coastal rivers and agrees with a previous analysis of otolith chemistry that suggested larvae probably move into the sea rather than remain in estuaries. It appears likely that the dispersal strategy of P. maraena would enable recolonization of rivers that experience localized extinction provided that connectivity between freshwater habitats and the sea is sufficient to permit migration and that enough source populations remain intact to support viability of the wider population.

  7. The manufacture and assessment of tissue microarrays: suggestions and criteria for analysis, with breast cancer as an example.

    Science.gov (United States)

    Pinder, Sarah E; Brown, John P; Gillett, Cheryl; Purdie, Colin A; Speirs, Valerie; Thompson, Alastair M; Shaaban, Abeer M

    2013-03-01

    Tissue microarray (TMA) is an established and valuable tool, particularly in translational research and clinical trials, allowing resource-efficient use, and high-throughput profiling, of large numbers of tumours. Despite this, there is little evidence, or guidance, on the optimum manufacture, use and assessment of TMAs. Here we review some of the literature, using breast cancer as an example, to highlight good practice and pitfalls in the design and manufacture of TMAs. Issues, such as the size, number, spacing and layout of cores, as well as the assessment and reporting of studies using TMAs are addressed. We make some suggestions regarding these challenges, and propose a checklist of features that should be considered in order to stimulate debate and improve the quality of data produced by TMA analysis. PMID:23087330

  8. Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns

    Directory of Open Access Journals (Sweden)

    Fischer Lukáš

    2007-11-01

    Full Text Available Abstract Background Plant hybrid proline-rich proteins (HyPRPs are putative cell wall proteins consisting, usually, of a repetitive proline-rich (PR N-terminal domain and a conserved eight-cysteine motif (8 CM C-terminal domain. Understanding the evolutionary dynamics of HyPRPs might provide not only insight into their so far elusive function, but also a model for other large protein families in plants. Results We have performed a phylogenetic analysis of HyPRPs from seven plant species, including representatives of gymnosperms and both monocot and dicot angiosperms. Every species studied possesses a large family of 14–52 HyPRPs. Angiosperm HyPRPs exhibit signs of recent major diversification involving, at least in Arabidopsis and rice, several independent tandem gene multiplications. A distinct subfamily of relatively well-conserved C-type HyPRPs, often with long hydrophobic PR domains, has been identified. In most of gymnosperm (pine HyPRPs, diversity appears within the C-type group while angiosperms have only a few of well-conserved C-type representatives. Atypical (glycine-rich or extremely short N-terminal domains apparently evolved independently in multiple lineages of the HyPRP family, possibly via inversion or loss of sequences encoding proline-rich domains. Expression profiles of potato and Arabidopsis HyPRP genes exhibit instances of both overlapping and complementary organ distribution. The diversified non-C-type HyPRP genes from recently amplified chromosomal clusters in Arabidopsis often share their specialized expression profiles. C-type genes have broader expression patterns in both species (potato and Arabidopsis, although orthologous genes exhibit some differences. Conclusion HyPRPs represent a dynamically evolving protein family apparently unique to seed plants. We suggest that ancestral HyPRPs with long proline-rich domains produced the current diversity through ongoing gene duplications accompanied by shortening

  9. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase

    Directory of Open Access Journals (Sweden)

    Dugas Sandra L

    2003-07-01

    Full Text Available Abstract Background The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects. Results Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the γ-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (γ-Proteobacteria possess similar plasmid-encoded arsC sequences. Conclusion The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

  10. THE STRATEGIC PLANNING (SWOT ANALYSIS OUTCOMES AND SUGGESTIONS ACCORDING TO THE STUDENTS AND THE LECTURERS WITHIN THE DISTANCE EDUCATION SYSTEM

    Directory of Open Access Journals (Sweden)

    Tugba Yanpar YELKEN

    2012-04-01

    Full Text Available In recent years, strategic planning has become one of the subjects that many institutions work on to ensure the intuitions’ appropriate management based on realistic results. Therefore, this planning has to be taken into account and should provide planning direction on the bases of its results. Basically, the manager of strategic planning, leadership and strategic thinking and to act to help planners designed the tools, processes and concepts is a group. At the same time, the organization of the development and effective strategies will help to place. The purpose of this research is to provide SWOT (Strengths, Weaknesses, Opportunities and Threats analysis and to present new suggestions based on the opinions of students in the distance education system. In this work, we have applied Survey Method. The study group has consisted of 70 students and 11 instructors of Mersin Vocational School of Higher Education (MVSHE. All the data was surveyed during the spring semester of 2009. In the development of the questionnaire, a relevant literature has been investigated. Also, expert opinion has also been provided for the survey materials and survey articles. The questionnaire is finalized according to the expert’s opinion. The questionnaire was applied in the internet environment to both the students and the instructors. The outcomes of the survey have been evaluated quantatively along the direction of the survey’s fundamental question: “What are your views on strategic planning (SWOT of distance education?” The suggestions have been made about the distance learning education based on the findings of the survey.

  11. Largescale Transcriptomics Analysis Suggests Over-Expression of BGH3, MMP9 and PDIA3 in Oral Squamous Cell Carcinoma.

    Science.gov (United States)

    He, Yuan; Shao, Fangyang; Pi, Weidong; Shi, Cong; Chen, Yujia; Gong, Diping; Wang, Bingjie; Cao, Zhiwei; Tang, Kailin

    2016-01-01

    Oral squamous cell carcinoma (OSCC) has been reported as the most prevalent cancer of the head and neck region, while early diagnosis remains challenging. Here we took a comprehensive bioinformatics study on microarray data of 326 OSCC clinical samples with control of 165 normal tissues. The cell interaction pathways of ECM-receptor interaction and focal adhesion were found to be significantly regulated in OSCC samples. Further analysis of the topological properties and expression consistency identified that three hub genes in the gene interaction network, MMP9, PDIA3 and BGH3, were consistently up-expressed in OSCC samples. When being validated on additional microarray datasets of 41 OSCC samples, the validation rate of over-expressed BGH3, MMP9, and PDIA3 reached 90%, 90% and 84% respectively. At last, immuno-histochemical assays were done to test the protein expression of the three genes on newly collected clinical samples of 35 OSCC, 20 samples of pre-OSCC stage, and 12 normal oral mucosa specimens. Their protein expression levels were also found to progressively increase from normal mucosa to pre-OSCC stage and further to OSCC (ANOVA p = 0.000), suggesting their key roles in OSCC pathogenesis. Based on above solid validation, we propose BGH3, MMP9 and PDIA3 might be further explored as potential biomarkers to aid OSCC diagnosis.

  12. Largescale Transcriptomics Analysis Suggests Over-Expression of BGH3, MMP9 and PDIA3 in Oral Squamous Cell Carcinoma.

    Directory of Open Access Journals (Sweden)

    Yuan He

    Full Text Available Oral squamous cell carcinoma (OSCC has been reported as the most prevalent cancer of the head and neck region, while early diagnosis remains challenging. Here we took a comprehensive bioinformatics study on microarray data of 326 OSCC clinical samples with control of 165 normal tissues. The cell interaction pathways of ECM-receptor interaction and focal adhesion were found to be significantly regulated in OSCC samples. Further analysis of the topological properties and expression consistency identified that three hub genes in the gene interaction network, MMP9, PDIA3 and BGH3, were consistently up-expressed in OSCC samples. When being validated on additional microarray datasets of 41 OSCC samples, the validation rate of over-expressed BGH3, MMP9, and PDIA3 reached 90%, 90% and 84% respectively. At last, immuno-histochemical assays were done to test the protein expression of the three genes on newly collected clinical samples of 35 OSCC, 20 samples of pre-OSCC stage, and 12 normal oral mucosa specimens. Their protein expression levels were also found to progressively increase from normal mucosa to pre-OSCC stage and further to OSCC (ANOVA p = 0.000, suggesting their key roles in OSCC pathogenesis. Based on above solid validation, we propose BGH3, MMP9 and PDIA3 might be further explored as potential biomarkers to aid OSCC diagnosis.

  13. Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon.

    Science.gov (United States)

    Sato, Jun J; Ohdachi, Satoshi D; Echenique-Diaz, Lazaro M; Borroto-Páez, Rafael; Begué-Quiala, Gerardo; Delgado-Labañino, Jorge L; Gámez-Díez, Jorgelino; Alvarez-Lemus, José; Nguyen, Son Truong; Yamaguchi, Nobuyuki; Kita, Masaki

    2016-01-01

    The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised. PMID:27498968

  14. Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).

    Science.gov (United States)

    Yang, Ji; Gu, Hongya; Yang, Ziheng

    2004-01-01

    Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (omega = d(N)/ d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication. PMID:14743314

  15. Overlapping communities reveal rich structure in large-scale brain networks during rest and task conditions.

    Science.gov (United States)

    Najafi, Mahshid; McMenamin, Brenton W; Simon, Jonathan Z; Pessoa, Luiz

    2016-07-15

    Large-scale analysis of functional MRI data has revealed that brain regions can be grouped into stable "networks" or communities. In many instances, the communities are characterized as relatively disjoint. Although recent work indicates that brain regions may participate in multiple communities (for example, hub regions), the extent of community overlap is poorly understood. To address these issues, here we investigated large-scale brain networks based on "rest" and task human functional MRI data by employing a mixed-membership Bayesian model that allows each brain region to belong to all communities simultaneously with varying membership strengths. The approach allowed us to 1) compare the structure of disjoint and overlapping communities; 2) determine the relationship between functional diversity (how diverse is a region's functional activation repertoire) and membership diversity (how diverse is a region's affiliation to communities); 3) characterize overlapping community structure; 4) characterize the degree of non-modularity in brain networks; 5) study the distribution of "bridges", including bottleneck and hub bridges. Our findings revealed the existence of dense community overlap that was not limited to "special" hubs. Furthermore, the findings revealed important differences between community organization during rest and during specific task states. Overall, we suggest that dense overlapping communities are well suited to capture the flexible and task dependent mapping between brain regions and their functions. PMID:27129758

  16. Separating cyclostationary signals from spectrally overlapping interference

    Institute of Scientific and Technical Information of China (English)

    GUO Jie; LIU Yun; YE Zhi-hui; SONG Tie-cheng; SHEN Lian-feng

    2006-01-01

    This paper studies an algorithm about separating spectmlly overlapping signals using the cyclostationary properties of signals.On the basis of direct sequence spread system (DSSS),frequency shift filter is added into the receiver of the communication system.Although the structure of frequency shift filter is more complicated than the time-domain filter,it uses both time correlations and frequency spectrum correlations so it can achieve better performances on separating the overlapping signals.After the analysis of cyclostationary characteristic and frequency spectrum correlation,the structure of the frequency shift filter can be gained.Then,a self-adaptive algorithm is utilized for the purpose of achieving optimum multidimensional tap weights of frequency shift components.The simulation results indicate that this method can efficiently separate overlapping signals,and its error rate is lower than the time-domain filter or DSSS system by two orders of magnitude on the condition that high-power interference is added into the system.

  17. Combining Density and Overlap (CoDO): A New Method for Assessing the Significance of Overlap Among Subgraphs

    CERN Document Server

    Magner, Abram; Grama, Ananth

    2016-01-01

    Algorithms for detecting clusters (including overlapping clusters) in graphs have received significant attention in the research community. A closely related important aspect of the problem -- quantification of statistical significance of overlap of clusters, remains relatively unexplored. This paper presents the first theoretical and practical results on quantifying statistically significant interactions between clusters in networks. Such problems commonly arise in diverse applications, ranging from social network analysis to systems biology. The paper addresses the problem of quantifying the statistical significance of the observed overlap of the two clusters in an Erd\\H{o}s-R\\'enyi graph model. The analytical framework presented in the paper assigns a $p$-value to overlapping subgraphs by combining information about both the sizes of the subgraphs and their edge densities in comparison to the corresponding values for their overlapping component. This $p$-value is demonstrated to have excellent discriminati...

  18. Structural analysis of the essential resuscitation promoting factor YeaZ suggests a mechanism of nucleotide regulation through dimer reorganization.

    Directory of Open Access Journals (Sweden)

    Inci Aydin

    Full Text Available BACKGROUND: The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC state. METHODOLOGY/PRINCIPAL FINDINGS: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the 'on' and 'off' states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD. CONCLUSIONS/SIGNIFICANCE: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD.

  19. Prevention of overlapping prescriptions of psychotropic drugs by community pharmacists.

    Science.gov (United States)

    Shimane, Takuya; Matsumoto, Toshihiko; Wada, Kiyoshi

    2012-10-01

    The nonmedical use or abuse of prescription drugs, including psychotropic medicines, is a growing health problem in Japan. Patient access to psychotropic drugs, specifically from the oversupply of medications due to overlapping prescriptions, may increase the risk of drug abuse and dependence. However, very little is known about such overlapping prescriptions. Today, the dispensing of prescriptions is generally moving from inside to outside of hospitals, with psychotropic drugs mainly dispensed at community pharmacies. In this study, we used health insurance claims (i.e., receipts) for dispensing as the main source of information in an investigation of overlapping prescriptions of psychotropic drugs. A total of 119 patients were found to have received overlapping prescriptions, as identified by community pharmacists who were members of the Saitama Pharmaceutical Association, using patient medication records, followed by medication counseling and prescription notes for the patient. According to our findings, the most frequently overlapping medication was etizolam. Etizolam can be prescribed for more than 30 days since it is not regulated under Japanese law as a "psychotropic drug." Generally, when a drug can be prescribed for a greater number of days, it increases the likelihood of an overlapping prescription during the same period. As a result, the long-term prescription of etizolam increases the risk of overlapping prescriptions. We also found that the patients who received overlapping prescriptions of etizolam were mostly elderly and the most common pattern was prescription from both internal medicine and orthopedics physicians. Etizolam has wide range of indications that are covered by health insurance. Our results suggest that patients who received overlapping prescriptions of etizolam may receive prescriptions from different prescribers for different purposes. Therefore, it may be appropriate to regulate etizolam as a "psychotropic drug" under Japanese law

  20. Biogeochemical analysis of ancient Pacific Cod bone suggests Hg bioaccumulation was linked to paleo sea level rise and climate change

    Directory of Open Access Journals (Sweden)

    Maribeth S. Murray

    2015-02-01

    Full Text Available Deglaciation at the end of the Pleistocene initiated major changes in ocean circulation and distribution. Within a brief geological time, large areas of land were inundated by sea-level rise and today global sea level is 120 m above its minimum stand during the last glacial maximum. This was the era of modern sea shelf formation; climate change caused coastal plain flooding and created broad continental shelves with innumerable consequences to marine and terrestrial ecosystems and human populations. In Alaska, the Bering Sea nearly doubled in size and stretches of coastline to the south were flooded, with regional variability in the timing and extent of submergence. Here we suggest how past climate change and coastal flooding are linked to mercury bioaccumulation that could have had profound impacts on past human populations and that, under conditions of continued climate warming, may have future impacts. Biogeochemical analysis of total mercury (tHg and 13C/15N ratios in the bone collagen of archaeologically recovered Pacific Cod (Gadus macrocephalus bone shows high levels of tHg during early/mid-Holocene. This pattern cannot be linked to anthropogenic activity or to food web trophic changes, but may result from natural phenomena such as increases in productivity, carbon supply and coastal flooding driven by glacial melting and sea-level rise. The coastal flooding could have led to increased methylation of Hg in newly submerged terrestrial land and vegetation. Methylmercury is bioaccumulated through aquatic food webs with attendant consequences for the health of fish and their consumers, including people. This is the first study of tHg levels in a marine species from the Gulf of Alaska to provide a time series spanning nearly the entire Holocene and we propose that past coastal flooding resulting from climate change had the potential to input significant quantities of Hg into marine food webs and subsequently to human consumers.

  1. Analysis of memory T lymphocyte activity following stimulation with overlapping HLA-A*2402, A*0101 and Cw*0402 restricted CMV pp65 peptides

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    Provenzano Maurizio

    2005-05-01

    Full Text Available Abstract The continuous efforts aimed at the identification of new immune epitopes across the MHC system has led to the discovery that more than one peptide may be restricted to the same HLA antigen and function as an immune determinant for that association. The aim of this study was to compare the ability of two overlapping peptides, the nonamer (9-mer cytomegalovirus (CMV pp65341–349 (QYDPVAALF and the decamer (10-mer CMV pp65341–350 (QYDPVAALFF, and the esadecamer (16-mer peptide containing both the 9-mer and 10-mer sequences, CMV pp65340–355 (RQYDPVAALFFFDIDL, to stimulate and maintain over time a T cell immune reactivation by HLA-A*2402, A*0101, and Cw*0402 cells from CMV-seropositive subjects. The 9-mer, 10-mer, and 16-mer peptides effectively stimulated CTLs from HLA-A*2402, HLA-A*0101, and HLA-Cw*0402 CMV seropositive donors. This data confirms that both the 9-mer and the 10-mer peptides are promiscuous and are not restricted to a single HLA antigen. CMV pp65341–349 and CMV pp65341–350 have the ability to produce CMV-specific CTLs in subjects with several different HLA types, presenting a practical advantage over other peptides that are restricted only to a single HLA antigen, and thus being optimal for CMV adoptive immune therapy. Moreover, since the 16-mer peptide encompasses both the 9-mer and 10-mer peptides, it may be better than either of these peptides for CMV adoptive immune therapy.

  2. Item Overlap Correlations: Definitions, Interpretations, and Implications.

    Science.gov (United States)

    Hsu, Louis M.

    1994-01-01

    Item overlap coefficient (IOC) formulas are discussed, providing six warnings about their calculation and interpretation and some explanations of why item overlap influences the Minnesota Multiphasic Personality Inventory and the Millon Clinical Multiaxial Inventory factor structures. (SLD)

  3. Bifurcation Analysis of an Existing Mathematical Model Reveals Novel Treatment Strategies and Suggests Potential Cure for Type 1 Diabetes

    DEFF Research Database (Denmark)

    Nielsen, Kenneth Hagde Mandrup; Ottesen, Johnny T.; Pociot, Flemming

    2014-01-01

    Type 1 diabetes is a disease with serious personal and socioeconomic consequences that has attracted the attention of modellers recently. But as models of this disease tend to be complicated, there has been only limited mathematical analysis to date. Here we address this problem by providing a...... bifurcation analysis of a previously published mathematical model for the early stages of type 1 diabetes in diabetes-prone NOD mice, which is based on the data available in the literature. We also show positivity and the existence of a family of attracting trapping regions in the positive 5D cone, converging...

  4. Bifurcation Analysis of an Existing Mathematical Model Reveals Novel Treatment Strategies and Suggests Potential Cure for Type 1 Diabetes

    DEFF Research Database (Denmark)

    Nielsen, Kenneth Hagde Mandrup; Ottesen, Johnny T.; Pociot, Flemming

    2014-01-01

    Type 1 diabetes is a disease with serious personal and socioeconomic consequences that has attracted the attention of modellers recently. But as models of this disease tend to be complicated, there has been only limited mathematical analysis to date. Here we address this problem by providing...... a bifurcation analysis of a previously published mathematical model for the early stages of type 1 diabetes in diabetes-prone NOD mice, which is based on the data available in the literature. We also show positivity and the existence of a family of attracting trapping regions in the positive 5D cone, converging...

  5. Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes.

    Directory of Open Access Journals (Sweden)

    Christopher T Brown

    Full Text Available Recent studies have suggested a bacterial role in the development of autoimmune disorders including type 1 diabetes (T1D. Over 30 billion nucleotide bases of Illumina shotgun metagenomic data were analyzed from stool samples collected from four pairs of matched T1D case-control subjects collected at the time of the development of T1D associated autoimmunity (i.e., autoantibodies. From these, approximately one million open reading frames were predicted and compared to the SEED protein database. Of the 3,849 functions identified in these samples, 144 and 797 were statistically more prevalent in cases and controls, respectively. Genes involved in carbohydrate metabolism, adhesions, motility, phages, prophages, sulfur metabolism, and stress responses were more abundant in cases while genes with roles in DNA and protein metabolism, aerobic respiration, and amino acid synthesis were more common in controls. These data suggest that increased adhesion and flagella synthesis in autoimmune subjects may be involved in triggering a T1D associated autoimmune response. Extensive differences in metabolic potential indicate that autoimmune subjects have a functionally aberrant microbiome. Mining 16S rRNA data from these datasets showed a higher proportion of butyrate-producing and mucin-degrading bacteria in controls compared to cases, while those bacteria that produce short chain fatty acids other than butyrate were higher in cases. Thus, a key rate-limiting step in butyrate synthesis is more abundant in controls. These data suggest that a consortium of lactate- and butyrate-producing bacteria in a healthy gut induce a sufficient amount of mucin synthesis to maintain gut integrity. In contrast, non-butyrate-producing lactate-utilizing bacteria prevent optimal mucin synthesis, as identified in autoimmune subjects.

  6. Coupling otolith microstructure analysis and hydrographic backtracking suggests a mechanism for the 2000s North Sea herring recruitment failure

    DEFF Research Database (Denmark)

    Ross, Stine Dalmann; Payne, Mark; Worsøe Clausen, Lotte;

    2012-01-01

    .g. average temperature experienced, time available for feeding and spawning origin) to reconstruct the recent history of the larvae. A mixed‐modelling approach was then employed to analyse the combined data: after correcting for the effect of the other variables, a significant reduction in larval growth rate......, associated with the onset of the reduced recruitment, was identified. These results suggest that the reduced recruitment is associated with a reduction in the growth rate of the larval survivors, most probably through changes in either the amount or quality of the available food. Furthermore, this study...

  7. Toxicogenomic Analysis Suggests Chemical-Induced Sexual Dimorphism in the Expression of Metabolic Genes in Zebrafish Liver

    OpenAIRE

    Xun Zhang; Choong Yong Ung; Siew Hong Lam; Jing Ma; Yu Zong Chen; Louxin Zhang; Zhiyuan Gong; Baowen Li

    2012-01-01

    Differential gene expression in two sexes is widespread throughout the animal kingdom, giving rise to sex-dimorphic gene activities and sex-dependent adaptability to environmental cues, diets, growth and development as well as susceptibility to diseases. Here, we present a study using a toxicogenomic approach to investigate metabolic genes that show sex-dimorphic expression in the zebrafish liver triggered by several chemicals. Our analysis revealed that, besides the known genes for xenobioti...

  8. Diffuse interstitial lung disease: overlaps and uncertainties

    Energy Technology Data Exchange (ETDEWEB)

    Walsh, Simon L.F.; Hansell, David M. [Royal Brompton Hospital, Department of Radiology, London (United Kingdom)

    2010-08-15

    Histopathological analysis of lung biopsy material allows the diagnosis of idiopathic interstitial pneumonias; however, the strength of this diagnosis is sometimes subverted by interobserver variation and sampling. The American Thoracic Society and European Respiratory Society recommendations of 2002 provide a framework for the diagnosis of interstitial lung disease (ILD) and proposed an integrated clinical, radiological and histopathological approach. These recommendations represent a break with tradition by replacing the 'gold standard' of histopathology with the combined 'silver standards' of clinical, imaging and histopathological information. One of the pitfalls of a rigid classification system for the diagnosis of interstitial lung disease is its failure to accommodate the phenomenon of overlapping disease patterns. This article reviews the various ways that interstitial lung disease may be classified and discusses their applicability. In addition the issue of overlap disease patterns is considered in the context of histopathological interobserver variation and sampling error and how a pigeonhole approach to disease classification may overlook these hybrid entities. (orig.)

  9. Unusual flux-distance relationship for pulsars suggested by analysis of the Australia national telescopy facility pulsar catalogue

    Energy Technology Data Exchange (ETDEWEB)

    Singleton, John [Los Alamos National Laboratory; Perez, M R [Los Alamos National Laboratory; Singleton, J [Los Alamos National Laboratory; Ardavan, H [UNIV OF CAMBRIDGE; Ardavan, A [UNIV OF OXFORD

    2009-01-01

    We analyze pulsar fluxes at 1400 MHz (S(1400)) and distances d taken from the Australia National Telescope Facility (ATNF) Pulsar Catalogue. Under the assumption that pulsar populations in different parts of the Galaxy are similar, we find that either (a) pulsar fluxes diminish with distance according to a non-standard power law (we suggest S(1400){proportional_to} 1/d rather than {proportional_to} 1/d{sup 2}) or (b) that there are very significant (i.e. order of magnitude) errors in the distance estimates quoted in the ATNF Catalogue. The former conclusion (a) supports a recent model for pulsar emission that has also successfully explained the frequency spectrum of the Crab pulsar over 16 orders of magnitude of frequency, whilst alternative (b) would necessitate a radical re-evaluation of both the dispersion method for estimating pulsar distances and current ideas about the distribution of pulsars within our Galaxy.

  10. Three-Dimensional Analysis of Budding Sites and Released Virus Suggests a Revised Model for HIV-1 Morphogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Carlson, L.; Simon, M.; Briggs, J. A. G.; Glass, B.; Riches, J. D.; Johnson, M. C.; Muller, B.; Grunewald, K.; Krausslich, H.-G.

    2008-12-11

    Current models of HIV-1 morphogenesis hold that newly synthesized viral Gag polyproteins traffic to and assemble at the cell membrane into spherical protein shells. The resulting late-budding structure is thought to be released by the cellular ESCRT machinery severing the membrane tether connecting it to the producer cell. Using electron tomography and scanning transmission electron microscopy, we find that virions have a morphology and composition distinct from late-budding sites. Gag is arranged as a continuous but incomplete sphere in the released virion. In contrast, late-budding sites lacking functional ESCRT exhibited a nearly closed Gag sphere. The results lead us to propose that budding is initiated by Gag assembly, but is completed in an ESCRT-dependent manner before the Gag sphere is complete. This suggests that ESCRT functions early in HIV-1 release - akin to its role in vesicle formation - and is not restricted to severing the thin membrane tether.

  11. Choosing optimal exposure times for XRF core-scanning: Suggestions based on the analysis of geological reference materials

    Science.gov (United States)

    Huang, Jyh-Jaan; Löwemark, Ludvig; Chang, Queenie; Lin, Tzu-Yu; Chen, Huei-Fen; Song, Sheng-Rong; Wei, Kuo-Yen

    2016-04-01

    X-ray fluorescence (XRF) core-scanning is a fast and nondestructive technique to assess elemental variations of unprocessed sediments. However, although the exposure time of XRF-scanning directly affects the scanning counts and total measurement time, only a few studies have considered the influence of exposure time during the scan. How to select an optimal exposure time to achieve reliable results and reduce the total measurement time is an important issue. To address this question, six geological reference materials from the Geological Survey of Japan (JLK-1, JMS-1, JMS-2, JSD-1, JSD-2, and JSD-3) were scanned by the Itrax-XRF core scanner using the Mo- and the Cr-tube with different exposure times to allow a comparison of scanning counts with absolute concentrations. The regression lines and correlation coefficients of elements that are generally used in paleoenvironmental studies were examined for the different exposure times and X-ray tubes. The results show that for those elements with relatively high concentrations or high detectability, the correlation coefficients are higher than 0.90 for all exposure times. In contrast, for the low detectability or low concentration elements, the correlation coefficients are relatively low, and improve little with increased exposure time. Therefore, we suggest that the influence of different exposure times is insignificant for the accuracy of the measurements. Thus, caution must be taken when interpreting the results of elements with low detectability, even when the exposure times are long and scanning counts are reasonably high.

  12. Transcriptome analysis suggests that starch synthesis may proceed via multiple metabolic routes in high yielding potato cultivars.

    Directory of Open Access Journals (Sweden)

    Kacper Piotr Kaminski

    Full Text Available BACKGROUND: Glucose-6-phosphate is imported into the amyloplast of potato tubers and thought to constitute the precursor for starch synthesis in potato tubers. However, recently it was shown that glucose-1-phosphate can also be imported into the amyloplast and incorporated into starch via an ATP independent mechanism under special conditions. Nonetheless, glucose-6-phosphate is believed to be the quantitatively important precursor for starch synthesis in potato. PRINCIPAL FINDING: Potato tubers of the high yielding cv Kuras had low gene expression of plastidial phophoglucomutase (PGM and normal levels of transcripts for other enzymes involved in starch metabolism in comparison with medium and low yielding cultivars as determined by DeepSAGE transcriptome profiling. The decrease in PGM activity in Kuras was confirmed by measuring the enzyme activity from potato tuber extracts. Contrary to expectations, this combination lead to a higher level of intracellular glucose-1-phosphate (G1P in Kuras suggesting that G1P is directly imported into plastids and can be quantitatively important for starch synthesis under normal conditions in high yielding cultivars. SIGNIFICANCE: This could open entirely new possibilities for metabolic engineering of the starch metabolism in potato via the so far uncharacterized G1P transporter. The perspectives are to increase yield and space efficiency of this important crop. In the light of the increasing demands imposed on agriculture to support a growing global population this presents an exciting new possibility.

  13. Analysis of C3 suggests three periods of positive selection events and different evolutionary patterns between fish and mammals.

    Directory of Open Access Journals (Sweden)

    Fanxing Meng

    Full Text Available BACKGROUND: The third complement component (C3 is a central protein of the complement system conserved from fish to mammals. It also showed distinct characteristics in different animal groups. Striking features of the fish complement system were unveiled, including prominent levels of extrahepatic expression and isotypic diversity of the complement components. The evidences of the involvement of complement system in the enhancement of B and T cell responses found in mammals indicated that the complement system also serves as a bridge between the innate and adaptive responses. For the reasons mentioned above, it is interesting to explore the evolutionary process of C3 genes and to investigate whether the huge differences between aquatic and terrestrial environments affected the C3 evolution between fish and mammals. METHODOLOGY/PRINCIPAL FINDINGS: Analysis revealed that these two groups of animals had experienced different evolution patterns. The mammalian C3 genes were under purifying selection pressure while the positive selection pressure was detected in fish C3 genes. Three periods of positive selection events of C3 genes were also detected. Two happened on the ancestral lineages to all vertebrates and mammals, respectively, one happened on early period of fish evolutionary history. CONCLUSIONS/SIGNIFICANCE: Three periods of positive selection events had happened on C3 genes during history and the fish and mammals C3 genes experience different evolutionary patterns for their distinct living environments.

  14. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Directory of Open Access Journals (Sweden)

    Guido Valverde

    Full Text Available The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD, Wari (Middle Horizon, 800-1000 AD and Ychsma (Late Intermediate Period, 1000-1450 AD. We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  15. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Science.gov (United States)

    Valverde, Guido; Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars; Llamas, Bastien; Haak, Wolfgang

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD), Wari (Middle Horizon, 800-1000 AD) and Ychsma (Late Intermediate Period, 1000-1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast. PMID:27248693

  16. Analysis of gene expression profile of TPM3-ALK positive anaplastic large cell lymphoma reveals overlapping and unique patterns with that of NPM-ALK positive anaplastic large cell lymphoma.

    Science.gov (United States)

    Bohling, Sandra D; Jenson, Stephen D; Crockett, David K; Schumacher, Jonathan A; Elenitoba-Johnson, Kojo S J; Lim, Megan S

    2008-03-01

    Anaplastic large cell lymphoma (ALCL) comprises a group of non-Hodgkin lymphomas characterized by the expression of the CD30/Ki-1 antigen. A subset of ALCL is characterized by chromosomal translocations involving the anaplastic lymphoma kinase (ALK) gene on chromosome 2. While the most common translocation is the t(2;5)(p23;q35) involving the nucleophosmin (NPM) gene on chromosome 5, up to 12 other translocations partners of the ALK gene have been identified. One of these is the t(1;2)(q25;p23) which results in the formation of the chimeric protein TPM3-ALK. While several of the signaling pathways induced by NPM-ALK have been elucidated, those involved in ALCLs harboring TPM3-ALK are largely unknown. In order to investigate the expression profiles of ALCLs carrying the NPM-ALK and TPM3-ALK fusions, we carried out cDNA microarray analysis of two ALCL tissue samples, one expressing the NPM-ALK fusion protein and the other the TPM3-ALK fusion protein. RNA was extracted from snap-frozen tissues, labeled with fluorescent dyes and analyzed using cDNAs microarray containing approximately 9,200 genes and expressed sequence tags (ESTs). Quantitative fluorescence RT-PCR was performed to validate the cDNA microarray data on nine selected gene targets. Our results show a significant overlap of genes deregulated in the NPM-ALK and TPM-ALK positive lymphomas. These deregulated genes are involved in diverse cellular functions, such as cell cycle regulation, apoptosis, proliferation, and adhesion. Interestingly, a subset of the genes was distinct in their expression pattern in the two types of lymphomas. More importantly, many genes that were not previously associated with ALK positive lymphomas were identified. Our results demonstrate the overlapping and unique transcriptional patterns associated with the NPM-ALK and TPM3-ALK fusions in ALCL.

  17. Transcriptome analysis and RNA interference of cockroach phototransduction indicate three opsins and suggest a major role for TRPL channels

    Directory of Open Access Journals (Sweden)

    Andrew S French

    2015-07-01

    Full Text Available Our current understanding of insect phototransduction is based on a small number of species, but insects occupy many different visual environments. We created the retinal transcriptome of a nocturnal insect, the cockroach, Periplaneta americana to identify proteins involved in the earliest stages of compound eye phototransduction, and test the hypothesis that different visual environments are reflected in different molecular contributions to function. We assembled five novel mRNAs: two green opsins, one UV opsin, and one each TRP and TRPL ion channel homologs. One green opsin mRNA (pGO1 was 100-1000 times more abundant than the other opsins (pGO2 and pUVO, while pTRPL mRNA was 10 times more abundant than pTRP, estimated by transcriptome analysis or quantitative PCR (qPCR. Electroretinograms were used to record photoreceptor responses. Gene-specific in vivo RNA interference (RNAi was achieved by injecting long (596-708 bp double-stranded RNA into head hemolymph, and verified by qPCR. RNAi of the most abundant green opsin reduced both green opsins by more than 97% without affecting UV opsin, and gave a maximal reduction of 75% in ERG amplitude seven days after injection that persisted for at least 19 days. RNAi of pTRP and pTRPL genes each specifically reduced the corresponding mRNA by 90%. Electroretinogram reduction by pTRPL RNAi was slower than for opsin, reaching 75% attenuation by 21 days, without recovery at 29 days. pTRP RNAi attenuated ERG much less; only 30% after 21 days. Combined pTRP plus pTRPL RNAi gave only weak evidence of any cooperative interactions. We conclude that silencing retinal genes by in vivo RNAi using long dsRNA is effective, that visible light transduction in Periplaneta is dominated by pGO1, and that pTRPL plays a major role in cockroach phototransduction.

  18. Overlapped frequency-time division multiplexing

    Institute of Scientific and Technical Information of China (English)

    JIANG Hui; LI Dao-ben

    2009-01-01

    A technique named overlapped frequency-time division multiplexing (OVFTDM)) is proposed in this article. The technique is derived from Nyquist system and frequency-time division multiplexing system. When the signals are compactly overlapped without the orthogonality in time domain, the technique is named overlapped time division multiplexing (OVTDM), whereas when signals are compactly overlapped without the orthogonality in frequency domain, the technique is called overlapped frequency division multiplexing (OVFDM). To further improve spectral efficiency, the OVFTDM in which signals are overlapped both in frequency domain and in time domain is explored. OVFTDM does not depend on orthogonality whatever in time domain or in frequency domain like Nyquist system or OFDM system, but on the convolutional constraint relationship among signals. Therefore, not only the spectral efficiency but also the reliability is improved. The simulations verify the validity of this theory.

  19. LLVM-based overlapped executable code generator

    OpenAIRE

    V. Aranov; A. Terentiev

    2014-01-01

    Overlapped executable code is an attractive artifact of obfuscation technology not yet widely covered and researched. Overlapped code and opaque predicates technologies together allows creation of prominent software obfuscation technologies featuring both obscure executable code and code protected from patching due to hard-to-track relations with other code. The paper provides polynomial algorithm to generate overlapped executable code using LLVM framework and discuss results of the generatio...

  20. Correlated Edge Overlaps in Multiplex Networks

    CERN Document Server

    Baxter, Gareth J; da Costa, Rui A; Dorogovtsev, Sergey N; Mendes, José F F

    2016-01-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local tree-likeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and non-overlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions.

  1. Overlap syndromes among autoimmune liver diseases

    Institute of Scientific and Technical Information of China (English)

    Christian Rust; Ulrich Beuers

    2008-01-01

    The three major immune disorders of the liver are autoimmune hepatitis (AIH),primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC).Variant forms of these diseases are generally called overlap syndromes,although there has been no standardised definition.Patients with overlap syndromes present with both hepatitic and cholestatic serum liver tests and have histological features of AIH and PBC or PSC.The AIH-PBC overlap syndrome is the most common form,affecting almost 10% of adults with AIH or PBC.Single cases of AIH and autoimmune cholangitis (AMA-negative PBC) overlap syndrome have also been reported.The AIH-PSC overlap syndrome is predominantly found in children,adolescents and young adults with AIH or PSC.Interestingly,transitions from one autoimmune to another have also been reported in a minority of patients,especially transitions from PBC to AIH-PBC overlap syndrome.Overlap syndromes show a progressive course towards liver cirrhosis and liver failure without treatment.Therapy for overlap syndromes is empiric,since controlled trials are not available in these rare disorders.Anticholestatic therapy with ursodeoxycholic acid is usually combined with immunosuppressive therapy with corticosteroids and/or azathioprine in both AIH-PBC and AIH-PSC overlap syndromes.In end-stage disease,liver transplantation is the treatment of choice.

  2. The Entropy of an Overlapping Dynamical System

    CERN Document Server

    Barnsley, Michael F; Vince, Andrew

    2011-01-01

    The term "overlapping" refers to a certain fairly simple type of piecewise continuous function from the unit interval to itself and also to a fairly simple type of iterated function system (IFS) on the unit interval. A correspondence between these two classes of objects is used (1) to find a necessary and sufficient condition for a fractal transformation from the attractor of one overlapping IFS to the attractor of another overlapping IFS to be a homeomorphism and (2) to find a formula for the topological entropy of the dynamical system associated with an overlapping function.

  3. Peer Network Overlap in Twin, Sibling, and Friend Dyads

    Science.gov (United States)

    McGuire, Shirley; Segal, Nancy L.

    2013-01-01

    Research suggests that sibling–peer connections are important for understanding adolescent problem behaviors. Using a novel behavioral genetic design, the current study investigated peer network overlap in 300 child–child pairs (aged 7-13 years) in 5 dyad types: monozygotic (MZ), dizygotic twins, full siblings (FSs), friend pairs, and virtual…

  4. Market positioning: the shifting effects of niche overlap

    NARCIS (Netherlands)

    J. Bruggeman; D. Grunow; M.A.A.M. Leenders; I. Vermeulen; J.G. Kuilman

    2012-01-01

    Organizational ecology models of market dynamics emphasize the competition-inducing role of inter-organizational niche overlap—targeting similar market niches increases competitive pressure and thus reduces organizations’ fitness. Recent studies, however, have suggested that moderate niche overlap m

  5. Interaction of spatially overlapping standing electromagnetic solitons in plasmas

    International Nuclear Information System (INIS)

    Numerical investigations on mutual interactions between two spatially overlapping standing electromagnetic solitons in a cold unmagnetized plasma are reported. It is found that an initial state comprising of two overlapping standing solitons evolves into different end states, depending on the amplitudes of the two solitons and the phase difference between them. For small amplitude solitons with zero phase difference, we observe the formation of an oscillating bound state whose period depends on their initial separation. These results suggest the existence of a bound state made of two solitons in the relativistic cold plasma fluid model.

  6. A global survey of aerosol-liquid water cloud overlap based on four years of CALIPSO-CALIOP data

    Directory of Open Access Journals (Sweden)

    A. Devasthale

    2010-09-01

    Full Text Available The presence of aerosols over highly reflective liquid water cloud tops poses a big challenge in simulating their radiative impacts. Particularly, absorbing aerosols, such as smoke, may have significant impact in such situations and even change the sign of net radiative forcing. Until now, it was not possible to obtain information on such overlap events realistically from the existing passive satellite sensors. However, the CALIOP instrument onboard NASA's CALIPSO satellite allows us to examine these events with an unprecedented accuracy.

    Using four years of collocated CALIPSO 5 km Aerosol and Cloud Layer Version 3 Products (June 2006–May 2010, we quantify, for the first time, the macrophysical characteristics of overlapping aerosol and water cloud layers globally. We investigate seasonal variability in these characteristics over six latitude bands to understand the hemispheric differences. We compute a the percentage cases when such overlap is seen globally and seasonally when all aerosol types are included (AAO case in the analysis, b the joint histograms of aerosol layer base height and cloud layer top height, and c the joint histograms of aerosol and cloud geometrical thicknesses in such overlap cases. We also investigate frequency of smoke aerosol-cloud overlap (SAO case.

    The results show a distinct seasonality in overlap frequency in both AAO and SAO cases. Globally, the frequency is highest during JJA months in AAO case, while for the SAO case, it is highest in SON months. The seasonal mean overlap frequency can regionally exceed 20% in AAO case and 10% in SAO case. There is a tendency that the vertical separation between aerosol and cloud layers increases from high to low latitude regions in the both hemispheres. In about 5–10% cases the vertical distance between aerosol and cloud layers is less than 100 m, while about in 45–60% cases it less than a kilometer in the annual means for different latitudinal bands

  7. Presentation of dynamically overlapping auditory messages in user interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Papp, A.L.

    1997-09-01

    This dissertation describes a methodology and example implementation for the dynamic regulation of temporally overlapping auditory messages in computer-user interfaces. The regulation mechanism exists to schedule numerous overlapping auditory messages in such a way that each individual message remains perceptually distinct from all others. The method is based on the research conducted in the area of auditory scene analysis. While numerous applications have been engineered to present the user with temporally overlapped auditory output, they have generally been designed without any structured method of controlling the perceptual aspects of the sound. The method of scheduling temporally overlapping sounds has been extended to function in an environment where numerous applications can present sound independently of each other. The Centralized Audio Presentation System is a global regulation mechanism that controls all audio output requests made from all currently running applications. The notion of multimodal objects is explored in this system as well. Each audio request that represents a particular message can include numerous auditory representations, such as musical motives and voice. The Presentation System scheduling algorithm selects the best representation according to the current global auditory system state, and presents it to the user within the request constraints of priority and maximum acceptable latency. The perceptual conflicts between temporally overlapping audio messages are examined in depth through the Computational Auditory Scene Synthesizer. At the heart of this system is a heuristic-based auditory scene synthesis scheduling method. Different schedules of overlapped sounds are evaluated and assigned penalty scores. High scores represent presentations that include perceptual conflicts between over-lapping sounds. Low scores indicate fewer and less serious conflicts. A user study was conducted to validate that the perceptual difficulties predicted by

  8. Climate-induced range overlap among closely related species

    Science.gov (United States)

    Krosby, Meade; Wilsey, Chad B.; McGuire, Jenny L.; Duggan, Jennifer M.; Nogeire, Theresa M.; Heinrichs, Julie A.; Tewksbury, Joshua J.; Lawler, Joshua J.

    2015-09-01

    Contemporary climate change is causing large shifts in biotic distributions, which has the potential to bring previously isolated, closely related species into contact. This has led to concern that hybridization and competition could threaten species persistence. Here, we use bioclimatic models to show that future range overlap by the end of the century is predicted for only 6.4% of isolated, congeneric species pairs of New World birds, mammals and amphibians. Projected rates of climate-induced overlap are higher for birds (11.6%) than for mammals (4.4%) or amphibians (3.6%). As many species will have difficulty tracking shifting climates, actual rates of future overlap are likely to be far lower, suggesting that hybridization and competition impacts may be relatively modest.

  9. Overlap between empathy, teamwork and integrative approach to patient care.

    Science.gov (United States)

    Hojat, Mohammadreza; Bianco, Joseph A; Mann, Douglas; Massello, David; Calabrese, Leonard H

    2014-10-14

    Abstract Background: Empathy, teamwork and an integrative approach to patient care share common denominators such as interpersonal skills and understanding patients' concerns. Thus, a significant overlap among measures of empathy, teamwork and integrative approach to patient care is expected. Aim: This study examined the magnitude of overlap (shared variance) among three measures of empathy, teamwork and an integrative approach to patient care. Methods: Three-hundred seventy-three medical students completed the Jefferson Scale of Empathy (JSE), the Jefferson Scale of Attitudes toward Physician-Nurse Collaboration (JSAPNC) and Integrative Patient Care (IPC). Results: Significant overlaps were found among the three measures (p teamwork and IPC support the common denominator assumption. The findings that IPC shares common variance with empathy and teamwork have implications for medical education curriculum, suggesting that implementation of integrative patient care can improve empathic engagement in patient care and orientation toward teamwork.

  10. DIMENSIONS OF SELF-AFFINESETS WITH OVERLAPS

    Institute of Scientific and Technical Information of China (English)

    华苏

    2003-01-01

    The authors develop an algorithm to show that a class of self-affine sets with overlaps canbe viewed as sofic affine-invariant sets without overlaps, thus by using the results of [11] and[10], the Hausdorff and Minkowski dimensions are determined.

  11. Hypnosis, suggestion, and suggestibility: an integrative model.

    Science.gov (United States)

    Lynn, Steven Jay; Laurence, Jean-Roch; Kirsch, Irving

    2015-01-01

    This article elucidates an integrative model of hypnosis that integrates social, cultural, cognitive, and neurophysiological variables at play both in and out of hypnosis and considers their dynamic interaction as determinants of the multifaceted experience of hypnosis. The roles of these variables are examined in the induction and suggestion stages of hypnosis, including how they are related to the experience of involuntariness, one of the hallmarks of hypnosis. It is suggested that studies of the modification of hypnotic suggestibility; cognitive flexibility; response sets and expectancies; the default-mode network; and the search for the neurophysiological correlates of hypnosis, more broadly, in conjunction with research on social psychological variables, hold much promise to further understanding of hypnosis.

  12. GEOMETRIC QUALITY ASSESSMENT OF LIDAR DATA BASED ON SWATH OVERLAP

    Directory of Open Access Journals (Sweden)

    A. Sampath

    2016-06-01

    degrees of slope It is suggested that 4000-5000 points are uniformly sampled in the overlapping regions of the point cloud, and depending on the surface roughness, to measure the discrepancy between swaths. Care must be taken to sample only areas of single return points only. Point-to-Plane distance based data quality measures are determined for each sample point. These measurements are used to determine the above mentioned parameters. This paper details the measurements and analysis of measurements required to determine these metrics, i.e. Discrepancy Angle, Mean and RMSD of errors in flat regions and horizontal errors obtained using measurements extracted from sloping regions (slope greater than 10 degrees. The research is a result of an ad-hoc joint working group of the US Geological Survey and the American Society for Photogrammetry and Remote Sensing (ASPRS Airborne Lidar Committee.

  13. Geometric Quality Assessment of LIDAR Data Based on Swath Overlap

    Science.gov (United States)

    Sampath, A.; Heidemann, H. K.; Stensaas, G. L.

    2016-06-01

    ) It is suggested that 4000-5000 points are uniformly sampled in the overlapping regions of the point cloud, and depending on the surface roughness, to measure the discrepancy between swaths. Care must be taken to sample only areas of single return points only. Point-to-Plane distance based data quality measures are determined for each sample point. These measurements are used to determine the above mentioned parameters. This paper details the measurements and analysis of measurements required to determine these metrics, i.e. Discrepancy Angle, Mean and RMSD of errors in flat regions and horizontal errors obtained using measurements extracted from sloping regions (slope greater than 10 degrees). The research is a result of an ad-hoc joint working group of the US Geological Survey and the American Society for Photogrammetry and Remote Sensing (ASPRS) Airborne Lidar Committee.

  14. Bayesian Overlapping Community Detection in Dynamic Networks

    CERN Document Server

    Ghorbani, Mahsa; Khodadadi, Ali

    2016-01-01

    Detecting community structures in social networks has gained considerable attention in recent years. However, lack of prior knowledge about the number of communities, and their overlapping nature have made community detection a challenging problem. Moreover, many of the existing methods only consider static networks, while most of real world networks are dynamic and evolve over time. Hence, finding consistent overlapping communities in dynamic networks without any prior knowledge about the number of communities is still an interesting open research problem. In this paper, we present an overlapping community detection method for dynamic networks called Dynamic Bayesian Overlapping Community Detector (DBOCD). DBOCD assumes that in every snapshot of network, overlapping parts of communities are dense areas and utilizes link communities instead of common node communities. Using Recurrent Chinese Restaurant Process and community structure of the network in the last snapshot, DBOCD simultaneously extracts the numbe...

  15. Motor Protein Accumulation on Antiparallel Microtubule Overlaps.

    Science.gov (United States)

    Kuan, Hui-Shun; Betterton, Meredith D

    2016-05-10

    Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. Overlap motor density profiles and motor trajectories resemble experimental measurements. The phase diagram of the model is similar to the single-filament case for low switching rate, while for high switching rate we find a new (to our knowledge) low density-high density-low density-high density phase. The overlap center region, far from the overlap ends, has a constant motor density as one would naïvely expect. However, rather than following a simple binding equilibrium, the center motor density depends on total overlap length, motor speed, and motor switching rate. The size of the crowded boundary layer near the overlap ends is also dependent on the overlap length and switching rate in addition to the motor speed and bulk concentration. The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity. PMID:27166811

  16. Motor Protein Accumulation on Antiparallel Microtubule Overlaps

    Science.gov (United States)

    Kuan, Hui-Shun; Betterton, Meredith D.

    2016-05-01

    Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process (TASEP) for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. Overlap motor density profiles and motor trajectories resemble experimental measurements. The phase diagram of the model is similar to the single-filament case for low switching rate, while for high switching rate we find a new low density-high density-low density-high density phase. The overlap center region, far from the overlap ends, has a constant motor density as one would naively expect. However, rather than following a simple binding equilibrium, the center motor density depends on total overlap length, motor speed, and motor switching rate. The size of the crowded boundary layer near the overlap ends is also dependent on the overlap length and switching rate in addition to the motor speed and bulk concentration. The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity.

  17. Riflessioni e Proposte sulle Unita' di Analisi per l'Analisi del Discorso (Didattico) (Reflections and Suggestions Concerning the Units of Analysis for Discourse Analysis).

    Science.gov (United States)

    Landolfi, Liliana

    1995-01-01

    After reviewing units of discourse analysis generally used by sociolinguists, this article reports on a study conducted in university English-as-a-Second-Language classes in Los Angeles to show differences between interactions in and outside of class and proposes a broader frame of analysis to include both the turn and the exchange systems. (CFM)

  18. Conceptual overlap between moral norms and anticipated regret in the prediction of intention: implications for theory of planned behaviour research.

    Science.gov (United States)

    Newton, Joshua D; Newton, Fiona J; Ewing, Michael T; Burney, Sue; Hay, Margaret

    2013-01-01

    Moral norms and anticipated regret are widely used extensions to the theory of planned behaviour, yet there is some evidence to suggest that these constructs may conceptually overlap as predictors of intention. Two health-related behaviours with distinct moral implications (Study 1: organ donation registration, N = 352 and Study 2: condom usage, N = 1815) were therefore examined to ascertain whether moral norms and anticipated regret are indeed conceptually distinct. While evidence consistent with conceptual overlap was identified in Study 1, the evidence for such overlap in Study 2 was more ambiguous. In Study 3, a meta-analysis of existing literature revealed that the relationship between moral norms and anticipated regret was moderated by the extent of the moral implications arising from the behaviour under examination. Taken together, these findings suggest that conceptual overlap between moral norms and anticipated regret is more likely to occur among behaviours with obvious moral implications. Researchers wishing to examine the predictive utility of moral norms and anticipated regret among such behaviours would therefore be advised to aggregate these measures to form a composite variable (personal norms). PMID:23256489

  19. Motor protein accumulation on antiparallel microtubule overlaps

    CERN Document Server

    Kuan, Hui-Shun

    2015-01-01

    Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process (TASEP) for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. The center region, far from the overlap ends, has a constant motor density as one would na\\"ively expect. However, rather than following a simple binding equilibrium, the center ...

  20. Open to Suggestion.

    Science.gov (United States)

    Journal of Reading, 1987

    1987-01-01

    Offers (1) suggestions for improving college students' study skills; (2) a system for keeping track of parent, teacher, and community contacts; (3) suggestions for motivating students using tic tac toe; (4) suggestions for using etymology to improve word retention; (5) a word search grid; and (6) suggestions for using postcards in remedial reading…

  1. SCLERODERMA OVERLAP SYNDROME: A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Diwakar K

    2014-06-01

    Full Text Available Overlap syndrome is a condition in which the patient presents with features of two or more diseases. These rheumatic conditions can co-exist in various combinations and are not rare, as myopathy or myositis co-exist in scleroderma in up to3 7% of scleroderma patients. 1 Here we present a case of 49 years old patient of overlap syndrome (Scleroderma (LcSS/Myositis (Dermatomyositis.

  2. Detecting overlapping coding sequences in virus genomes

    Directory of Open Access Journals (Sweden)

    Brown Chris M

    2006-02-01

    Full Text Available Abstract Background Detecting new coding sequences (CDSs in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs. Results In a previous paper we introduced a new statistic – MLOGD (Maximum Likelihood Overlapping Gene Detector – for detecting and analysing overlapping CDSs. Here we present (a an improved MLOGD statistic, (b a greatly extended suite of software using MLOGD, (c a database of results for 640 virus sequence alignments, and (d a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment. Conclusion MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs – in particular overlapping or short CDSs – and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at http://guinevere.otago.ac.nz/mlogd.html.

  3. Correlated edge overlaps in multiplex networks

    Science.gov (United States)

    Baxter, Gareth J.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions.

  4. Locality and topology with fat link overlap actions

    CERN Document Server

    Kovács, T G

    2003-01-01

    We study the locality and topological properties of fat link clover overlap (FCO) actions. We find that a small amount of fattening (2-4 steps of APE or 1 step of HYP) already results in greatly improved properties compared to the Wilson overlap (WO). We present a detailed study of the localisation of the FCO and its connection to the density of low modes of $A^\\dagger A$. In contrast to the Wilson overlap, on quenched gauge backgrounds we do not find any dependence of the localization of the FCO on the gauge coupling. This suggests that the FCO remains local in the continuum limit. The FCO also faithfully reproduces the zero mode wave functions of typical lattice instantons, not like the Wilson overlap. After a general discussion of different lattice definitions of the topological charge we also show that the FCO together with the Boulder charge are likely to satisfy the index theorem in the continuum limit. Finally, we present a high statistics computation of the quenched topological susceptibility with the...

  5. Resolution of overlapping skin auto-fluorescence for development of non-invasive applications

    Science.gov (United States)

    Su, Yu-Zheng; Lin, Li-Wu; Chen, Chuen-Yau; Hung, Min-Wei; Huang, Kuo-Cheng

    2010-08-01

    Skin auto-fluorescence spectra can provide useful biological information, but the obtained spectrum is overlapped and is difficult to distinguish each contributed component. We applied the genetic algorithm to decompose the overlapping spectrum. First, we simulate the overlapping spectral to confirm our feasible algorithm. The skin auto-fluorescence spectra were obtained from the normal human skin with 337 nm excitation light source. The nicotinamide adenine dinucleotid (NADH) and flavin adenine dinucleotide (FAD) are accurately decomposed and demonstrated. The developed algorithm can be widely applied to achieve qualitative and quantitative analysis for overlapping spectra.

  6. Quantitative analysis of Plasmodium ookinete motion in three dimensions suggests a critical role for cell shape in the biomechanics of malaria parasite gliding motility.

    Science.gov (United States)

    Kan, Andrey; Tan, Yan-Hong; Angrisano, Fiona; Hanssen, Eric; Rogers, Kelly L; Whitehead, Lachlan; Mollard, Vanessa P; Cozijnsen, Anton; Delves, Michael J; Crawford, Simon; Sinden, Robert E; McFadden, Geoffrey I; Leckie, Christopher; Bailey, James; Baum, Jake

    2014-05-01

    Motility is a fundamental part of cellular life and survival, including for Plasmodium parasites--single-celled protozoan pathogens responsible for human malaria. The motile life cycle forms achieve motility, called gliding, via the activity of an internal actomyosin motor. Although gliding is based on the well-studied system of actin and myosin, its core biomechanics are not completely understood. Currently accepted models suggest it results from a specifically organized cellular motor that produces a rearward directional force. When linked to surface-bound adhesins, this force is passaged to the cell posterior, propelling the parasite forwards. Gliding motility is observed in all three life cycle stages of Plasmodium: sporozoites, merozoites and ookinetes. However, it is only the ookinetes--formed inside the midgut of infected mosquitoes--that display continuous gliding without the necessity of host cell entry. This makes them ideal candidates for invasion-free biomechanical analysis. Here we apply a plate-based imaging approach to study ookinete motion in three-dimensional (3D) space to understand Plasmodium cell motility and how movement facilitates midgut colonization. Using single-cell tracking and numerical analysis of parasite motion in 3D, our analysis demonstrates that ookinetes move with a conserved left-handed helical trajectory. Investigation of cell morphology suggests this trajectory may be based on the ookinete subpellicular cytoskeleton, with complementary whole and subcellular electron microscopy showing that, like their motion paths, ookinetes share a conserved left-handed corkscrew shape and underlying twisted microtubular architecture. Through comparisons of 3D movement between wild-type ookinetes and a cytoskeleton-knockout mutant we demonstrate that perturbation of cell shape changes motion from helical to broadly linear. Therefore, while the precise linkages between cellular architecture and actomyosin motor organization remain unknown, our

  7. Host plant-associated population variation in the carob moth Ectomyelois ceratoniae in Iran: A geometric morphometric analysis suggests a nutritional basis.

    Science.gov (United States)

    Mozaffarian, Fariba; Sarafrazi, Alimorad; Ganbalani, Gadir Nouri

    2007-01-01

    The carob moth, Ectomyelois ceratoniae (Zeller, 1839) (Lepidoptera: Pyralidae), is the most important pest of pomegranate in Iran. As it has been rarely recorded on other host plants, control methods have mostly been focused on its populations on pomegranate. In this study, shapes and sizes of wings were compared in populations on 4 host plants (pomegranate, fig, pistachio and walnut) using a landmark-based geometric morphometric method, and analysis of partial warp scores and centroid sizes. The results showed significantly smaller wing size in populations on pomegranate and a significant host plant-associated shape difference among populations as a consequence of allometric growth. This suggests that the wing size and shape differences among test populations may not have a genetic basis and could happen because of differences in the nutritional content of host plants. The results of the analysis suggest that the female carob moth lays her eggs on host plants that provide suitable conditions for hatching. The larger size of moths on hosts other than pomegranate showed that some host plants such as fig, pistachio and walnut can provide for increased stored nutritional reserves by larvae that may result in more successful over-wintering and higher fecundity in adults. This suggests that in spite of the more extensive activity of carob moth on pomegranate in Iran, populations on other host plants can have an important effect on expanding pest population sizes in following years which should be considered in control methods.

  8. Wavelet fractal character of overlapping signal

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A new method based on the combining of the wavelet theory with the fractal theory and named wavelet fractal peak position method (WFPPM) is introduced to extract the number of the components and the relevant peak positions from overlapping signals in chemistry. The overlapping signal is first transformed into continuous wavelet transform value of time domain in certain dilation range via continuous wavelet transform (CWT), and then changed into capacity dimensions (Dc). The number of the components and the relevant positions of overlapping peaks can be identified easily according to the change of Dc. An investigation concerning the influence of different dilation ranges on the peak positions extracted by WFPPM is also provided. Studies show that WFPPM is and efficient tool for extracting the peak positions and identifying the number of peaks from unresolved signals, even wht\\en this kind of overlapping is significantly serious. Relative errors of less than 1.0% in peak are found when WFPPM is used in the processing of the cadmium(Ⅱ)-indium(Ⅲ) mixture system. The analytical results demonstrate that the desired peak positions can be extracted conveniently, accurately and rapidly from and unresolved signal via WFPPM. Tremendous developing and applications based on currently reported WFPPM in extracting overlapping signals would be expected in the near futrue.

  9. Genomic and Functional Overlap between Somatic and Germline Chromosomal Rearrangements

    Directory of Open Access Journals (Sweden)

    Sebastiaan van Heesch

    2014-12-01

    Full Text Available Genomic rearrangements are a common cause of human congenital abnormalities. However, their origin and consequences are poorly understood. We performed molecular analysis of two patients with congenital disease who carried de novo genomic rearrangements. We found that the rearrangements in both patients hit genes that are recurrently rearranged in cancer (ETV1, FOXP1, and microRNA cluster C19MC and drive formation of fusion genes similar to those described in cancer. Subsequent analysis of a large set of 552 de novo germline genomic rearrangements underlying congenital disorders revealed enrichment for genes rearranged in cancer and overlap with somatic cancer breakpoints. Breakpoints of common (inherited germline structural variations also overlap with cancer breakpoints but are depleted for cancer genes. We propose that the same genomic positions are prone to genomic rearrangements in germline and soma but that timing and context of breakage determines whether developmental defects or cancer are promoted.

  10. An Overlapping Clustering Approach for Routing in Wireless Sensor Networks

    OpenAIRE

    Zhenquan Qin; Can Ma; Lei Wang; Jiaqi Xu; Bingxian Lu

    2013-01-01

    The design and analysis of routing algorithm is an important issue in wireless sensor networks (WSNs). Most traditional geographical routing algorithms cannot achieve good performance in duty-cycled networks. In this paper, we propose a k-connected overlapping clustering approach with energy awareness, namely, k-OCHE, for routing in WSNs. The basic idea of this approach is to select a cluster head by energy availability (EA) status. The k-OCHE scheme adopts a sleep scheduling strategy of CKN,...

  11. Transient brain activity disentangles fMRI resting-state dynamics in terms of spatially and temporally overlapping networks.

    Science.gov (United States)

    Karahanoğlu, Fikret Işik; Van De Ville, Dimitri

    2015-07-16

    Dynamics of resting-state functional magnetic resonance imaging (fMRI) provide a new window onto the organizational principles of brain function. Using state-of-the-art signal processing techniques, we extract innovation-driven co-activation patterns (iCAPs) from resting-state fMRI. The iCAPs' maps are spatially overlapping and their sustained-activity signals temporally overlapping. Decomposing resting-state fMRI using iCAPs reveals the rich spatiotemporal structure of functional components that dynamically assemble known resting-state networks. The temporal overlap between iCAPs is substantial; typically, three to four iCAPs occur simultaneously in combinations that are consistent with their behaviour profiles. In contrast to conventional connectivity analysis, which suggests a negative correlation between fluctuations in the default-mode network (DMN) and task-positive networks, we instead find evidence for two DMN-related iCAPs consisting the posterior cingulate cortex that differentially interact with the attention network. These findings demonstrate how the fMRI resting state can be functionally decomposed into spatially and temporally overlapping building blocks using iCAPs.

  12. Central European parasitic flatworms of the family Renicolidae Dollfus, 1939 (Trematoda: Plagiorchiida): molecular and comparative morphological analysis rejects the synonymization of Renicola pinguis complex suggested by Odening.

    Science.gov (United States)

    Heneberg, Petr; Sitko, Jiljí; Bizos, Jiří; Horne, Elizabeth C

    2016-10-01

    The Renicolidae are digenean parasites of piscivorous and molluscivorous birds. Although they exhibit few morphological autapomorphies and are highly variable, the numerous suggested re-classifications within the family have never been supported by any molecular analyses. We address the possible synonymization of species within the Renicola pinguis complex suggested previously by Odening. We provide and analyse sequences of two nuclear (ITS2, 28S rDNA) and two mitochondrial (CO1, ND1) DNA loci of central European species of the Renicolidae, namely Renicola lari, Renicola pinguis and Renicola sternae sp. n., and we also provide first sequences of Renicola sloanei. The combined molecular and comparative morphological analysis confirms the previously questioned validity of the three Renicola spp. of highly similar morphology, which display strict niche separation in terms of host specificity and selectivity. We identify two previously unreported clades within the genus Renicola; however, only one of them is supported by the analysis of adult worms. We also provide comparative measurements of the three examined closely related central European renicolids, and describe the newly proposed tern-specialized species Renicola sternae sp. n., which was previously repeatedly misidentified as Renicola paraquinta. Based on the extensive dataset collected in 1962-2015, we update the host spectrum of Renicolidae parasitizing central European birds (Renicola bretensis, R. lari, Renicola mediovitellata, R. pinguis, Renicola secunda and R. sternae sp. n.) and discuss their host-specific prevalence and intensity of infections. PMID:27356772

  13. A global survey of aerosol-liquid water cloud overlap based on four years of CALIPSO-CALIOP data

    Science.gov (United States)

    Devasthale, A.; Thomas, M. A.

    2011-02-01

    Simulating the radiative impacts of aerosols located above liquid water clouds presents a significant challenge. In particular, absorbing aerosols, such as smoke, may have significant impact in such situations and even change the sign of net radiative forcing. It is not possible to reliably obtain information on such overlap events from existing passive satellite sensors. However, the CALIOP instrument onboard NASA's CALIPSO satellite allows us to examine these events with unprecedented accuracy. Using four years of collocated CALIPSO 5 km Aerosol and Cloud Layer Version 3 Products (June 2006-May 2010), we quantify, for the first time, the characteristics of overlapping aerosol and water cloud layers globally. We investigate seasonal variability in these characteristics over six latitude bands to understand the hemispheric differences when all aerosol types are included in the analysis (the AAO case). We also investigate frequency of smoke aerosol-cloud overlap (the SAO case). Globally, the frequency is highest during the JJA months in the AAO case, while for the SAO case, it is highest in the SON months. The seasonal mean overlap frequency can regionally exceed 20% in the AAO case and 10% in the SAO case. In about 5-10% cases the vertical distance between aerosol and cloud layers is less than 100 m, while about in 45-60% cases it less than a kilometer in the annual means for different latitudinal bands. In about 70-80% cases, aerosol layers are less than a kilometer thick, while in about 18-22% cases they are 1-2 km thick. The frequency of aerosol layers 2-3 km thick is about 4-5% in the tropical belts during overlap events. Over the regions where high aerosol loadings are present, the overlap frequency can be up to 50% higher when quality criteria on aerosol/cloud feature detection are relaxed. Over the polar regions, more than 50% of the overlapping aerosol layers have optical thickness less than 0.02, but the contribution from the relatively optically thicker

  14. A global survey of aerosol-liquid water cloud overlap based on four years of CALIPSO-CALIOP data

    Directory of Open Access Journals (Sweden)

    A. Devasthale

    2011-02-01

    Full Text Available Simulating the radiative impacts of aerosols located above liquid water clouds presents a significant challenge. In particular, absorbing aerosols, such as smoke, may have significant impact in such situations and even change the sign of net radiative forcing. It is not possible to reliably obtain information on such overlap events from existing passive satellite sensors. However, the CALIOP instrument onboard NASA's CALIPSO satellite allows us to examine these events with unprecedented accuracy. Using four years of collocated CALIPSO 5 km Aerosol and Cloud Layer Version 3 Products (June 2006–May 2010, we quantify, for the first time, the characteristics of overlapping aerosol and water cloud layers globally. We investigate seasonal variability in these characteristics over six latitude bands to understand the hemispheric differences when all aerosol types are included in the analysis (the AAO case. We also investigate frequency of smoke aerosol-cloud overlap (the SAO case. Globally, the frequency is highest during the JJA months in the AAO case, while for the SAO case, it is highest in the SON months. The seasonal mean overlap frequency can regionally exceed 20% in the AAO case and 10% in the SAO case. In about 5–10% cases the vertical distance between aerosol and cloud layers is less than 100 m, while about in 45–60% cases it less than a kilometer in the annual means for different latitudinal bands. In about 70–80% cases, aerosol layers are less than a kilometer thick, while in about 18–22% cases they are 1–2 km thick. The frequency of aerosol layers 2–3 km thick is about 4–5% in the tropical belts during overlap events. Over the regions where high aerosol loadings are present, the overlap frequency can be up to 50% higher when quality criteria on aerosol/cloud feature detection are relaxed. Over the polar regions, more than 50% of the overlapping aerosol layers have optical thickness less than 0.02, but the contribution from

  15. Manufacturer's Suggested Retail Prices

    NARCIS (Netherlands)

    Rosenkranz, S.

    2003-01-01

    Based on arguments of the `reference- dependent' theory of consumer choice we assume that a retailer's discount of a manufacturer's suggested retail price changes consumers' demand. We can show that the producer benefits from suggesting a retail price. If consumers are additionally sufficiently `los

  16. Overlapping community detection using weighted consensus clustering

    Indian Academy of Sciences (India)

    LINTAO YANG; ZETAI YU; JING QIAN; SHOUYIN LIU

    2016-10-01

    Many overlapping community detection algorithms have been proposed. Most of them are unstable and behave non-deterministically. In this paper, we use weighted consensus clustering for combining multiple base covers obtained by classic non-deterministic algorithms to improve the quality of the results. We first evaluate a reliability measure for each community in all base covers and assign a proportional weight to each one. Then we redefine the consensus matrix that takes into account not only the common membership of nodes, but also the reliability of the communities. Experimental results on both artificial and real-world networks show that our algorithm can find overlapping communities accurately.

  17. FREQUENCY OVERLAPPED SIGNAL IDENTIFICATION USING BLIND SOURCE SEPARATION

    Institute of Scientific and Technical Information of China (English)

    WANG Junfeng; SHI Tielin; HE Lingsong; YANG Shuzi

    2006-01-01

    The concepts, principles and usages of principal component analysis (PCA) and independent component analysis (ICA) are interpreted. Then the algorithm and methodology of ICA-based blind source separation (BSS), in which the pre-whitened based on PCA for observed signals is used, are researched. Aiming at the mixture signals, whose frequency components are overlapped by each other, a simulation of BSS to separate this type of mixture signals by using theory and approach of BSS has been done. The result shows that the BSS has some advantages what the traditional methodology of frequency analysis has not.

  18. Topology of dynamical lattice configurations including results from overlap fermions

    CERN Document Server

    Bruckmann, Falk; Gruber, Florian; Lippert, Thomas; Schäfer, Andreas

    2011-01-01

    We investigate how the topological charge density in lattice QCD simulations is affected by violations of chiral symmetry caused by the fermion action. To this end we compare lattice configurations generated with a number of different actions including first configurations generated with exact overlap quarks. We visualize the topological profiles after mild smearing. In the topological charge correlator we measure the size of the positive core, which is known to vanish in the continuum limit. To leading order we find the core size to scale linearly with the lattice spacing with the same coefficient for all actions, even including quenched simulations. In the subleading term the different actions vary over a range of about 10%. Our findings suggest that non-chiral lattice actions at current lattice spacings do not differ much for observables related to topology, both among themselves and compared to overlap fermions.

  19. Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma

    Science.gov (United States)

    Amato, Teresa; Abate, Francesco; Piccaluga, Pierpaolo; Iacono, Michele; Fallerini, Chiara; Renieri, Alessandra; De Falco, Giulia; Ambrosio, Maria Raffaella; Mourmouras, Vaselious; Ogwang, Martin; Calbi, Valeria; Rabadan, Roul; Hummel, Michael; Pileri, Stefano; Bellan, Cristiana

    2016-01-01

    Objectives: Recent studies using next-generation sequencing (NGS) analysis disclosed the importance of the intrinsic activation of the B-cell receptor (BCR) pathway in the pathogenesis of sporadic Burkitt lymphoma (sBL) due to mutations of TCF3/ID3 genes. Since no definitive data are available on the genetic landscape of endemic Burkitt (eBL), we first assessed the mutation frequency of TCF3/ID3 in eBL compared with sBL and subsequently the somatic hypermutation status of the BCR to answer whether an extrinsic activation of BCR signaling could also be demonstrated in Burkitt lymphoma. Methods: We assessed the mutations of TCF3/ID3 by RNAseq and the BCR status by NGS analysis of the immunoglobulin genes (IGs). Results: We detected mutations of TCF3/ID3 in about 30% of the eBL cases. This rate is significantly lower than that detected in sBL (64%). The NGS analysis of IGs revealed intraclonal diversity, suggesting an active targeted somatic hypermutation process in eBL compared with sBL. Conclusions: These findings support the view that the antigenic pressure plays a key role in the pathogenetic pathways of eBL, which may be partially distinct from those driving sBL development. PMID:26712879

  20. Using Model-based Overlapping Seed Expansion to detect highly overlapping community structure

    CERN Document Server

    McDaid, Aaron F

    2010-01-01

    As research into community finding in social networks progresses, there is a need for algorithms capable of detecting overlapping community structure. Many algorithms have been proposed in recent years that are capable of assigning each node to more than a single community. The performance of these algorithms tends to degrade when the ground-truth contains a more highly overlapping community structure, with nodes assigned to more than two communities. Such highly overlapping structure is likely to exist in many social networks, such as Facebook friendship networks. In this paper we present a scalable algorithm, MOSES, based on a statistical model of community structure, which is capable of detecting highly overlapping community structure, especially when there is variance in the number of communities each node is in. In evaluation on synthetic data MOSES is found to be superior to existing algorithms, especially at high levels of overlap. We demonstrate MOSES on real social network data by analyzing the netwo...

  1. [Therapy and suggestion].

    Science.gov (United States)

    Barrucand, D; Paille, F

    1986-12-01

    Therapy and suggestion are closely related. That is clear for the ancient time: primitive medicine gives a good place to the Word. In plant, animal or mineral remedies, the suggestion is clearly preponderant. Towards the end of the 19th century, the "Ecole de Nancy" sets up a real theory of the suggestion, and Bernheim, its leader, bases hypnosis, then psychotherapy on this concept. Thereafter Coué will bring up the "conscious autosuggestion". Today, despite the progress of scientific medicine, the part of suggestion is still very important in medical therapy (with or without drugs), or in chirurgical therapy; this part is also very important in psychotherapies, whatever has been said in this field. This has to be known and used consciously in the doctor-patient relation, which is always essential in the therapeutic effectiveness.

  2. The clinical and genetic features of the COPD asthma overlap syndrome

    Science.gov (United States)

    Hardin, Megan; Cho, Michael; McDonald, Merry-Lynn; Beaty, Terri; Ramsdell, Joe; Bhatt, Surya; van Beek, Edwin J. R.; Make, Barry J.; Crapo, James D.; Silverman, Edwin K.; Hersh, Craig P.

    2014-01-01

    Background Individuals with COPD and asthma are an important but poorly characterized group. The genetic determinants of COPD-asthma overlap have not been studied. Objective Identify clinical features and genetic risk factors for COPD-asthma overlap. Methods Subjects were current or former smoking non-Hispanic whites (NHW) or African-Americans (AA) with COPD. Overlap subjects reported a history of physician-diagnosed asthma before the age of 40. We compared clinical and radiographic features between COPD and overlap subjects. We performed genome-wide association studies (GWAS) in the NHW and AA populations, and combined these results in a meta-analysis. Results More women and African Americans reported a history of asthma. Overlap subjects had more severe and more frequent respiratory exacerbations, less emphysema, and greater airway wall thickness compared to subjects with COPD alone. The NHW GWAS identified SNPs in CSMD1 (rs11779254, P=1.57×10−6) and SOX5(rs59569785, P=1.61×10−6) and the meta-analysis identified SNPs in the gene GPR65 (rs6574978, P=1.18×10−7) associated with COPD-asthma overlap. Conclusions Overlap subjects have more exacerbations, less emphysema and more airway disease for any degree of lung function impairment compared to COPD alone. We identified novel genetic variants associated with this syndrome. COPD-asthma overlap is an important syndrome and may require distinct clinical management. PMID:24876173

  3. Power Divergences in Overlapping Wilson Lines

    OpenAIRE

    Berwein, Matthias

    2014-01-01

    We discuss the divergence structure of Wilson line operators with partially overlapping segments on the basis of the cyclic Wilson loop as an explicit example. The generalized exponentiation theorem is used to show the exponentiation and factorization of power divergences for certain linear combinations of associated loop functions.

  4. Power divergences in overlapping Wilson lines

    Science.gov (United States)

    Berwein, Matthias

    2016-01-01

    We discuss the divergence structure of Wilson line operators with partially overlapping segments on the basis of the cyclic Wilson loop as an explicit example. The generalized exponentiation theorem is used to show the exponentiation and factorization of power divergences for certain linear combinations of associated loop functions.

  5. Parallelizing SLPA for Scalable Overlapping Community Detection

    Directory of Open Access Journals (Sweden)

    Konstantin Kuzmin

    2015-01-01

    Full Text Available Communities in networks are groups of nodes whose connections to the nodes in a community are stronger than with the nodes in the rest of the network. Quite often nodes participate in multiple communities; that is, communities can overlap. In this paper, we first analyze what other researchers have done to utilize high performance computing to perform efficient community detection in social, biological, and other networks. We note that detection of overlapping communities is more computationally intensive than disjoint community detection, and the former presents new challenges that algorithm designers have to face. Moreover, the efficiency of many existing algorithms grows superlinearly with the network size making them unsuitable to process large datasets. We use the Speaker-Listener Label Propagation Algorithm (SLPA as the basis for our parallel overlapping community detection implementation. SLPA provides near linear time overlapping community detection and is well suited for parallelization. We explore the benefits of a multithreaded programming paradigm and show that it yields a significant performance gain over sequential execution while preserving the high quality of community detection. The algorithm was tested on four real-world datasets with up to 5.5 million nodes and 170 million edges. In order to assess the quality of community detection, at least 4 different metrics were used for each of the datasets.

  6. Overlapping Community Detection based on Network Decomposition

    Science.gov (United States)

    Ding, Zhuanlian; Zhang, Xingyi; Sun, Dengdi; Luo, Bin

    2016-04-01

    Community detection in complex network has become a vital step to understand the structure and dynamics of networks in various fields. However, traditional node clustering and relatively new proposed link clustering methods have inherent drawbacks to discover overlapping communities. Node clustering is inadequate to capture the pervasive overlaps, while link clustering is often criticized due to the high computational cost and ambiguous definition of communities. So, overlapping community detection is still a formidable challenge. In this work, we propose a new overlapping community detection algorithm based on network decomposition, called NDOCD. Specifically, NDOCD iteratively splits the network by removing all links in derived link communities, which are identified by utilizing node clustering technique. The network decomposition contributes to reducing the computation time and noise link elimination conduces to improving the quality of obtained communities. Besides, we employ node clustering technique rather than link similarity measure to discover link communities, thus NDOCD avoids an ambiguous definition of community and becomes less time-consuming. We test our approach on both synthetic and real-world networks. Results demonstrate the superior performance of our approach both in computation time and accuracy compared to state-of-the-art algorithms.

  7. A Note On Computing Set Overlap Classes

    OpenAIRE

    Charbit, Pierre; Habib, Michel; Limouzy, Vincent; de Montgolfier, Fabien; Raffinot, Mathieu; Rao, Michaël

    2007-01-01

    Let ${\\cal V}$ be a finite set of $n$ elements and ${\\cal F}=\\{X_1,X_2, \\ldots , X_m\\}$ a family of $m$ subsets of ${\\cal V}.$ Two sets $X_i$ and $X_j$ of ${\\cal F}$ overlap if $X_i \\cap X_j \

  8. Autism and ADHD: Overlapping and Discriminating Symptoms

    Science.gov (United States)

    Mayes, Susan Dickerson; Calhoun, Susan L.; Mayes, Rebecca D.; Molitoris, Sarah

    2012-01-01

    Children with ADHD and autism have some similar features, complicating a differential diagnosis. The purpose of our study was to determine the degree to which core ADHD and autistic symptoms overlap in and discriminate between children 2-16 years of age with autism and ADHD. Our study demonstrated that 847 children with autism were easily…

  9. Empirical Study of Corporate Social Responsibility Overlap Based on Multidimensional Scaling Analysis%基于多维尺度分析的企业社会责任重叠测评实证研究

    Institute of Scientific and Technical Information of China (English)

    孙键; 赵红; 赵宇彤; 胡锋

    2011-01-01

    目前学界的研究已经从讨论企业为什么要履行企业社会责任(CSR)逐步转变为探讨如何履行CSR.创新性地提出了CSR重叠的概念并提出了利用多维尺度分析(MDS)方法模型对CSR重叠进行测评,选取了5家煤炭企业做了实证研究,结果显示该方法能够清晰的解读CSR重叠背后的因素,企业应该围绕"硬责任"和"软责任"两大维度制定相应CSR发展策略.%The academic research interests has move from studying why enterprise take CSR to how should enterprise take CSR. This paper innovative proposes the concept of CSR overlap and MDS model for measuring CSR overlap.The empirical research is also conducted by selecting 5 coal mine companies. The study results indicate that the MDS model can uncover the factors behind the CSR overlap.The companies should focus on the two dimensions "soft responsibility"and "hard responsibility" to develop appropriate CSR strategies.

  10. Segmentation, Inference and Classification of Partially Overlapping Nanoparticles

    KAUST Repository

    Chiwoo Park,

    2013-03-01

    This paper presents a method that enables automated morphology analysis of partially overlapping nanoparticles in electron micrographs. In the undertaking of morphology analysis, three tasks appear necessary: separate individual particles from an agglomerate of overlapping nano-objects; infer the particle\\'s missing contours; and ultimately, classify the particles by shape based on their complete contours. Our specific method adopts a two-stage approach: the first stage executes the task of particle separation, and the second stage conducts simultaneously the tasks of contour inference and shape classification. For the first stage, a modified ultimate erosion process is developed for decomposing a mixture of particles into markers, and then, an edge-to-marker association method is proposed to identify the set of evidences that eventually delineate individual objects. We also provided theoretical justification regarding the separation capability of the first stage. In the second stage, the set of evidences become inputs to a Gaussian mixture model on B-splines, the solution of which leads to the joint learning of the missing contour and the particle shape. Using twelve real electron micrographs of overlapping nanoparticles, we compare the proposed method with seven state-of-the-art methods. The results show the superiority of the proposed method in terms of particle recognition rate.

  11. Direct and indirect effects in the regulation of overlapping promoters

    DEFF Research Database (Denmark)

    Bendtsen, Kristian Moss; Erdossy, Janos; Csiszovski, Zsolt;

    2011-01-01

    Optimal response to environmental stimuli often requires activation of certain genes and repression of others. Dual function regulatory proteins play a key role in the differential regulation of gene expression. While repression can be achieved by any DNA binding protein through steric occlusion...... of RNA polymerase in the promoter region, activation often requires a surface on the regulatory protein to contact RNAP and thus facilitate transcription initiation. RNAP itself is also a DNA binding protein, therefore it can function as a transcriptional repressor. Searching the Escherichia coli...... promoter database we found that ~14% of the identified 'forward' promoters overlap with a promoter oriented in the opposite direction. In this article we combine a mathematical model with experimental analysis of synthetic regulatory regions to investigate interference of overlapping promoters. We find...

  12. Analysis of biosurfactants from industrially-viable Pseudomonas strain isolated from crude oil suggests how rhamnolipids congeners affect on emulsification property and antimicrobial activity

    Directory of Open Access Journals (Sweden)

    Palashpriya eDas

    2014-12-01

    Full Text Available Rhamnolipid biosurfactants produced mainly by Pseudomonas sp. had been reported to possess a wide range of potential industrial application. These biosurfactants are produced as monorhamnolipid (MRL and di-rhamnolipid (DRL congeners. The present study deals with rhamnolipid biosurfactants produced by three bacterial isolates from crude oil. Biosurfactants produced by one of the strains (named as IMP67 was found to be very efficacious based on its critical micelle concentration (CMC value and hydrocarbon emulsification property. Strikingly, antimicrobial and anti-biofilm potential of this biosurfactant were higher than biosurfactants produced by other two strains. Thin layer chromatography (TLC analysis and rhamnose quantification showed that the rhamnolipids of IMP67 had more MRL congeners than biosurfactants of the other two strains. Emulsification and antimicrobial actions were affected by manual change of MRL and DRL congener proportions. Increase of MRL proportion enhanced emulsification index and antimicrobial property to Gram negative bacteria. This result indicated that the ratio of MRL and DRL affect the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In consistent, rhamnolipids of IMP67 reduced the MIC of some antibiotics against bacteria, suggesting the potential of biosurfactant as antibiotics synergist.

  13. Analysis of striatal transcriptome in mice overexpressing human wild-type alpha-synuclein supports synaptic dysfunction and suggests mechanisms of neuroprotection for striatal neurons

    Directory of Open Access Journals (Sweden)

    Cabeza-Arvelaiz Yofre

    2011-12-01

    Full Text Available Abstract Background Alpha synuclein (SNCA has been linked to neurodegenerative diseases (synucleinopathies that include Parkinson's disease (PD. Although the primary neurodegeneration in PD involves nigrostriatal dopaminergic neurons, more extensive yet regionally selective neurodegeneration is observed in other synucleinopathies. Furthermore, SNCA is ubiquitously expressed in neurons and numerous neuronal systems are dysfunctional in PD. Therefore it is of interest to understand how overexpression of SNCA affects neuronal function in regions not directly targeted for neurodegeneration in PD. Results The present study investigated the consequences of SNCA overexpression on cellular processes and functions in the striatum of mice overexpressing wild-type, human SNCA under the Thy1 promoter (Thy1-aSyn mice by transcriptome analysis. The analysis revealed alterations in multiple biological processes in the striatum of Thy1-aSyn mice, including synaptic plasticity, signaling, transcription, apoptosis, and neurogenesis. Conclusion The results support a key role for SNCA in synaptic function and revealed an apoptotic signature in Thy1-aSyn mice, which together with specific alterations of neuroprotective genes suggest the activation of adaptive compensatory mechanisms that may protect striatal neurons in conditions of neuronal overexpression of SNCA.

  14. Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8.

    Directory of Open Access Journals (Sweden)

    Archana Shenoy

    Full Text Available BACKGROUND: The Microprocessor, containing the RNA binding protein Dgcr8 and RNase III enzyme Drosha, is responsible for processing primary microRNAs to precursor microRNAs. The Microprocessor regulates its own levels by cleaving hairpins in the 5'UTR and coding region of the Dgcr8 mRNA, thereby destabilizing the mature transcript. METHODOLOGY/PRINCIPAL FINDINGS: To determine whether the Microprocessor has a broader role in directly regulating other coding mRNA levels, we integrated results from expression profiling and ultra high-throughput deep sequencing of small RNAs. Expression analysis of mRNAs in wild-type, Dgcr8 knockout, and Dicer knockout mouse embryonic stem (ES cells uncovered mRNAs that were specifically upregulated in the Dgcr8 null background. A number of these transcripts had evolutionarily conserved predicted hairpin targets for the Microprocessor. However, analysis of deep sequencing data of 18 to 200nt small RNAs in mouse ES, HeLa, and HepG2 indicates that exonic sequence reads that map in a pattern consistent with Microprocessor activity are unique to Dgcr8. CONCLUSION/SIGNIFICANCE: We conclude that the Microprocessor's role in directly destabilizing coding mRNAs is likely specifically targeted to Dgcr8 itself, suggesting a specialized cellular mechanism for gene auto-regulation.

  15. Perceived Non-Overlap of Objects in an Audiovisual Stream/Bounce Display

    Directory of Open Access Journals (Sweden)

    Yousuke Kawachi

    2011-10-01

    Full Text Available In a stream/bounce display in which two identical visual objects move toward each other, coincide (completely overlap, and then move apart, the objects can be perceived as either streaming through or bouncing off each other. Despite the perceptual ambiguity in this display, the streaming percept is dominant. However, a sound burst presented at the time that the objects coincide facilitates the bouncing percept. Herein, we report a perceptual phenomenon in which the overlap between objects is illusorily perceived as a non-overlap in the stream/bounce display accompanied with sound. In the experiment, the amount of overlap between two objects was systematically manipulated in the presence/absence of a sound. Observers were asked to judge whether the two objects overlapped with each other and then asked whether the objects appeared to stream through or bounce off each other. The results were consistent with those of previous studies showing that sound promoted the bouncing percept. Most importantly, the sound presentation facilitated the perception of a non-overlap between the objects instead of a physical overlap, suggesting that the momentary overlap was inadequately perceived. We discuss the possibility that an abrupt sound temporally interrupts visual processing such as the formation of dynamic object representations.

  16. Attitudes to Suggestions

    Institute of Scientific and Technical Information of China (English)

    PETER; JOHNSON

    2007-01-01

    As an Australian expat teaching English in China for over four years, I often encourage my students to not only learn the English language but also try to understand Western culture. This includes the fact that Westerners frequently initiate proactive suggestions on any aspects of soci-

  17. On the overlap between bilingual language control and domain-general executive control.

    Science.gov (United States)

    Branzi, Francesca M; Calabria, Marco; Boscarino, Maria Lucrezia; Costa, Albert

    2016-05-01

    We explored the overlap between bilingual language control (bLC) and domain-general executive control (EC) by focusing on inhibitory control processes. We tested 62 bilinguals in linguistic and non-linguistic switching tasks for two types of costs, such as the n-1 shift cost and the n-2 repetition cost. In order to explore the involvement of inhibitory control in bLC and EC, we assessed the pattern of switch costs in the two tasks and then we correlated them between tasks. Results showed reduced n-2 repetition costs as compared to n-1 shift costs in the linguistic task only, suggesting that small amount of inhibition were deployed when switching between languages. Importantly, neither the n-1 shift costs nor the n-2 repetition costs were correlated between tasks. These results, supported by additional evidence from the ex-Gaussian analysis, suggest that inhibitory control is differently involved in bLC and in EC. PMID:27043252

  18. On the acoustics of overlapping laughter in conversational speech

    NARCIS (Netherlands)

    Truong, Khiet P.; Trouvain, Jürgen

    2012-01-01

    The social nature of laughter invites people to laugh together. This joint vocal action often results in overlapping laughter. In this paper, we show that the acoustics of overlapping laughs are different from non-overlapping laughs. We found that overlapping laughs are stronger prosodically marked

  19. Pollination niche overlap between a parasitic plant and its host.

    Science.gov (United States)

    Ollerton, Jeff; Stott, Adrian; Allnutt, Emma; Shove, Sam; Taylor, Chloe; Lamborn, Ellen

    2007-03-01

    Niche theory predicts that species which share resources should evolve strategies to minimise competition for those resources, or the less competitive species would be extirpated. Some plant species are constrained to co-occur, for example parasitic plants and their hosts, and may overlap in their pollination niche if they flower at the same time and attract the same pollinators. Using field observations and experiments between 1996 and 2006, we tested a series of hypotheses regarding pollination niche overlap between a specialist parasitic plant Orobanche elatior (Orobanchaceae) and its host Centaurea scabiosa (Asteraceae). These species flower more or less at the same time, with some year-to-year variation. The host is pollinated by a diverse range of insects, which vary in their effectiveness, whilst the parasite is pollinated by a single species of bumblebee, Bombus pascuorum, which is also an effective pollinator of the host plant. The two species therefore have partially overlapping pollination niches. These niches are not finely subdivided by differential pollen placement, or by diurnal segregation of the niches. We therefore found no evidence of character displacement within the pollination niches of these species, possibly because pollinators are not a limiting resource for these plants. Direct observation of pollinator movements, coupled with experimental manipulations of host plant inflorescence density, showed that Bombus pascuorum only rarely moves between inflorescences of the host and the parasite and therefore the presence of one plant is unlikely to be facilitating pollination in the other. This is the first detailed examination of pollination niche overlap in a plant parasite system and we suggest avenues for future research in relation to pollination and other shared interactions between parasitic plants and their hosts.

  20. Suggestions for Teaching Practice

    Institute of Scientific and Technical Information of China (English)

    ZHAN Na-na

    2013-01-01

    Teacher development and teaching practice(TP) have caught the eyes of researchers at home and abroad for many years. Many western scholars hold that reflective teaching is an efficient way to promote teacher development, but traditional TP is prevailing in China. Based on the merits and demerits of traditional TP and reflective TP, the author hopes to provide some suggestions for the people involved to promote the development of teacher education.

  1. Analysis of problems during molybdenum resources development in China and suggestions%中国钼矿资源开发问题分析及对策

    Institute of Scientific and Technical Information of China (English)

    闫兴虎

    2013-01-01

    针对中国钼矿资源开发所存在的地质勘查过度投入、产能盲目扩涨、采选产品附加值低、产品市场恶性竞争、企业抗风险能力较弱、矿山安全环境问题突出等问题,提出坚持中国钼采选业的可持续发展政策的建议,包括:健全钼矿资源可供性分析,实行钼矿资源勘查差别化政策;提高钼行业准入条件,严格生产配额管理;出台兼并重组政策,提高行业集中度;鼓励技术创新,提高产品附加值;坚持开发与环境保护协调发展。%Aiming at the problems during molybdenum resources development ,such as excessive investment in geological exploration ,blind expansion of production capacity ,mining products with low added value ,vicious competition in product markets ,enterprise weak anti-risk capability ,mine safety and environment problems etc .,corresponding suggestions were put out ,which promote sustainable development policy of molybdenum mining industry in China .The suggestions include improve the analysis of availability of molybdenum resources ,implement differentiated policies in molybdenum exploration ,increase access conditions and implement quota management in molybdenum industry ,increase the industry concentration , encourage technological innovation to increase additional products value ,and geological exploration and environment protection develop coordinately .

  2. A stochastic model for detecting overlapping and hierarchical community structure.

    Directory of Open Access Journals (Sweden)

    Xiaochun Cao

    Full Text Available Community detection is a fundamental problem in the analysis of complex networks. Recently, many researchers have concentrated on the detection of overlapping communities, where a vertex may belong to more than one community. However, most current methods require the number (or the size of the communities as a priori information, which is usually unavailable in real-world networks. Thus, a practical algorithm should not only find the overlapping community structure, but also automatically determine the number of communities. Furthermore, it is preferable if this method is able to reveal the hierarchical structure of networks as well. In this work, we firstly propose a generative model that employs a nonnegative matrix factorization (NMF formulization with a l(2,1 norm regularization term, balanced by a resolution parameter. The NMF has the nature that provides overlapping community structure by assigning soft membership variables to each vertex; the l(2,1 regularization term is a technique of group sparsity which can automatically determine the number of communities by penalizing too many nonempty communities; and hence the resolution parameter enables us to explore the hierarchical structure of networks. Thereafter, we derive the multiplicative update rule to learn the model parameters, and offer the proof of its correctness. Finally, we test our approach on a variety of synthetic and real-world networks, and compare it with some state-of-the-art algorithms. The results validate the superior performance of our new method.

  3. MOHCS: Towards Mining Overlapping Highly Connected Subgraphs

    CERN Document Server

    Lin, Xiahong; Chen, Kefei; Chiu, David K Y

    2008-01-01

    Many networks in real-life typically contain parts in which some nodes are more highly connected to each other than the other nodes of the network. The collection of such nodes are usually called clusters, communities, cohesive groups or modules. In graph terminology, it is called highly connected graph. In this paper, we first prove some properties related to highly connected graph. Based on these properties, we then redefine the highly connected subgraph which results in an algorithm that determines whether a given graph is highly connected in linear time. Then we present a computationally efficient algorithm, called MOHCS, for mining overlapping highly connected subgraphs. We have evaluated experimentally the performance of MOHCS using real and synthetic data sets from computer-generated graph and yeast protein network. Our results show that MOHCS is effective and reliable in finding overlapping highly connected subgraphs. Keywords-component; Highly connected subgraph, clustering algorithms, minimum cut, m...

  4. DNA sequence analysis suggests that cytb-nd1 PCR-RFLP may not be applicable to sandfly species identification throughout the Mediterranean region.

    Science.gov (United States)

    Llanes-Acevedo, Ivonne Pamela; Arcones, Carolina; Gálvez, Rosa; Martin, Oihane; Checa, Rocío; Montoya, Ana; Chicharro, Carmen; Cruz, Susana; Miró, Guadalupe; Cruz, Israel

    2016-03-01

    Molecular methods are increasingly used for both species identification of sandflies and assessment of their population structure. In general, they are based on DNA sequence analysis of targets previously amplified by PCR. However, this approach requires access to DNA sequence facilities, and in some circumstances, it is time-consuming. Though DNA sequencing provides the most reliable information, other downstream PCR applications are explored to assist in species identification. Thus, it has been recently proposed that the amplification of a DNA region encompassing partially both the cytochrome-B (cytb) and the NADH dehydrogenase 1 (nd1) genes followed by RFLP analysis with the restriction enzyme Ase I allows the rapid identification of the most prevalent species of phlebotomine sandflies in the Mediterranean region. In order to confirm the suitability of this method, we collected, processed, and molecularly analyzed a total of 155 sandflies belonging to four species including Phlebotomus ariasi, P. papatasi, P. perniciosus, and Sergentomyia minuta from different regions in Spain. This data set was completed with DNA sequences available at the GenBank for species prevalent in the Mediterranean basin and the Middle East. Additionally, DNA sequences from 13 different phlebotomine species (P. ariasi, P. balcanicus, P. caucasicus, P. chabaudi, P. chadlii, P. longicuspis, P. neglectus, P. papatasi, P. perfiliewi, P. perniciosus, P. riouxi, P. sergenti, and S. minuta), from 19 countries, were added to the data set. Overall, our molecular data revealed that this PCR-RFLP method does not provide a unique and specific profile for each phlebotomine species tested. Intraspecific variability and similar RFLP patterns were frequently observed among the species tested. Our data suggest that this method may not be applicable throughout the Mediterranean region as previously proposed. Other molecular approaches like DNA barcoding or phylogenetic analyses would allow a more

  5. Non-omega-overlapping TRSs are UN

    OpenAIRE

    Smith, Connor; Kahrs, Stefan

    2016-01-01

    This paper solves problem #79 of RTA's list of open problems --- in the positive. If the rules of a TRS do not overlap w.r.t. substitutions of infinite terms then the TRS has unique normal forms. We solve the problem by reducing the problem to one of consistency for ``similar'' constructor term rewriting systems. For this we introduce a new proof technique. We define a relation $\\invariant$ that is consistent by construction, and which --- if transitive --- would coincide wi...

  6. Depression-Burnout Overlap in Physicians

    OpenAIRE

    Walter Wurm; Katrin Vogel; Anna Holl; Christoph Ebner; Dietmar Bayer; Sabrina Mörkl; Istvan-Szilard Szilagyi; Erich Hotter; Hans-Peter Kapfhammer; Peter Hofmann

    2016-01-01

    Background Whether burnout is a distinct phenomenon rather than a type of depression and whether it is a syndrome, limited to three “core” components (emotional exhaustion, depersonalization and low personal accomplishment) are subjects of current debate. We investigated the depression-burnout overlap, and the pertinence of these three components in a large, representative sample of physicians. Methods In a cross-sectional study, all Austrian physicians were invited to answer a questionnaire ...

  7. Function approximation using adaptive and overlapping intervals

    Energy Technology Data Exchange (ETDEWEB)

    Patil, R.B.

    1995-05-01

    A problem common to many disciplines is to approximate a function given only the values of the function at various points in input variable space. A method is proposed for approximating a function of several to one variable. The model takes the form of weighted averaging of overlapping basis functions defined over intervals. The number of such basis functions and their parameters (widths and centers) are automatically determined using given training data and a learning algorithm. The proposed algorithm can be seen as placing a nonuniform multidimensional grid in the input domain with overlapping cells. The non-uniformity and overlap of the cells is achieved by a learning algorithm to optimize a given objective function. This approach is motivated by the fuzzy modeling approach and a learning algorithms used for clustering and classification in pattern recognition. The basics of why and how the approach works are given. Few examples of nonlinear regression and classification are modeled. The relationship between the proposed technique, radial basis neural networks, kernel regression, probabilistic neural networks, and fuzzy modeling is explained. Finally advantages and disadvantages are discussed.

  8. 大学生炒股行为分析及建议%Analysis and Suggestion on College Students ' Stocks Behavior

    Institute of Scientific and Technical Information of China (English)

    王婷; 刘阿幸

    2016-01-01

    我国股市的发展吸引了越来越多的投资者,其中包括许多在校大学生。他们有的是学习证券投资相关专业的学生,有的则与专业无关,但这种现象是否值得提倡仍需要讨论。通过对相关大学生炒股情况的调查,揭示了大学生炒股的动因,并对大学生炒股行为进行了利弊分析,同时对如何正确引导大学生炒股提出建议。%The stock market is rapidly developing in our country, and it has attracted more and more investors including many undergraduate college students who either studies the security analysis and investment or not. This phenomenon should be discussed. Through the survey results about the college students' stocks behavior, the paper reveals the reason of the be-havior, analyses the advantages and disadvantages of it, and gives suggestions to guide the behavior correctly.

  9. Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available A group of intrinsically disordered, hydrophilic proteins—Late Embryogenesis Abundant (LEA proteins—has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

  10. Analysis of multi-domain hypothetical proteins containing iron-sulphur clusters and fad ligands reveal rieske dioxygenase activity suggesting their plausible roles in bioremediation.

    Science.gov (United States)

    Sathyanarayanan, Nitish; Nagendra, Holenarasipur Gundurao

    2012-01-01

    'Conserved hypothetical' proteins pose a challenge not just for functional genomics, but also to biology in general. As long as there are hundreds of conserved proteins with unknown function in model organisms such as Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae, any discussion towards a 'complete' understanding of these biological systems will remain a wishful thinking. Insilico approaches exhibit great promise towards attempts that enable appreciating the plausible roles of these hypothetical proteins. Among the majority of genomic proteins, two-thirds in unicellular organisms and more than 80% in metazoa, are multi-domain proteins, created as a result of gene duplication events. Aromatic ring-hydroxylating dioxygenases, also called Rieske dioxygenases (RDOs), are class of multi-domain proteins that catalyze the initial step in microbial aerobic degradation of many aromatic compounds. Investigations here address the computational characterization of hypothetical proteins containing Ferredoxin and Flavodoxin signatures. Consensus sequence of each class of oxidoreductase was obtained by a phylogenetic analysis, involving clustering methods based on evolutionary relationship. A synthetic sequence was developed by combining the consensus, which was used as the basis to search for their homologs via BLAST. The exercise yielded 129 multidomain hypothetical proteins containing both 2Fe-2S (Ferredoxin) and FNR (Flavodoxin) domains. In the current study, 40 proteins with N-terminus 2Fe-2S domain and C-terminus FNR domain are characterized, through homology modelling and docking exercises which suggest dioxygenase activity indicating their plausible roles in degradation of aromatic moieties.

  11. Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates BCAR1 and Suggests a Causal Variant

    DEFF Research Database (Denmark)

    Boardman-Pretty, Freya; Smith, Andrew J. P.; Cooper, Jackie;

    2015-01-01

    Carotid intima-media thickness (IMT) is a marker of subclinical atherosclerosis that can predict cardiovascular disease events over traditional risk factors. This study examined the BCAR1-CFDP1-TMEM170A locus on chromosome 16, associated with carotid IMT and coronary artery disease in the IMT and...... with slower IMT progression in women (P=0.04) but not in men. Meta-analysis of 5 cohort studies also supported a protective effect of the A allele on common carotid IMT in women only (women: β=-0.0047, P=1.63×10-4; men: β=-0.0029, P=0.0678). Two hundred fourteen noncoding variants in strong linkage...... associations of rs4888378 with BCAR1 in vascular tissues. Molecular studies suggest the lead SNP as a potentially causal SNP at the BCAR1-CFDP1-TMEM170A locus, and expression quantitative trait loci studies implicate BCAR1 as the causal gene. This variant showed stronger effects on common carotid IMT in women...

  12. 格林-巴利综合征/急性脊髓炎重叠综合征的临床特点及机制分析%Clinical characteristics and mechanism analysis of GBS/AM overlap syndrome

    Institute of Scientific and Technical Information of China (English)

    郭芳; 张拥波; 王瑞金

    2016-01-01

    Objective Patients presenting with Guillain - Barre’ syndrome(GBS)and acute myelitis(AM),either simultaneously or consecutively,have been defined as GBS/ AM overlap syndrome. We performed a website - based study to evaluate the clinical course,biological and neuroimaging characteristics,therapy and outcomes of GBS/ AM overlap syndrome. Methods We mainly performed website - based research based on articles in cases presented with GBS/ AM overlap syndrome. A total of 18 cases were included. Clinical and prognosis data were ana-lyzed. Results The mean age of patients with GBS / AM overlap syndrome was 20. 5 years old,the predominance of cases found at younger ages could be attributed to higher exposures to triggering factors(88. 9% ),as infection or vaccination. The clinical presentations of patients with GBS/AM overlap syndrome were various. There were many atypical clinical presentations,besides the common presentations,such as limb weakness (94. 4% ),sensory disturbance(83. 3% ),sensory level(72. 2% ),and urinary disturbance(66. 7% ). Nerve conduction study revealed acute demyelinating polyneuropathy in 12(66. 7% )patients,while acute axonal polyneuropathy in 6(33. 3% )patients. Abnormality in the spinal cord MRI was detected in 100% of patients. Immunotherapies were prescribed in 100% of patients. The outcome of patients with GBS / AM overlap syn-drome was good in 10 patients(55. 6% ),while 7 patients(38. 9% )had poor outcomes,1 patient(5. 6% )died. All the patients had a monophasic disease course. Conclusion The clinical presentations of patients with GBS/ AM overlap syndrome were various. The common feature of GBS,clinical presentation and imaging data of AM,is help for diagnosing GBS / AM overlap syndrome. Immunotherapies were mostly steroid and intravenous immunoglobulin. The total outcomes were relatively good.%目的:明确格林-巴利综合征(GBS)和急性脊髓炎(AM)重叠综合征的临床表现、实验室检查、电生理及影像学特

  13. Analysis of Human Rotaviruses from a Single Location Over an 18-Year Time Span Suggests that Protein Coadaption Influences Gene Constellations

    Science.gov (United States)

    Zhang, Shu; McDonald, Paul W.; Thompson, Travis A.; Dennis, Allison F.; Akopov, Asmik; Kirkness, Ewen F.; Patton, John T.

    2014-01-01

    ABSTRACT Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution. IMPORTANCE Rotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by

  14. Biochemical Analysis of Pathogenic Ligand-Dependent FGFR2 Mutations Suggests Distinct Pathophysiological Mechanisms for Craniofacial and Limb Abnormalities in Human Skeletal Disorders

    Energy Technology Data Exchange (ETDEWEB)

    Ibrahimi,O.; Zhang, F.; Eliseenkova, A.; Itoh, N.; Linhardt, R.; Mohammadi, M.

    2004-01-01

    Gain-of-function missense mutations in FGF receptor 2 (FGFR2) are responsible for a variety of craniosynostosis syndromes including Apert syndrome (AS), Pfeiffer syndrome (PS) and Crouzon syndrome (CS). Unlike the majority of FGFR2 mutations, S252W and P253R AS mutations and a D321A PS mutation retain ligand-dependency and are also associated with severe limb pathology. In addition, a recently identified ligand-dependent S252L/A315S double mutation in FGFR2 was shown to cause syndactyly in the absence of craniosynostosis. Here, we analyze the effect of the canonical AS mutations, the D321A PS mutation and the S252L/A315S double mutation on FGFR2 ligand binding affinity and specificity using surface plasmon resonance. Both AS mutations and the D321A PS mutation, but not the S252L/A315S double mutation, increase the binding affinity of FGFR2c to multiple FGFs expressed in the cranial suture. Additionally, all four pathogenic mutations also violate FGFR2c ligand binding specificity and enable this receptor to bind FGF10. Based on our data, we propose that an increase in mutant FGFR2c binding to multiple FGFs results in craniosynostosis, whereas binding of mutant FGFR2c to FGF10 results in severe limb pathology. Structural and biophysical analysis shows that AS mutations in FGFR2b also enhance and violate FGFR2b ligand binding affinity and specificity, respectively. We suggest that elevated AS mutant FGFR2b signaling may account for the dermatological manifestations of AS.

  15. Phylogenetic analysis of New World screwworm fly, Cochliomyia hominivorax, suggests genetic isolation of some Caribbean island populations following colonization from South America.

    Science.gov (United States)

    McDonagh, L; García, R; Stevens, J R

    2009-06-01

    Larval infestations of the New World screwworm (NWS) fly, Cochliomyia hominivorax, cause considerable economic losses through the direct mortality and reduced production of livestock. Since the 1950s, NWS populations in North and Central America have been the target of virtually continuous eradication attempts by sterile insect technique (SIT). Nevertheless, in some areas, such as Jamaica, SIT-based control programmes have failed. Reasons for the failure of SIT-based programmes in some locations are unknown, but it is hypothesized that failure may be related to the mating incompatibility between sterile and wild flies or to the existence of sexually incompatible cryptic species. Accordingly, the current research investigates intraspecific phylogenetic relationships and associated biogeographic patterns between NWS populations from the Caribbean and South America, which represent those populations involved in, or earmarked for, forthcoming SIT programmes. Uniquely, this study also includes analyses of two North American samples, collected in Texas in 1933 and 1953 prior to initiation of the SIT-based eradication programme. The study utilizes three nucleotide datasets: elongation factor-1alpha (nuclear); cytochrome oxidase subunit 1 (mitochondrial), and 12S rRNA (mitochondrial). Phylogenetic analysis of these data, representing populations from across the Caribbean, South America and Texas, indicates sub-structuring of fly populations on several of the larger Caribbean islands, suggesting a period of isolation and/or founder effects following colonization from South America; significantly, our findings do not support a North American origin for Cuban flies. The importance of these findings in the light of proposed SIT programmes in the region is discussed. PMID:19335826

  16. A spatially explicit metapopulation model and cattle trade analysis suggests key determinants for the recurrent circulation of rift valley Fever virus in a pilot area of madagascar highlands.

    Directory of Open Access Journals (Sweden)

    Gaëlle Nicolas

    2014-12-01

    Full Text Available Rift Valley fever (RVF is a vector-borne zoonotic disease that causes high morbidity and mortality in ruminants. In 2008-2009, a RVF outbreak affected the whole Madagascar island, including the Anjozorobe district located in Madagascar highlands. An entomological survey showed the absence of Aedes among the potential RVF virus (RVFV vector species identified in this area, and an overall low abundance of mosquitoes due to unfavorable climatic conditions during winter. No serological nor virological sign of infection was observed in wild terrestrial mammals of the area, suggesting an absence of wild RVF virus (RVFV reservoir. However, a three years serological and virological follow-up in cattle showed a recurrent RVFV circulation. The objective of this study was to understand the key determinants of this unexpected recurrent transmission. To achieve this goal, a spatial deterministic discrete-time metapopulation model combined with cattle trade network was designed and parameterized to reproduce the local conditions using observational data collected in the area. Three scenarios that could explain the RVFV recurrent circulation in the area were analyzed: (i RVFV overwintering thanks to a direct transmission between cattle when viraemic cows calve, vectors being absent during the winter, (ii a low level vector-based circulation during winter thanks to a residual vector population, without direct transmission between cattle, (iii combination of both above mentioned mechanisms. Multi-model inference methods resulted in a model incorporating both a low level RVFV winter vector-borne transmission and a direct transmission between animals when viraemic cows calve. Predictions satisfactorily reproduced field observations, 84% of cattle infections being attributed to vector-borne transmission, and 16% to direct transmission. These results appeared robust according to the sensitivity analysis. Interweaving between agricultural works in rice fields

  17. Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Soares Fernando A

    2011-04-01

    Full Text Available Abstract Background Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+ and recurrent head and neck squamous cell carcinoma (HNSCC may increase our understanding of the complex biology of this disease. Methods Tumor samples were obtained from untreated HNSCC patients undergoing surgery. Patients were classified according to pathologic lymph node status (positive or negative or tumor recurrence (recurrent or non-recurrent tumor after treatment (surgery with neck dissection followed by radiotherapy. Using microarray gene expression, we screened tumor samples according to modules comprised by genes in the same pathway or functional category. Results The most frequent alterations were the repression of modules in negative lymph node (N0 and in non-recurrent tumors rather than induction of modules in N+ or in recurrent tumors. N0 tumors showed repression of modules that contain cell survival genes and in non-recurrent tumors cell-cell signaling and extracellular region modules were repressed. Conclusions The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway

  18. Analysis and implementation suggestions concerning new accounting system in college%高校新会计制度的分析与实施建议

    Institute of Scientific and Technical Information of China (English)

    郭海平

    2014-01-01

    This paper makes a comparative analysis on the old and new accounting system of colleges from the as-pects of accounting basis , financial report system structure , the basic content and the accounting subject and puts forward the following suggestions concerning the transformation from the old accounting system to the new : divide the business transaction , choose the reasonable accounting basis , find out the assets value , standardize assets man-agement , check fixed assets , compensate for fixed assets depreciation , clean the running account , incorporate the infrastructure account into the overall account , strengthen the supporting system to promote the financial informati-zation .and strengthen the construction of the accounting team , improve the accounting management level.%从会计核算基础、财务报告体系结构、基本内容和会计科目等方面,对两种高校会计制度进行了比较分析,并对新会计制度的实施提出了应正确划分经济业务,选择合理的记账基础;摸清资产“家底”,规范资产管理;清查固定资产,补提固定资产折旧;清理往来账项,将基建账并入“大账”;加强配套建设,推进财务信息化和加强财会队伍建设,以期提高财会管理水平的建议。

  19. MERRF/MELAS overlap syndrome due to the m.3291T>C mutation.

    Science.gov (United States)

    Liu, Kaiming; Zhao, Hui; Ji, Kunqian; Yan, Chuanzhu

    2014-03-01

    We report the case of a 19-year-old Chinese female harboring the m.3291T>C mutation in the MT-TL1 gene encoding the mitochondrial transfer RNA for leucine. She presented with a complex phenotype characterized by progressive cerebellar ataxia, frequent myoclonus seizures, recurrent stroke-like episodes, migraine-like headaches with nausea and vomiting, and elevated resting lactate blood level. It is known that the myoclonus epilepsy with ragged-red fibers (MERRF) is characterized by cerebellar ataxia and myoclonus epilepsy, while that the mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is characterized by recurrent stroke-like episodes, migraine-like headaches, and elevated resting lactate blood level. So the patient's clinical manifestations suggest the presence of a MERRF/MELAS overlap syndrome. Muscle biopsy of the patient showed the presence of numerous scattered ragged-red fibers, some cytochrome c oxidase-deficient fibers, and several strongly succinate dehygrogenase-reactive vessels, suggestive of a mitochondrial disorder. Direct sequencing of the complete mitochondrial genome of the proband revealed no mutations other than the T-to-C transition at nucleotide position 3291. Restriction fragment length polymorphism analysis of the proband and her family revealed maternal inheritance of the mutation in a heteroplasmic manner. The analysis of aerobic respiration and glycolysis demonstrated that the fibroblasts from the patient had mitochondrial dysfunction. Our results suggest that the m.3291T>C is pathogenic. This study is the first to describe the m.3291T>C mutation in association with the MERRF/MELAS overlap syndrome.

  20. Group Lasso with Overlaps: the Latent Group Lasso approach

    CERN Document Server

    Obozinski, Guillaume; Vert, Jean-Philippe

    2011-01-01

    We study a norm for structured sparsity which leads to sparse linear predictors whose supports are unions of prede ned overlapping groups of variables. We call the obtained formulation latent group Lasso, since it is based on applying the usual group Lasso penalty on a set of latent variables. A detailed analysis of the norm and its properties is presented and we characterize conditions under which the set of groups associated with latent variables are correctly identi ed. We motivate and discuss the delicate choice of weights associated to each group, and illustrate this approach on simulated data and on the problem of breast cancer prognosis from gene expression data.

  1. 正面小重叠碰撞工况模拟研究与实车优化分析%Simulation research and optimal analysis for small overlap frontal crashworthiness of a real car

    Institute of Scientific and Technical Information of China (English)

    刘珍海; 乔磊磊; 岳国辉; 陈现岭; 张凯

    2012-01-01

    美国高速公路安全保险协会(Insurance Institute for Highway Safety,IIHS)2012年颁布的正面小重叠碰撞试验方法及评价规程,对进军美国市场的中国车企提出了挑战。本文根据IIHS协会的试验方法及评价规程,用相关性分析后的有限元模型,对某实车进行了正面小重叠碰撞仿真分析。试验中,汽车以64.4km/h的速度撞击刚性壁障,重叠率为25%。试验后对碰撞车的车体结构、约束系统/假人运动学、假人伤害测量三方面进行评价,加权得到正面小重叠碰撞工况的总等级。分析结果为:车体结构得到“边缘”的评级;针对初始结果,从车体结构和材料两方面进行优化,优化后车体结构评级为“良好”。提出结构耐撞性能、约束系统集成方面的建议,为后续车辆安全性能开发提供参考。%A crash-test protocol and rating guidelines for small-overlap frontal-crashworthiness, which was released by the Insurance Institute for Highway Safety (IIHS) in August 2012, is a challenge to China's enterprises intending to enter the US automotive market. Small-overlap frontal barrier crash tests on a real vehicle in the authors' company were simulated and analyzed using the correlated FE model according to the protocol and guidelines. The tests were conducted at 64.4 km/h and 25% overlap, with rating based on vehicle structures, restraints and dummy kinematics, and dummy injury measures, and with the overall rating obtained by weighting of each individual rating. The original results indicate that the structure rating is "Marginal". After optimizing the structure and material according to the original results, the structure obtains "Good" rating. Some strategies for structure crashworthiness and restraints are summarized to offer references for new car safety.

  2. Influence of slice overlap on positron emission tomography image quality

    Science.gov (United States)

    McKeown, Clare; Gillen, Gerry; Dempsey, Mary Frances; Findlay, Caroline

    2016-02-01

    PET scans use overlapping acquisition beds to correct for reduced sensitivity at bed edges. The optimum overlap size for the General Electric (GE) Discovery 690 has not been established. This study assesses how image quality is affected by slice overlap. Efficacy of 23% overlaps (recommended by GE) and 49% overlaps (maximum possible overlap) were specifically assessed. European Association of Nuclear Medicine (EANM) guidelines for calculating minimum injected activities based on overlap size were also reviewed. A uniform flood phantom was used to assess noise (coefficient of variation, (COV)) and voxel accuracy (activity concentrations, Bq ml-1). A NEMA (National Electrical Manufacturers Association) body phantom with hot/cold spheres in a background activity was used to assess contrast recovery coefficients (CRCs) and signal to noise ratios (SNR). Different overlap sizes and sphere-to-background ratios were assessed. COVs for 49% and 23% overlaps were 9% and 13% respectively. This increased noise was difficult to visualise on the 23% overlap images. Mean voxel activity concentrations were not affected by overlap size. No clinically significant differences in CRCs were observed. However, visibility and SNR of small, low contrast spheres (⩽13 mm diameter, 2:1 sphere to background ratio) may be affected by overlap size in low count studies if they are located in the overlap area. There was minimal detectable influence on image quality in terms of noise, mean activity concentrations or mean CRCs when comparing 23% overlap with 49% overlap. Detectability of small, low contrast lesions may be affected in low count studies—however, this is a worst-case scenario. The marginal benefits of increasing overlap from 23% to 49% are likely to be offset by increased patient scan times. A 23% overlap is therefore appropriate for clinical use. An amendment to EANM guidelines for calculating injected activities is also proposed which better reflects the effect overlap size has

  3. Surfaces and spaces: troubleshooting the study of dietary niche space overlap between North American stem primates and rodents

    Science.gov (United States)

    Prufrock, Kristen A.; López-Torres, Sergi; Silcox, Mary T.; Boyer, Doug M.

    2016-06-01

    Dental topographic metrics provide quantitative, biologically meaningful data on the three-dimensional (3D) form of teeth. In this study, three dental topographic metrics (Dirichlet normal energy (DNE), relief index (RFI), and orientation patch count rotated (OPCR)) are used to evaluate the presence of dietary niche overlap between North American plesiadapoid primates (Plesiadapidae, Carpolestidae, and Saxonellidae) and early rodents. Calculation of these metrics requires researchers to modify the 3D surface models of the teeth by cropping them to a region of interest and/or orienting them. The current study therefore also examines the error introduced by cropping and orientation, and evaluates the contribution of these metrics to the niche overlap hypothesis. Our results indicate that cropping creates significantly more variation in RFI than DNE. Furthermore, orientation is an even larger source of variation in the calculation of RFI than cropping. Orientation does not strongly influence OPCR values. However, none of these sources of error are significant enough to undermine the extent to which these metrics can speak to the niche overlap hypothesis. The DNE and RFI results suggest that carpolestids and saxonellids had very different molar morphologies from early rodents, and thus these groups were not adapted to consume the same resources. Some plesiadapids show similar levels of occlusal curvature, relief, and complexity to early rodents. The plesiadapid Chiromyoides, which has distinctively low cusps and weak shearing crest development, has molars that are the most rodent-like of all taxa compared. This suggests that Chiromyoides had a dietary niche that overlapped with early rodents and would have been the most likely to be competing over food resources. Results from the plesiadapoid-rodent dental topographic analysis highlight the utility of DNE for detecting more fine-scaled differences in occlusal surface morphology than OPCR, whereas RFI provided valuable

  4. Overlap Quark Propagator in Coulomb Gauge QCD

    CERN Document Server

    Mercado, Ydalia Delgado; Schröck, Mario

    2014-01-01

    The chirally symmetric Overlap quark propagator is explored in Coulomb gauge. This gauge is well suited for studying the relation between confinement and chiral symmetry breaking, since confinement can be attributed to the infrared divergent Lorentz-vector dressing function. Using quenched gauge field configurations on a $20^4$ lattice, the quark propagator dressing functions are evaluated, the dynamical quark mass is extracted and the chiral limit of these quantities is discussed. By removing the low-lying modes of the Dirac operator, chiral symmetry is artificially restored. Its effect on the dressing functions is discussed.

  5. Technology initiatives with government/business overlap

    Science.gov (United States)

    Knapp, Robert H., Jr.

    2015-03-01

    Three important present-day technology development settings involve significant overlap between government and private sectors. The Advanced Research Project Agency for Energy (ARPA-E) supports a wide range of "high risk, high return" projects carried out in academic, non-profit or private business settings. The Materials Genome Initiative (MGI), based in the White House, aims at radical acceleration of the development process for advanced materials. California public utilities such as Pacific Gas & Electric operate under a structure of financial returns and political program mandates that make them arms of public policy as much as independent businesses.

  6. Probing the topological structure of the QCD vacuum with overlap fermions

    International Nuclear Information System (INIS)

    Overlap fermions implement exact chiral symmetry on the lattice and are thus an appropriate tool for investigating the chiral and topological structure of the QCD vacuum. We study various chiral and topological aspects on Luescher-Weisz-type quenched gauge field configurations using overlap fermions as a probe. Particular emphasis is placed upon the analysis of the spectral density and the localisation properties of the eigenmodes as well as on the local structure of topological charge fluctuations. (orig.)

  7. Probing the topological structure of the QCD vacuum with overlap fermions

    International Nuclear Information System (INIS)

    Overlap fermions implement exact chiral symmetry on the lattice and are thus an appropriate tool for investigating the chiral and topological structure of the QCD vacuum. We study various chiral and topological aspects on Luescher-Weisz-type quenched gauge field configurations using overlap fermions as a probe. Particular emphasis is placed upon the analysis of the spectral density and the localisation properties of the eigenmodes as well as on the local structure of topological charge fluctuations

  8. Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1

    Directory of Open Access Journals (Sweden)

    Bonander Nicklas

    2008-07-01

    Full Text Available Abstract Background We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strain, V5 hxt1-7Δ, in which only HXT1-7 had been deleted. In this study, we compared the transcriptome of the resultant strain, V5.TM6*P, with that of its wild-type parent, V5, at different glucose concentrations. Results cDNA array analyses revealed that alterations in gene expression that occur when transitioning from a respiro-fermentative (V5 to a respiratory (V5.TM6*P strain, are very similar to those in cells undergoing a diauxic shift. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4 (in complex with Hap2, 3, 5, Cat8 and Mig1, and used this in combination with verified binding consensus sequences to identify genes likely to be regulated by one or more of these. Of the induced genes in our dataset, 77% had binding sites for the Hap complex, with 72% having at least two. In addition, 13% were found to have a binding site for Cat8 and 21% had a binding site for Mig1. Unexpectedly, both the up- and down-regulation of many of the genes in our dataset had a clear glucose dependence in the parent V5 strain that was not present in V5.TM6*P. This indicates that the relief of glucose repression is already operable at much higher glucose concentrations than is widely accepted and suggests that glucose sensing might occur inside the cell. Conclusion Our dataset gives a remarkably complete view of the involvement of genes in the TCA cycle, glyoxylate cycle and respiratory chain in the expression of the phenotype of V5.TM6*P. Furthermore, 88% of the transcriptional response of the induced genes in our dataset can be related to the potential

  9. Current situation analysis and suggestions of employee turnover in military hospital%军队医院聘用人员离职现状分析及对策

    Institute of Scientific and Technical Information of China (English)

    陈莉莉; 路文亮; 刘文颖; 高鹏; 魏巍; 许树根

    2015-01-01

    目的:为医院管理者对聘用人员管理并有效留住人才提供依据和建议。方法通过采用问卷调查和统计分析的方法进行讨论。结果离职人员从专业看,护理比例最高(47.92%);从学历看,本科比例最高(42.36%)、大专为(36.11%);从在院工作时间看,1~3年最多(38.19%);从职称看,初级技术职务最多(79.17%);离职原因主要为家庭原因(33.33%)、寻求外部职业机会(31.25%)。结论医院聘用初级技术人员,特别是护士离职较严重,要求医院管理者加大对聘用人员的人文关怀和职业规划引导,确保人才队伍的可持续发展。%Objective To provide suggestions for effective human resources management of hospital .Methods Question-naire and statistic analysis was used during the discussion .Results From the point of the position , the turn over rate of nursing was highest (47.92%).From the perspective of education background , undergraduate degree took up 42.36% while college degree took up 36.11%.And the turnover rate of employees whose work time lasts for 1 to 3 years was highest (38.19%).Primary title took up to 79.17%;The main reasons for employee turnover were family issues (33.33%) and outside job opportunities (31.25%).Conclu-sion The main turnover group is the primary title employee , especially the nursing .This requires more humanistic care and better ca-reer planning on the current employees to ensure the stability of our talents .

  10. The Cause Analysis of Scaling and Controlling Suggestions of the Oilfields%渤西油田群结垢成因分析及控制建议

    Institute of Scientific and Technical Information of China (English)

    赵德喜

    2013-01-01

    渤西油田群歧口18-1、歧口17-2平台水源井和生产水系统存在结垢现象,一定程度的影响了油田正常生产。通过对现场工艺流程的调研、垢样组分以及水型与结垢关系的分析,确定了现场垢样主要为CaCO3垢,现场水样为NaHCO3型水,水样本身有很大的结垢倾向;结合ScaleChem软件对温度、压力、pH值等关键因素进行了结垢趋势预测研究,明确温度、压力突变是结垢发生的主要外因。根据调研分析结果,提出了切实可行的现场结垢控制建议。%Water wells and production water systems in QK18-1, QK17-2 of Boxi group oilfield exist scaling phenomenon that seriously affects the normal production. By way of investigating the process, analyzing the components of scale and scaling relations with Water type ,We reach a conclusion that the field scale is mainly CaCO3 scale, the type of field water is NaHCO3 and this water system has serious scaling tendency. In addition, We made a study on the relation between the scaling tendency and the surroundings such as temperature, pressure and pH with ScaleChem software, which make us know that the main reasons of external fouling occurs are high temperature and pressure jump. According to the results of the analysis, the feasible suggestions for scaling control is given.

  11. Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus

    Directory of Open Access Journals (Sweden)

    de Kroon Gerard HJ

    2010-07-01

    Full Text Available Abstract Background Water Rails (Rallus aquaticus inhabit fragmented freshwater wetlands across their Palearctic distribution. Disjunct populations are now thought to be morphologically similar over their vast geographic range, though four subspecies had been recognized previously. The fossil record suggests that Water Rails (R. aquaticus were already spread across the Palearctic by the Pleistocene ~2 million years ago, and the oldest fossil remains thought to be closely related to the common ancestor of water rails date from the Pliocene. Results To investigate population structure in Water Rails at the genetic level we sequenced three independent loci: 686 base pairs (bp of the mitochondrial DNA COI barcode; 618 bp of the intron ADH5; and 746 bp of the exon PTPN12. Phylogeographic analysis revealed that Water Rails breeding in eastern Asia (R. a. indicus, also known as the Brown-cheeked Rail are strongly differentiated from the Water Rails in Western and Middle Asia and Europe (R. a. aquaticus and R. a. korejewi. The Kimura 3-parameter plus Gamma COI genetic distance between these two geographic groups was > 3%, and they differed by 18 diagnostic substitutions commensurate with differences between recently diverged sister species of birds. In spite of the low number of variable sites, the two nuclear loci supported this split. We estimated the split of the Brown-cheeked Rail and the Water Rail to have occurred ~534,000 years ago (95% CI 275,000-990,000 years ago. Fragmentation of the widespread ancestral population and eventual speciation of water rails is likely attributable to vicariance by a barrier formed by glacial cycles, continuous uplift of the Tibetan Plateau and increased sedimentation in deserts in southern Asia that originated in the Miocene. Conclusions Water Rails from East Asia were genetically differentiated from the ones breeding in Europe and Western to Middle Asia. Most of the genetic signal was from mitochondrial COI, and

  12. Risk Factors for Dysmotility, Acid Reflux Symptoms, and Overlap Using FSSG in Japan

    Directory of Open Access Journals (Sweden)

    Seiji Shiota

    2012-01-01

    Full Text Available Aims. FSSG {frequency scale for the symptoms of gastroesophageal reflux disease (GERD} was developed as a diagnostic tool for dysmotility and acid reflux symptoms. We first used FSSG to investigate the prevalence and risk factors for dysmotility and acid reflux symptoms and overlap of the two symptoms in a Japanese population. Methods. A cross-sectional survey was performed in Japanese underwent the routine medical examination. Dysmotility and acid reflux symptom were diagnosed by using FSSG. Subjects met both criteria were considered as overlap group. Results. Among 778 subjects, 395 persons were included in the final analyses. Dysmotility symptoms were found in 32.6% and acid reflux symptoms in 20.5%. Their overlap was found in 13.9% of all 395 subjects, which in 42.6% of dysmotility symptoms and 67.9% of acid reflux symptoms. Multiple logistic analysis showed that female gender was significantly associated with dysmotility symptoms compared with controls. Female gender, smoking, and hiatus hernia were significantly associated with overlap. Smoking was significantly associated with overlap compared with dysmotility symptoms alone and acid reflux symptoms alone. Conclusions. Overlap between dysmotility and acid reflux symptoms was common in Japan. Smoking was an independent risk factor for overlap among two symptoms.

  13. Activation of words with phonological overlap

    Directory of Open Access Journals (Sweden)

    Claudia K. Friedrich

    2013-08-01

    Full Text Available Multiple lexical representations overlapping with the input (cohort neighbors are temporarily activated in the listener’s mental lexicon when speech unfolds in time. Activation for cohort neighbors appears to rapidly decline as soon as there is mismatch with the input. However, it is a matter of debate whether or not they are completely excluded from further processing. We recorded behavioral data and event-related brain potentials (ERPs in auditory-visual word onset priming during a lexical decision task. As primes we used the first two syllables of spoken German words. In a carrier word condition, the primes were extracted from spoken versions of the target words (ano-ANORAK 'anorak'. In a cohort neighbor condition, the primes were taken from words that overlap with the target word up to the second nucleus (ana- taken from ANANAS 'pineapple'. Relative to a control condition, where primes and targets were unrelated, lexical decision responses for cohort neighbors were delayed. This reveals that cohort neighbors are disfavored by the decision processes at the behavioral front end. In contrast, left-anterior ERPs reflected long-lasting facilitated processing of cohort neighbors. We interpret these results as evidence for extended parallel processing of cohort neighbors. That is, in parallel to the preparation and elicitation of delayed lexical decision responses to cohort neighbors, aspects of the processing system appear to keep track of those less efficient candidates.

  14. Non-perturbative renormalisation for overlap fermions

    International Nuclear Information System (INIS)

    Using non-perturbative techniques we have found the renormalisation factor, Z, in the RI-MOM scheme for quark bilinear operators in quenched QCD. We worked with overlap fermions using the Luescher-Weisz gauge action. Our calculation was performed at β = 8.45 at a lattice spacing of 1/a=2.1 GeV using a value of ρ = 1.4. Our results show good agreement between the vector and the axial vector in the zero mass limit. This shows that overlap fermions have good chiral properties. To attempt to improve the discretisation errors in our results we subtracted the O(a2) terms in one-loop lattice perturbation theory from the Monte Carlo Green functions. In particular we paid attention to the operators for the observable left angle x right angle. We found a value for the renormalisation constants ZMSv2b and ZMSv2a just less than 1.9 at μ = 1/a = 2.1 GeV. (orig.)

  15. Contact resistance and overlapping capacitance in flexible sub-micron long oxide thin-film transistors for above 100 MHz operation

    Science.gov (United States)

    Münzenrieder, Niko; Salvatore, Giovanni A.; Petti, Luisa; Zysset, Christoph; Büthe, Lars; Vogt, Christian; Cantarella, Giuseppe; Tröster, Gerhard

    2014-12-01

    In recent years new forms of electronic devices such as electronic papers, flexible displays, epidermal sensors, and smart textiles have become reality. Thin-film transistors (TFTs) are the basic blocks of the circuits used in such devices and need to operate above 100 MHz to efficiently treat signals in RF systems and address pixels in high resolution displays. Beyond the choice of the semiconductor, i.e., silicon, graphene, organics, or amorphous oxides, the junctionless nature of TFTs and its geometry imply some limitations which become evident and important in devices with scaled channel length. Furthermore, the mechanical instability of flexible substrates limits the feature size of flexible TFTs. Contact resistance and overlapping capacitance are two parasitic effects which limit the transit frequency of transistors. They are often considered independent, while a deeper analysis of TFTs geometry imposes to handle them together; in fact, they both depend on the overlapping length (LOV) between source/drain and the gate contacts. Here, we conduct a quantitative analysis based on a large number of flexible ultra-scaled IGZO TFTs. Devices with three different values of overlap length and channel length down to 0.5 μm are fabricated to experimentally investigate the scaling behavior of the transit frequency. Contact resistance and overlapping capacitance depend in opposite ways on LOV. These findings establish routes for the optimization of the dimension of source/drain contact pads and suggest design guidelines to achieve megahertz operation in flexible IGZO TFTs and circuits.

  16. An empirical assessment of the overlap between sexual victimization and sex offending.

    Science.gov (United States)

    Jennings, Wesley G; Zgoba, Kristen M; Maschi, Tina; Reingle, Jennifer M

    2014-12-01

    There has been a recent proliferation in the number of studies that are investigating the phenomenon that has been coined the victim-offender overlap. There has been noticeably less attention toward examining the sexual victimization and sex offending overlap. Acknowledging this gap in the literature, the present study provides an assessment of this overlap among a large sample of male prisoners with a focus on the cycle of violence hypothesis. Bivariate results reveal a considerable degree of overlap between sexual victimization and sex offending, and multivariate results estimated from a series of bivariate probit models simultaneously assessing both outcomes suggest that experiencing emotional abuse early on in the life-course is a robust risk factor for experiencing sexual victimization and demonstrating sex offending behavior. Furthermore, being physically neglected and witnessing family violence also emerged as significant risk factors for sexual victimization. Study limitations and policy implications are also discussed. PMID:23864522

  17. Advanced brain aging: relationship with epidemiologic and genetic risk factors, and overlap with Alzheimer disease atrophy patterns.

    Science.gov (United States)

    Habes, M; Janowitz, D; Erus, G; Toledo, J B; Resnick, S M; Doshi, J; Van der Auwera, S; Wittfeld, K; Hegenscheid, K; Hosten, N; Biffar, R; Homuth, G; Völzke, H; Grabe, H J; Hoffmann, W; Davatzikos, C

    2016-01-01

    We systematically compared structural imaging patterns of advanced brain aging (ABA) in the general-population, herein defined as significant deviation from typical BA to those found in Alzheimer disease (AD). The hypothesis that ABA would show different patterns of structural change compared with those found in AD was tested via advanced pattern analysis methods. In particular, magnetic resonance images of 2705 participants from the Study of Health in Pomerania (aged 20-90 years) were analyzed using an index that captures aging atrophy patterns (Spatial Pattern of Atrophy for Recognition of BA (SPARE-BA)), and an index previously shown to capture atrophy patterns found in clinical AD (Spatial Patterns of Abnormality for Recognition of Early Alzheimer's Disease (SPARE-AD)). We studied the association between these indices and risk factors, including an AD polygenic risk score. Finally, we compared the ABA-associated atrophy with typical AD-like patterns. We observed that SPARE-BA had significant association with: smoking (Ppatterns of atrophy were partially overlapping with, but notably deviating from those typically found in AD. Subjects with ABA had higher SPARE-AD values; largely due to the partial spatial overlap of associated patterns in temporal regions. The AD polygenic risk score was significantly associated with SPARE-AD but not with SPARE-BA. Our findings suggest that ABA is likely characterized by pathophysiologic mechanisms that are distinct from, or only partially overlapping with those of AD. PMID:27045845

  18. A case study of discordant overlapping meta-analyses: vitamin d supplements and fracture.

    Directory of Open Access Journals (Sweden)

    Mark J Bolland

    Full Text Available BACKGROUND: Overlapping meta-analyses on the same topic are now very common, and discordant results often occur. To explore why discordant results arise, we examined a common topic for overlapping meta-analyses- vitamin D supplements and fracture. METHODS AND FINDINGS: We identified 24 meta-analyses of vitamin D (with or without calcium and fracture in a PubMed search in October 2013, and analysed a sample of 7 meta-analyses in the highest ranking general medicine journals. We used the AMSTAR tool to assess the quality of the meta-analyses, and compared their methodologies, analytic techniques and results. Applying the AMSTAR tool suggested the meta-analyses were generally of high quality. Despite this, there were important differences in trial selection, data extraction, and analytical methods that were only apparent after detailed assessment. 25 trials were included in at least one meta-analysis. Four meta-analyses included all eligible trials according to the stated inclusion and exclusion criteria, but the other 3 meta-analyses "missed" between 3 and 8 trials, and 2 meta-analyses included apparently ineligible trials. The relative risks used for individual trials differed between meta-analyses for total fracture in 10 of 15 trials, and for hip fracture in 6 of 12 trials, because of different outcome definitions and analytic approaches. The majority of differences (11/16 led to more favourable estimates of vitamin D efficacy compared to estimates derived from unadjusted intention-to-treat analyses using all randomised participants. The conclusions of the meta-analyses were discordant, ranging from strong statements that vitamin D prevents fractures to equally strong statements that vitamin D without calcium does not prevent fractures. CONCLUSIONS: Substantial differences in trial selection, outcome definition and analytic methods between overlapping meta-analyses led to discordant estimates of the efficacy of vitamin D for fracture prevention

  19. Genome-wide Gene Expression Analysis of Mucosal Colonic Biopsies and Isolated Colonocytes Suggests a Continuous Inflammatory State in the Lamina Propria of Patients with Quiescent Ulcerative Colitis

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Hansen, Morten; Olsen, Jørgen;

    2010-01-01

    syndrome (controls, n = 10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure...

  20. Trophic overlap between native and invasive stream crayfish

    Science.gov (United States)

    Magoulick, Daniel D.; Piercey, Glenn L.

    2016-01-01

    We examined trophic dynamics of a stream food web where invasive Orconectes neglectusappear to be displacing native O. eupunctus in the Spring River drainage of the Ozark Highlands, Missouri and Arkansas, USA. We collected crayfish species and possible food sources seasonally from a site of sympatry on the South Fork Spring River. We determined diet overlap and potential for competition between O. eupunctus and O. neglectus, and investigated seasonal variation using carbon and nitrogen stable isotope analyses and gut content analyses. Gut content analysis showed both species of crayfish consumed mainly detritus during summer and spring, with other prey categories varying by species and season. Stable isotope analysis showed that O. eupunctus and O. neglectus relied on invertebrates as a major energy and nutrient source throughout summer, autumn, and spring, and the two species showed differences in their stable isotope signatures during spring and summer, but not autumn. Given the trophic overlap between O. eupunctus and O. neglectus, there is a potential for the two species to compete for food and to be ecologically redundant. Ecological redundancy can lead to reduced effects on ecosystem function post-invasion, and therefore examining ecological redundancy of potential invaders should be a conservation priority.

  1. A Social Network Model Exhibiting Tunable Overlapping Community Structure

    NARCIS (Netherlands)

    Liu, D.; Blenn, N.; Van Mieghem, P.F.A.

    2012-01-01

    Social networks, as well as many other real-world networks, exhibit overlapping community structure. In this paper, we present formulas which facilitate the computation for characterizing the overlapping community structure of networks. A hypergraph representation of networks with overlapping commun

  2. Analysis of school authorities´ concepts and suggestions on bullying - doi: 10.4025/actascieduc.v36i1.21940

    Directory of Open Access Journals (Sweden)

    José Leon Crochík

    2014-02-01

    Full Text Available Interviews by school authorities from five public primary schools inSão Paulo,São Paulo State,Brazilwere analyzed. The contents of the interviews by school principals and pedagogical coordinators investigated (1 the manner they understood bullying, especially with regard to their determinations; (2 their proposals for combating the problem; (3 the relationship between their understanding of the phenomenon and the suggestions against it. Results showed that the authorities that perceived the social determination on school violence had the best structured suggestions against the phenomenon, with regard to its understanding by students and teachers. On the other hand, others, foregrounded on a more reductionist stance which made difficult the perception of bulling within the school milieu, suggested activities which were not relevant to the factors that produced it and thus not efficacious in their attacking the phenomenon.

  3. 对企业管理案例分析的几点建议%About business management case analysis several suggestions

    Institute of Scientific and Technical Information of China (English)

    张爱民

    2012-01-01

    This article case reading and the analysis method has carried on the preliminary discussion to the university industry and commerce management science curriculum, stressed carries on to the case reading step and the analysis basic mentality has combed. Based on this proposed management case reading and analysis several skills, the coach pupils carry on the management case discussion and the analysis by the time to the teacher in the case teaching have the help.%探讨高校企业管理学课程中案例的阅读与分析方法,梳理案例阅读步骤和分析的基本思路,提出管理案例阅读与分析的几个技巧。

  4. Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease

    OpenAIRE

    Lu, Yue; He, Xin; Zhong, Sheng

    2007-01-01

    OSCAR is a web platform for cluster and cross-species analysis of microarray data. It provides a comprehensive but friendly environment to both users and algorithm developers. For users, OSCAR provides cluster tools for both single and multiple species data, together with interactive analysis features. For single species data, OSCAR currently provides Hierarchical Clustering, K-means, partition around medoids (PAM), Self-Organizing Map (SOM), Tight Clustering and a novel algorithm called ‘Con...

  5. Social externalities, overlap and the poverty trap.

    Science.gov (United States)

    Kim, Young-Chul; Loury, Glenn C

    2014-12-01

    Previous studies find that some social groups are stuck in poverty traps because of network effects. However, these studies do not carefully analyze how these groups overcome low human capital investment activities. Unlike previous studies, the model in this paper includes network externalities in both the human capital investment stage and the subsequent career stages. This implies that not only the current network quality, but also the expectations about future network quality affect the current investment decision. Consequently, the coordinated expectation among the group members can play a crucial role in the determination of the final state. We define "overlap" for some initial skill ranges, whereby the economic performance of a group can be improved simply by increasing expectations of a brighter future. We also define "poverty trap" for some ranges, wherein a disadvantaged group is constrained by its history, and we explore the egalitarian policies to mobilize the group out of the trap.

  6. Novel overlapping coding sequences in Chlamydia trachomatis

    DEFF Research Database (Denmark)

    Jensen, Klaus Thorleif; Petersen, Lise; Falk, Søren;

    2006-01-01

    Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein...... coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853...... that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several...

  7. Grid adaptation using chimera composite overlapping meshes

    Science.gov (United States)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1994-01-01

    The objective of this paper is to perform grid adaptation using composite overlapping meshes in regions of large gradient to accurately capture the salient features during computation. The chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using trilinear interpolation. Application to the Euler equations for shock reflections and to shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well-resolved.

  8. Grid adaption using Chimera composite overlapping meshes

    Science.gov (United States)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1993-01-01

    The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.

  9. Fusion protein gene nucleotide sequence similarities, shared antigenic sites and phylogenetic analysis suggest that phocid distemper virus 2 and canine distemper virus belong to the same virus entity.

    NARCIS (Netherlands)

    I.K.G. Visser (Ilona); R.W.J. van der Heijden (Roger); M.W.G. van de Bildt (Marco); M.J.H. Kenter (Marcel); C. Örvell; A.D.M.E. Osterhaus (Albert)

    1993-01-01

    textabstractNucleotide sequencing of the fusion protein (F) gene of phocid distemper virus-2 (PDV-2), recently isolated from Baikal seals (Phoca sibirica), revealed an open reading frame (nucleotides 84 to 2075) with two potential in-frame ATG translation initiation codons. We suggest that the secon

  10. The clinical and genetic features of COPD-asthma overlap syndrome.

    Science.gov (United States)

    Hardin, Megan; Cho, Michael; McDonald, Merry-Lynn; Beaty, Terri; Ramsdell, Joe; Bhatt, Surya; van Beek, Edwin J R; Make, Barry J; Crapo, James D; Silverman, Edwin K; Hersh, Craig P

    2014-08-01

    Individuals with chronic obstructive pulmonary disease (COPD) and asthma are an important but poorly characterised group. The genetic determinants of COPD and asthma overlap have not been studied. The aim of this study was to identify clinical features and genetic risk factors for COPD and asthma overlap. Subjects were current or former smoking non-Hispanic whites or African-Americans with COPD. Overlap subjects reported a history of physician-diagnosed asthma before the age of 40 years. We compared clinical and radiographic features between COPD and overlap subjects. We performed genome-wide association studies (GWAS) in the non-Hispanic whites and African-American populations, and combined these results in a meta-analysis. More females and African-Americans reported a history of asthma. Overlap subjects had more severe and more frequent respiratory exacerbations, less emphysema and greater airway wall thickness compared to subjects with COPD alone. The non-Hispanic white GWAS identified single nucleotide polymorphisms in the genes CSMD1 (rs11779254, p=1.57 × 10(-6)) and SOX5 (rs59569785, p=1.61 × 10(-6)) and the meta-analysis identified single nucleotide polymorphisms in the gene GPR65 (rs6574978, p=1.18 × 10(-7)) associated with COPD and asthma overlap. Overlap subjects have more exacerbations, less emphysema and more airway disease for any degree of lung function impairment compared to COPD alone. We identified novel genetic variants associated with this syndrome. COPD and asthma overlap is an important syndrome and may require distinct clinical management. PMID:24876173

  11. Separation and sequence detection of overlapped fingerprints: experiments and first results

    Science.gov (United States)

    Kärgel, Rainer; Giebel, Sascha; Leich, Marcus; Dittmann, Jana

    2011-11-01

    Latent fingerprints provide vital information in modern crime scene investigation. On frequently touched surfaces the fingerprints may overlap which poses a major problem for forensic analysis. In order to make such overlapping fingerprints available for analysis, they have to be separated. An additional evaluation of the sequence in which the fingerprints were brought onto the surface can help to reconstruct the progression of events. Advances in both tasks can considerably aid crime investigation agencies and are the subject of this work. Here, a statistical approach, initially devised for the separation of overlapping text patterns by Tonazzini et al.,1 is employed to separate overlapping fingerprints. The method involves a maximum a posteriori estimation of the single fingerprints and the mixing coefficients, computed by an expectation-maximization algorithm. A fingerprint age determination feature based on corrosion is evaluated for sequence estimation. The approaches are evaluated using 30 samples of overlapping latent fingerprints on two different substrates. The fingerprint images are acquired with a non-destructive chromatic white light surface measurement device, each sample containing exactly two fingerprints that overlap in the center of the image. Since forensic investigations rely on manual assessment of acquired fingerprints by forensics experts, a subjective scale ranging from 0 to 8 is used to rate the separation results. Our results indicate that the chosen method can separate overlapped fingerprints which exhibit strong differences in contrast, since results gradually improve with the growing contrast difference of the overlapping fingerprints. Investigating the effects of corrosion leads to a reliable determination of the fingerprints' sequence as the timespan between their leaving increases.

  12. Geometrical constraint experimental determination of Raman lidar overlap profile.

    Science.gov (United States)

    Li, Jian; Li, Chengcai; Zhao, Yiming; Li, Jing; Chu, Yiqi

    2016-06-20

    A simple experimental method to determine the overlap profile of Raman lidar is presented in this paper. Based on Mie and Raman backscattering signals and a geometrically constrained condition, the overlap profile of a Raman lidar system can be determined. Our approach simultaneously retrieves the lidar ratio of aerosols, which is one of the most important sources of uncertainty in the overlap profile determination. The results indicate that the overlap factor is significantly influenced by the lidar ratio in experimental methods. A representative case study indicates that the correction of the overlap profile obtained by this method is practical and feasible. PMID:27409119

  13. Evaluation of a Highly Anticlastic Panel with Tow Overlaps

    Science.gov (United States)

    Wu, K. Chauncey; Gurdal, Zafer

    2007-01-01

    A rectangular, variable-stiffness panel with tow overlaps was manufactured using an advanced tow placement machine. The cured panel had large anticlastic imperfections, with measured amplitudes of over two times the average panel thickness. These imperfections were not due to the overall steered-fiber layup or the tow overlaps, but instead resulted from local asymmetries in the laminate that were caused by a manufacturing oversight. In the nominal panel layup, fiber angles vary linearly from 60 degrees on the panel axial centerline to 30 degrees on the parallel edges. A geometrically nonlinear analysis was performed with a -280 degree Fahrenheit thermal load to simulate the postcure cooldown to room temperature. The predicted geometric imperfections correlated well with the measured panel shape. Unique structural test fixtures were then developed which greatly reduced these imperfections, but they also caused prestresses in the panel. Surface imperfections measured after the panel was installed in the test fixtures were used with nonlinear finite element analyses to predict these fixturing-induced prestresses. These prestresses were also included in structural analyses of panel end compression to failure, and the analytical results compared well with test data when both geometric and material nonlinearities were included.

  14. Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

    Science.gov (United States)

    Sood, Mariam R; Sereno, Martin I

    2016-08-01

    Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:27061771

  15. Application of Non-overlapping Mortar Finite Element Method to Electromagnetic Analysis%非重叠Mortar有限元法在电磁分析中的应用

    Institute of Scientific and Technical Information of China (English)

    刘守豹; 阮江军; 彭迎; 杜志叶; 黄道春; 王栋

    2011-01-01

    The mortar element method (MEM) is a new domain decomposition technique. MEM allows to take benefit of the presence of the subdomains in order to choose the discretization method, which is best adapted to the local behavior of the solution of the partial differential equation. In mortar finite element method (MFEI~I) a discretized mortar space is introduced to approximate the original continuous function space. The continuity of degree of freedoms across the non-conforming interface is ensured by the surface integration in a weak sense. The MFEM could "Mortar" the inter face between subdomains effectively. This paper gave the fundamental of non-overlapping MFEM (NO-MFEM); the procedures of calculating the mortar condition were discussed; the calculation and construction of the global matrix was proposed. By two dimensional static magnetic model and three dimensional electrostatic model, the validity of NO-MFEM was proved. This work is fundamental for extending MFEM to the other applications in computational electromagnetics.%Mortar元法(mortarelement method,MEM)是一种新型区域分解算法,它允许将求解区域分解为多个子域,在各个区域以最适合子域特征的方式离散。在各个区域的交界面上,边界节点不要求逐点匹配,而是通过建立加权积分形式的Mortar条件使得交界面上的传递条件在分布意义上满足。Mortar有限元法(mortar finite element method,MFEM)将MEM和有限元法(finite element method,FEM)相结合,在各区域中分别使用FEM网格离散,区域的交界面上通

  16. Fusion protein gene nucleotide sequence similarities, shared antigenic sites and phylogenetic analysis suggest that phocid distemper virus 2 and canine distemper virus belong to the same virus entity.

    OpenAIRE

    Visser, Ilona; Heijden, Roger; van de Bildt, Marco; Kenter, Marcel; Örvell, C.; Osterhaus, Albert

    1993-01-01

    textabstractNucleotide sequencing of the fusion protein (F) gene of phocid distemper virus-2 (PDV-2), recently isolated from Baikal seals (Phoca sibirica), revealed an open reading frame (nucleotides 84 to 2075) with two potential in-frame ATG translation initiation codons. We suggest that the second in-frame ATG triplet at positions 264 to 266 initiates the translation, resulting in a protein of 537 amino acid residues with a calculated M(r) of 63,035. The putative F1/F2 cleavage site, locat...

  17. Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

    Directory of Open Access Journals (Sweden)

    Eroukova Veronika

    2008-12-01

    Full Text Available Abstract Background Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, ~4700 strains for increased sensitivity to paromomycin, which targets the process of protein synthesis. Results As expected, our analysis indicated that the majority of deletion strains (134 with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45, cellular component biogenesis and organization (28, DNA maintenance (21, transport (20, others (38 and unknown (39. These may represent minor cellular target sites (side-effects for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. Conclusion We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s.

  18. Gene expression analysis of parthenogenetic embryonic development of the pea aphid, Acyrthosiphon pisum, suggests that aphid parthenogenesis evolved from meiotic oogenesis.

    Directory of Open Access Journals (Sweden)

    Dayalan G Srinivasan

    Full Text Available Aphids exhibit a form of phenotypic plasticity, called polyphenism, in which genetically identical females reproduce sexually during one part of the life cycle and asexually (via parthenogenesis during the remainder of the life cycle. The molecular basis for aphid parthenogenesis is unknown. Cytological observations of aphid parthenogenesis suggest that asexual oogenesis evolved either through a modification of meiosis or from a mitotic process. As a test of these alternatives, we assessed the expression levels and expression patterns of canonical meiotic recombination and germline genes in the sexual and asexual ovaries of the pea aphid, Acyrthosiphon pisum. We observed expression of all meiosis genes in similar patterns in asexual and sexual ovaries, with the exception that some genes encoding Argonaute-family members were not expressed in sexual ovaries. In addition, we observed that asexual aphid tissues accumulated unspliced transcripts of Spo11, whereas sexual aphid tissues accumulated primarily spliced transcripts. In situ hybridization revealed Spo11 transcript in sexual germ cells and undetectable levels of Spo11 transcript in asexual germ cells. We also found that an obligately asexual strain of pea aphid produced little spliced Spo11 transcript. Together, these results suggest that parthenogenetic oogenesis evolved from a meiosis-like, and not a mitosis-like, process and that the aphid reproductive polyphenism may involve a modification of Spo11 gene activity.

  19. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  20. Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns

    OpenAIRE

    Fischer Lukáš; Cvrčková Fatima; Dvořáková Lenka

    2007-01-01

    Abstract Background Plant hybrid proline-rich proteins (HyPRPs) are putative cell wall proteins consisting, usually, of a repetitive proline-rich (PR) N-terminal domain and a conserved eight-cysteine motif (8 CM) C-terminal domain. Understanding the evolutionary dynamics of HyPRPs might provide not only insight into their so far elusive function, but also a model for other large protein families in plants. Results We have performed a phylogenetic analysis of HyPRPs from seven plant species, i...

  1. 国内冷链物流发展现状与对策%Simple Analysis on Status and Suggestion on Domestic Cold Chain Logistics

    Institute of Scientific and Technical Information of China (English)

    漆莼

    2012-01-01

    With the development of economy and the rise of living level, people's concern has turned to the quality of the product from the previous quantity. To better satisfy people's demand on food, cold chain logistics is playing a more and more important role. In this article, the basic meaning of cold chain logistics was initially introduced. Then, with cold chain logistics measurements from abroad, aiming the existing prob- lems at home, in terms of "cold" and "chain", the paper put forward some reasonable suggestions. And in the "chain" perspective, detailed suggestions are offered to the government, industry organization and companies themselves respectively.%随着经济的发展和人们生活水平的提高,人们的消费观念逐渐从原来的单一数量化向如今的多元质量化转变,为了满足消费者需求,保证食品的新鲜、营养和安全,冷链物流体系发挥着越来越重要的作用。首先介绍了冷链物流的基本内涵,然后阐述了目前国内冷链物流的特征,之后结合国外发展冷链物流的一些具体做法.针对国内冷链物流存在的问题从“冷”和“链”两方面提出了一些对策,其中在“链”的角度上,重点从政府、行业组织和企业自身三个方面给出了具体的对策建议。

  2. Overlapping Spreading Centers: Implications from Crack Growth Simulation by the Displacement Discontinuity Method

    Science.gov (United States)

    Sempere, Jean-Christophe; MacDonald, Ken C.

    1986-02-01

    Overlapping spreading centers (OSC's) are a fundamental aspect of accretionary processes at intermediate and fast-spreading centers and typically occur at deep points along the axial depth profile. They have a characteristic geometry consisting of two en echelon overlapping, curving ridges separated by an elongated depression. The length to width ratio of this overlap basin is typically 3∶1. We have been successful in reproducing the overlapping spreading center geometry by modelling the growth of two initially parallel elastic cracks of given length and offset in a tensile stress field at infinity. A boundary element displacement discontinuity method was used to solve this problem. Our calculated results are compared with seafloor observations in terms of the size and shape of the overlap region. For small OSC's, there is a very good agreement between calculations and observations but, for large ones, the overlap basin tends to be longer than our predicted results indicate. This suggests that the assumptions made in the model (i.e., perfectly elastic, isotropic and homogeneous medium) are perhaps valid for the brittle lid above the magma chamber that underlies OSC's with small offsets (OSC's with large offsets. Our modelling shows that the initial interaction of closely spaced surface ruptures along spreading centers is to deflect away from one another as they approach. The deflection will be the greatest for small misalignments of the fracture systems, thus even minor misalignments of the spreading centers may result in the development of OSC's. Where the misalignment is less than the width of the cracking front, the fracture systems may meet head-on creating a saddle point along the axial depth profile. Our results support the hypothesis suggested by Macdonald et al. [1984] in which overlapping spreading centers develop where two magmatic pulses migrate toward each other along the strike of the spreading center following fracture systems and magmatic conduits

  3. Enzymatic assembly of overlapping DNA fragments.

    Science.gov (United States)

    Gibson, Daniel G

    2011-01-01

    Three methods for assembling multiple, overlapping DNA molecules are described. Each method shares the same basic approach: (i) an exonuclease removes nucleotides from the ends of double-stranded (ds) DNA molecules, exposing complementary single-stranded (ss) DNA overhangs that are specifically annealed; (ii) the ssDNA gaps of the joined molecules are filled in by DNA polymerase, and the nicks are covalently sealed by DNA ligase. The first method employs the 3'-exonuclease activity of T4 DNA polymerase (T4 pol), Taq DNA polymerase (Taq pol), and Taq DNA ligase (Taq lig) in a two-step thermocycled reaction. The second method uses 3'-exonuclease III (ExoIII), antibody-bound Taq pol, and Taq lig in a one-step thermocycled reaction. The third method employs 5'-T5 exonuclease, Phusion® DNA polymerase, and Taq lig in a one-step isothermal reaction and can be used to assemble both ssDNA and dsDNA. These assembly methods can be used to seamlessly construct synthetic and natural genes, genetic pathways, and entire genomes and could be very useful for molecular engineering tools. PMID:21601685

  4. Overlapping Zone Partitioning Localisation Technique for RFID

    Directory of Open Access Journals (Sweden)

    Kavi K. Khedo

    2010-04-01

    Full Text Available Basically used for contactless identification, Radio Frequency Identification (RFID technology was originallythought as a complement for the drawbacks of the Barcode. Due to its capabilities and on-going drop in cost,researchers have started to look into other areas where RFID can be employed. One such area of research isReal-Time Location Tracking (RTLT, especially for indoor environments. While technologies such as Ultra-Sound, Infrared, WiFi, Bluetooth and GSM have been considered for indoor localisation, their requirements forline of sight and/or prohibitive cost have hindered their successful adoption. We are therefore presenting a lowcostsolution using RFID technology which we refer to as the ‘Overlapping Zone Partitioning’ (OZP techniquethat can be implemented using basic off-the-shelf RFID Readers and which has been derived from the zonebasedlocalisation technique. We have successfully implemented OZP and evaluated its performance. It hasbeen found that its accuracy is enhanced by nearly 40% in comparison to a normal zone-based localisationsystem. Its performance in terms of correct zone classification is within the range of 80-90%.

  5. Some Indices of Alphabet Overlap Graph

    Institute of Scientific and Technical Information of China (English)

    Rong Yang; Zhao-Lan Yang; He-Ping Zhang

    2012-01-01

    The undirected de Bruijn graph is often used as the model of communication network for its useful properties,such as short diameter,small maximum vertex degree.In this paper,we consider the alphabet overlap graph G(k,d,s):the vertex set V ={vㄧv =(v1…vk); vi ∈ {1,2,…,d},i =1,2,…,k}; they are distinct and two vertices u =(u1…uk) and v =(v1…vk) are adjacent if and only if us+i =vi or vs+i =ui (i =1,2,…,k-s).In particular,when s =1,G(k,d,s) is just an undirected de Bruijn graph.First,we give a formula to calculate the vertex degree of G(k,d,s).Then,we use the corollary of Menger's theorem to prove that the connectivity of G(k,d,s) is 2ds-2d2s-k for s ≥ k/2.

  6. A model of residential energy end-use in Canada: Using conditional demand analysis to suggest policy options for community energy planners

    International Nuclear Information System (INIS)

    We applied conditional demand analysis (CDA) to estimate the average annual energy use of various electrical and natural gas appliances, and derived energy reductions associated with certain appliance upgrades and behaviours. The raw data came from 9773 Canadian households, and comprised annual electricity and natural gas use, and responses to >600 questions on dwelling and occupant characteristics, appliances, heating and cooling equipment, and associated behaviours. Replacing an old (>10 years) refrigerator with a new one was estimated to save 100 kW h/year; replacing an incandescent lamp with a CFL/LED lamp was estimated to save 20 kW h/year; and upgrading an old central heating system with a new one was estimated to save 2000 kW h/year. This latter effect was similar to that of reducing the number of walls exposed to the outside. Reducing the winter thermostat setpoint during occupied, waking hours was estimated to lower annual energy use by 200 kW h/°C-reduction, and lowering the thermostat setting overnight in winter relative to the setting during waking hours (night-time setback) was estimated to have a similar effect. This information may be used by policy-makers to optimize incentive programs, information campaigns, or other energy use change instruments. - Highlights: ► Conditional demand analysis (CDA) applied to data from 9773 Canadian households. ► Energy savings associated with certain appliance upgrades estimated. ► Energy savings associated with thermostat behaviours estimated. ► Policy-makers can use findings to optimize incentives and information campaigns

  7. 我国农田化肥施用现状分析及建议%Analysis and Suggestions of Agricultural Fertilizer Application in China

    Institute of Scientific and Technical Information of China (English)

    杨慧; 刘立晶; 刘忠军; 商稳奇; 曲晓健

    2014-01-01

    The paper analyzed the current situation of fertilizers used in farmland in China , found problems of excessive fertilization and poor efficiency .The Unreasonable fertilization led to waste of money and power , environment pollution , threat of food safety,etc.Several suggestions,including policy, crop varieties, different fertilization,fertilizer varieties and so on were given , to ensure high yield of crop ,low investment , and environment protection .%综述了目前我国农田的化肥施用现状,指出了其中存在的化肥施用过量、利用率低等问题。同时,分析了不合理施肥造成的资金、能源浪费,环境污染,食品安全受到威胁等严重后果。从政策、作物品种、施肥制度、肥料品种、施肥新技术等方面提出几点建议,以达到确保作物增产的同时,达到减少投入、环境友好的效果。

  8. Taiyuan city waterlogging causes analysis and countermeasure suggestions%太原市城市内涝的原因分析及对策建议

    Institute of Scientific and Technical Information of China (English)

    徐迎春

    2014-01-01

    The paper interprets the concept of urban waterlogging,analyzes urban waterlogging causes,and puts forward waterlogging preventing suggestions from two phases of major flood season preparation phase and in-flood season emergency phase,and finally points out that:continuously improving drainage pipeline and discharging capacities are the key to controlling urban waterlogging for drainage facility management and mainte-nancer.%解释了城市内涝的含义,对产生城市内涝的主要原因进行了分析,并从主汛期前准备、主汛期中防汛应急两个阶段提出了防止内涝的对策建议,并指出不断完善排水管网,提高泄洪能力,加强对排水设施的管理和维护是遏制城市内涝的关键。

  9. Military Demand Analysis and Suggestions about Submarine Torpedo Launching System%潜艇鱼雷发射系统军事需求及对策分析

    Institute of Scientific and Technical Information of China (English)

    马亮; 李伟; 于大方

    2011-01-01

    潜艇鱼雷发射系统是潜艇武器系统的重要组成部分,其战技性能直接影响潜艇整体作战效能.本文针对潜艇鱼雷发射系统研究与建设现状,结合未来海战中潜艇作战行动的特点,分析了潜艇鱼雷发射系统的最新军事需求.通过分析鱼雷发射系统的综合指标要求,指出了其未来的发展趋势和涉及的关键技术,特别强调了鱼雷发射系统的整体性要求,并提出了几点建议.%Torpedo launching system is a key component of submarine weapon system, and its performance influences submarine's operational effectiveness. Considering the current research and development situations of submarine torpedo launching system, the new military demand for the submarine torpedo launching system in accordance with the future submarine combat is analyzed in this paper. By analyzing the composite index for torpedo launching system, the developing trend and the key technologies of the system are pointed out with emphasis on integrity demand, and some suggestions are offered.

  10. Status analysis and suggestions of the Road greening of Wuchang%武昌区道路绿化现状分析与建议

    Institute of Scientific and Technical Information of China (English)

    梁黎薇

    2014-01-01

    Through literature review and the status quo of WuChang area road greening on-the-spot investigation, summarized the WuChang district border trees, green belt, the characteristics of plant landscape, and analyzes the insufficiency of current WuChang, according to the actual situation of WuChang, put forward effective suggestions for future development of road greening.%本文通过查阅文献资料和对武昌区辖区内道路绿化现状进行实地调查,归纳总结了武昌区道路行道树树种运用、绿化带植物配置特点、绿化景观效果等,并分析概括出武昌区道路绿化现存的不足之处,根据武昌区实际情况,提出今后城区道路绿化发展的有效建议。

  11. Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes.

    Science.gov (United States)

    Srivastava, Vaibhav; Weber, Joseph R; Malm, Erik; Fouke, Bruce W; Bulone, Vincent

    2016-01-01

    S-acylation is a reversible post-translational modification of proteins known to be involved in membrane targeting, subcellular trafficking, and the determination of a great variety of functional properties of proteins. The aim of this work was to identify S-acylated proteins in poplar. The use of an acyl-biotin exchange method and mass spectrometry allowed the identification of around 450 S-acylated proteins, which were subdivided into three major groups of proteins involved in transport, signal transduction, and response to stress, respectively. The largest group of S-acylated proteins was the protein kinase superfamily. Soluble N-ethylmaleimide-sensitive factor-activating protein receptors, band 7 family proteins and tetraspanins, all primarily related to intracellular trafficking, were also identified. In addition, cell wall related proteins, including cellulose synthases and other glucan synthases, were found to be S-acylated. Twenty four of the identified S-acylated proteins were also enriched in detergent-resistant membrane microdomains, suggesting S-acylation plays a key role in the localization of proteins to specialized plasma membrane subdomains. This dataset promises to enhance our current understanding of the various functions of S-acylated proteins in plants. PMID:27148305

  12. Prioritization and burden analysis of rare variants in 208 candidate genes suggest they do not play a major role in CAKUT.

    Science.gov (United States)

    Nicolaou, Nayia; Pulit, Sara L; Nijman, Isaac J; Monroe, Glen R; Feitz, Wout F J; Schreuder, Michiel F; van Eerde, Albertien M; de Jong, Tom P V M; Giltay, Jacques C; van der Zwaag, Bert; Havenith, Marlies R; Zwakenberg, Susan; van der Zanden, Loes F M; Poelmans, Geert; Cornelissen, Elisabeth A M; Lilien, Marc R; Franke, Barbara; Roeleveld, Nel; van Rooij, Iris A L M; Cuppen, Edwin; Bongers, Ernie M H F; Giles, Rachel H; Knoers, Nine V A M; Renkema, Kirsten Y

    2016-02-01

    The leading cause of end-stage renal disease in children is attributed to congenital anomalies of the kidney and urinary tract (CAKUT). Familial clustering and mouse models support the presence of monogenic causes. Genetic testing is insufficient as it mainly focuses on HNF1B and PAX2 mutations that are thought to explain CAKUT in 5–15% of patients. To identify novel, potentially pathogenic variants in additional genes, we designed a panel of genes identified from studies on familial forms of isolated or syndromic CAKUT and genes suggested by in vitro and in vivo CAKUT models. The coding exons of 208 genes were analyzed in 453 patients with CAKUT using next-generation sequencing. Rare truncating, splice-site variants, and non-synonymous variants, predicted to be deleterious and conserved, were prioritized as the most promising variants to have an effect on CAKUT. Previously reported disease-causing mutations were detected, but only five were fully penetrant causal mutations that improved diagnosis. We prioritized 148 candidate variants in 151 patients, found in 82 genes, for follow-up studies. Using a burden test, no significant excess of rare variants in any of the genes in our cohort compared with controls was found. Thus, in a study representing the largest set of genes analyzed in CAKUT patients to date, the contribution of previously implicated genes to CAKUT risk was significantly smaller than expected, and the disease may be more complex than previously assumed. PMID:26489027

  13. Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions.

    Directory of Open Access Journals (Sweden)

    Niamh M C Connolly

    Full Text Available Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK, re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult.

  14. 加快宁夏信用类债券发行的对策与建议%Analysis and suggestions on issuing debenture bonds of Ningxia

    Institute of Scientific and Technical Information of China (English)

    兰勇

    2014-01-01

    近年来,发行企业债券、短期融资券和中期票据等信用类债券已逐渐成为我国企业融资的主要手段。本文对宁夏发行信用类债券与周边省区进行了比较,分析了宁夏信用类债券发行规模小的主要因素。在阐述全国信用类债券发行市场环境和借鉴发达地区企业发行信用类债券经验的基础上,提出了加快宁夏发行信用类债券的若干建议。%In recent years, issuing credit bonds, such as enterprise bond, short-term financing bond, and medium-term note, have gradually become the main means of enterprises' financing in China. The paper gives a comparison on issuing credit bonds between Ningxia and its neighboring provinces, and analyzes on the main factors affecting issuing credit bonds. Moreover, built on the introductions of China's financial environment and learning experiences from developed regions on issuing credit bonds, it puts forward some suggestions on issuing credit bonds of Ningxia.

  15. 苏宁云商商业模式分析及发展建议%Analysis of Commercial Model and Developing Suggestions about Suning

    Institute of Scientific and Technical Information of China (English)

    王喆薇

    2015-01-01

    With the rapid development of online shopping and the rise of electronic commerce, more and more enterprises into the internet. At the same time, with the rapid development of e-commerce, the online retail industry has also brought impact onto the traditional retail industry, promoting the innovation of the business model. Suning was produced under such a background. Firstly, analyzing Suning model, found the innovation and mode of operation, and then discusses the existing cloud business model, and finally development suggestions are put forward.%随着网购的兴起和电子商务的蓬勃发展,越来越多的企业涌上互联网。在电子商务快速发展的同时,网上零售业也给传统零售业带来了冲击,促使其创新商业模式。苏宁云商就是在这样一种背景下产生的。文章首先对苏宁云商的商业模式进行分析,发现其创新点和运作方式,然后探讨云商模式存在的问题,最后对苏宁云商的未来提出发展建议。

  16. 电信运营商IPTV发展困境分析及应对建议%Analysis of the IPTV Predicament and Suggestions for Telecommunication Operators

    Institute of Scientific and Technical Information of China (English)

    刘山

    2012-01-01

    IPTV作为三网融合的典型应用,拥有广阔的前景,目前作为IPTV推进主体之一的电信运营商,在发展中却面临着诸多的困难和巨大挑战。该文对电信运营商目前在IPTV发展上所面临的困境进行了深入分析,并提出电信运营商应对的策略建议,为电信运营商IPTV下一步发展战略的制定提供借鉴和参考。%As the demonstration application of tri-network convergence of telecommunications networks, cable TV networks and the internet, IPTV has a broad prospect of development. However, the telecommunication operators which are the main driving force of IPTV are facing many dififculties and chalenges. This paper deeply analyzes the dififculties faced by the operators in IPTV development, and then proposes some strategies and suggestions for references.

  17. A convergent overlapping domain decomposition method for total variation minimization

    KAUST Repository

    Fornasier, Massimo

    2010-06-22

    In this paper we are concerned with the analysis of convergent sequential and parallel overlapping domain decomposition methods for the minimization of functionals formed by a discrepancy term with respect to the data and a total variation constraint. To our knowledge, this is the first successful attempt of addressing such a strategy for the nonlinear, nonadditive, and nonsmooth problem of total variation minimization. We provide several numerical experiments, showing the successful application of the algorithm for the restoration of 1D signals and 2D images in interpolation/inpainting problems, respectively, and in a compressed sensing problem, for recovering piecewise constant medical-type images from partial Fourier ensembles. © 2010 Springer-Verlag.

  18. Non-overlapping domain decomposition methods in structural mechanics

    CERN Document Server

    Gosselet, Pierre; 10.1007/BF02905857

    2012-01-01

    The modern design of industrial structures leads to very complex simulations characterized by nonlinearities, high heterogeneities, tortuous geometries... Whatever the modelization may be, such an analysis leads to the solution to a family of large ill-conditioned linear systems. In this paper we study strategies to efficiently solve to linear system based on non-overlapping domain decomposition methods. We present a review of most employed approaches and their strong connections. We outline their mechanical interpretations as well as the practical issues when willing to implement and use them. Numerical properties are illustrated by various assessments from academic to industrial problems. An hybrid approach, mainly designed for multifield problems, is also introduced as it provides a general framework of such approaches.

  19. A suggested procedure for resolving an anomaly in least-squares data analysis known as ''Peelle's Pertinent Puzzle'' and the general implications for nuclear data evaluation

    International Nuclear Information System (INIS)

    Modern nuclear-data evaluation methodology is based largely on statistical inference, with the least-squares technique being chosen most often to generate best estimates for physical quantities and their uncertainties. It has been observed that those least-squares evaluations which employ covariance matrices based on absolute errors that are derived directly from the reported experimental data often tend to produce results which appear to be too low. This anomaly is discussed briefly in this report, and a procedure for resolving it is suggested. The method involves employing data uncertainties which are derived from errors expressed in percent. These percent errors are used, in conjunction with reasonable a priori estimates for the quantities to be evaluated, to derive the covariance matrices which are required for applications of the least-squares procedure. This approach appears to lead to more rational weighting of the experimental data and, thus, to more realistic evaluated results than are obtained when the errors are based on the actual data. The procedure is very straightforward when only one parameter must be estimated. However, for those evaluation exercises involving more than one parameter, this technique demands that a priori estimates be provided at the outset for all of the parameters in question. Then, the least-squares method is applied iteratively to produce a sequence of sets of estimated values which are anticipated to convergence toward a particular set of parameters which one then designates as the ''best'' evaluated results from the exercise. It is found that convergence usually occurs very rapidly when the a priori estimates approximate the final solution reasonably well

  20. Microarray analysis and functional tests suggest the involvement of expansins in the early stages of symbiosis of the arbuscular mycorrhizal fungus Glomus intraradices on tomato (Solanum lycopersicum).

    Science.gov (United States)

    Dermatsev, Vladimir; Weingarten-Baror, Carmiya; Resnick, Nathalie; Gadkar, Vijay; Wininger, Smadar; Kolotilin, Igor; Mayzlish-Gati, Einav; Zilberstein, Avia; Koltai, Hinanit; Kapulnik, Yoram

    2010-01-01

    Arbuscular mycorrhizal (AM) symbiosis occurs between fungi of the phylum Glomeromycota and most terrestrial plants. However, little is known about the molecular symbiotic signalling between AM fungi (AMFs) and non-leguminous plant species. We sought to further elucidate the molecular events occurring in tomato, a non-leguminous host plant, during the early, pre-symbiotic stage of AM symbiosis, i.e. immediately before and after contact between the AMF (Glomus intraradices) and the host. We adopted a semi-synchronized AMF root infection protocol, followed by genomic-scale, microarray-based, gene expression profiling at several defined time points during pre-symbiotic AM stages. The microarray results suggested differences in the number of differentially expressed genes and in the differential regulation of several functional groups of genes at the different time points examined. The microarray results were validated and one of the genes induced during contact between AMF and tomato, the expansin-like EXLB1, was functionally analysed. Expansins, encoded by a large multigene family, facilitate plant cell expansion. However, no biological or biochemical function has yet been established for plant-originated expansin-like proteins. EXLB1 transcripts were localized early during the association to cells that may perceive the fungal signal, and later during the association in close proximity to sites of AMF hypha-root colonization. Moreover, in transgenic roots, we demonstrated that a reduction in the steady-state level of EXLB1 transcript was correlated with a reduced rate of infection, reduced arbuscule expansion and reduced AMF spore formation.

  1. 物联网感知层信息安全分析与建议%Analysis and suggestion on information security of Internet of Things perceptual layer

    Institute of Scientific and Technical Information of China (English)

    马纪丰; 梁浩

    2012-01-01

    Internet of Things (IOT) , with the help of perception technology, aims to build a total connection network between human and things. Since the conception of IOT was proposed, IOT has been largely promoted and actively developed by the governments, research institutions and enterprises. As perception layer is the major source of IOT information, its information security is the most important issue during the development of IOT. This paper studies the key information technologies and security threats of perception layer, and then analyzes and summarizes the existing security mechanism. Finally, this paper gives security measures and suggestions on the current security concerns on the perception layer.%物联网是以感知为目的,实现人与人、人与物、物与人全面互联的网络.其概念一经提出,得到了各国政府、科研机构以及各类企业的大力推广和积极发展.感知层作为物联网信息获取的主要来源,其信息安全问题是物联网发展所面临的首要问题.对物联网感知层的信息获取方式以及存在的安全威胁进行了研究,并对现有的安全防护机制进行了分析和总结.最后,针对感知层目前存在的信息安全问题及其技术的发展趋势,提出了相应的应对建议措施.

  2. Candidate gene analysis of tooth agenesis identifies novel mutations in six genes and suggests significant role for WNT and EDA signaling and allele combinations.

    Science.gov (United States)

    Arte, Sirpa; Parmanen, Satu; Pirinen, Sinikka; Alaluusua, Satu; Nieminen, Pekka

    2013-01-01

    Failure to develop complete dentition, tooth agenesis, is a common developmental anomaly manifested most often as isolated but also as associated with many developmental syndromes. It typically affects third molars or one or few other permanent teeth but severe agenesis is also relatively prevalent. Here we report mutational analyses of seven candidate genes in a cohort of 127 probands with non-syndromic tooth agenesis. 82 lacked more than five permanent teeth excluding third molars, called as oligodontia. We identified 28 mutations, 17 of which were novel. Together with our previous reports, we have identified two mutations in MSX1, AXIN2 and EDARADD, five in PAX9, four in EDA and EDAR, and nine in WNT10A. They were observed in 58 probands (44%), with a mean number of missing teeth of 11.7 (range 4 to 34). Almost all of these probands had severe agenesis. Only few of the probands but several relatives with heterozygous genotypes of WNT10A or EDAR conformed to the common type of non-syndromic tooth agenesis, incisor-premolar hypodontia. Mutations in MSX1 and PAX9 affected predominantly posterior teeth, whereas both deciduous and permanent incisors were especially sensitive to mutations in EDA and EDAR. Many mutations in EDAR, EDARADD and WNT10A were present in several families. Biallelic or heterozygous genotypes of WNT10A were observed in 32 and hemizygous or heterozygous genotypes of EDA, EDAR or EDARADD in 22 probands. An EDARADD variant were in seven probands present together with variants in EDAR or WNT10A, suggesting combined phenotypic effects of alleles in distinct genes. PMID:23991204

  3. Candidate gene analysis of tooth agenesis identifies novel mutations in six genes and suggests significant role for WNT and EDA signaling and allele combinations.

    Directory of Open Access Journals (Sweden)

    Sirpa Arte

    Full Text Available Failure to develop complete dentition, tooth agenesis, is a common developmental anomaly manifested most often as isolated but also as associated with many developmental syndromes. It typically affects third molars or one or few other permanent teeth but severe agenesis is also relatively prevalent. Here we report mutational analyses of seven candidate genes in a cohort of 127 probands with non-syndromic tooth agenesis. 82 lacked more than five permanent teeth excluding third molars, called as oligodontia. We identified 28 mutations, 17 of which were novel. Together with our previous reports, we have identified two mutations in MSX1, AXIN2 and EDARADD, five in PAX9, four in EDA and EDAR, and nine in WNT10A. They were observed in 58 probands (44%, with a mean number of missing teeth of 11.7 (range 4 to 34. Almost all of these probands had severe agenesis. Only few of the probands but several relatives with heterozygous genotypes of WNT10A or EDAR conformed to the common type of non-syndromic tooth agenesis, incisor-premolar hypodontia. Mutations in MSX1 and PAX9 affected predominantly posterior teeth, whereas both deciduous and permanent incisors were especially sensitive to mutations in EDA and EDAR. Many mutations in EDAR, EDARADD and WNT10A were present in several families. Biallelic or heterozygous genotypes of WNT10A were observed in 32 and hemizygous or heterozygous genotypes of EDA, EDAR or EDARADD in 22 probands. An EDARADD variant were in seven probands present together with variants in EDAR or WNT10A, suggesting combined phenotypic effects of alleles in distinct genes.

  4. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon

    Science.gov (United States)

    Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast. PMID:27248693

  5. Structural Analysis of the Plakin Domain of Bullous Pemphigiod Antigen1 (BPAG1) Suggests That Plakins are Members of the Spectrin Superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Jefferson,J.; Ciatto, C.; Shapiro, l.; Liem, R.

    2007-01-01

    Bullous pemphigoid antigen 1 (BPAG1) is a member of the plakin family of proteins. The plakins are multi-domain proteins that have been shown to interact with microtubules, actin filaments and intermediate filaments, as well as proteins found in cellular junctions. These interactions are mediated through different domains on the plakins. The interactions between plakins and components of specialized cell junctions such as desmosomes and hemidesmosomes are mediated through the so-called plakin domain, which is a common feature of the plakins. We report the crystal structure of a stable fragment from BPAG1, residues 226-448, defined by limited proteolysis of the whole plakin domain. The structure, determined by single-wavelength anomalous diffraction phasing from a selenomethionine-substituted crystal at 3.0 {angstrom} resolution, reveals a tandem pair of triple helical bundles closely related to spectrin repeats. Based on this structure and analysis of sequence conservation, we propose that the architecture of plakin domains is defined by two pairs of spectrin repeats interrupted by a putative Src-Homology 3 (SH3) domain.

  6. Recent Male-Mediated Gene Flow over a Linguistic Barrier in Iberia, Suggested by Analysis of a Y-Chromosomal DNA Polymorphism

    Science.gov (United States)

    Hurles, Matthew E.; Veitia, Reiner; Arroyo, Eduardo; Armenteros, Manuel; Bertranpetit, Jaume; Pérez-Lezaun, Anna; Bosch, Elena; Shlumukova, Maria; Cambon-Thomsen, Anne; McElreavey, Ken; López de Munain, Adolfo; Röhl, Arne; Wilson, Ian J.; Singh, Lalji; Pandya, Arpita; Santos, Fabrício R.; Tyler-Smith, Chris; Jobling, Mark A.

    1999-01-01

    Summary We have examined the worldwide distribution of a Y-chromosomal base-substitution polymorphism, the T/C transition at SRY-2627, where the T allele defines haplogroup 22; sequencing of primate homologues shows that the ancestral state cannot be determined unambiguously but is probably the C allele. Of 1,191 human Y chromosomes analyzed, 33 belong to haplogroup 22. Twenty-nine come from Iberia, and the highest frequencies are in Basques (11%; n=117) and Catalans (22%; n=32). Microsatellite and minisatellite (MSY1) diversity analysis shows that non-Iberian haplogroup-22 chromosomes are not significantly different from Iberian ones. The simplest interpretation of these data is that haplogroup 22 arose in Iberia and that non-Iberian cases reflect Iberian emigrants. Several different methods were used to date the origin of the polymorphism: microsatellite data gave ages of 1,650, 2,700, 3,100, or 3,450 years, and MSY1 gave ages of 1,000, 2,300, or 2,650 years, although 95% confidence intervals on all of these figures are wide. The age of the split between Basque and Catalan haplogroup-22 chromosomes was calculated as only 20% of the age of the lineage as a whole. This study thus provides evidence for direct or indirect gene flow over the substantial linguistic barrier between the Indo-European and non–Indo-European–speaking populations of the Catalans and the Basques, during the past few thousand years. PMID:10521311

  7. Axial anomaly and index of the overlap hypercube operator

    International Nuclear Information System (INIS)

    The overlap hypercube fermion is constructed by inserting a lattice fermion with hypercubic couplings into the overlap formula. One obtains an exact Ginsparg-Wilson fermion, which is more complicated than the standard overlap fermion, but which has improved practical properties and is of current interest for use in numerical simulations. Here we deal with conceptual aspects of the overlap hypercube Dirac operator. Specifically, we evaluate the axial anomaly and the index, demonstrating that the correct classical continuum limit is recovered. Our derivation is non-perturbative and therefore valid in all topological sectors. At the non-perturbative level this result had previously only been shown for the standard overlap Dirac operator with Wilson kernel. The new techniques which we develop to accomplish this also for hypercubic kernels are of a general nature and have the potential to be extended to overlap Dirac operators with even more general kernels. (orig.)

  8. 如何避免会话中的重叠和干扰%How to Avoid Overlapping and Interruption in Conversation

    Institute of Scientific and Technical Information of China (English)

    徐冬梅; 李婷

    2015-01-01

    Both overlapping and interruption impede the fluency of discourse between the speakers. Firstly, overlapping is con-cerned with conversational principles and conversation analysis. On the one hand, overlapping violates the maxim of quantity and quality in conversational principle put forward by Grice;on the other hand, overlapping takes place at the transition relevance place (TRP) where turn-taking happens. Interruption, however, has nothing to do with this principle. But it breaks the continuity of the turn-constructional unite(TCU), leading to an impolite consequence.To some degree, it is an impolite behavior. In a word, overlap-ping and interruption have negative impacts on daily conversation. Therefore,several suggestions are put forward to avoid or save their occurrences.%会话中的重叠(overlapping)和干扰(interruption)既有相同点,也有极大的不同.首先,重叠与会话原则(Conversational Principles)和会话分析(Conversation Analysis)有关.一方面,重叠的发生违反了格莱斯的会话原则中的量的原则(maxim of quantity)和质的原则(maxim of quality);另一方面,重叠一般是发生在话语转换位置(Transition Relevance Place/TRP)的完结处,也就是发生话语轮换(turn-taking)的地方.干扰和会话原则无关,但它会中断轮换结构单元(Turn-Constructional Units/TCU)的连续性,导致当前说话者(current speaker)无法完整表达其话语.因此,从某种程度上说干扰是一种不礼貌的行为.尽管重叠与礼貌无关,但它也会影响交流的顺利进行.所以,文章最后提出了几大预防和补救措施.

  9. Analysis of Immune Response Markers in Jorge Lobo's Disease Lesions Suggests the Occurrence of Mixed T Helper Responses with the Dominance of Regulatory T Cell Activity

    Science.gov (United States)

    Azevedo, Michelle de C. S.; Rosa, Patricia S.; Soares, Cleverson T.; Fachin, Luciana R. V.; Baptista, Ida Maria F. D.; Woods, William J.; Garlet, Gustavo P.

    2015-01-01

    Jorge Lobo’s disease (JLD) is a chronic infection that affects the skin and subcutaneous tissues. Its etiologic agent is the fungus Lacazia loboi. Lesions are classified as localized, multifocal, or disseminated, depending on their location. Early diagnosis and the surgical removal of lesions are the best therapeutic options currently available for JLD. The few studies that evaluate the immunological response of JLD patients show a predominance of Th2 response, as well as a high frequency of TGF-β and IL-10 positive cells in the lesions; however, the overall immunological status of the lesions in terms of their T cell phenotype has yet to be determined. Therefore, the objective of this study was to evaluate the pattern of Th1, Th2, Th17 and regulatory T cell (Treg) markers mRNA in JLD patients by means of real-time PCR. Biopsies of JLD lesions (N = 102) were classified according to their clinical and histopathological features and then analyzed using real-time PCR in order to determine the expression levels of TGF-β1, FoxP3, CTLA4, IKZF2, IL-10, T-bet, IFN-γ, GATA3, IL-4, IL-5, IL-13, IL-33, RORC, IL-17A, IL-17F, and IL-22 and to compare these levels to those of healthy control skin (N = 12). The results showed an increased expression of FoxP3, CTLA4, TGF-β1, IL-10, T-bet, IL-17F, and IL-17A in lesions, while GATA3 and IL-4 levels were found to be lower in diseased skin than in the control group. When the clinical forms were compared, TGF-β1 was found to be highly expressed in patients with a single localized lesion while IL-5 and IL-17A levels were higher in patients with multiple/disseminated lesions. These results demonstrate the occurrence of mixed T helper responses and suggest the dominance of regulatory T cell activity, which could inhibit Th-dependent protective responses to intracellular fungi such as L. loboi. Therefore, Tregs may play a key role in JLD pathogenesis. PMID:26700881

  10. Probabilistic tsunami hazard assessment for Makran considering recently suggested larger maximum magnitudes and sensitivity analysis for GNSS-based early warning

    Science.gov (United States)

    Zamora, N.; Hoechner, A.; Babeyko, A. Y.

    2014-12-01

    Iran and Pakistan are countries frequently affected by destructive earthquakes, as for instance, the magnitude 6.6 Bam earthquake in 2003 in Iran with about 30 000 casualties, or the magnitude 7.6 Kashmir earthquake 2005 in Pakistan with about 80'000 casualties. Both events took place inland, but in terms of magnitude, even significantly larger events can be expected to happen offshore, at the Makran subduction zone. This small subduction zone is seismically rather quiescent, nevertheless a tsunami caused by a thrust event in 1945 (Balochistan earthquake) led to about 4000 casualties. Nowadays, the coastal regions are more densely populated and vulnerable to similar events. Furthermore, some recent publications discuss the possiblity of rather rare huge magnitude 9 events at the Makran subduction zone. We analyze the seismicity at the subduction plate interface and generate various synthetic earthquake catalogs spanning 100000 years. All the events are projected onto the plate interface using scaling relations and a tsunami model is run for every scenario. The tsunami hazard along the coast is computed and presented in the form of annual probability of exceedance, probabilistic tsunami height for different time periods and other measures. We show how the hazard reacts to variation of the Gutenberg-Richter parameters and maximum magnitudes.We model the historic Balochistan event and its effect in terms of coastal wave heights. Finally, we show how an effective tsunami early warning could be achieved by using an array of high-precision real-time GNSS (Global Navigation Satellite System) receivers along the coast by applying it to the 1945 event and by performing a sensitivity analysis.

  11. A Model-Based Framework to Overlap Product Development Activities

    OpenAIRE

    Viswanathan Krishnan; Steven D. Eppinger; Whitney, Daniel E.

    1997-01-01

    Intense competition in many industries forces manufacturing firms to develop new, higher quality products at an increasingly rapid pace. Overlapping product development activities is an important component of concurrent product development that can help firms develop products faster. However, since product development activities may be coupled in complex ways, overlapping interrelated activities can present many difficulties. Without careful management of the overlapped product development pr...

  12. Do Neutrino Wave Functions Overlap and Does it Matter?

    CERN Document Server

    Li, Cheng-Hsien

    2016-01-01

    Studies of neutrinos commonly ignore anti-symmetrization of their wave functions. This implicitly assumes that either spatial wave functions for neutrinos with approximately the same momentum do not overlap or their overlapping has no measurable consequences. We examine these assumptions by considering the evolution of three-dimensional neutrino wave packets (WPs). We find that it is perfectly adequate to treat accelerator and reactor neutrinos as separate WPs for typical experimental setup. While solar and supernova neutrinos correspond to overlapping WPs, they can be treated effectively as non-overlapping for analyses of their detection.

  13. 我国DTP药房的SWOT分析及发展建议%SWOT Analysis and Development Suggestion on DTP Pharmacy in China

    Institute of Scientific and Technical Information of China (English)

    杨显辉; 张晓霞

    2015-01-01

    目的:探寻我国直销患者(DTP)药房所处的市场环境,找出DTP药房发展的优势、劣势、机会和威胁,有针对性地提出建议。方法:运用态势分析法(SWOT),对我国DTP药房模式的优势、内部劣势、外部机会、面临的威胁进行分析,对我国DTP药房的发展提出了建议。结果:DTP药房可以成为医药企业利润新的增长点;该市场模式在产品、服务及区域竞争等方面存在优势,但在资源需求和认知度方面劣势明显;其市场环境中,良好的医药政策、公众用药多元化及企业品牌的树立为其提供了良好的市场机会,但医药体制以及竞争日益激烈的市场环境也对其发展产生了极大威胁。结论:为实现DTP药房的良好发展,国家应给予政策支持,医药企业应在服务水平、管理能力、集约化规模化经营及创新型等方面,采取切实可行的措施。%Objective: To investigate the market conditions and explore the strengths and weaknesses, opportunities and threats for the development of the direct-to-patient (DTP) pharmacy, and make recommendations for its development. Methods:The market environment, such as the advantages, internal weaknesses, external opportunities and threats of the DTP pharmacy was analyzed and summarized by the SWOT (strengths, weakness, opportunity, threats) analysis method. Results:The DTP pharmacy could become a new proift growth point of the pharmaceutical companies. This market model has the advantages in aspects of products, services and regional competition, but it has the obvious disadvantages in terms of resource requirements and awareness. With good medical policy, diversiifed medication habits of the public and corporate image building, the DTP pharmacy has good market opportunities;however, there are still threats such as the medical system and the increasingly iferce market competition. Conclusion:In order to achieve good development of

  14. Detecting overlapping instances in microscopy images using extremal region trees.

    Science.gov (United States)

    Arteta, Carlos; Lempitsky, Victor; Noble, J Alison; Zisserman, Andrew

    2016-01-01

    In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains - for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations - a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance.

  15. Online monitoring of the laser brazing of titanium overlap joints

    Science.gov (United States)

    Schmitt, R.; Vielhaber, K.; Donst, D.; Klocke, F.

    2007-06-01

    Image processing and thermography for its own are very versatile and established measurement techniques for many years. However, the combination of these two measurement technologies opens a new field of applications. The online monitoring of the laser-brazing of titanium overlap joints is such a new application. The laser brazing process for overlap joining of formed titanium sheets for the production of heat exchangers is presently being investigated at the Fraunhofer IPT. In comparison to conventional furnace brazing the laser brazing technology decreases substantially the heat impact and thus reduces the thermal material damage in the parts due to local selective heating in a laser beam focal spot. Even though the process is stable, errors in the brazing seam such as pores or unacceptable material oxidation can occur. To ensure a high quality an online process monitoring or even process control is necessary. But since the surface remains unchanged during this brazing process no geometrical inspection of the surface can be conducted. Therefore today's quality assurance performs x-ray or destructive testing. This paper demonstrates how the use of thermography in combination with image processing allows a machine integrated online monitoring of the laser brazing process. First the basic principals are presented which cover the fields of heat coupling, heat transmission and heat distribution as well as the temperature emission of light and the spectral properties of the laser beam shaping optic and so lead to the optical set-up. Then analysis algorithms are derived which characterize the process, detect process failures and make a seam tracking possible.

  16. Detecting overlapping instances in microscopy images using extremal region trees.

    Science.gov (United States)

    Arteta, Carlos; Lempitsky, Victor; Noble, J Alison; Zisserman, Andrew

    2016-01-01

    In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains - for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations - a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance. PMID:25980675

  17. Progress Testing: Critical Analysis and Suggested Practices

    Science.gov (United States)

    Albanese, Mark; Case, Susan M.

    2016-01-01

    Educators have long lamented the tendency of students to engage in rote memorization in preparation for tests rather than engaging in deep learning where they attempt to gain meaning from their studies. Rote memorization driven by objective exams has been termed a steering effect. Progress testing (PT), in which a comprehensive examination…

  18. Analysis about Unbalanced International Payment and Suggestions

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ 1.The cause of unbalanced international payment Since the implementation of reform and opening-up from the end of 1970's,due to the economic development and the gradually improved reliance on import,China used to witness the situation that exchange supply could not meet the demand, foreign exchange became a kind of resource in shortage. Therefore, we had to try every way to promote the export and increase the exchange reserve, it was an important economic task during that period.

  19. Nested Genetic Algorithm for Resolving Overlapped Spectral Bands

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A nested genetic algorithm, including genetic parameter level and genetic implemented level for peak parameters, was proposed and applied for resolving overlapped spectral bands. By the genetic parameter level, parameters of genetic algorithm were optimized; moreover, the number of overlapped peaks was determined simultaneously. Then parameters of individual peaks were computed with the genetic implemented level.

  20. Overlaps of Partial Neel States and Bethe States

    CERN Document Server

    Foda, O

    2015-01-01

    Partial Neel states are generalizations of the ordinary Neel (classical anti-ferromagnet) state that can have arbitrary integer spin. We study overlaps of these states with Bethe states. We first identify this overlap with a partial version of reflecting-boundary domain-wall partition function, and then derive various determinant representations for off-shell and on-shell Bethe states.

  1. Probing the chiral phase transition of Nf=2 clover fermions with valence overlap fermions

    International Nuclear Information System (INIS)

    Overlap fermions are a powerful tool for investigating the chiral and topological structure of the vacuum and the thermal states of QCD. We study various chiral and topological aspects of the finite temperature phase transition of Nf=2 flavours of O(a) improved Wilson fermions, using valence overlap fermions as a probe. Particular emphasis is placed upon the analysis of the spectral density and the localisation properties of the eigenmodes as well as on the local structure of topological charge fluctuations in the vicinity of the chiral phase transition. The calculations are done on 163 x 8 lattices generated by the DIK collaboration. (orig.)

  2. LHON/MELAS overlap syndrome associated with a mitochondrial MTND1 gene mutation.

    Science.gov (United States)

    Blakely, Emma L; de Silva, Rajith; King, Andrew; Schwarzer, Verena; Harrower, Tim; Dawidek, Gervase; Turnbull, Douglass M; Taylor, Robert W

    2005-05-01

    Pathogenic point mutations in the mitochondrial MTND1 gene have previously been described in association with two distinct clinical phenotypes -- Leber hereditary optic neuropathy (LHON) and mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). Here we report the first heteroplasmic mitochondrial DNA (mtDNA) point mutation (3376G>A) in the MTND1 gene associated with an overlap syndrome comprising the clinical features of both LHON and MELAS. Muscle histochemistry revealed subtle mitochondrial abnormalities, while biochemical analysis showed an isolated complex I deficiency. Our findings serve to highlight the growing importance of mutations in mitochondrial complex I structural genes in MELAS and its associated overlap syndromes.

  3. Non-perturbative renormalization of overlap quark bilinears on domain wall fermion configurations

    CERN Document Server

    Liu, Zhaofeng; Yang, Yi-Bo; Dong, Shao-Jing; Glatzmaier, Michael; Gong, Ming; Liu, Keh-Fei; Li, Anyi; Zhang, Jian-Bo

    2013-01-01

    We present renormalization constants of overlap quark bilinear operators on 2+1-flavor domain wall fermion configurations. Both overlap and domain wall fermions have chiral symmetry on the lattice. The scale independent renormalization constant for the local axial vector current is computed using a Ward Identity. The renormalization constants for the scalar, pseudoscalar and vector current are calculated in the RI-MOM scheme. Results in the MS-bar scheme are obtained by using perturbative conversion ratios. The analysis uses in total six ensembles with lattice sizes 24^3x64 and 32^3x64.

  4. Separation of overlapping linear frequency modulated (LFM) signals using the fractional fourier transform.

    Science.gov (United States)

    Cowell, David M J; Freear, Steven

    2010-10-01

    Linear frequency modulated (LFM) excitation combined with pulse compression provides an increase in SNR at the receiver. LFM signals are of longer duration than pulsed signals of the same bandwidth; consequently, in many practical situations, maintaining temporal separation between echoes is not possible. Where analysis is performed on individual LFM signals, a separation technique is required. Time windowing is unable to separate signals overlapping in time. Frequency domain filtering is unable to separate signals with overlapping spectra. This paper describes a method to separate time-overlapping LFM signals through the application of the fractional Fourier transform (FrFT), a transform operating in both time and frequency domains. A short introduction to the FrFT and its operation and calculation are presented. The proposed signal separation method is illustrated by application to a simulated ultrasound signal, created by the summation of multiple time-overlapping LFM signals and the component signals recovered with ±0.6% spectral error. The results of an experimental investigation are presented in which the proposed separation method is applied to time-overlapping LFM signals created by the transmission of a LFM signal through a stainless steel plate and water-filled pipe.

  5. Compressed Sensing Inspired Image Reconstruction from Overlapped Projections

    Directory of Open Access Journals (Sweden)

    Lin Yang

    2010-01-01

    Full Text Available The key idea discussed in this paper is to reconstruct an image from overlapped projections so that the data acquisition process can be shortened while the image quality remains essentially uncompromised. To perform image reconstruction from overlapped projections, the conventional reconstruction approach (e.g., filtered backprojection (FBP algorithms cannot be directly used because of two problems. First, overlapped projections represent an imaging system in terms of summed exponentials, which cannot be transformed into a linear form. Second, the overlapped measurement carries less information than the traditional line integrals. To meet these challenges, we propose a compressive sensing-(CS- based iterative algorithm for reconstruction from overlapped data. This algorithm starts with a good initial guess, relies on adaptive linearization, and minimizes the total variation (TV. Then, we demonstrated the feasibility of this algorithm in numerical tests.

  6. Piles, Tabs and Overlaps in Navigation among Documents

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Rønne; Hornbæk, Kasper Anders Søren

    2010-01-01

    Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles. In an experim......Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles....... In an experiment we compared 11 participants’ navigation with these variations and found strong task effects. Overall, overlapping windows were preferred and their structured layout worked well with some tasks. Surprisingly, tabbed documents were efficient in tasks requiring simply finding a document. Piled...... on document navigation and its support by piling....

  7. Sending Hidden Data via Google Suggest

    CERN Document Server

    Bialczak, Piotr; Szczypiorski, Krzysztof

    2011-01-01

    Google Suggest is a service incorporated within Google Web Search which was created to help user find the right search phrase by proposing the autocompleting popular phrases while typing. The paper presents a new network steganography method called StegSuggest which utilizes suggestions generated by Google Suggest as a hidden data carrier. The detailed description of the method's idea is backed up with the analysis of the network traffic generated by the Google Suggest to prove its feasibility. The traffic analysis was also performed to discover the occurrence of two TCP options: Window Scale and Timestamp which StegSuggest uses to operate. Estimation of method steganographic bandwidth proves that it is possible to insert 100 bits of steganogram into every suggestions list sent by Google Suggest service.

  8. Analytical Approximation of the Deconvolution of Strongly Overlapping Broad Fluorescence Bands

    Science.gov (United States)

    Dubrovkin, J. M.; Tomin, V. I.; Ushakou, D. V.

    2016-09-01

    A method for deconvoluting strongly overlapping spectral bands into separate components that enables the uniqueness of the deconvolution procedure to be monitored was proposed. An asymmetric polynomial-modified function subjected to Fourier filtering (PMGFS) that allowed more accurate and physically reasonable band shapes to be obtained and also improved significantly the deconvolution convergence was used as the band model. The method was applied to the analysis of complexation in solutions of the molecular probe 4'-(diethylamino)-3-hydroxyflavone with added LiCl. Two-band fluorescence of the probe in such solutions was the result of proton transfer in an excited singlet state and overlapped strongly with stronger spontaneous emission of complexes with the ions. Physically correct deconvolutions of overlapping bands could not always be obtained using available software.

  9. Communication: Unambiguous comparison of many-electron wavefunctions through their overlaps

    Science.gov (United States)

    Plasser, Felix; González, Leticia

    2016-07-01

    A simple and powerful method for comparing many-electron wavefunctions constructed at different levels of theory is presented. By using wavefunction overlaps, it is possible to analyze the effects of varying wavefunction models, molecular orbitals, and one-electron basis sets. The computation of wavefunction overlaps eliminates the inherent ambiguity connected to more rudimentary wavefunction analysis protocols, such as visualization of orbitals or comparing selected physical observables. Instead, wavefunction overlaps allow processing the many-electron wavefunctions in their full inherent complexity. The presented method is particularly effective for excited state calculations as it allows for automatic monitoring of changes in the ordering of the excited states. A numerical demonstration based on multireference computations of two test systems, the selenoacrolein molecule and an iridium complex, is presented.

  10. Study of the structure of the QCD vacuum by means of overlap fermions; Untersuchung der Struktur des QCD-Vakuums mit Hilfe von Overlap-Fermionen

    Energy Technology Data Exchange (ETDEWEB)

    Weinberg, Volker

    2008-12-15

    In this thesis the structure of the QCD vacuum and the nature of the chiral phase transition were studied by means of overlap fermions. The main topic of the theiss lies in the study of the infrared long-range aspects shown by the low-lying eigenmodes of the overlap operator. For the characterization of the structure and dimension of an arbitray density embedded in the four-dimensional space-time diverse analysis tools were developed. These are applied both at low temperature (T=0) in the valence-quark approximation of QCD and in the environment of the high-temperature phase transition of the full QCD for the description of the structure of the modes and the topological density, as well as for the analysis of the local self-duality of the basing gauge fields.

  11. An extension to artifact-free projection overlaps

    International Nuclear Information System (INIS)

    Purpose: In multipinhole single photon emission computed tomography, the overlapping of projections has been used to increase sensitivity. Avoiding artifacts in the reconstructed image associated with projection overlaps (multiplexing) is a critical issue. In our previous report, two types of artifact-free projection overlaps, i.e., projection overlaps that do not lead to artifacts in the reconstructed image, were formally defined and proved, and were validated via simulations. In this work, a new proposition is introduced to extend the previously defined type-II artifact-free projection overlaps so that a broader range of artifact-free overlaps is accommodated. One practical purpose of the new extension is to design a baffle window multipinhole system with artifact-free projection overlaps. Methods: First, the extended type-II artifact-free overlap was theoretically defined and proved. The new proposition accommodates the situation where the extended type-II artifact-free projection overlaps can be produced with incorrectly reconstructed portions in the reconstructed image. Next, to validate the theory, the extended-type-II artifact-free overlaps were employed in designing the multiplexing multipinhole spiral orbit imaging systems with a baffle window. Numerical validations were performed via simulations, where the corresponding 1-pinhole nonmultiplexing reconstruction results were used as the benchmark for artifact-free reconstructions. The mean square error (MSE) was the metric used for comparisons of noise-free reconstructed images. Noisy reconstructions were also performed as part of the validations. Results: Simulation results show that for noise-free reconstructions, the MSEs of the reconstructed images of the artifact-free multiplexing systems are very similar to those of the corresponding 1-pinhole systems. No artifacts were observed in the reconstructed images. Therefore, the testing results for artifact-free multiplexing systems designed using the

  12. Major role for a 3p21 region and lack of involvement of the t(3;8) breakpoint region in the development of renal cell carcinoma suggested by loss of heterozygosity analysis

    NARCIS (Netherlands)

    van den Berg, Anke; Hulsbeek, MMF; deJong, D; Kok, K; Veldhuis, PMJF; Roche, J; Buys, CHCM

    1996-01-01

    In a loss of heterozygosity analysis of 3p, we examined 44 sporadic cases of renal cell carcinoma (RCC) and matched normal tissue with 18 markers distributed over the whole p-arm. The majority of these markers clustered in three regions that have been suggested to be involved in the development of R

  13. BSPM: A NEW MECHANISM FOR "OVERLAP-MATCHING EXPRESSIONS" IN DPI

    Institute of Scientific and Technical Information of China (English)

    Li Zheng; Yu Nenghai; Li Yang

    2010-01-01

    Nowadays,using Deterministic Finite Automata (DFA) or Non-deterministic Finite Automata (NFA) to parse regular expressions is the most popular way for Deep Packet Inspection (DPI),and the research about DPI focuses on the improvement of DFA to reduce memory. However,most of the existing literature ignores a special kind of "overlap-matching expression",which causes states explosion and takes quite a large part in the DPI rules. To solve this problem,in this paper a new mechanism is proposed based on bitmap. We start with a simple regular expression to describe "overlap-matching expressions" and state the problem. Then,after calculating the terrible number of exploded states for this kind of expressions,the procedure of Bitmap-based Soft Parallel Mechanism (BSPM) is described. Based on BSPM,we discuss all the different types of "overlap-matching expressions" and give optimization suggestions of them separately. Finally,experiment results prove that BSPM can give an excellent performance on solving the problem stated above,and the optimization suggestions are also effective for the memory reduction on all types of "overlap-matching expressions".

  14. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online.

  15. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online. PMID:27671928

  16. Overlapping ion structures in the mid-altitude cusp under northward IMF: signature of dual lobe reconnection?

    Directory of Open Access Journals (Sweden)

    F. Pitout

    2012-03-01

    Full Text Available On some rare occasions, data from the Cluster Ion Spectrometer (CIS in the mid-altitude cusp reveal overlapping ion populations under northward interplanetary magnetic field (IMF. While the poleward part of the cusp exhibits the expected reverse dispersion due to lobe reconnection, its equatorward part shows a second ion population at higher-energy that coexists with the low energy tail of the dispersion. This second population is either dispersionless or slightly dispersed with energies increasing with increasing latitudes, indicative of lobe reconnection as well. Our analysis of a case that occurred 3 September 2002 when the IMF stayed northward for more than two hours suggests that the second population comes from the opposite hemisphere and is very likely on newly-closed field lines. We interpret this overlap of cusp populations as a clear mid-altitude signature of re-closed magnetic field lines by double lobe reconnection (reconnection in both hemispheres under northward IMF. This interpretation is supported by modelling performed with the Cooling model and an MHD model.

  17. Study on Spectral Overlap Model for Energy Transfer between J-Mult iplets in Rare Earth-Doped Crystals

    Institute of Scientific and Technical Information of China (English)

    王殿元; 夏上达; 尹民

    2003-01-01

    Based on the experimental data of KY3F10∶Tm3+ reported by Diaf, Kushida′s spectral overlap model (SOM) of energy transfer between J-multiplets was studied. Firstly, with the help of the Inokuti-Hirayama and Yokota-Tanimoto models, the luminescence decay curve of 3H4 of Tm3+ ion was fitted, and the fitted values of corresponding interaction parameters CDA of energy transfer and CDD of energy migration were obtained. Secondly, by compared with Kushida′s SOM in which the relevant Judd-Ofelt approximative transition rates are known, the average overlap integrals of SDD and SDA were obtained. For SDD, how to treat the contribution of the electronic-dipole (ED) crystal field transition forbidden by C4v site symmetry in the calculation of SDD was discussed. For SDA we suggested that, by including the contribution of the phonon sidebands in the analysis of oscillator strength of transition, Kushida′s SOM of ED-ED resonant energy transfer rate can be extended to non-resonant phonon-assisted D-A energy transfer. The strengths and widths of phonon sidebands in this example were discussed, and the results were reasonably good.

  18. Hybrid Self Organizing Map for Overlapping Clusters

    OpenAIRE

    M.N.M. Sap; Ehsan Mohebi

    2008-01-01

    The Kohonen self organizing map is an excellent tool in exploratoryphase of data mining and pattern recognition. The SOM is a popular tool that maps high dimensional space into a small number of dimensions by placing similar elements close together, forming clusters. Recently researchers found that to capture the uncertainty involved in cluster analysis, it is not necessary to have crisp boundaries in some clustering operations. In this paper to overcomethe uncertainty, a two-level clustering...

  19. Contact resistance and overlapping capacitance in flexible sub-micron long oxide thin-film transistors for above 100 MHz operation

    Energy Technology Data Exchange (ETDEWEB)

    Münzenrieder, Niko, E-mail: muenzenrieder@ife.ee.ethz.ch; Salvatore, Giovanni A.; Petti, Luisa; Zysset, Christoph; Büthe, Lars; Vogt, Christian; Cantarella, Giuseppe; Tröster, Gerhard [Electronics Laboratory Swiss Federal Institute of Technology (ETH) Zürich, Gloriastrasse 35, 8092 Zürich (Switzerland)

    2014-12-29

    In recent years new forms of electronic devices such as electronic papers, flexible displays, epidermal sensors, and smart textiles have become reality. Thin-film transistors (TFTs) are the basic blocks of the circuits used in such devices and need to operate above 100 MHz to efficiently treat signals in RF systems and address pixels in high resolution displays. Beyond the choice of the semiconductor, i.e., silicon, graphene, organics, or amorphous oxides, the junctionless nature of TFTs and its geometry imply some limitations which become evident and important in devices with scaled channel length. Furthermore, the mechanical instability of flexible substrates limits the feature size of flexible TFTs. Contact resistance and overlapping capacitance are two parasitic effects which limit the transit frequency of transistors. They are often considered independent, while a deeper analysis of TFTs geometry imposes to handle them together; in fact, they both depend on the overlapping length (L{sub OV}) between source/drain and the gate contacts. Here, we conduct a quantitative analysis based on a large number of flexible ultra-scaled IGZO TFTs. Devices with three different values of overlap length and channel length down to 0.5 μm are fabricated to experimentally investigate the scaling behavior of the transit frequency. Contact resistance and overlapping capacitance depend in opposite ways on L{sub OV}. These findings establish routes for the optimization of the dimension of source/drain contact pads and suggest design guidelines to achieve megahertz operation in flexible IGZO TFTs and circuits.

  20. Disentangling the Overlap Between Employee Engagement and Passion

    Directory of Open Access Journals (Sweden)

    Gaja Zager Kocjan

    2015-07-01

    Full Text Available With the emergence of positive psychology and the subsequent positive organizational behavior movement, focusing on the employee experience and factors of positive psychological states in employees has come to the forefront. In recent years, several studies have emphasized the practical value of employee engagement and passion (the dualistic model of passion; Vallerand et al., 2003 in predicting various positive individual and organizational outcomes (e.g., performance, well-being. Although engagement and passion seem relatively easy to spot at first glance, they are rather difficult to define and distinguish one from another. Therefore, the aim of the present article is to provide a comprehensive discussion on the shared aspects and conceptual differences between these two constructs within the work environment. The most noticeable overlap is proposed to exist between engagement and harmonious passion. It concerns the common underlying development mechanism, a very strong motivational force to engage in one's work, strong identification with work, and similar relationships with various antecedents and consequences. It is suggested that broader scope theories (such as the self-determination theory should be taken into consideration in order to unify common findings from both theoretical backgrounds and overcome redundancy and the risk of multiplication of concepts in positive psychology.

  1. Overlapped partitioning for ensemble classifiers of P300-based brain-computer interfaces.

    Science.gov (United States)

    Onishi, Akinari; Natsume, Kiyohisa

    2014-01-01

    A P300-based brain-computer interface (BCI) enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300). In this study, we evaluated ensemble linear discriminant analysis (LDA) classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA), or none. The results show that an ensemble stepwise LDA (SWLDA) classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance.

  2. Overlapped partitioning for ensemble classifiers of P300-based brain-computer interfaces.

    Directory of Open Access Journals (Sweden)

    Akinari Onishi

    Full Text Available A P300-based brain-computer interface (BCI enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300. In this study, we evaluated ensemble linear discriminant analysis (LDA classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA, or none. The results show that an ensemble stepwise LDA (SWLDA classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance.

  3. Genetic overlap among intelligence and other candidate endophenotypes for schizophrenia

    NARCIS (Netherlands)

    Aukes, Maartje F; Alizadeh, Behrooz Z; Sitskoorn, Margriet M; Kemner, Chantal; Ophoff, Roel A; Kahn, René S

    2009-01-01

    BACKGROUND: A strategy to improve genetic studies of schizophrenia involves the use of endophenotypes. Information on overlapping genetic contributions among endophenotypes may provide additional power, reveal biological pathways, and have practical implications for genetic research. Several cogniti

  4. Overlapping Communities Detection Based on Link Partition in Directed Networks

    Directory of Open Access Journals (Sweden)

    Qingyu Zou

    2013-09-01

    Full Text Available Many complex systems can be described as networks to comprehend both the structure and the function. Community structure is one of the most important properties of complex networks. Detecting overlapping communities in networks have been more attention in recent years, but the most of approaches to this problem have been applied to the undirected networks. This paper presents a novel approach based on link partition to detect overlapping communities structure in directed networks. In contrast to previous researches focused on grouping nodes, our algorithm defines communities as groups of directed links rather than nodes with the purpose of nodes naturally belong to more than one community. This approach can identify a suitable number of overlapping communities without any prior knowledge about the community in directed networks. We evaluate our algorithm on a simple artificial network and several real-networks. Experimental results demonstrate that the algorithm proposed is efficient for detecting overlapping communities in directed networks.  

  5. On the interpretation of wave function overlaps in quantum dots

    DEFF Research Database (Denmark)

    Stobbe, Søren; Hvam, Jørn Märcher; Lodahl, Peter

    2011-01-01

    The spontaneous emission rate of excitons strongly confined in quantum dots (QDs) is proportional to the overlap integral of electron and hole envelope wave functions. A common and intuitive interpretation of this result is that the spontaneous emission rate is proportional to the probability...... that the electron and the hole are located at the same point or region in space, i.e., they must coincide spatially to recombine. Here, we show that this interpretation is not correct even loosely speaking. By general mathematical considerations we compare the envelope wave function overlap, the exchange overlap...... integral, and the probability of electrons and holes coinciding, and find that the frequency dependence of the envelope wave function overlap integral is very different from that expected from the common interpretation. We show that these theoretical considerations lead to predictions for measurements. We...

  6. 42 CFR 73.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-10-01

    ... genetically modified. (d) Overlap select agents or toxins that meet any of the following criteria are excluded... Equine Encephalitis virus (c) Genetic Elements, Recombinant Nucleic Acids, and Recombinant Organisms:...

  7. Understanding asthma-chronic obstructive pulmonary disease overlap syndrome.

    Science.gov (United States)

    Wurst, Keele E; Kelly-Reif, Kaitlin; Bushnell, Greta A; Pascoe, Steven; Barnes, Neil

    2016-01-01

    Asthma-chronic obstructive pulmonary disease overlap syndrome (ACOS) is a loosely-defined clinical entity referring to patients who exhibit characteristics of both asthma and chronic obstructive pulmonary disease (COPD). Clinical definitions and classifications for ACOS vary widely, which impacts our understanding of prevalence, diagnosis and treatment of the condition. This literature review was therefore conducted to characterize the prevalence of ACOS and the effect of different disease definitions on these estimates, as this has not previously been explored. From an analysis of English language literature published from 2000 to 2014, the estimated prevalence of ACOS ranges from 12.1% to 55.2% among patients with COPD and 13.3%-61.0% among patients with asthma alone. This variability is linked to differences in COPD and asthma diagnostic criteria, disease ascertainment methods (spirometry-based versus clinical or symptom-based diagnoses and claims data), and population characteristics including age, gender and smoking. Understanding the reasons for differences in prevalence estimates of ACOS across the literature may help guide decision making on the most appropriate criteria for defining ACOS and aid investigators in designing future ACOS clinical studies aimed at effective treatment.

  8. Optical axis jitter rejection for double overlapped adaptive optics systems

    Science.gov (United States)

    Luo, Qi; Luo, Xi; Li, Xinyang

    2016-04-01

    Optical axis jitters, or vibrations, which arise from wind shaking and structural oscillations of optical platforms, etc., cause a deleterious impact on the performance of adaptive optics systems. When conventional integrators are utilized to reject such high frequency and narrow-band disturbance, the benefits are quite small despite their acceptable capabilities to reject atmospheric turbulence. In our case, two suits of complete adaptive optics systems called double overlapped adaptive optics systems (DOAOS) are used to counteract both optical jitters and atmospheric turbulence. A novel algorithm aiming to remove vibrations is proposed by resorting to combine the Smith predictor and notch filer. With the help of loop shaping method, the algorithm will lead to an effective and stable controller, which makes the characteristics of error transfer function close to notch filters. On the basis of the spectral analysis of observed data, the peak frequency and bandwidth of vibrations can be identified in advance. Afterwards, the number of notch filters and their parameters will be determined using coordination descending method. The relationship between controller parameters and filtering features is discussed, and the robustness of the controller against varying parameters of the control object is investigated. Preliminary experiments are carried out to validate the proposed algorithms. The overall control performance of DOAOS is simulated. Results show that time delays are a limit of the performance, but the algorithm can be successfully implemented on our systems, which indicate that it has a great potential to reject jitters.

  9. Phenotype of asthma-chronic obstructive pulmonary disease overlap syndrome

    OpenAIRE

    Rhee, Chin Kook

    2015-01-01

    Many patients with asthma or chronic obstructive pulmonary disease (COPD) have overlapping characteristics of both diseases. By spirometric definition, patients with both fixed airflow obstruction (AO) and bronchodilator reversibility or fixed AO and bronchial hyperresponsiveness can be considered to have asthma-COPD overlap syndrome (ACOS). However, patients regarded to have ACOS by spirometric criteria alone are heterogeneous and can be classified by phenotype. Eosinophilic inflammation, a ...

  10. Regional security overlaps in EU-Turkey affairs

    OpenAIRE

    Nielsen, Søren Cramer

    2013-01-01

    Throughout this project I analyze how the EU security community operates to secure dependable expectations of peaceful outcomes through its security cooperation with Turkey. This is done by examining EU security overlaps in the Turkey-EU security cooperation, Turkey EU-accession and the EU-Turkish energy security cooperation in the Caspian region with a focus on the Nabucco project. I conclude that the integration of Turkey into the EU security community reveals overlapping security concerns ...

  11. A novel symbol overlapping FFH-OCDMA system

    Institute of Scientific and Technical Information of China (English)

    Chengbin Shen(沈成彬); Chen Wu(吴琛); Jinhui Yu(于金辉); Ge Fan(范戈)

    2004-01-01

    @@ A novel symbol overlapping optical fast frequency-hop code-division multiple access(FFH-OCDMA)sys-tem is proposed,and its bit error rate(BER)performance is investigated under consideration of avalanchephotonic diode(APD)noise auid thermal noise.An experimental symbol overlapping(SO)FFH-OCDMAtestbed is developed and some experimental results axe given.The theoretical and experimental resultsshow that the system is apt to implement and has larger throughput.

  12. Evaluating Overlapping Communities with the Conductance of their Boundary Nodes

    OpenAIRE

    Havemann, Frank; Gläser, Jochen; Heinz, Michael; Struck, Alexander

    2012-01-01

    Usually the boundary of a community in a network is drawn between nodes and thus crosses its outgoing links. If we construct overlapping communities by applying the link-clustering approach nodes and links interchange their roles. Therefore, boundaries must drawn through the nodes shared by two or more communities. For the purpose of community evaluation we define a conductance of boundary nodes of overlapping communities analogously to the graph conductance of boundary-crossing links used to...

  13. Cooperative Games with Overlapping Coalitions: Charting the Tractability Frontier

    OpenAIRE

    Zick, Yair; Chalkiadakis, Georgios; Elkind, Edith; Markakis, Evangelos

    2014-01-01

    In many multiagent scenarios, agents distribute resources, such as time or energy, among several tasks. Having completed their tasks and generated profits, task payoffs must be divided among the agents in some reasonable manner. Cooperative games with overlapping coalitions (OCF games) are a recent framework proposed by Chalkiadakis et al. (2010), generalizing classic cooperative games to the case where agents may belong to more than one coalition. Having formed overlapping coalitions and div...

  14. Detecting overlapping protein complexes in protein-protein interaction networks

    OpenAIRE

    Nepusz, Tamás; Yu, Haiyuan; Paccanaro, Alberto

    2012-01-01

    We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a...

  15. Satisfying assignments of Random Boolean CSP: Clusters and Overlaps

    OpenAIRE

    Istrate, Gabriel

    2007-01-01

    The distribution of overlaps of solutions of a random CSP is an indicator of the overall geometry of its solution space. For random $k$-SAT, nonrigorous methods from Statistical Physics support the validity of the ``one step replica symmetry breaking'' approach. Some of these predictions were rigorously confirmed in \\cite{cond-mat/0504070/prl} \\cite{cond-mat/0506053}. There it is proved that the overlap distribution of random $k$-SAT, $k\\geq 9$, has discontinuous support. Furthermore, Achliop...

  16. Hereditary hemorrhagic telangiectasia and juvenile polyposis: an overlap of syndromes

    Energy Technology Data Exchange (ETDEWEB)

    Poletto, Erica D.; Levin, Terry L. [Montefiore Medical Center, Department of Radiology, Bronx, NY (United States); Trinh, Angela M. [Albert Einstein College of Medicine, Bronx, NY (United States); Loizides, Anthony M. [Children' s Hospital at Montefiore, Department of Pediatric Gastroenterology, Bronx, NY (United States)

    2010-07-15

    Hereditary hemorrhagic telangiectasia (HHT) (Osler-Weber-Rendu syndrome) is a syndrome characterized by multiorgan telangiectases and arteriovenous malformations. A subset of patients with a mutation in the MADH4 gene on chromosome 18 exhibits an overlapping syndrome of HHT and juvenile polyposis (JPS). We present one such family. Genetic testing is warranted when either HHT or JPS is diagnosed, as early recognition of this syndrome overlap allows appropriate management of these patients. (orig.)

  17. Hybrid Self Organizing Map for Overlapping Clusters

    Directory of Open Access Journals (Sweden)

    M.N.M. Sap

    2008-12-01

    Full Text Available The Kohonen self organizing map is an excellent tool in exploratoryphase of data mining and pattern recognition. The SOM is a popular tool that maps high dimensional space into a small number of dimensions by placing similar elements close together, forming clusters. Recently researchers found that to capture the uncertainty involved in cluster analysis, it is not necessary to have crisp boundaries in some clustering operations. In this paper to overcomethe uncertainty, a two-level clustering algorithm based on SOM which employs the rough set theory is proposed. The two-level stage Rough SOM (first using SOM to produce the prototypes that are then clustered in the second stage is found to perform well and more accurate compared with the proposed crisp clustering method (Incremental SOM and reduces the errors.

  18. A Bayesian variable selection procedure to rank overlapping gene sets

    Directory of Open Access Journals (Sweden)

    Skarman Axel

    2012-05-01

    Full Text Available Abstract Background Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prioritize gene sets, such as the genes in a given molecular pathway, have been described. In many cases, these methods test one gene set at a time, and therefore do not consider overlaps among the pathways. Here, we present a Bayesian variable selection method to prioritize gene sets that overcomes this limitation by considering all gene sets simultaneously. We applied Bayesian variable selection to differential expression to prioritize the molecular and genetic pathways involved in the responses to Escherichia coli infection in Danish Holstein cows. Results We used a Bayesian variable selection method to prioritize Kyoto Encyclopedia of Genes and Genomes pathways. We used our data to study how the variable selection method was affected by overlaps among the pathways. In addition, we compared our approach to another that ignores the overlaps, and studied the differences in the prioritization. The variable selection method was robust to a change in prior probability and stable given a limited number of observations. Conclusions Bayesian variable selection is a useful way to prioritize gene sets while considering their overlaps. Ignoring the overlaps gives different and possibly misleading results. Additional procedures may be needed in cases of highly overlapping pathways that are hard to prioritize.

  19. Management Model of Resources Equilibrium Distribution among Overlapping-Generations

    Institute of Scientific and Technical Information of China (English)

    Jiang Xuemin; Li Ling

    2004-01-01

    The overlapping generation models the western scholars have designed from various perspectives to address different kinds of issues do not reflect Chinese emerging political and economic problems, and cannot be entirely and blindly applied to Chinese practical situation. In this paper the authors endeavor to incorporate some western scholars' research results into their own research findings to present overlapping generations model theory in a new perspective through establishing an overlapping generations theory on population including articulation of concepts and theorems of biological generation, economic generation and social generation and the overlapping periods in biological generation and two overlapping periods in economic generation among three generations. This management model with equilibrium distribution of resource wealth includes overlapping generations length model (δ),equilibrium transfer model (θ) and a complete model on equilibrium distribution among generations (δ-θ).The model provides quantitative basis for the creation of resource management system, and fills in a theoretical gap in this discipline in China. Besides,it furnishes a new methodology and manipulable tool for Chinese government to establish a comprehensive management information bank for many sectors such as economic trade, population, science and technology, education, human resource, natural resource and environment, agriculture, forestry,industry, mining and energy.

  20. Molecular and clinical characterization of patients with overlapping 10p deletions.

    Science.gov (United States)

    Lindstrand, Anna; Malmgren, Helena; Verri, Annapia; Benetti, Elisa; Eriksson, Maud; Nordgren, Ann; Anderlid, Britt-Marie; Golovleva, Irina; Schoumans, Jacqueline; Blennow, Elisabeth

    2010-05-01

    Chromosome 10p terminal deletions have been associated with DiGeorge phenotype, and within the same genomic region haploinsufficiency of GATA3 causes the HDR syndrome (hypoparathyroidism, sensorineural deafness, renal dysplasia). We have performed detailed molecular analysis of four patients with partial overlapping 10p deletions by using FISH-mapping, array-CGH, and custom-designed high-resolution oligonucleotide array. All four patients had mental retardation and speech impairment and three of them showed variable signs of HDR syndrome. In addition, two patients had autistic behaviors and had similar dysmorphic features giving them a striking physical resemblance. A review of the literature identified 10 previously published cases with similar 10p deletions and reliable molecular or molecular cytogenetic mapping data. The combined information of present and previous cases suggests that partial deletions of 10p14-p15 represent a syndrome with a distinct and more severe phenotype than previously assumed. The main characteristics include severe mental retardation, language impairment, autistic behavior, and characteristic clinical features. A critical region involved in mental retardation and speech impairment is defined within 1.6 Mb in 10p15.3. In addition, deletion of 4.3 Mb within 10p14 is associated with autism and characteristic clinical findings. PMID:20425828

  1. Overlapping patterns of neural activity for different forms of novelty in fMRI

    Directory of Open Access Journals (Sweden)

    Colin Shaun Hawco

    2014-09-01

    Full Text Available When stimuli are presented multiple times, the neural response to repeated stimuli is reduced relative to novel stimuli (repetition suppression. Responses to different types of novelty were examined. Stimulus novelty was examined by contrasting first vs. second presentation of triads of objects during memory encoding. Semantic novelty was contrasted by comparing unrelated (semantically novel triads of objects to triads in which all three objects were related (e.g. all objects were tools. In recognition, associative novelty was examined by contrasting rearranged triads (previously seen objects in a new association with intact triads. Activity was observed in posterior regions (occipital and fusiform, with the largest extent of activity for stimulus novelty and smallest for associational novelty. Frontal activity was also observed in stimulus and semantic novelty. Additional analysis indicated that the hemodynamic response in voxels identified in the stimulus and semantic novelty contrasts was modulated by reaction time on a trial-by-trial basis. That is, the duration of the hemodynamic response was driven by reaction time. This was not the case for associative novelty. The high level of overlap across different forms of novelty suggests a similar mechanism for reduced neural activity, which may be related to reduced visual processing time. This is consistent with a facilitation model of repetition suppression, which posits a reduced peak and duration of neuronal firing for repeated stimuli.

  2. Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

    Directory of Open Access Journals (Sweden)

    Brian T. Weinert

    2013-08-01

    Full Text Available Recent studies have shown that lysines can be posttranslationally modified by various types of acylations. However, except for acetylation, very little is known about their scope and cellular distribution. We mapped thousands of succinylation sites in bacteria (E. coli, yeast (S. cerevisiae, human (HeLa cells, and mouse liver tissue, demonstrating widespread succinylation in diverse organisms. A majority of succinylation sites in bacteria, yeast, and mouse liver were acetylated at the same position. Quantitative analysis of succinylation in yeast showed that succinylation was globally altered by growth conditions and mutations that affected succinyl-coenzyme A (succinyl-CoA metabolism in the tricarboxylic acid cycle, indicating that succinylation levels are globally affected by succinyl-CoA concentration. We preferentially detected succinylation on abundant proteins, suggesting that succinylation occurs at a low level and that many succinylation sites remain unidentified. These data provide a systems-wide view of succinylation and its dynamic regulation and show its extensive overlap with acetylation.

  3. Quantitative analysis of overlapping XPS peaks by spectrum reconstruction

    DEFF Research Database (Denmark)

    Graat, Peter C.J.; Somers, Marcel A. J.

    1998-01-01

    The composition and thickness of thin iron oxide iron were evaluated from Fe 2p spectra as measured by X-ray photoelectron spectroscopy. To this end the experimental spectra were reconstructed from reference spectra of the constituents Fe/sup 0/, Fe/sup 2+/ and Fe/sup 3+/. The background contribu...

  4. Local-global overlap in diversity informs mechanisms of bacterial biogeography.

    Science.gov (United States)

    Livermore, Joshua A; Jones, Stuart E

    2015-11-01

    Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local-global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among 'patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.

  5. Niche convergence suggests functionality of the nocturnal fovea

    Directory of Open Access Journals (Sweden)

    Gillian L. Moritz

    2014-07-01

    Full Text Available The fovea is a declivity of the retinal surface associated with maximum visual acuity. Foveae are widespread across vertebrates, but among mammals they are restricted to haplorhine primates (tarsiers, monkeys, apes, and humans, which are primarily diurnal. Thus primates have long contributed to the prevailing view that the fovea is a functional adaptation to diurnal color vision. The foveae of nocturnal taxa, such as tarsiers, are widely interpreted as vestigial traits and therefore evidence of a diurnal ancestry. This enduring premise has been central to adaptive hypotheses on the origins of anthropoid primates; however, the question of whether the fovea of tarsiers is a functionless anachronism or a nocturnal adaptation remains open. To address this question, we focused on the diets of tarsiers (Tarsius and scops owls (Otus, two taxa united by numerous anatomical homoplasies, including foveate vision. A functional interpretation of these homoplasies predicts dietary convergence and competition. This prediction can be tested with an analysis of carbon and nitrogen stable isotopes in tissues, which integrate dietary information. As predicted, the isotopic niches of Tarsius and Otus overlapped. In both Borneo and the Philippines, the δ13C values were indistinguishable, whereas the δ15N values of Otus were marginally higher than those of Tarsius. Our results indicate that both diets consisted mainly of ground-dwelling prey and raise the possibility of some resource partitioning. Taken together, our isotopic analysis supports a functional interpretation of the many homoplasies shared by tarsiers and scops owls, including a retinal fovea. We suggest that the fovea might function similarly in tarsiers and scops owls by calibrating the auditory localization pathway. The integration of auditory localization and visual fixation during prey detection and acquisition might be critical at low light levels.

  6. A new approach to study of seabird-fishery overlap: Connecting chick feeding with parental foraging and overlap with fishing vessels

    Directory of Open Access Journals (Sweden)

    Junichi Sugishita

    2015-07-01

    Full Text Available Incidental fisheries bycatch is recognised as a major threat to albatross populations worldwide. However, fishery discards and offal produced in large quantities might benefit some scavenging seabirds. Here, we demonstrate an integrated approach to better understand the ecological ramifications of fine-scale overlap between seabirds and fisheries. As a case study, we examined whether foraging in association with a fishing vessel is advantageous for chick provisioning in terms of quantity of food delivered to chicks, in northern royal albatross (Diomedea sanfordi at Taiaroa Head, New Zealand. Fine-scale overlap between albatrosses and vessels was quantified by integrating GPS tracking and Vessel Monitoring Systems (VMS. Meal size delivered to chicks was measured using custom-designed nest balances, and monitoring of attendance of adults fitted with radio transmitters was used in conjunction with time-lapse photography at the nest allowed us to allocate each feeding event to a specific parent. The combination of these techniques enabled comparison of meal sizes delivered to chicks with parental foraging trip durations with or without fishing vessels association. A total of 45 foraging trips and associated chick feeding events were monitored during the chick-rearing period in 2012. Differences in the meal size and foraging trip duration relative to foraging overlap with fisheries were examined using a linear mixed-effect model, adjusted for chick age. Our results, based on three birds, suggest that foraging in association with vessels does not confer an advantage for chick feeding for this population that demonstrated low rates of overlap while foraging. The integrated research design presented can be applied to other seabird species that are susceptible to bycatch, and offers a valuable approach to evaluate habitat quality by linking habitat use and foraging success in terms of total amount of food delivered to offspring.

  7. A Case of Successful Use of Hypnosis in the Treatment of Parasomnia Overlap Disorder.

    Science.gov (United States)

    Kohler, William C; Kurz, Peter J; Kohler, Elizabeth A

    2015-01-01

    A young male patient was successfully treated for parasomnia overlap disorder (POD) using hypnosis. In 2006, this 16-year-old patient underwent a clinical evaluation for episodes of sleep talking, sleepwalking, and dream enactment. This initial assessment was followed by polysomnographic evaluation, a brain MRI, and three sessions of treatment using hypnosis. From the beginning, until the last contact in December 2011, benefits from the hypnotic suggestions were noted and documented. PMID:24738970

  8. Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

    OpenAIRE

    Xie, Mengshuang

    2016-01-01

    Mengshuang Xie, Wei Wang, Shuang Dou, Liwei Cui, Wei Xiao Department of Pulmonary Medicine, Qilu Hospital, Shandong University, Jinan, People’s Republic of China Background: The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evalua...

  9. Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

    OpenAIRE

    Xie M; Wang W; Dou S; Cui L; Xiao W

    2016-01-01

    Mengshuang Xie, Wei Wang, Shuang Dou, Liwei Cui, Wei Xiao Department of Pulmonary Medicine, Qilu Hospital, Shandong University, Jinan, People’s Republic of China Background: The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evaluation of ...

  10. Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

    OpenAIRE

    Xie, Mengshuang; Wang, Wei; Dou, Shuang; Cui, Liwei; Xiao, Wei

    2016-01-01

    Background The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evaluation of emphysema noninvasively. We investigated the value of quantitative CT measurements of emphysema in the diagnosis of ACOS. Methods This study included 404 participants; 151 asthm...

  11. The binding sites for cocaine and dopamine in the dopamine transporter overlap

    OpenAIRE

    Beuming, Thijs; Kniazeff, Julie; Bergmann, Marianne L; Shi, Lei; Gracia, Luis; Raniszewska, Klaudia; Newman, Amy Hauck; Javitch, Jonathan A.; Weinstein, Harel; Gether, Ulrik; Loland, Claus J

    2008-01-01

    Cocaine is a widely abused substance with psychostimulant effects that are attributed to inhibition of the dopamine transporter (DAT). We present molecular models for DAT binding of cocaine and cocaine analogs constructed from the high-resolution structure of the bacterial transporter homolog LeuT. Our models suggest that the binding site for cocaine and cocaine analogs is deeply buried between transmembrane segments 1, 3, 6 and 8, and overlaps with the binding sites for the substrates dopami...

  12. Optical Study of Flow and Combustion in an HCCI Engine with Negative Valve Overlap

    Science.gov (United States)

    Wilson, Trevor S.; Xu, Hongming; Richardson, Steve; Wyszynski, Miroslaw L.; Megaritis, Thanos

    2006-07-01

    One of the most widely used methods to enable Homogeneous Charge Compression Ignition (HCCI) combustion is using negative valve overlapping to trap a sufficient quantity of hot residual gas. The characteristics of air motion with specially designed valve events having reduced valve lift and durations associated with HCCI engines and their effect on subsequent combustion are not yet fully understood. In addition, the ignition process and combustion development in such engines are very different from those in conventional spark-ignition or diesel compression ignition engines. Very little data has been reported concerning optical diagnostics of the flow and combustion in the engine using negative valve overlapping. This paper presents an experimental investigation into the in-cylinder flow characteristics and combustion development in an optical engine operating in HCCI combustion mode. PIV measurements have been taken under motored engine conditions to provide a quantitative flow characterisation of negative valve overlap in-cylinder flows. The ignition and combustion process was imaged using a high resolution charge coupled device (CCD) camera and the combustion imaging data was supplemented by simultaneously recorded in-cylinder pressure data which assisted the analysis of the images. It is found that the flow characteristics with negative valve overlapping are less stable and more valve event driven than typical spark ignition in-cylinder flows, while the combustion initiation locations are not uniformly distributed.

  13. Visualising inter-subject variability in fMRI using threshold-weighted overlap maps.

    Science.gov (United States)

    Seghier, Mohamed L; Price, Cathy J

    2016-01-01

    Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects, and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis, and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage. PMID:26846561

  14. Instrument Identification in Polyphonic Music: Feature Weighting to Minimize Influence of Sound Overlaps

    Directory of Open Access Journals (Sweden)

    Goto Masataka

    2007-01-01

    Full Text Available We provide a new solution to the problem of feature variations caused by the overlapping of sounds in instrument identification in polyphonic music. When multiple instruments simultaneously play, partials (harmonic components of their sounds overlap and interfere, which makes the acoustic features different from those of monophonic sounds. To cope with this, we weight features based on how much they are affected by overlapping. First, we quantitatively evaluate the influence of overlapping on each feature as the ratio of the within-class variance to the between-class variance in the distribution of training data obtained from polyphonic sounds. Then, we generate feature axes using a weighted mixture that minimizes the influence via linear discriminant analysis. In addition, we improve instrument identification using musical context. Experimental results showed that the recognition rates using both feature weighting and musical context were 84.1 for duo, 77.6 for trio, and 72.3 for quartet; those without using either were 53.4, 49.6, and 46.5 , respectively.

  15. Instrument Identification in Polyphonic Music: Feature Weighting to Minimize Influence of Sound Overlaps

    Science.gov (United States)

    Kitahara, Tetsuro; Goto, Masataka; Komatani, Kazunori; Ogata, Tetsuya; Okuno, Hiroshi G.

    2006-12-01

    We provide a new solution to the problem of feature variations caused by the overlapping of sounds in instrument identification in polyphonic music. When multiple instruments simultaneously play, partials (harmonic components) of their sounds overlap and interfere, which makes the acoustic features different from those of monophonic sounds. To cope with this, we weight features based on how much they are affected by overlapping. First, we quantitatively evaluate the influence of overlapping on each feature as the ratio of the within-class variance to the between-class variance in the distribution of training data obtained from polyphonic sounds. Then, we generate feature axes using a weighted mixture that minimizes the influence via linear discriminant analysis. In addition, we improve instrument identification using musical context. Experimental results showed that the recognition rates using both feature weighting and musical context were 84.1[InlineEquation not available: see fulltext.] for duo, 77.6[InlineEquation not available: see fulltext.] for trio, and 72.3[InlineEquation not available: see fulltext.] for quartet; those without using either were 53.4, 49.6, and 46.5[InlineEquation not available: see fulltext.], respectively.

  16. Diet History Questionnaire: Suggested Citations

    Science.gov (United States)

    Use of the Diet History Questionnaire and Diet*Calc Analysis Software for publication purposes should contain a citation which includes version information for the software, questionnaire, and nutrient database.

  17. Morphological similarity and ecological overlap in two rotifer species.

    Directory of Open Access Journals (Sweden)

    Carmen Gabaldón

    Full Text Available Co-occurrence of cryptic species raises theoretically relevant questions regarding their coexistence and ecological similarity. Given their great morphological similitude and close phylogenetic relationship (i.e., niche retention, these species will have similar ecological requirements and are expected to have strong competitive interactions. This raises the problem of finding the mechanisms that may explain the coexistence of cryptic species and challenges the conventional view of coexistence based on niche differentiation. The cryptic species complex of the rotifer Brachionus plicatilis is an excellent model to study these questions and to test hypotheses regarding ecological differentiation. Rotifer species within this complex are filtering zooplankters commonly found inhabiting the same ponds across the Iberian Peninsula and exhibit an extremely similar morphology-some of them being even virtually identical. Here, we explore whether subtle differences in body size and morphology translate into ecological differentiation by comparing two extremely morphologically similar species belonging to this complex: B. plicatilis and B. manjavacas. We focus on three key ecological features related to body size: (1 functional response, expressed by clearance rates; (2 tolerance to starvation, measured by growth and reproduction; and (3 vulnerability to copepod predation, measured by the number of preyed upon neonates. No major differences between B. plicatilis and B. manjavacas were found in the response to these features. Our results demonstrate the existence of a substantial niche overlap, suggesting that the subtle size differences between these two cryptic species are not sufficient to explain their coexistence. This lack of evidence for ecological differentiation in the studied biotic niche features is in agreement with the phylogenetic limiting similarity hypothesis but requires a mechanistic explanation of the coexistence of these species not

  18. Hierarchical Overlapping Clustering of Network Data Using Cut Metrics

    CERN Document Server

    Gama, Fernando; Ribeiro, Alejandro

    2016-01-01

    A novel method to obtain hierarchical and overlapping clusters from network data -i.e., a set of nodes endowed with pairwise dissimilarities- is presented. The introduced method is hierarchical in the sense that it outputs a nested collection of groupings of the node set depending on the resolution or degree of similarity desired, and it is overlapping since it allows nodes to belong to more than one group. Our construction is rooted on the facts that a hierarchical (non-overlapping) clustering of a network can be equivalently represented by a finite ultrametric space and that a convex combination of ultrametrics results in a cut metric. By applying a hierarchical (non-overlapping) clustering method to multiple dithered versions of a given network and then convexly combining the resulting ultrametrics, we obtain a cut metric associated to the network of interest. We then show how to extract a hierarchical overlapping clustering structure from the aforementioned cut metric. Furthermore, the so-called overlappi...

  19. Increasing efficiency in intermediate band solar cells with overlapping absorptions

    Science.gov (United States)

    Krishna, Akshay; Krich, Jacob J.

    2016-07-01

    Intermediate band (IB) materials are promising candidates for realizing high efficiency solar cells. In IB photovoltaics, photons are absorbed in one of three possible electronic transitions—valence to conduction band, valence to intermediate band, or intermediate to conduction band. With fully concentrated sunlight, when the band gaps have been chosen appropriately, the highest efficiency IB solar cells require that these three absorptions be non-overlapping, so absorbed photons of fixed energy contribute to only one transition. The realistic case of overlapping absorptions, where the transitions compete for photons, is generally considered to be a source of loss. We show that overlapping absorptions can in fact lead to significant improvements in IB solar cell efficiencies, especially for IB that are near the middle of the band gap. At low to moderate concentration, the highest efficiency requires overlapping absorptions. We use the detailed-balance method and indicate how much overlap of the absorptions is required to achieve efficiency improvements, comparing with some known cases. These results substantially broaden the set of materials that can be suitable for high-efficiency IB solar cells.

  20. Bayesian method for system reliability assessment of overlapping pass/fail data

    Institute of Scientific and Technical Information of China (English)

    Zhipeng Hao; Shengkui Zeng; Jianbin Guo

    2015-01-01

    For high reliability and long life systems, system pass/fail data are often rare. Integrating lower-level data, such as data drawn from the subsystem or component pass/fail testing, the Bayesian analysis can improve the precision of the system reli-ability assessment. If the multi-level pass/fail data are overlapping, one chal enging problem for the Bayesian analysis is to develop a likelihood function. Since the computation burden of the existing methods makes them infeasible for multi-component systems, this paper proposes an improved Bayesian approach for the system reliability assessment in light of overlapping data. This approach includes three steps: fristly searching for feasible paths based on the binary decision diagram, then screening feasible points based on space partition and constraint decomposition, and final y sim-plifying the likelihood function. An example of a satel ite rol ing control system demonstrates the feasibility and the efficiency of the proposed approach.

  1. Imperfect competition in an overlapping generations model : a case for fiscal policy

    OpenAIRE

    d'Aspremont-Lynden, Claude; Dos Santos Ferreira, Rodolphe

    1995-01-01

    Imperfect competition is a meaningful feature for macroeconomic analysis only to the extent that it leads to properties qualitatively different from those obtained under perfect competition. In particular, we have to wonder how imperfect competition per se may found an effective fiscal policy. For that matter we consider a simple overlapping generations model with firms acting as Cournot oligopolists in the good market. Through fiscal policy, a government, keeping the stock of money constant, re...

  2. Overlapping Domain Decomp osition Finite Difference Algorithm for Compact Difference Scheme of the Heat Conduction Equation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong-mei

    2015-01-01

    In this paper, a modified additive Schwarz finite difference algorithm is applied in the heat conduction equation of the compact difference scheme. The algorithm is on the basis of domain decomposition and the subspace correction. The basic train of thought is the introduction of the units function decomposition and reasonable distribution of the overlap of correction. The residual correction is conducted on each subspace while the computation is completely parallel. The theoretical analysis shows that this method is completely characterized by parallel.

  3. Automatic correction scheme for the temperature dependent overlap function of CHM15k ceilometers

    Science.gov (United States)

    Haefele, Alexander; Poltera, Yann; Hervo, Maxime

    2016-04-01

    Imperfections in a lidar's overlap function lead to artefacts in the background, range and overlap corrected lidar signals. These artefacts can erroneously be interpreted as aerosol gradient or, in extreme cases, as cloud base leading to false cloud detection. A correct specification of the overlap function is hence crucial to use automatic elastic lidars (ceilometers) for the detection of the planetary boundary layer or low clouds. In this study an algorithm is presented to correct such artefacts. It is based on the assumption of a homogeneous boundary layer and a correct specification of the overlap function down to a minimum range, which must be situated within the boundary layer. The strength of the algorithm lies in a sophisticated quality check scheme which allows to reliably identify favorable atmospheric conditions. The algorithm has been applied to 2 years of data from a CHM15k ceilometer from Lufft. Backscatter signals corrected for background, range and overlap have been compared using the overlap function provided by the manufacturer and the one corrected with the presented algorithm. Differences between corrected and uncorrected signals reach up to 45% in the first 300m above ground. The amplitude of the correction turned out to be temperature dependent being larger for higher temperatures. A linear model of the correction as a function of the instrument's internal temperature has been derived from the experimental data. Case studies and a statistical analysis of the strongest gradient derived from corrected signals reveal that the temperature model is capable to correct overlap artefacts with high quality, in particular such due to diurnal variations. The presented correction method has the potential to significantly improve the detection of the boundary layer with gradient based methods because it removes false candidates and hence simplifies the attribution of the detected gradients to the planetary boundary layer. A particularly high benefit can be

  4. Negative Valve Overlap Reforming Chemistry in Low-Oxygen Environments

    Energy Technology Data Exchange (ETDEWEB)

    Szybist, James P [ORNL; Steeper, Richard R. [Sandia National Laboratories (SNL); Splitter, Derek A [ORNL; Kalaskar, Vickey B [ORNL; Pihl, Josh A [ORNL; Daw, C Stuart [ORNL

    2014-01-01

    Fuel injection into the negative valve overlap (NVO) period is a common method for controlling combustion phasing in homogeneous charge compression ignition (HCCI) and other forms of advanced combustion. When fuel is injected into O2-deficient NVO conditions, a portion of the fuel can be converted to products containing significant levels of H2 and CO. Additionally, other short chain hydrocarbons are produced by means of thermal cracking, water-gas shift, and partial oxidation reactions. The present study experimentally investigates the fuel reforming chemistry that occurs during NVO. To this end, two very different experimental facilities are utilized and their results are compared. One facility is located at Oak Ridge National Laboratory, which uses a custom research engine cycle developed to isolate the NVO event from main combustion, allowing a steady stream of NVO reformate to be exhausted from the engine and chemically analyzed. The other experimental facility, located at Sandia National Laboratories, uses a dump valve to capture the exhaust from a single NVO event for analysis. Results from the two experiments are in excellent trend-wise agreement and indicate that the reforming process under low-O2 conditions produces substantial concentrations of H2, CO, methane, and other short-chain hydrocarbon species. The concentration of these species is found to be strongly dependent on fuel injection timing and injected fuel type, with weaker dependencies on NVO duration and initial temperature, indicating that NVO reforming is kinetically slow. Further, NVO reforming does not require a large energy input from the engine, meaning that it is not thermodynamically expensive. The implications of these results on HCCI and other forms of combustion are discussed in detail.

  5. Detection of multiple velocity components in partially overlapping emitting regions

    CERN Document Server

    Mertens, F

    2016-01-01

    Velocity measurements made from multiple-epoch astronomical images of evolving objects with optically thin continuum emission (e.g. as relativistic jets or expanding supernova shells) may be confused as a result of the overlap of semi-transparent features moving at different speeds. Multi-scale wavelet decomposition can be effectively applied to identify and track such overlapping features, provided that their respective structural responses can be separated over the spatial scales used for the decomposition. We developed a new method that combines the stacked cross-correlation with the wavelet-based image segmentation and evaluation (WISE) technique of decomposition of two-dimensional structures, to separate and track dominant spatial responses of overlapping evolving features. The method is tested on a set of simulated images of a stratified relativistic jet, demonstrating the robust detection of both the faster spine and the slower sheath speeds. The method is applied to mutliple-epoch images from the MOJA...

  6. Iterative methods for overlap and twisted mass fermions

    Energy Technology Data Exchange (ETDEWEB)

    Chiarappa, T. [Univ. di Milano Bicocca (Italy); Jansen, K.; Shindler, A.; Wetzorke, I. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Nagai, K.I. [Wuppertal Univ. (Gesamthochschule) (Germany). Fachbereich Physik; Papinutto, M. [INFN Sezione di Roma Tre, Rome (Italy); Scorzato, L. [European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT), Villazzano (Italy); Urbach, C. [Liverpool Univ. (United Kingdom). Dept. of Mathematical Sciences; Wenger, U. [ETH Zuerich (Switzerland). Inst. fuer Theoretische Physik

    2006-09-15

    We present a comparison of a number of iterative solvers of linear systems of equations for obtaining the fermion propagator in lattice QCD. In particular, we consider chirally invariant overlap and chirally improved Wilson (maximally) twisted mass fermions. The comparison of both formulations of lattice QCD is performed at four fixed values of the pion mass between 230 MeV and 720 MeV. For overlap fermions we address adaptive precision and low mode preconditioning while for twisted mass fermions we discuss even/odd preconditioning. Taking the best available algorithms in each case we find that calculations with the overlap operator are by a factor of 30-120 more expensive than with the twisted mass operator. (orig.)

  7. Overlapped flowers yield detection using computer-based interface

    Directory of Open Access Journals (Sweden)

    Anuradha Sharma

    2016-09-01

    Full Text Available Precision agriculture has always dealt with the accuracy and timely information about agricultural products. With the help of computer hardware and software technology designing a decision support system that could generate flower yield information and serve as base for management and planning of flower marketing is made so easy. Despite such technologies, some problem still arise, for example, a colour homogeneity of a specimen which cannot be obtained similar to actual colour of image and overlapping of image. In this paper implementing a new ‘counting algorithm’ for overlapped flower is being discussed. For implementing this algorithm, some techniques and operations such as colour image segmentation technique, image segmentation, using HSV colour space and morphological operations have been used. In this paper used two most popular colour space; those are RGB and HSV. HSV colour space decouples brightness from a chromatic component in the image, by which it provides better result in case for occlusion and overlapping.

  8. The eigSUMR inverter for overlap fermion

    CERN Document Server

    Cundy, Nigel

    2015-01-01

    We discuss the usage and applicability of deflation methods for the overlap lattice Dirac operator, focussing on calculating the eigenvalues using a method similar to the eigCG algorithm used for other Dirac operators. The overlap operator, which contains several theoretical advantages over other formulations of lattice Quantum Chromodynamics, is more computationally expensive because it requires the computation of the matrix sign function. The principle change made compared to deflation methods for other formulations of lattice QCD is that it is necessary for best performance to tune or relax the accuracy of the matrix sign function as the computation proceeds. We adapt the eigCG algorithm for two inversion algorithms for overlap fermions, GMRESR(relCG) and GMRESR(relSUMR). Before deflation, the rate of convergence of these routines in terms of iterations is similar, but, since the Shifted Unitary Minimal Residual (SUMR) algorithm only requires one call to the matrix sign function compared to the two calls r...

  9. Flight performance and feather quality: paying the price of overlapping moult and breeding in a tropical highland bird.

    Directory of Open Access Journals (Sweden)

    Maria Angela Echeverry-Galvis

    Full Text Available A temporal separation of energetically costly life history events like reproduction and maintenance of the integumentary system is thought to be promoted by selection to avoid trade-offs and maximize fitness. It has therefore remained somewhat of a paradox that certain vertebrate species can undergo both events simultaneously. Identifying potential costs of overlapping two demanding life history stages will further our understanding of the selection pressures that shape the temporal regulation of life history events in vertebrates. We studied free-living tropical Slaty brush-finches (Atlapetes schistaceus, in which individuals spontaneously overlap reproduction and moult or undergo both events in separation. To assess possible costs of such an overlap we quantified feather quality and flight performance of individuals in different states. We determined individual's life history state by measuring gonad size and scoring moult stage, and collected a newly grown 7(th primary wing feather for later analysis of feather quality. Finally, we quantified flight performance for each individual in the wild. Overlapping individuals produced lighter and shorter wing feathers than individuals just moulting, with females decreasing feather quality more strongly during the overlap than males. Moreover, overlapping individuals had a reduced flight speed during escape flights, while their foraging flight speed was unaffected. Despite overlappers being larger and having a smaller wing area, their lower body mass resulted in a similar wing load as in breeders or moulters. Individuals measured repeatedly in different states also showed significant decreases in feather quality and escape flight speed during the overlap. Reduced escape flight speed may represent a major consequence of the overlap by increasing predation risk. Our data document costs to undergoing two life history stages simultaneously, which likely arise from energetic trade-offs. Impairments in

  10. Risk of New-Onset Atrial Fibrillation in Elderly Patients with the Overlap Syndrome: A Retrospective Cohort Study

    Institute of Scientific and Technical Information of China (English)

    Harsha V. Ganga; Sanjeev U. Nair; Venkata K. Puppala; Wayne L. Miller

    2013-01-01

    Objective Co-existence of obstructive sleep apnea (OSA) and chronic obstructive pulmonary disease (COPD) is referred to as overlap syndrome. Overlap patients have greater degree of hypoxia and pulmonary hypertension than patients with OSA or COPD alone. Studies showed that elderly patients with OSA alone do not have increased risk of atrial fibrillation (AF) but it is not known if overlap patients have higher risk of AF. Objective To determine whether elderly patients with overlap syndrome have an increased risk of AF. Methods In this single center, community-based retrospective cohort analysis, data were collected on 2,873 patients > 65 years of age without AF, presenting in the year 2006. Patients were divided into OSA group (n = 60), COPD group (n = 416), overlap syndrome group (n = 28) and group with no OSA or COPD (n = 2369). The primary endpoint was incidence of new-onset AF over the following two years. Logistic regression was performed to adjust for heart failure (HF), coronary artery disease, hypertension (HTN), cerebrovascular disease, cardiac valve disorders, diabetes mellitus, hyperlipidemia, chronic kidney disease (CKD) and obesity. Results The incidence of AF was 10% in COPD group, 6% in OSA group and 21% in overlap syndrome group (P < 0.05). After adjusting for age, sex, HF, CKD, and HTN, patients with overlap syndrome demonstrated a significant association with new-onset AF (OR = 3.66, P = 0.007). HF, CKD and HTN were also significantly associated with new-onset AF (P < 0.05). Conclusion Among elderly patients, the presence of overlap syndrome is associated with a marked increase in risk of new-onset AF as compared to the presence of OSA or COPD alone.

  11. Detect overlapping and hierarchical community structure in networks

    CERN Document Server

    Shen, Huawei; Cai, Kai; Hu, Mao-Bin

    2008-01-01

    Clustering and community structure is crucial for many network systems and the related dynamic processes. It has been shown that communities are usually overlapping and hierarchical. However, previous methods investigate these two properties of community structure separately. This paper propose an algorithm (EAGLE) to detect both the overlapping and hierarchical properties of complex community structure together. This algorithm deals with the set of maximal cliques and adopts an agglomerative framework. The quality function of modularity is extended to evaluate the goodness of a cover. The examples of application to real world networks give excellent results.

  12. Suggestions on photons and fermions

    CERN Document Server

    Alvargonzalez, R

    2007-01-01

    In this paper we suggest a configuration of photons consistent with a spin $\\hbar$, and a configuration of the fermions coherent with a spin $\\hbar/2$. These suggested configurations open the way to further analyses which lead to the following conclusions: - There cannot exist elementary particles of spin $\\hbar/2$ with a mass inferior to $1m_e$ or with a radius greater than $1l_e$. - The electrostatic force derives from the centrifugal forces inherent to the spin and are propagated by photons. - The derivation of the electrostatic force explains the existence of positive and negative charges and Coulomb's law. - The enormous differences between the centrifugal forces and the centripetal forces at the surface of the protons give rise to quantic fluctuations of space which generate the energy flows necessary for equilibrium. These energy flows can explain gravitation and the strong force. - The mass of the proton, $m_p$, and the mass of the neutron, $m_n$, must each have a concrete value required for the cohes...

  13. Niche overlap in allotopic and syntopic populations of sexually interacting ground-hopper species

    Institute of Scientific and Technical Information of China (English)

    Axel Hochkirch; Julia Gr(o)ning

    2012-01-01

    There is accumulating evidence that sexual interactions among species (reproductive interference) could have dramatic effects for species' coexistence.It has been shown that the fitness of individuals can be substantially reduced as a consequence of reproductive interference.This might subsequently lead to displacement of a species (sexual exclusion).On the other hand,some evolutionary and ecological mechanisms might enable species to coexist,such as the divergence of mate recognition systems (reproductive character displacement),habitat partitioning,clumped dispersion patterns or different colonization capabilities.We have previously shown that the two ground-hopper species Tetrix subulata and Tetrix ceperoi interact sexually in the laboratory as well as in the field.At sites where both species co-occur niche overlap was high,suggesting that coexistence is maintained by different niche breadths rather than by habitat partitioning.To test the hypothesis that habitat partitioning does not contribute to species' coexistence,we examined whether allotopic and syntopic populations of these two species differ in niche overlap (competitive release).Our results show that niche overlap is higher in syntopic than in allotopic populations,suggesting that the site-specific habitat structure (heterogeneity) has a stronger influence on microhabitat utilization than the presence of heterospecifics.Hence,our data do not support the hypothesis that habitat partitioning plays a substantial role for the coexistence of these sexually interacting species.

  14. Genetics, Cognition and Neurobiology of Schizotypal Personality: A Review of the Overlap with Schizophrenia

    Directory of Open Access Journals (Sweden)

    Ulrich eEttinger

    2014-02-01

    Full Text Available Schizotypy refers to a set of temporally stable traits that are observed in the general population and that resemble the signs and symptoms of schizophrenia. Here, we review evidence from studies on genetics, cognition, perception, motor and oculomotor control, brain structure, brain function and psychopharmacology in schizotypy. We specifically focused on identifying areas of overlap between schizotypy and schizophrenia. Evidence was corroborated that significant overlap exists between the two, covering the behavioural, brain structural and functional as well molecular levels. In particular, several studies showed that individuals with high levels of schizotypal traits exhibit alterations in neurocognitive task performance and underlying brain function similar to the deficits seen in patients with schizophrenia. Studies of brain structure have shown both volume reductions and increases in schizotypy, pointing to schizophrenia-like deficits as well as possible protective or compensatory mechanisms. Experimental pharmacological studies have shown that high levels of schizotypy are associated with (i enhanced dopaminergic response in striatum following administration of amphetamine and (ii improvement of cognitive performance following administration of antipsychotic compounds. Together, this body of work suggests that schizotypy shows overlap with schizophrenia across multiple behavioural and neurobiological domains, suggesting that the study of schizotypal traits may be useful in improving our understanding of the aetiology of schizophrenia.

  15. Topology of dynamical lattice configurations including results from dynamical overlap fermions

    CERN Document Server

    Bruckmann, Falk; Gruber, Florian; Lippert, Thomas; Schäfer, Andreas

    2011-01-01

    We investigate how the topological charge density in lattice QCD simulations is affected by violations of chiral symmetry in different fermion actions. To this end we compare lattice configurations generated with a number of different actions including first configurations generated with exact overlap quarks. We visualize the topological profiles after mild smearing. In the topological charge correlator we measure the size of the positive core, which is known to vanish in the continuum limit. To leading order we find the core size to scale linearly with the lattice spacing with the same coefficient for all actions, even including quenched simulations. In the subleading term the different actions vary over a range of about 10 %. Our findings suggest that non-chiral lattice actions at current lattice spacings do not differ much for this specific observable related to topology, both among themselves and compared to overlap fermions.

  16. Neuroimaging supports behavioral personality assessment: Overlapping activations during reflective and impulsive risk taking.

    Science.gov (United States)

    Pletzer, Belinda; M Ortner, Tuulia

    2016-09-01

    Personality assessment has been challenged by the fact that different assessment methods (implicit measures, behavioral measures and explicit rating scales) show little or no convergence in behavioral studies. In this neuroimaging study we address for the first time, whether different assessment methods rely on separate or overlapping neuronal systems. Fifty nine healthy adult participants completed two objective personality tests of risk propensity: the more implicit Balloon Analogue Risk Task (BART) and the more explicit Game of Dice Task (GDT). Significant differences in activation, as well as connectivity patterns between both tasks were observed. In both tasks, risky decisions yielded significantly stronger activations than safe decisions in the bilateral caudate, as well as the bilateral Insula. The finding of overlapping brain areas validates different assessment methods, despite their behavioral non-convergence. This suggests that neuroimaging can be an important tool of validation in the field of personality assessment. PMID:27373370

  17. Neuroimaging supports behavioral personality assessment: Overlapping activations during reflective and impulsive risk taking.

    Science.gov (United States)

    Pletzer, Belinda; M Ortner, Tuulia

    2016-09-01

    Personality assessment has been challenged by the fact that different assessment methods (implicit measures, behavioral measures and explicit rating scales) show little or no convergence in behavioral studies. In this neuroimaging study we address for the first time, whether different assessment methods rely on separate or overlapping neuronal systems. Fifty nine healthy adult participants completed two objective personality tests of risk propensity: the more implicit Balloon Analogue Risk Task (BART) and the more explicit Game of Dice Task (GDT). Significant differences in activation, as well as connectivity patterns between both tasks were observed. In both tasks, risky decisions yielded significantly stronger activations than safe decisions in the bilateral caudate, as well as the bilateral Insula. The finding of overlapping brain areas validates different assessment methods, despite their behavioral non-convergence. This suggests that neuroimaging can be an important tool of validation in the field of personality assessment.

  18. Coeliac disease and autoimmune disease-genetic overlap and screening

    NARCIS (Netherlands)

    Lundin, Knut E. A.; Wijmenga, Cisca

    2015-01-01

    Coeliac disease is a treatable, gluten-induced disease that often occurs concurrently with other autoimmune diseases. In genetic studies since 2007, a partial genetic overlap between these diseases has been revealed and further insights into the pathophysiology of coeliac disease and autoimmunity ha

  19. Track with overlapping links for dry coal extrusion pumps

    Science.gov (United States)

    Saunders, Timothy; Brady, John D

    2014-01-21

    A chain for a particulate material extrusion pump includes a plurality of links, each of the plurality of links having a link body and a link ledge, wherein each link ledge of the plurality of links at least partially overlaps the link body of an adjacent one of the plurality of links.

  20. A Laser Lock System using Multiple Overlapping Beams

    Science.gov (United States)

    Harper, Stuart; Francis, Ben; Erickson, Christopher; Durfee, Dallin

    2010-10-01

    We describe a system wherein the lock of trapping, ionizing, and ion resonance lasers for a Sr experiment are bootstrapped together in a single neutral atom vapor cell. This is done by overlapping beams to optically pump the atoms into the necessary states.

  1. Two Fractal Overlap Time Series: Earthquakes and Market Crashes

    OpenAIRE

    Chakrabarti, Bikas K.; Arnab Chatterjee; Pratip Bhattacharyya

    2007-01-01

    We find prominent similarities in the features of the time series for the (model earthquakes or) overlap of two Cantor sets when one set moves with uniform relative velocity over the other and time series of stock prices. An anticipation method for some of the crashes have been proposed here, based on these observations.

  2. Two-fractal overlap time series: Earthquakes and market crashes

    Indian Academy of Sciences (India)

    Bikas K Chakrabarti; Arnab Chatterjee; Pratip Bhattacharyya

    2008-08-01

    We find prominent similarities in the features of the time series for the (model earthquakes or) overlap of two Cantor sets when one set moves with uniform relative velocity over the other and time series of stock prices. An anticipation method for some of the crashes have been proposed here, based on these observations.

  3. 9 CFR 121.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-01-01

    ... in paragraph (b) of this section that have been genetically modified. (d) Overlap select agents or... OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS POSSESSION, USE... elements, recombinant nucleic acids, and recombinant organisms: (1) Nucleic acids that can...

  4. Separation of the overlapping effects in spectra for WDXRF using the Rietveld method

    International Nuclear Information System (INIS)

    This work presents a new methodology for the overlapping spectra separation obtained by the technique of wavelength dispersion X-ray fluorescence (WDXRF). This methodology allows to improve the conventional analytic results and to facilitate the determination of chemical species of a same element without chemical separation, by means of the separation of coming spectra of electronic transitions of valence electrons or chemical effects in internal electrons. With the software 'GSAS-EXPGUI' and the method of Rietveld overcomes the problem of overlapping lines of the present species in the sample and it facilitates the determination of the same ones simultaneously, without the need of samples patterns and calibration curves, what means an expressive gain in relation to other techniques. The preparation of the surface of the sample for the collection of the spectrum represents a critical stage for the acting of the analysis whose effects can be minimized being used the refinement of Rietveld, that allows the determination of the relationships of the intensities of the lines put upon by means of mathematical models, what establishes the basic conditions for obtaining of more precise results in the quantitative analysis. In the case of the determination of chemical species it can separate, for example Cr (III), Cr (VI) and Fe (II), Fe(III) that present overlapping of almost 100%. (author)

  5. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  6. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    Alammouri, Ahmad Mohammad Abdel-Karim

    2015-12-06

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.

  7. Genetic overlap between Alzheimer's disease and Parkinson's disease at the MAPT locus.

    Science.gov (United States)

    Desikan, R S; Schork, A J; Wang, Y; Witoelar, A; Sharma, M; McEvoy, L K; Holland, D; Brewer, J B; Chen, C-H; Thompson, W K; Harold, D; Williams, J; Owen, M J; O'Donovan, M C; Pericak-Vance, M A; Mayeux, R; Haines, J L; Farrer, L A; Schellenberg, G D; Heutink, P; Singleton, A B; Brice, A; Wood, N W; Hardy, J; Martinez, M; Choi, S H; DeStefano, A; Ikram, M A; Bis, J C; Smith, A; Fitzpatrick, A L; Launer, L; van Duijn, C; Seshadri, S; Ulstein, I D; Aarsland, D; Fladby, T; Djurovic, S; Hyman, B T; Snaedal, J; Stefansson, H; Stefansson, K; Gasser, T; Andreassen, O A; Dale, A M

    2015-12-01

    We investigated the genetic overlap between Alzheimer's disease (AD) and Parkinson's disease (PD). Using summary statistics (P-values) from large recent genome-wide association studies (GWAS) (total n=89 904 individuals), we sought to identify single nucleotide polymorphisms (SNPs) associating with both AD and PD. We found and replicated association of both AD and PD with the A allele of rs393152 within the extended MAPT region on chromosome 17 (meta analysis P-value across five independent AD cohorts=1.65 × 10(-7)). In independent datasets, we found a dose-dependent effect of the A allele of rs393152 on intra-cerebral MAPT transcript levels and volume loss within the entorhinal cortex and hippocampus. Our findings identify the tau-associated MAPT locus as a site of genetic overlap between AD and PD, and extending prior work, we show that the MAPT region increases risk of Alzheimer's neurodegeneration. PMID:25687773

  8. Individual foraging strategies reveal niche overlap between endangered galapagos pinnipeds.

    Directory of Open Access Journals (Sweden)

    Stella Villegas-Amtmann

    Full Text Available Most competition studies between species are conducted from a population-level approach. Few studies have examined inter-specific competition in conjunction with intra-specific competition, with an individual-based approach. To our knowledge, none has been conducted on marine top predators. Sympatric Galapagos fur seals (Arctocephalus galapagoensis and sea lions (Zalophus wollebaeki share similar geographic habitats and potentially compete. We studied their foraging niche overlap at Cabo Douglas, Fernandina Island from simultaneously collected dive and movement data to examine spatial and temporal inter- and intra-specific competition. Sea lions exhibited 3 foraging strategies (shallow, intermediate and deep indicating intra-specific competition. Fur seals exhibited one foraging strategy, diving predominantly at night, between 0-80 m depth and mostly at 19-22 h. Most sea lion dives also occurred at night (63%, between 0-40 m, within fur seals' diving depth range. 34% of sea lions night dives occurred at 19-22 h, when fur seals dived the most, but most of them occurred at dawn and dusk, when fur seals exhibited the least amount of dives. Fur seals and sea lions foraging behavior overlapped at 19 and 21 h between 0-30 m depths. Sea lions from the deep diving strategy exhibited the greatest foraging overlap with fur seals, in time (19 h, depth during overlapping time (21-24 m, and foraging range (37.7%. Fur seals foraging range was larger. Cabo Douglas northwest coastal area, region of highest diving density, is a foraging "hot spot" for both species. Fur seals and sea lions foraging niche overlap occurred, but segregation also occurred; fur seals primarily dived at night, while sea lions exhibited night and day diving. Both species exploited depths and areas exclusive to their species. Niche breadth generally increases with environmental uncertainty and decreased productivity. Potential competition between these species could be greater during

  9. T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs.

    Directory of Open Access Journals (Sweden)

    Andréa Barbosa de Melo

    Full Text Available The yellow fever vaccines (YF-17D-204 and 17DD are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env and nonstructural (NS proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4(+ and CD8(+ T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines.

  10. In silico analysis suggests repurposing of ibuprofen for prevention and treatment of EBOLA virus disease [v1; ref status: indexed, http://f1000r.es/5bs

    Directory of Open Access Journals (Sweden)

    Veljko Veljkovic

    2015-05-01

    Full Text Available The large 2014/2015 Ebola virus outbreak in West Africa points out the urgent need to develop new preventive and therapeutic approaches that are effective against Ebola viruses and  can be rapidly utilized. Recently, a simple theoretical criterion for the virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection was proposed. Using this method the ‘drug space’ was screened and 267 approved and 382 experimental drugs as candidates for treatment of the Ebola virus disease (EVD have been selected. Detailed analysis of these drugs revealed the non-steroidal anti-inflammatory drug ibuprofen as an inexpensive, widely accessible and minimally toxic candidate for prevention and treatment of EVD. Furthermore, the molecular mechanism underlying this possible protective effect of ibuprofen against EVD is suggested in this article.

  11. Diet overlap between juvenile flatfish and the invasive round goby in the central Baltic Sea

    Science.gov (United States)

    Ustups, D.; Bergström, U.; Florin, A. B.; Kruze, E.; Zilniece, D.; Elferts, D.; Knospina, E.; Uzars, D.

    2016-01-01

    The present study offers a comprehensive analysis of changes in the abundance and diet composition of juvenile flounder (Platichthys flesus) and turbot (Psetta maxima), along with other dominant coastal fish species, before and after the establishment of the alien round goby off an exposed stretch of coast in the eastern Baltic Sea. In the study area, the round goby (Neogobius melanostomus) was recorded for the first time in 2009. After a few years of low abundance, a sharp increase in the population occurred. After the round goby invasion, flatfish juveniles exhibited an increased diet overlap with other species and had a lower feeding success, reflecting an increase in resource competition. For juvenile turbot, the increase was mainly caused by the round goby, while for flounder it was due to both the round goby and the lesser sandeel (Ammodytes tobianus). Juvenile turbot, whose dominant food item before the round goby establishment had been mysids, shifted their diet towards Crangon crangon, reflecting a decrease in mysid abundance by three orders of magnitude and a concurrent doubling in C. crangon abundance in the habitat. At the same time a significant decrease in turbot recruitment was observed. Juvenile flounder had the widest food spectrum of the studied species. When the availability of the primary food item, Bathyporeia pilosa, decreased, flounder juveniles adapted by increasing the share of zooplankton in their diets. No changes in flounder feeding success and recruitment were observed. However, the recruitment estimates of flounder and turbot show an increasing co-variation after the round goby invasion, suggesting that recruitment of the species may currently be regulated by processes in the common nursery habitat.

  12. Clinical comparison of 10q26 overlapping deletions: delineating the critical region for urogenital anomalies.

    Science.gov (United States)

    Vera-Carbonell, Ascensión; López-González, Vanesa; Bafalliu, Juan Antonio; Ballesta-Martínez, María J; Fernández, Asunción; Guillén-Navarro, Encarna; López-Expósito, Isabel

    2015-04-01

    The 10q26 deletion syndrome is a clinically heterogeneous disorder. The most common phenotypic characteristics include pre- and/or postnatal growth retardation, microcephaly, developmental delay/intellectual disability and a facial appearance consisting of a broad nasal bridge with a prominent nose, low-set malformed ears, strabismus, and a thin vermilion of the upper lip. In addition, limb and cardiac anomalies as well as urogenital anomalies are occasionally observed. In this report, we describe three unrelated females with 10q26 terminal deletions who shared clinical features of the syndrome, including urogenital defects. Cytogenetic studies showed an apparently de novo isolated deletion of the long arm of chromosome 10, with breakpoints in 10q26.1, and subsequent oligo array-CGH analysis confirmed the terminal location and defined the size of the overlapping deletions as ∼ 13.46, ∼ 9.31 and ∼ 9.17 Mb. We compared the phenotypic characteristics of the present patients with others reported to have isolated deletions and we suggest that small 10q26.2 terminal deletions may be associated with growth retardation, developmental delay/intellectual disability, craniofacial features and external genital anomalies whereas longer terminal deletions affecting the 10q26.12 and/or 10q26.13 regions may be responsible for renal/urinary tract anomalies. We propose that the haploinsufficiency of one or several genes located in the 10q26.12-q26.13 region may contribute to the renal or urinary tract pathogenesis and we highlight the importance of FGFR2 and probably of CTBP2 as candidate genes. PMID:25655674

  13. Environmental Niche Overlap between Common and Dusky Dolphins in North Patagonia, Argentina

    Science.gov (United States)

    Svendsen, Guillermo Martín; Romero, María Alejandra; Williams, Gabriela Noemí; Gagliardini, Domingo Antonio; Crespo, Enrique Alberto; Dans, Silvana Laura; González, Raúl Alberto

    2015-01-01

    Research on the ecology of sympatric dolphins has increased worldwide in recent decades. However, many dolphin associations such as that between common dolphins (Delphinus delphis) and dusky dolphins (Lagenorhynchus obscurus) are poorly understood. The present study was conducted in the San Matías Gulf (SMG) ecosystem (North Patagonia, Argentina) where a high diet overlap among both species was found. The main objective of the present work was to explore the niche overlap of common and dusky dolphins in the habitat and temporal dimensions. The specific aims were (a) to evaluate the habitat use strategies of both species through a comparison of their group attributes (social composition, size and activity), and (b) to evaluate their habitat preferences and habitat overlap through Environmental Niche modeling considering two oceanographic seasons. To accomplish these aims, we used a historic database of opportunistic and systematic records collected from 1983 to 2011. Common and dusky dolphins exhibited similar patterns of group size (from less than 10 to more than 100 individuals), activity (both species use the area to feed, nurse, and copulate), and composition (adults, juveniles, and mothers with calves were observed for both species). Also, both species were observed travelling and feeding in mixed-species groups. Specific overlap indices were higher for common dolphins than for dusky dolphins, but all indices were low, suggesting that they are mainly segregated in the habitat dimension. In the case of common dolphins, the best habitats were located in the northwest of the gulf far from the coast. In the warm season they prefer areas with temperate sea surface and in the cold season they prefer areas with relatively high variability of sea surface temperature. Meanwhile, dusky dolphins prefer areas with steep slopes close to the coast in the southwestern sector of the gulf in both seasons. PMID:26091542

  14. Environmental Niche Overlap between Common and Dusky Dolphins in North Patagonia, Argentina.

    Directory of Open Access Journals (Sweden)

    Guillermo Martín Svendsen

    Full Text Available Research on the ecology of sympatric dolphins has increased worldwide in recent decades. However, many dolphin associations such as that between common dolphins (Delphinus delphis and dusky dolphins (Lagenorhynchus obscurus are poorly understood. The present study was conducted in the San Matías Gulf (SMG ecosystem (North Patagonia, Argentina where a high diet overlap among both species was found. The main objective of the present work was to explore the niche overlap of common and dusky dolphins in the habitat and temporal dimensions. The specific aims were (a to evaluate the habitat use strategies of both species through a comparison of their group attributes (social composition, size and activity, and (b to evaluate their habitat preferences and habitat overlap through Environmental Niche modeling considering two oceanographic seasons. To accomplish these aims, we used a historic database of opportunistic and systematic records collected from 1983 to 2011. Common and dusky dolphins exhibited similar patterns of group size (from less than 10 to more than 100 individuals, activity (both species use the area to feed, nurse, and copulate, and composition (adults, juveniles, and mothers with calves were observed for both species. Also, both species were observed travelling and feeding in mixed-species groups. Specific overlap indices were higher for common dolphins than for dusky dolphins, but all indices were low, suggesting that they are mainly segregated in the habitat dimension. In the case of common dolphins, the best habitats were located in the northwest of the gulf far from the coast. In the warm season they prefer areas with temperate sea surface and in the cold season they prefer areas with relatively high variability of sea surface temperature. Meanwhile, dusky dolphins prefer areas with steep slopes close to the coast in the southwestern sector of the gulf in both seasons.

  15. Spectral-overlap approach to multiframe superresolution image reconstruction.

    Science.gov (United States)

    Cohen, Edward; Picard, Richard H; Crabtree, Peter N

    2016-05-20

    Various techniques and algorithms have been developed to improve the resolution of sensor-aliased imagery captured with multiple subpixel-displaced frames on an undersampled pixelated image plane. These dealiasing algorithms are typically known as multiframe superresolution (SR), or geometric SR to emphasize the role of the focal-plane array. Multiple low-resolution (LR) aliased frames of the same scene are captured and allocated to a common high-resolution (HR) reconstruction grid, leading to the possibility of an alias-free reconstruction, as long as the HR sampling rate is above the Nyquist rate. Allocating LR-frame irradiances to HR frames requires the use of appropriate weights. Here we present a novel approach in the spectral domain to calculating exactly weights based on spatial overlap areas, which we call the spectral-overlap (SO) method. We emphasize that the SO method is not a spectral approach but rather an approach to calculating spatial weights that uses spectral decompositions to exploit the array properties of the HR and LR pixels. The method is capable of dealing with arbitrary aliasing factors and interframe motions consisting of in-plane translations and rotations. We calculate example reconstructed HR images (the inverse problem) from synthetic aliased images for integer and for fractional aliasing factors. We show the utility of the SO-generated overlap-area weights in both noniterative and iterative reconstructions with known or unknown aliasing factor. We show how the overlap weights can be used to generate the Green's function (pixel response function) for noniterative dealiasing. In addition, we show how the overlap-area weights can be used to generate synthetic aliased images (the forward problem). We compare the SO approach to the spatial-domain geometric approach of O'Rourke and find virtually identical high accuracy but with significant enhancements in speed for SO. We also compare the SO weights to interpolated weights and find that

  16. Overlap of primary biliary cirrhosis and primary sclerosing cholangitis – a rare coincidence or a new syndrome

    Directory of Open Access Journals (Sweden)

    Arun Jeevagan

    2010-05-01

    Full Text Available Arun JeevaganGeneral Medicine, Ipswich NHS Hospital, Ipswich, UKBackground: Overlap syndrome has been introduced to the field of hepatology to describe the coexistence of two or more autoimmune hepatic conditions in the same individual. This is a rare clinical case of a patient diagnosed with primary biliary cirrhosis (PBC who later developed primary sclerosing cholangitis (PSC. This is a unique case as no other cases with a similar pattern have been reported. Overlap syndrome does not include the coexistence of PBC and PSC as a distinctive syndrome so far.Case report: A middle-aged woman suffering from PBC for 17 years got admitted with clinical and biochemical features of cholestatic syndrome. A provisional diagnosis of worsening PBC was proved wrong by magnetic resonance cholangiopancreatography, which revealed typical benign stricture and dilatation of common bile duct with typical beading appearance suggestive of PSC. The patient was stented and treated with an increased dose of ursodeoxycholic acid (UDCA which improved the symptoms and the biochemical picture.Conclusion: This is a clear overlap of PBC–PSC. It is very difficult to say whether it is a rare coincidence or a new overlap syndrome, but there are no clear guidelines for management of these patients. Currently, the treatment involves endoscopic duct dilatation, UDCA, and regular follow-ups to rule out hepato-biliary tumor occurrence.Keywords: primary biliary cirrhosis, primary sclerosing cholangitis, hepatic overlap syndrome

  17. Home-range size and overlap within an introduced population of the Cuban Knight Anole, Anolis equestris (Squamata: Iguanidae

    Directory of Open Access Journals (Sweden)

    Paul M. Richards

    2011-07-01

    Full Text Available Many studies have investigated the spatial relationships of terrestrial lizards, but arboreal species remain poorly studiedbecause they are difficult to observe. The conventional view of home-range size and overlap among territorial, polygynous species of lizards is that: (1 male home ranges are larger than those of females; (2 male home ranges usually encompass, or substantiallyoverlap, those of several females; and (3 male home-range overlap varies but often is minimal, but female home ranges frequently overlap extensively. However, the paucity of pertinent studies makes it difficult to generalize these patterns to arboreal lizards. Weinvestigated home-range size and overlap in the arboreal Knight Anole, Anolis equestris, and compared our findings to published home-range data for 15 other species of Anolis. Using radiotelemetry and mark-recapture/resight techniques, we analyzed the home rangesof individuals from an introduced population of Knight Anoles in Miami, Florida. The home ranges of both sexes substantially overlapped those of the same- and different-sex individuals. In addition, male and female home ranges did not differ significantly, an unusual observation among lizard species. If one compares both male and female home ranges to those of other Anolis species, Knight Anoles have significantly larger home ranges, except for two species for which statistical comparisons were not possible. Our results suggest that home ranges and sex-specific spatial arrangements of canopy lizards may differ from those of more terrestrial species.

  18. Phenotype of asthma-chronic obstructive pulmonary disease overlap syndrome.

    Science.gov (United States)

    Rhee, Chin Kook

    2015-07-01

    Many patients with asthma or chronic obstructive pulmonary disease (COPD) have overlapping characteristics of both diseases. By spirometric definition, patients with both fixed airflow obstruction (AO) and bronchodilator reversibility or fixed AO and bronchial hyperresponsiveness can be considered to have asthma-COPD overlap syndrome (ACOS). However, patients regarded to have ACOS by spirometric criteria alone are heterogeneous and can be classified by phenotype. Eosinophilic inflammation, a history of allergic disease, and smoke exposure are important components in the classification of ACOS. Each phenotype has a different underlying pathophysiology, set of characteristics, and prognosis. Medical treatment for ACOS should be tailored according to phenotype. A narrower definition of ACOS that includes both spirometric and clinical criteria is needed. PMID:26161009

  19. On Evaluation of Overlap Integrals with Noninteger Principal Quantum Numbers

    Institute of Scientific and Technical Information of China (English)

    I.I.Guseinov; B.A.Mamedov

    2004-01-01

    By use of complete orthonormal sets of ψα exponential-type orbitals (ψα-ETOs,α=1,0,-1,-2,...) the series expansion formulas for the noninteger n Slater-type orbitals (NISTOs) in terms of integer n Slater-type orbitals (ISTOs) are derived. These formulas enable us to express the overlap integrals with NISTOs through the overlap integrals over ISTOs with the same and different screening constants. By calculating concrete cases the convergence of the series for arbitrary values of noninteger principal quantum numbers and screening constants of NISTOs and internuclear distances is tested. The accuracy of the results is quite high for quantum numbers, screening constants and location of STOs.

  20. On Evaluation of Overlap Integrals with Noninteger Principal Quantum Numbers

    Institute of Scientific and Technical Information of China (English)

    I.I. Guseinov; B.A. Mamedov

    2004-01-01

    By use of complete orthonormal sets of ψα exponential-type orbitals (ψα-ETOs, α = 1, 0,-1,-2, ...) the series expansion formulas for the noninteger n* Slater-type orbitals (NISTOs) in terms of integer n Slater-type orbitals(ISTOs) are derived. These formulas enable us to express the overlap integrals with NISTOs through the overlap integrals over ISTOs with the same and different screening constants. By calculating concrete cases the convergence of the series for arbitrary values of noninteger principal quantum numbers and screening constants of NISTOs and internuclear distances is tested. The accuracy of the results is quite high for quantum numbers, screening constants and location of STOs.

  1. Hausdorff dimension of self-similar sets with overlaps

    Institute of Scientific and Technical Information of China (English)

    DENG QiRong; John HARDING; HU TianYou

    2009-01-01

    We provide a simple formula to compute the Hausdorff dimension of the attractor of an overlapping iterated function system of contractive similarities satisfying a certain collection of assumptions. This formula is obtained by associating a non-overlapping infinite iterated function system to an iterated function system satisfying our assumptions and using the results of Moran to compute the Hausdorff dimension of the attractor of this infinite iterated function system,thus showing that the Hausdorff dimension of the attractor of this infinite iterated function system agrees with that of the attractor of the original iterated function system.Our methods are applicable to some iterated function systems that do not satisfy the finite type condition recently introduced by Ngai and Wang.

  2. Discriminating crop and other canopies by overlapping binary image layers

    Science.gov (United States)

    Doi, Ryoichi

    2013-02-01

    For optimal management of agricultural fields by remote sensing, discrimination of the crop canopy from weeds and other objects is essential. In a digital photograph, a rice canopy was discriminated from a variety of weed and tree canopies and other objects by overlapping binary image layers of red-green-blue and other color components indicating the pixels with target canopy-specific (intensity) values based on the ranges of means ±(3×) standard deviations. By overlapping and merging the binary image layers, the target canopy specificity improved to 0.0015 from 0.027 for the yellow 1× standard deviation binary image layer, which was the best among all combinations of color components and means ±(3×) standard deviations. The most target rice canopy-likely pixels were further identified by limiting the pixels at different luminosity values. The discriminatory power was also visually demonstrated in this manner.

  3. DEMON: a Local-First Discovery Method for Overlapping Communities

    CERN Document Server

    Coscia, Michele; Giannotti, Fosca; Pedreschi, Dino

    2012-01-01

    Community discovery in complex networks is an interesting problem with a number of applications, especially in the knowledge extraction task in social and information networks. However, many large networks often lack a particular community organization at a global level. In these cases, traditional graph partitioning algorithms fail to let the latent knowledge embedded in modular structure emerge, because they impose a top-down global view of a network. We propose here a simple local-first approach to community discovery, able to unveil the modular organization of real complex networks. This is achieved by democratically letting each node vote for the communities it sees surrounding it in its limited view of the global system, i.e. its ego neighborhood, using a label propagation algorithm; finally, the local communities are merged into a global collection. We tested this intuition against the state-of-the-art overlapping and non-overlapping community discovery methods, and found that our new method clearly ou...

  4. Aceclofenac induced Stevens-Johnson/toxic epidermal necrolysis overlap syndrome

    Directory of Open Access Journals (Sweden)

    Kaderthambi Hajamohideen Nooru Ameen

    2013-01-01

    Full Text Available The purpose of this paper is to report a rare occurrence of Stevens-Johnson/Toxic epidermal necrolysis (SJS/TEN overlap syndrome after the use of aceclofenac. A 38 year old healthy adult male presented with rapidly evolving rash over face and upper body with ulceration of buccal mucosa and breathlessness after taking aceclofenac tablet. Naranjo score for this adverse drug event was six, thereby making it a probable adverse drug reaction. Despite aggressive fluid resuscitation and use of antihistamines and systemic steroids, patient′s health rapidly worsened and died within six hours of presentation. Aceclofenac induced SJS/TEN overlap is an extremely rare clinical association previously reported only once in medical literature. To the best of our knowledge, this is the first case report of such an association in the Indian population. We are presenting this case to highlight the serious adverse reactions possible from a routinely prescribed drug.

  5. Hausdorff dimension of self-similar sets with overlaps

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We provide a simple formula to compute the Hausdorff dimension of the attractor of an overlapping iterated function system of contractive similarities satisfying a certain collection of assumptions. This formula is obtained by associating a non-overlapping infinite iterated function system to an iterated function system satisfying our assumptions and using the results of Moran to compute the Hausdorff dimension of the attractor of this infinite iterated function system, thus showing that the Hausdorff dimension of the attractor of this infinite iterated function system agrees with that of the attractor of the original iterated function system. Our methods are applicable to some iterated function systems that do not satisfy the finite type condition recently introduced by Ngai and Wang.

  6. Auditing Complex Concepts in Overlapping Subsets of SNOMED

    Science.gov (United States)

    Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A.; Hripcsak, George

    2008-01-01

    Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries. PMID:18998838

  7. Pin diode calibration - beam overlap monitoring for low energy cooling

    Energy Technology Data Exchange (ETDEWEB)

    Drees, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Montag, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Thieberger, P. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-09-30

    We were trying to address the question whether or not the Pin Diodes, currently installed approximately 1 meter downstream of the RHIC primary collimators, are suitable to monitor a recombination signal from the future RHIC low energy cooling section. A maximized recombination signal, with the Au+78 ions being lost on the collimator, will indicate optimal Au-electron beam overlap as well as velocity matching of the electron beam in the cooling section.

  8. Multifunctional proteins revealed by overlapping clustering in protein interaction network

    OpenAIRE

    Becker, Emmanuelle; Robisson, Benoît; Chapple, Charles E.; Guénoche, Alain; Brun, Christine

    2011-01-01

    Motivation: Multifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters. Results: Here, we present Overlapping Cluster Generator (OCG), a novel clustering method which decomposes a network into overla...

  9. Unquenching the topological susceptibility with an overlap action

    CERN Document Server

    Kovács, T G

    2002-01-01

    We estimate the quark-mass dependence of the topological susceptibility with dynamical overlap and clover fermions. Unquenching effects on the susceptibility turn out to be well approximated by a reweighting of a quenched ensemble with a low-eigenmode truncation of the fermionic determinant. We find that it is most likely due to the explicit chiral symmetry breaking of the fermion action that present day dynamical simulations do not show the expected suppression of the topological susceptibility.

  10. The overlap between anxiety, depression, and obsessive-compulsive disorder

    OpenAIRE

    Goodwin, Guy M.

    2015-01-01

    The anxiety disorders include generalized anxiety disorder, specific phobia, social phobia, agoraphobia, and panic disorder. In addition to the specific symptoms of these disorders, there may be a common experience of anxiety and even dysphoria across the conditions, and of course recourse to the same drug or choice of drugs for treatment. This overlap probably occurs because of universal dimensions of distress or negative affectivity, a shared genetic predisposition, and a common neurobiolog...

  11. Node-Centric Detection of Overlapping Communities in Social Networks

    CERN Document Server

    Cohen, Yehonatan; Rubin, Amir

    2016-01-01

    We present NECTAR, a community detection algorithm that generalizes Louvain method's local search heuristic for overlapping community structures. NECTAR chooses dynamically which objective function to optimize based on the network on which it is invoked. Our experimental evaluation on both synthetic benchmark graphs and real-world networks, based on ground-truth communities, shows that NECTAR provides excellent results as compared with state of the art community detection algorithms.

  12. A Case of Overlapping Choriocapillaritis Syndromes: Multimodal Imaging Appraisal

    OpenAIRE

    Tatiana Kuznetcova; Bruno Jeannin; Herbort, Carl P.

    2012-01-01

    Purpose: To present a patient with overlapping choriocapillaritis syndromes who first presented as a typical case of multiple evanescent white dot syndrome (MEWDS) and later with characteristic findings compatible with multifocal choroiditis (MFC). Case Report: A 40-year-old myopic woman presented with a paracentral scotoma OS. Fundus examination revealed pale discolored areas around the optic disc corresponding to faintly hyperfluorescent areas on fluorescein angiography (FA). On indocya...

  13. Overlapping reliable control for a cable-stayed bridge benchmark

    OpenAIRE

    Bakule, Lubomir; Paulet-Crainiceanu, Fideliu; Rodellar Benedé, José; Rossell Garriga, Josep Maria

    2005-01-01

    The brief presents a reliable 1-out-2 reduced order control design strategy for a cable-stayed bridge benchmark using two overlapping subsystems and the linear quadratic Gaussian (LQG) design. Reliability with regard to controller failures is considered. Local controllers are designed for reduced order subsystems of expanded system. They are implemented and evaluated on the original overall system model. Two different sets of numerical experiments of reliable control design within 1-out-2 con...

  14. Overlapping cusp ion injections: An explanation invoking magnetopause reconnection

    OpenAIRE

    Lockwood, Mike

    1995-01-01

    An explanation of overlapping cusp ion injections is presented using the pulsating cusp model of the effects of magnetopause reconnection. It is shown that two populations of cusp ions, covering separated energy ranges, can be seen simultaneously by low- or mid-altitude satellites because of the combined effect of the acceleration and the straightening of newly-opened field lines as they evolve away from the reconnection site. Observations of such signatures, recently reported in data from th...

  15. Individual foraging strategies reveal niche overlap between endangered Galapagos pinnipeds

    OpenAIRE

    Stella Villegas-Amtmann; Jeglinski, Jana W.E.; Costa, Daniel P.; Robinson, Patrick W.; Fritz Trillmich

    2013-01-01

    Most competition studies between species are conducted from a population-level approach. Few studies have examined inter-specific competition in conjunction with intra-specific competition, with an individual-based approach. To our knowledge, none has been conducted on marine top predators. Sympatric Galapagos fur seals (Arctocephalus galapagoensis) and sea lions (Zalophus wollebaeki) share similar geographic habitats and potentially compete. We studied their foraging niche overlap at Cabo Do...

  16. Word segmentation of overlapping ambiguous strings during Chinese reading

    OpenAIRE

    Ma, Guojie; Li, Xingshan; Rayner, Keith

    2014-01-01

    In three experiments, we tested three possible mechanisms for segmenting overlapping ambiguous strings in Chinese reading. The first two characters and the last two characters in a 3-character ambiguous string could both constitute a word in the reported studies. The left-priority hypothesis assumes that the word on the left has an advantage in the competition and the other word cannot be processed until the word on the left is recognized. The independent processing hypothesis assumes that wo...

  17. Direct evaluation of overlap integrals between Slater-type-orbitals

    CERN Document Server

    Caola, Michael J

    2016-01-01

    We derive direct single-stage numerical evaluation of the electronic overlap integral between arbitrary atomic orbitals (including STOs). Integration is over cartesian co-ordinates, and replaces previous sums over 'special' functions. The results, in Mathematica 10 and Maple 18, agree with the literature to 8 digits. We briefly discuss possible use in quantum chemistry, including accuracy, algorithmic suitability and operating-system machine-implementation as an intrinsic function.

  18. Evaluation of the overlapping of posterior teeth in two techniques of improved interproximal panoramic program and standard panoramic

    Directory of Open Access Journals (Sweden)

    Goodarzi pour D

    2010-06-01

    Full Text Available "nBackground and Aims: Overlapping of the proximal surfaces of posterior teeth in the panoramic radiography is a major concern. Therefore, an option has been developed in the panoramic unit of Planmeca Promax, namely improved interproximal mode. This mode causes lower horizental angle with the teeth contact region during the unit rotation decreasing overlapping of the panoramic images of the posterior teeth especially premolar teeth. The present study was done to compare the overlapping of posterior teeth using two techniques of improved interproximal panoramic program and standard panoramic. "nMaterials and Methods: In this diagnostic study, 32 patients requiring panoramic radiographies at their posterior teeth during their routine diagnosis and treatment process with the mean age of 27.3 years were participated. No patients showed crowding of posterior teeth or missed and restored posterior teeth. The participants' panoramic radiographies were randomly taken by two techniques of improved interproximal panoramic and standard panoramic using Planmeca Promax device. The overlapping of the panoramic images was blindly assessed by an oral radiologist. The overlapping in both techniques was reported by frequency and percentage. The comparisons were done by Chi-square test between two techniques and the odds ratio of overlapping was estimated using regression analysis. "nResults: In standard panoramic techniques, 38.5% (148 contacts of 384 contacts of the proximal surfaces overlapped while the overlapping of the proximal surfaces was observed in 18.8% (72 contacts of 384 overall contacts in improved interproximal technique. Significant differences were noted between two techniques regarding overlapping (P<0.001. Also 66.4% and 39.1% of 4-5 teeth contacts overlapped in standard and improved techniques. The values were reported to be 39.1% and 12.5% in contacts of 5-6 teeth and 10.2% and 4.7% in the contacts of 6-7 teeth in both techniques

  19. Strong genetic overlap between executive functions and intelligence.

    Science.gov (United States)

    Engelhardt, Laura E; Mann, Frank D; Briley, Daniel A; Church, Jessica A; Harden, K Paige; Tucker-Drob, Elliot M

    2016-09-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic influences on EFs are very high, even in middle childhood, but the extent to which these genetic influences overlap with those on intelligence is unclear. We examined genetic and environmental overlap between EFs and intelligence in a racially and socioeconomically diverse sample of 811 twins ages 7 to 15 years (M = 10.91, SD = 1.74) from the Texas Twin Project. A general EF factor representing variance common to inhibition, switching, working memory, and updating domains accounted for substantial proportions of variance in intelligence, primarily via a genetic pathway. General EF continued to have a strong, genetically mediated association with intelligence even after controlling for processing speed. Residual variation in general intelligence was influenced only by shared and nonshared environmental factors, and there remained no genetic variance in general intelligence that was unique of EF. Genetic variance independent of EF did remain, however, in a more specific perceptual reasoning ability. These results provide evidence that genetic influences on general intelligence are highly overlapping with those on EF. (PsycINFO Database Record

  20. Detection of multiple velocity components in partially overlapping emitting regions

    Science.gov (United States)

    Mertens, F.; Lobanov, A. P.

    2016-03-01

    Context. Velocity measurements made from multiple-epoch astronomical images of evolving objects with optically thin continuum emission (e.g. as relativistic jets or expanding supernova shells) may be confused as a result of the overlap of semi-transparent features moving at different speeds. Aims: Multi-scale wavelet decomposition can be effectively applied to identify and track such overlapping features, provided that their respective structural responses can be separated over the spatial scales used for the decomposition. Methods: We developed a new method that combines the stacked cross-correlation with the wavelet-based image segmentation and evaluation (WISE) technique of decomposition of two-dimensional structures, to separate and track dominant spatial responses of overlapping evolving features. Results: The method is tested on a set of simulated images of a stratified relativistic jet, demonstrating the robust detection of both the faster spine and the slower sheath speeds. The method is applied to mutliple-epoch images from the MOJAVE survey, revealing two different superluminal streams inside the jet in 3C 273 and the acceleration of the flow in 3C 120. Conclusions: The method can be applied to densely monitored objects with composite structural evolution such as the parsec-scale jet in M 87 or heavily resolved expanding supernova shells.

  1. Cluster-enhanced sparse approximation of overlapping ultrasonic echoes.

    Science.gov (United States)

    Mor, Etai; Aladjem, Mayer; Azoulay, Amnon

    2015-02-01

    Ultrasonic pulse-echo methods have been used extensively in non-destructive testing of layered structures. In acoustic measurements on thin layers, the resulting echoes from two successive interfaces overlap in time, making it difficult to assess the individual echo parameters. Over the last decade sparse approximation methods have been extensively used to address this issue. These methods employ a large dictionary of elementary functions (atoms) and attempt to select the smallest subset of atoms (sparsest approximation) that represent the ultrasonic signal accurately. In this paper we propose the cluster-enhanced sparse approximation (CESA) method for estimating overlapping ultrasonic echoes. CESA is specifically adapted to deal with a large number of signals acquired during an ultrasonic scan. It incorporates two principal algorithms. The first is a clustering algorithm, which divides a set of signals comprising an ultrasonic scan into groups of signals that can be approximated by the same set of atoms. The second is a two-stage iterative algorithm, which alternates between update of the atoms associated with each cluster, and re-clustering of the signals according to the updated atoms. Because CESA operates on clusters of signals, it achieves improved results in terms of approximation error and computation time compared with conventional sparse methods, which operate on each signal separately. The superior ability of CESA to approximate highly overlapping ultrasonic echoes is demonstrated through simulation and experiments on adhesively bonded structures. PMID:25643086

  2. How do keratinizing disorders and blistering disorders overlap?

    Science.gov (United States)

    Hamada, Takahiro; Tsuruta, Daisuke; Fukuda, Shunpei; Ishii, Norito; Teye, Kwesi; Numata, Sanae; Dainichi, Teruki; Karashima, Tadashi; Ohata, Chika; Furumura, Minao; Hashimoto, Takashi

    2013-02-01

    Inherited keratinizing disorders are caused by mutations in the genes encoding cornified cell envelope proteins, enzymes and their inhibitors, adhesion molecules, cytoskeletal proteins and others in the epidermis. These molecules are known to regulate differentiation, proliferation and cell adhesions. Intriguingly, some keratinizing disorders show blistering skin lesions, while some inherited blistering disorders show abnormal keratinization. Therefore, hereditary keratinizing and blistering diseases are closely related and show overlapping genetic backgrounds. In this review, we overviewed keratinizing and blistering disorders in terms of overlapping of the two disease groups. Gene mutations in desmosomal components cause striate keratoderma, Naxos disease, epidermolytic palmoplantar keratoderma and plakophilin deficiency, which first show skin fragility and blisters and later hyperkeratosis. Gene mutations in hemidesmosomal components cause various forms of epidermolysis bullosa, some of which show hyperkeratosis on the nails, palms and soles, in addition to blister formation. Diseases with gene mutations in calcium pump proteins are Darier disease and Hailey-Hailey disease, which show clinicopathological overlaps and develop both keratinizing and blistering skin lesions. Finally, gene mutations in epidermal keratins cause epidermolysis bullosa simplex, epidermolytic ichthyosis, superficial epidermolytic ichthyosis, epidermolytic palmoplantar keratoderma and pachyonychia congenita/focal palmoplantar keratoderma, which show thickening of the palms and soles with underlying blister formation. In general, responsible proteins for diseases developing both keratinizing and blistering conditions are adhesion molecules, calcium pump proteins and keratins, but not connexins, cornified cell envelop proteins, enzymes or inhibitors. It is still unknown how particular keratinizing diseases develop blisters and vice versa.

  3. Robust Mosaicking of Uav Images with Narrow Overlaps

    Science.gov (United States)

    Kim, J.; Kim, T.; Shin, D.; Kim, S. H.

    2016-06-01

    This paper considers fast and robust mosaicking of UAV images under a circumstance that each UAV images have very narrow overlaps in-between. Image transformation for image mosaicking consists of two estimations: relative transformations and global transformations. For estimating relative transformations between adjacent images, projective transformation is widely considered. For estimating global transformations, panoramic constraint is widely used. While perspective transformation is a general transformation model in 2D-2D transformation, this may not be optimal with weak stereo geometry such as images with narrow overlaps. While panoramic constraint works for reliable conversion of global transformation for panoramic image generation, this constraint is not applicable to UAV images in linear motions. For these reasons, a robust approach is investigated to generate a high quality mosaicked image from narrowly overlapped UAV images. For relative transformations, several transformation models were considered to ensure robust estimation of relative transformation relationship. Among them were perspective transformation, affine transformation, coplanar relative orientation, and relative orientation with reduced adjustment parameters. Performance evaluation for each transformation model was carried out. The experiment results showed that affine transformation and adjusted coplanar relative orientation were superior to others in terms of stability and accuracy. For global transformation, we set initial approximation by converting each relative transformation to a common transformation with respect to a reference image. In future work, we will investigate constrained relative orientation for enhancing geometric accuracy of image mosaicking and bundle adjustments of each relative transformation model for optimal global transformation.

  4. Overlapping Domain Decomposition Methods for Elliptic Quasi-Variational Inequalities Related to Impulse Control Problem with Mixed Boundary Conditions

    Indian Academy of Sciences (India)

    Mohamed Haiour; Salah Boulaaras

    2011-11-01

    In this paper we provide a maximum norm analysis of an overlapping Schwarz method on non-matching grids for quasi-variational inequalities related to impulse control problem with mixed boundary conditions. We provide that the discretization on every sub-domain converges in uniform norm. Furthermore, a result of approximation in uniform norm is given.

  5. THE OVERLAPPING DOMAIN DECOMPOSITION METHOD FOR HARMONIC EQUATION OVER EXTERIOR THREE-DIMENSIONAL DOMAIN

    Institute of Scientific and Technical Information of China (English)

    Ji-ming Wu; De-hao Yu

    2000-01-01

    In this paper, the overlapping domain decomposition method, which is based on the natural boundary reduction[1] and first suggested in [2], is applied to slove the exterior boundary value problem of harmonic equation over three-dimensional domain. The convergence and error estimates both for the continuous case and the discrete case are given. The contraction factor for the exterior spherical domain is also discussed. Moreover, numerical results are given which show that the accuracy and the convergence are in accord with the theoretical analyses.

  6. The binding sites for cocaine and dopamine in the dopamine transporter overlap

    DEFF Research Database (Denmark)

    Beuming, Thijs; Kniazeff, Julie; Bergmann, Marianne L;

    2008-01-01

    T. Our models suggest that the binding site for cocaine and cocaine analogs is deeply buried between transmembrane segments 1, 3, 6 and 8, and overlaps with the binding sites for the substrates dopamine and amphetamine, as well as for benztropine-like DAT inhibitors. We validated our models by detailed...... mutagenesis and by trapping the radiolabeled cocaine analog [3H]CFT in the transporter, either by cross-linking engineered cysteines or with an engineered Zn2+-binding site that was situated extracellularly to the predicted common binding pocket. Our data demonstrate the molecular basis for the competitive...

  7. Asthma-Chronic Obstructive Pulmonary Disease Overlap Syndrome: Nothing New Under the Sun.

    Science.gov (United States)

    Putcha, Nirupama; Wise, Robert A

    2016-08-01

    The debate about whether asthma and chronic obstructive pulmonary disease (COPD) are distinct clinical syndromes is not new; there is heightened interest in understanding the group of individuals with obstructive lung disease who seem to have elements of both conditions because recent studies have demonstrated increased risk for respiratory events and exacerbations. We describe the clinical characteristics of this subtype of disease and suggest 4 working definitions of individuals who would fall into the asthma-COPD overlap category. Understanding the mechanisms underlying these subtypes will hopefully lead into a better understanding of therapeutic strategies that can target specific pathobiologic pathways. PMID:27401623

  8. Xeroderma Pigmentosum-Trichothiodystrophy overlap patient with novel XPD/ERCC2 mutation

    DEFF Research Database (Denmark)

    Kralund, Henrik H; Ousager, Lilian; Jaspers, Nicolaas G;

    2013-01-01

    outcome from many of these mutations. We demonstrate a patient, believed to represent an overlap between XP and TTD/CS. In addition to other organ dysfunctions, the young man presented with Photosensitivity, Ichthyosis, Brittle hair, Impaired physical and mental development, Decreased fertility and Short...... stature (PIBIDS) suggestive of TTD, but lacking the almost patognomonic "tiger tail" banding of the hair under polarized light. Additionally, he developed basal cell carcinoma aged 28, as well as adult onset kidney failure, features normally not associated with TTD but rather XP/CS. His freckled...

  9. 工厂化水产养殖 LED 灯具选择的分析与建议%The Analysis and Suggestion of LED Lamp Selection in Industial Aquaculture Systems

    Institute of Scientific and Technical Information of China (English)

    宋昌斌; 高霄龙; 仇登高; 刘鹰; 王朝夕; 谢海忠; 杨华; 姚然; 王军喜

    2015-01-01

    This paper illustrates the importance of the LED light source in the recirculating aquaculture systems, introducing the current status of lighting in aquaculture workshop, and providing some useful analysis and suggestions in accordance with the required principle of three light environment parameters in fish and the requirements of lamps in specific contexts, which would be instructive and meaningful to how to choose the suitable LED lamps in aquaculture workshop.%阐述了LED光源对循环水养殖系统的重要性,介绍了养殖车间光照的现状,并根据鱼类对光环境三要素一般的适应需求规律、针对灯具在特定使用环境下的要求进行了分析与建议,对水产养殖车间如何正确选择LED灯具具有指导意义。

  10. 核电建设阶段大宗材料采购缺失分析和改进建议%Analysis and Improvement Suggestion for the Lack of Bulk Material Procurement during the Construction of Nuclear Power Plant

    Institute of Scientific and Technical Information of China (English)

    李冠英; 顾健

    2015-01-01

    Aiming at the importance and influence of lack of procurement for bulk materials during nuclear power plant construction, the design, procurement and construction management for bulk material are analyzed. Through analysis, referring to the problems during design, procurement and construction management, suggestions are given to countermeasures for all stage of work, with an aim to increase procurement efficiency and decrease the lack of procurement for bulk materials.%文章针对核电建设阶段大宗材料采购缺失重要性及缺失影响,进行了大宗材料采购时设计、采购、施工管理方面问题的分析.通过分析,针对大宗材料采购时设计、采购、施工管理问题提出了各阶段的工作对策,旨在提高采购效率、减小大宗材料的缺失率.

  11. 关于珠海渔女景区建筑更新改造的调研分析与建议%The Survey Analysis and Suggestions about Building Renewal and Transformation of Zhuhai Fishing-girl Scenic Area

    Institute of Scientific and Technical Information of China (English)

    林俊航

    2012-01-01

    旧城改造与城市更新在我国乃至世界各地已成为一个共同面临的问题,珠海渔女作为珠海市的城市地标景观,其景区内的建筑——旅游配套设施之旧况已难以满足日益增长的旅游服务需求,影响城市景观与城市印象。因此,通过实地踏勘调研分析.整合可靠数据,提出更新改造建议,为接下来的建筑改造设计提供思路和依据。%Transformation of the old city and city renewal in our country or even in the world has become a common problem we are facing now. The Fishing-girl, as the city-landmark-landscape of Zhuhai, the old condition of the construction of tourist facilities within the scenic area, has been difficult to meet the growing demand of tourism service and effects to the city- landscape and city-impression. Therefore, through field reconnaissance survey analysis, integrating reliability data, put forward renewal suggestions and make ideas and evidence for the following reconstruction of the building renovation design.

  12. Report of Two Siblings with Overlapping Features of Ellis-van Creveld and Weyers Acrodental Dysostosis

    Directory of Open Access Journals (Sweden)

    Devi C Shetty

    2012-01-01

    Full Text Available Skeletal dysplasias are a heterogenous group of disorders combining abnormalities in the skull and other skeletal bones. Weyers acrofacial dysostosis also known as Weyers acrodental dysostosis was first described in 1952, by Weyers, as a postaxial polydactyly, which had features distinct from, yet some in common with the Ellis-van Creveld Syndrome (EvC. Both the syndromes have been mapped to the same chromosome, 4p16. The cases reported here highlight the overlapping features of both syndromes, which are dissimilar in mode of inheritance and phenotypic severity, emphasizing the need for genetic analysis, to categorize these conditions.

  13. Partition of Unity for a Class of Nonlinear Parabolic Equation on Overlapping Non-Matching Grids

    Institute of Scientific and Technical Information of China (English)

    Qisheng Wang; Kang Deng; Zhiguang Xiong; Yunqing Huang

    2007-01-01

    A class of nonlinear parabolic equation on a polygonal domain Ω ( ) R2 is investigated in this paper. We introduce a finite element method on overlapping non-matching grids for the nonlinear parabolic equation based on the partition of unity method. We give the construction and convergence analysis for the semi-discrete and the fully discrete finite element methods. Moreover, we prove that the error of the discrete variational problem has good approximation properties. Our results are valid for any spatial dimensions. A numerical example to illustrate the theoretical results is also given.

  14. Spatial and Dietary Overlap Creates Potential for Competition between Red Snapper (Lutjanus campechanus and Vermilion snapper (Rhomboplites aurorubens.

    Directory of Open Access Journals (Sweden)

    William T Davis

    Full Text Available Understanding the complex nature of direct and indirect species interactions is a critical precursor to successful resource management. In the northern Gulf of Mexico fisheries ecosystem, red snapper (Lutjanus campechanus and vermilion snapper (Rhomboplites aurorubens are two commercially harvested species within a larger reef fish complex. These two species share similar habitats and diets; however, little is known about how these species partition habitat and dietary resources. In this study we examined the extent of spatial and dietary overlap between red snapper and vermilion snapper, and experimentally compared their feeding behavior. Field data from multiple gear types demonstrates that red snapper and vermilion snapper frequently cohabited reefs in the northern Gulf of Mexico, and Pianka's niche overlap indices suggest significantly overlapping diets. Experimental manipulations show that red snapper are the dominant forager of the two species, as red snapper foraging alone ate more shrimp per fish than vermilion snapper in both the single species (p = 0.003 and mixed species (p = 0.02 treatments. In addition, red snapper ate significantly more shrimp per fish in the mixed species treatment than in the single species treatment (p = 0.04. Vermilion snapper shrimp consumption per fish did not differ significantly between mixed and single species treatments. Cumulatively, our results suggest that spatial and dietary overlap could lead to competition between red and vermilion snapper in the study area; however, conclusively determining the existence of such competition would require further research.

  15. Spatial and Dietary Overlap Creates Potential for Competition between Red Snapper (Lutjanus campechanus) and Vermilion snapper (Rhomboplites aurorubens).

    Science.gov (United States)

    Davis, William T; Drymon, J Marcus; Powers, Sean P

    2015-01-01

    Understanding the complex nature of direct and indirect species interactions is a critical precursor to successful resource management. In the northern Gulf of Mexico fisheries ecosystem, red snapper (Lutjanus campechanus) and vermilion snapper (Rhomboplites aurorubens) are two commercially harvested species within a larger reef fish complex. These two species share similar habitats and diets; however, little is known about how these species partition habitat and dietary resources. In this study we examined the extent of spatial and dietary overlap between red snapper and vermilion snapper, and experimentally compared their feeding behavior. Field data from multiple gear types demonstrates that red snapper and vermilion snapper frequently cohabited reefs in the northern Gulf of Mexico, and Pianka's niche overlap indices suggest significantly overlapping diets. Experimental manipulations show that red snapper are the dominant forager of the two species, as red snapper foraging alone ate more shrimp per fish than vermilion snapper in both the single species (p = 0.003) and mixed species (p = 0.02) treatments. In addition, red snapper ate significantly more shrimp per fish in the mixed species treatment than in the single species treatment (p = 0.04). Vermilion snapper shrimp consumption per fish did not differ significantly between mixed and single species treatments. Cumulatively, our results suggest that spatial and dietary overlap could lead to competition between red and vermilion snapper in the study area; however, conclusively determining the existence of such competition would require further research.

  16. Concurrent partnerships in Cape Town, South Africa: race and sex differences in prevalence and duration of overlap

    Directory of Open Access Journals (Sweden)

    Roxanne Beauclair

    2015-02-01

    Full Text Available Introduction: Concurrent partnerships (CPs have been suggested as a risk factor for transmitting HIV, but their impact on the epidemic depends upon how prevalent they are in populations, the average number of CPs an individual has and the length of time they overlap. However, estimates of prevalence of CPs in Southern Africa vary widely, and the duration of overlap in these relationships is poorly documented. We aim to characterize concurrency in a more accurate and complete manner, using data from three disadvantaged communities of Cape Town, South Africa. Methods: We conducted a sexual behaviour survey (n=878 from June 2011 to February 2012 in Cape Town, using Audio Computer-Assisted Self-Interviewing to collect sexual relationship histories on partners in the past year. Using the beginning and end dates for the partnerships, we calculated the point prevalence, the cumulative prevalence and the incidence rate of CPs, as well as the duration of overlap for relationships begun in the previous year. Linear and binomial regression models were used to quantify race (black vs. coloured and sex differences in the duration of overlap and relative risk of having CPs in the past year. Results: The overall point prevalence of CPs six months before the survey was 8.4%: 13.4% for black men, 1.9% for coloured men, 7.8% black women and 5.6% for coloured women. The median duration of overlap in CPs was 7.5 weeks. Women had less risk of CPs in the previous year than men (RR 0.43; 95% CI: 0.32–0.57 and black participants were more at risk than coloured participants (RR 1.86; 95% CI: 1.17–2.97. Conclusions: Our results indicate that in this population the prevalence of CPs is relatively high and is characterized by overlaps of long duration, implying there may be opportunities for HIV to be transmitted to concurrent partners.

  17. Simple nonlinear models suggest variable star universality

    CERN Document Server

    Lindner, John F; Kia, Behnam; Hippke, Michael; Learned, John G; Ditto, William L

    2015-01-01

    Dramatically improved data from observatories like the CoRoT and Kepler spacecraft have recently facilitated nonlinear time series analysis and phenomenological modeling of variable stars, including the search for strange (aka fractal) or chaotic dynamics. We recently argued [Lindner et al., Phys. Rev. Lett. 114 (2015) 054101] that the Kepler data includes "golden" stars, whose luminosities vary quasiperiodically with two frequencies nearly in the golden ratio, and whose secondary frequencies exhibit power-law scaling with exponent near -1.5, suggesting strange nonchaotic dynamics and singular spectra. Here we use a series of phenomenological models to make plausible the connection between golden stars and fractal spectra. We thereby suggest that at least some features of variable star dynamics reflect universal nonlinear phenomena common to even simple systems.

  18. Overlap of Autism and Seizures: Understanding Cognitive Comorbidity

    Directory of Open Access Journals (Sweden)

    Neha Khetrapal

    2010-01-01

    Full Text Available This article introduces the concept of 'cognitive comorbidity,' which lays emphasis on common cognitive deficits that cut across different disorders. The concept is illustrated with the help of two commonly reported overlapping conditions (autism and epilepsy. It is further explained by concentrating on two important cognitive processes of facial emotional recognition and emotional memory, shown to be compromised in both conditions; and their underlying neural substrates. Cognitive comorbidity is then contrasted with 'comorbidity,' a term which is more commonly used for describing cognitive disorders. The paper closes by providing directions for rehabilitative and theoretical efforts that could be inspired by the newly introduced concept.

  19. Chaotic scattering in the regime of weakly overlapping resonances.

    Science.gov (United States)

    Dietz, B; Friedrich, T; Harney, H L; Miski-Oglu, M; Richter, A; Schäfer, F; Weidenmüller, H A

    2008-11-01

    We measure the transmission and reflection amplitudes of microwaves in a resonator coupled to two antennas at room temperature in the regime of weakly overlapping resonances and in a frequency range of 3-16GHz . Below 10.1GHz the resonator simulates a chaotic quantum system. The distribution of the elements of the scattering matrix S is not Gaussian. The Fourier coefficients of S are used for a best fit of the autocorrelation function of S to a theoretical expression based on random-matrix theory. We find very good agreement below but not above 10.1GHz .

  20. A NON-OVERLAPPED PRINTED MONOPOLE ANTENNA FOR UWB APPLICATIONS

    OpenAIRE

    ABDELHADI ASSIR; ABDELMAJID OUMNAD

    2011-01-01

    In this paper, a novel small ultra-wideband (UWB) printed monopole antenna, designed to operate in 3.1-10.6 GHz frequency band, is presented. The antenna is composed of five non-overlapped rectangular patches, a partial ground plane and a standard 50-Ω microstrip feed line. The overall size of the proposed antenna is 22.8 mm  29.5 mm  0.813 mm. The design procedure that we have used is based on a mixed integer genetic algorithm (GA) and the finite-difference time-domain (FDTD) method with u...

  1. DNA sequence and genetic analysis of the Rhodobacter capsulatus nifENX gene region: homology between NifX and NifB suggests involvement of NifX in processing of the iron-molybdenum cofactor.

    Science.gov (United States)

    Moreno-Vivian, C; Schmehl, M; Masepohl, B; Arnold, W; Klipp, W

    1989-04-01

    Rhodobacter capsulatus genes homologous to Klebsiella pneumoniae nifE, nifN and nifX were identified by DNA sequence analysis of a 4282 bp fragment of nif region A. Four open reading frames coding for a 51,188 (NifE), a 49,459 (NifN), a 17,459 (NifX) and a 17,472 (ORF4) dalton protein were detected. A typical NifA activated consensus promoter and two imperfect putative NifA binding sites were located in the 377 bp sequence in front of the nifE coding region. Comparison of the deduced amino acid sequences of R. capsulatus NifE and NifN revealed homologies not only to analogous gene products of other organisms but also to the alpha and beta subunits of the nitrogenase iron-molybdenum protein. In addition, the R. capsulatus nifE and nifN proteins shared considerable homology with each other. The map position of nifX downstream of nifEN corresponded in R. capsulatus and K. pneumoniae and the deduced molecular weights of both proteins were nearly identical. Nevertheless, R. capsulatus NifX was more related to the C-terminal end of NifY from K. pneumoniae than to NifX. A small domain of approximately 33 amino acid residues showing the highest degree of homology between NifY and NifX was also present in all nifB proteins analyzed so far. This homology indicated an evolutionary relationship of nifX, nifY and nifB and also suggested that NifX and NifY might play a role in maturation and/or stability of the iron-molybdenum cofactor. The open reading frame (ORF4) downstream of nifX in R. capsulatus is also present in Azotobacter vinelandii but not in K. pneumoniae.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2747620

  2. 中国建设银行核心竞争力SWOT分析及策略建议%SWOT Analysis of Core Competitiveness and Its Strategy and Suggestions for China Construction Bank

    Institute of Scientific and Technical Information of China (English)

    张继刚

    2014-01-01

    The core competence is the core problem of the research on strategic management,one of the most important goal is the pursuit of commercial banks in business management.With the opening of China’s financial industry to speed up,the entry of foreign banks will lower the core competitiveness in China's overall banking brings hitherto unknown challenge.Research on the core competitiveness of the state-owned commercial banks in China Construction Bank China represented is of practical significance and theoretical value.This paper puts forward a concept of the core competitiveness of commercial banks,and to determine the five aspects to enhance the core competitiveness of commercial banks.In order to build the principle and index system of evaluation of the core competitiveness of commercial banks.The Construction Bank China as an example,by qualitative analysis,using the SWOT analysis method.Based on the above analysis,are given in order to strengthen corporate governance,development and utilization of human resources,strategic positioning accuracy,improve the ability of technological innovation,innovation and use of the brand and strengthen the building of enterprise culture, to enhance the core competitiveness of Chinese Construction Bank some constructive suggestions.%核心竞争力是企业战略管理研究的核心问题,也是商业银行在经营管理中追求的最重要目标之一。随着中国金融业的对外开放加快,外资银行的进入无疑会对中国整体核心竞争力较低的银行业带来前所未有的挑战。研究以中国建设银行为代表的国有商业银行的核心竞争力问题具有一定的现实意义和理论价值。首先提出商业银行核心竞争力概念,并确定商业银行核心竞争力提升的五种方面。从而构建商业银行核心竞争力的评价原则和指标体系。以中国建设银行为例,从定性方面分析,运用SWOT分析方法。最后在以上分析的基础上,分

  3. Headaches and myofascial temporomandibular disorders: overlapping entities, separate managements?

    Science.gov (United States)

    Conti, P C R; Costa, Y M; Gonçalves, D A; Svensson, P

    2016-09-01

    There are relevant clinical overlaps between some of the painful temporomandibular disorders (TMD) and headache conditions that may hamper the diagnostic process and treatment. A non-systematic search for studies on the relationship between TMD and headaches was carried out in the following databases: PubMed, Cochrane Library and Embase. Important pain mechanisms contributing to the close association and complex relationship between TMD and headache disorders are as follows: processes of peripheral and central sensitisation which take place in similar anatomical areas, the possible impairment of the descending modulatory pain pathways and the processes of referred pain. In addition, the clinical examination does not always provide distinguishing information to differentiate between headaches and TMD. So, considering the pathophysiology and the clinical presentation of some types of headache and myofascial TMD, such overlap can be considered not only a matter of comorbid relationship, but rather a question of disorders where the distinction lines are sometimes hard to identify. These concerns are certainly reflected in the current classification systems of both TMD and headache where the clinical consequences of diagnosis such as headache attributed to or associated with TMD are uncertain. There are several similarities in terms of therapeutic strategies used to manage myofascial TMD and headaches. Considering all these possible levels of interaction, we reinforce the recommendation for multidisciplinary approaches, by a team of oro-facial pain specialists and a neurologist (headache specialist), to attain the most precise differential diagnosis and initiate the best and most efficient treatment. PMID:27191928

  4. A Greedy Algorithm for Neighborhood Overlap-Based Community Detection

    Directory of Open Access Journals (Sweden)

    Natarajan Meghanathan

    2016-01-01

    Full Text Available The neighborhood overlap (NOVER of an edge u-v is defined as the ratio of the number of nodes who are neighbors for both u and v to that of the number of nodes who are neighbors of at least u or v. In this paper, we hypothesize that an edge u-v with a lower NOVER score bridges two or more sets of vertices, with very few edges (other than u-v connecting vertices from one set to another set. Accordingly, we propose a greedy algorithm of iteratively removing the edges of a network in the increasing order of their neighborhood overlap and calculating the modularity score of the resulting network component(s after the removal of each edge. The network component(s that have the largest cumulative modularity score are identified as the different communities of the network. We evaluate the performance of the proposed NOVER-based community detection algorithm on nine real-world network graphs and compare the performance against the multi-level aggregation-based Louvain algorithm, as well as the original and time-efficient versions of the edge betweenness-based Girvan-Newman (GN community detection algorithm.

  5. A Case of Overlapping Choriocapillaritis Syndromes: Multimodal Imaging Appraisal

    Directory of Open Access Journals (Sweden)

    Tatiana Kuznetcova

    2012-01-01

    Full Text Available Purpose: To present a patient with overlapping choriocapillaritis syndromes who first presented as a typical case of multiple evanescent white dot syndrome (MEWDS and later with characteristic findings compatible with multifocal choroiditis (MFC. Case Report: A 40-year-old myopic woman presented with a paracentral scotoma OS. Fundus examination revealed pale discolored areas around the optic disc corresponding to faintly hyperfluorescent areas on fluorescein angiography (FA. On indocyanine green angiography (ICGA there was extensive peripapillary hypofluorescence and confluent hypofluorescent dots superiorly. According to the clinical picture, a diagnosis of MEWDS was made. In 4 weeks, the visual field reverted to normal together with almost complete regression of hypofluorescence on ICGA. However, 4 months later fundus examination revealed some scars, a finding not typical for MEWDS. Besides, she developed another scotoma 12 months later accompanied by photopsia and the fundus illustrated more numerous scars than one year earlier. ICGA showed hypofluorescent areas corresponding to the scotoma delineated by visual field testing. The pattern of this recurrence clearly corresponded to MFC. Conclusion: This case illustrates an overlap between two entities, MEWDS and MFC in two sequential episodes. FA and fundus autofluorescence accounted for the lesions and optical coherence tomography showed damage to the photoreceptor outer segments, but only ICGA correlated well with functional evolution.

  6. Optimizing packing fraction in granular media composed of overlapping spheres.

    Science.gov (United States)

    Roth, Leah K; Jaeger, Heinrich M

    2016-01-28

    What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution. Arbitrary particle shape is represented by a set of overlapping spheres of varying diameter, enabling us to approximate smooth surfaces with a resolution proportional to the number of spheres included. We discover a family of planar triangular particles, whose packing fraction of ϕ ∼ 0.73 is among the highest experimental results for disordered packings of frictionless particles. We investigate how ϕ depends on the arrangement of spheres comprising an individual particle and on the smoothness of the surface. We validate the simulations with experiments using 3D-printed copies of the simplest member of the family, a planar particle consisting of three overlapping spheres with identical radius. Direct experimental comparison with 3D-printed aspherical ellipsoids demonstrates that the triangular particles pack exceedingly well not only in the limit of large system size but also when confined to small containers. PMID:26592541

  7. Optimizing packing fraction in granular media composed of overlapping spheres.

    Science.gov (United States)

    Roth, Leah K; Jaeger, Heinrich M

    2016-01-28

    What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution. Arbitrary particle shape is represented by a set of overlapping spheres of varying diameter, enabling us to approximate smooth surfaces with a resolution proportional to the number of spheres included. We discover a family of planar triangular particles, whose packing fraction of ϕ ∼ 0.73 is among the highest experimental results for disordered packings of frictionless particles. We investigate how ϕ depends on the arrangement of spheres comprising an individual particle and on the smoothness of the surface. We validate the simulations with experiments using 3D-printed copies of the simplest member of the family, a planar particle consisting of three overlapping spheres with identical radius. Direct experimental comparison with 3D-printed aspherical ellipsoids demonstrates that the triangular particles pack exceedingly well not only in the limit of large system size but also when confined to small containers.

  8. Short-range spin glasses and Random Overlap Structures

    CERN Document Server

    Arguin, Louis-Pierre

    2010-01-01

    Properties of Random Overlap Structures (ROSt)'s constructed from the Edwards-Anderson (EA) Spin Glass model on $\\Z^d$ with periodic boundary conditions are studied. ROSt's are $\\N\\times\\N$ random matrices whose entries are the overlaps of spin configurations sampled from the Gibbs measure. Since the ROSt construction is the same for mean-field models (like the Sherrington-Kirkpatrick model) as for short-range ones (like the EA model), the setup is a good common ground to study the effect of dimensionality on the properties of the Gibbs measure. In this spirit, it is shown, using translation invariance, that the ROSt of the EA model possesses a local stability that is stronger than stochastic stability, a property known to hold at almost all temperatures in many spin glass models with Gaussian couplings. This fact is used to prove stochastic stability for the EA spin glass at all temperatures and for a wide range of coupling distributions. On the way, a theorem of Newman and Stein about the pure state decompo...

  9. Headaches and myofascial temporomandibular disorders: overlapping entities, separate managements?

    Science.gov (United States)

    Conti, P C R; Costa, Y M; Gonçalves, D A; Svensson, P

    2016-09-01

    There are relevant clinical overlaps between some of the painful temporomandibular disorders (TMD) and headache conditions that may hamper the diagnostic process and treatment. A non-systematic search for studies on the relationship between TMD and headaches was carried out in the following databases: PubMed, Cochrane Library and Embase. Important pain mechanisms contributing to the close association and complex relationship between TMD and headache disorders are as follows: processes of peripheral and central sensitisation which take place in similar anatomical areas, the possible impairment of the descending modulatory pain pathways and the processes of referred pain. In addition, the clinical examination does not always provide distinguishing information to differentiate between headaches and TMD. So, considering the pathophysiology and the clinical presentation of some types of headache and myofascial TMD, such overlap can be considered not only a matter of comorbid relationship, but rather a question of disorders where the distinction lines are sometimes hard to identify. These concerns are certainly reflected in the current classification systems of both TMD and headache where the clinical consequences of diagnosis such as headache attributed to or associated with TMD are uncertain. There are several similarities in terms of therapeutic strategies used to manage myofascial TMD and headaches. Considering all these possible levels of interaction, we reinforce the recommendation for multidisciplinary approaches, by a team of oro-facial pain specialists and a neurologist (headache specialist), to attain the most precise differential diagnosis and initiate the best and most efficient treatment.

  10. Growing networks of overlapping communities with internal structure.

    Science.gov (United States)

    Young, Jean-Gabriel; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J

    2016-08-01

    We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships, and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks. PMID:27627327

  11. Growing networks of overlapping communities with internal structure

    Science.gov (United States)

    Young, Jean-Gabriel; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J.

    2016-08-01

    We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships, and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks.

  12. 儿童龋病的相关因素分析及预防建议%Analysis of Related Factors of Children's Caries and Preventive Suggestions for It

    Institute of Scientific and Technical Information of China (English)

    詹杭; 陈樱

    2015-01-01

    Objective To discuss the related factors of children's caries and preventive suggestions for it. Methods An analysis was done on the condition of 200 children aged 5 years from urban and rural kindergartens in the chengxiang district in putian city who taken oral health examination. All the children were divided into dental caries group and non-dental caries group. The related factors of children's caries were observed and targeted preventive measures were taken positively. Results Among all the 200 children included in this investigation, 47.50% were found with caries. The proportion of children whose parents knew little about caries, as well as those who did not brush their teeth everyday, those who were not breast-feeding children, those who suffered from malnutrition, those who lived in rural area, and those who had a sweet tooth were higher in the dental caries group than in the non-dental caries group, P<0.05. Conclusion The incidence of children's caries is higher, and the related factors include lake of related knowledge, not brush teeth timely, diet, malnutrition. Targeted preventive suggestions showed be made to reduce the incidence of caries.%目的 探讨儿童龋病的相关因素分析及预防建议. 方法 整群选取2014年2月—2014年6月在莆田市城厢区的数所城乡幼儿园内进行口腔健康检查的200例5岁儿童的患病情况进行分析,儿童分为龋病组和非龋病组,观察比较儿童龋病的相关因素,并针对相关因素采取积极的预防措施. 结果 在参与调查的200名儿童中,龋病发生率为47.50%. 龋病组儿童家长缺乏龋病相关知识、未每天刷牙、非母乳喂养、营养不良、居住农村、喜爱甜食发生率均明显高于无龋病组儿童,差异具有统计学意义(P<0.05). 结论 儿童龋病发病率较高,相关因素包括缺乏相关知识、未及时刷牙、饮食、营养不良等,针对龋病因素采取预防措施,降低龋病发病率.

  13. Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression

    DEFF Research Database (Denmark)

    Lorenzen, Eline D; Simonsen, Bo T; Kat, Pieter W;

    2006-01-01

    disequilibrium and maximum-likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck....... of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess...... if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically...

  14. A Steady-State Kalman Predictor-Based Filtering Strategy for Non-Overlapping Sub-Band Spectral Estimation

    Directory of Open Access Journals (Sweden)

    Zenghui Li

    2014-12-01

    Full Text Available This paper focuses on suppressing spectral overlap for sub-band spectral estimation, with which we can greatly decrease the computational complexity of existing spectral estimation algorithms, such as nonlinear least squares spectral analysis and non-quadratic regularized sparse representation. Firstly, our study shows that the nominal ability of the high-order analysis filter to suppress spectral overlap is greatly weakened when filtering a finite-length sequence, because many meaningless zeros are used as samples in convolution operations. Next, an extrapolation-based filtering strategy is proposed to produce a series of estimates as the substitutions of the zeros and to recover the suppression ability. Meanwhile, a steady-state Kalman predictor is applied to perform a linearly-optimal extrapolation. Finally, several typical methods for spectral analysis are applied to demonstrate the effectiveness of the proposed strategy.

  15. A steady-state Kalman predictor-based filtering strategy for non-overlapping sub-band spectral estimation.

    Science.gov (United States)

    Li, Zenghui; Xu, Bin; Yang, Jian; Song, Jianshe

    2015-01-01

    This paper focuses on suppressing spectral overlap for sub-band spectral estimation, with which we can greatly decrease the computational complexity of existing spectral estimation algorithms, such as nonlinear least squares spectral analysis and non-quadratic regularized sparse representation. Firstly, our study shows that the nominal ability of the high-order analysis filter to suppress spectral overlap is greatly weakened when filtering a finite-length sequence, because many meaningless zeros are used as samples in convolution operations. Next, an extrapolation-based filtering strategy is proposed to produce a series of estimates as the substitutions of the zeros and to recover the suppression ability. Meanwhile, a steady-state Kalman predictor is applied to perform a linearly-optimal extrapolation. Finally, several typical methods for spectral analysis are applied to demonstrate the effectiveness of the proposed strategy. PMID:25609038

  16. Fundamental frequency height as a resource for the management of overlap in talk-in-interaction.

    OpenAIRE

    Kurtic, E.; Brown, G J; Wells, B

    2009-01-01

    Overlapping talk is common in talk-in-interaction. Much of the previous research on this topic agrees that speaker overlaps can be either turn competitive or noncompetitive. An investigation of the differences in prosodic design between these two classes of overlaps can offer insight into how speakers use and orient to prosody as a resource for turn competition. In this paper, we investigate the role of fundamental frequency (F0) as a resource for turn competition in overlapping speech. Ou...

  17. Systemic Inflammation in Older Adults With Asthma-COPD Overlap Syndrome

    OpenAIRE

    FU, JUAN-JUAN; Vanessa M. McDonald; Gibson, Peter G; Simpson, Jodie L.

    2014-01-01

    Purpose The role of systemic inflammation on asthma-COPD overlap syndrome is unknown. This study aimed to examine systemic inflammation in asthma-COPD overlap syndrome, and to identify associations between clinical characteristics and inflammatory mediators in asthma-COPD overlap syndrome. Methods In 108 adults older than 55 years comprising healthy controls (n=29), asthma (n=16), COPD (n=21) and asthma-COPD overlap syndrome (n=42), serum high sensitivity C-reactive protein and Interleukin 6 ...

  18. Evaluating spatial overlap and relatedness of white-tailed deer in a chronic wasting disease management zone.

    Science.gov (United States)

    Magle, Seth B; Samuel, Michael D; Van Deelen, Timothy R; Robinson, Stacie J; Mathews, Nancy E

    2013-01-01

    Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin's area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.

  19. Evaluating spatial overlap and relatedness of white-tailed deer in a chronic wasting disease management zone.

    Directory of Open Access Journals (Sweden)

    Seth B Magle

    Full Text Available Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection and genetic relatedness for female white-tailed deer in Wisconsin's area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.

  20. Evaluating spatial overlap and relatedness of white-tailed deer in a chronic wasting disease management zone

    Science.gov (United States)

    Samuel, Michael D.; Magle, Seth B.; Van Deelen, Timothy R.; Robinson, Stacie J.; Mathews, Nancy E.

    2013-01-01

    Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin’s area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.