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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

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

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    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.

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

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    Garmyn, Dominique; Augagneur, Yoann; Gal, Laurent; Vivant, Anne-Laure; Piveteau, Pascal

    2012-01-01

    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.

  4. 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.

  5. 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

    2014-07-03

    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.

  6. 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

  7. 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.

  8. 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

  9. 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...

  10. [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.

  11. Quantitative analysis of overlapping XPS peaks by spectrum reconstruction

    DEFF Research Database (Denmark)

    Graat, Peter C.J.; Somers, Marcel A. J.

    1998-01-01

    parameters. The values obtained for the oxide film thickness were compared with thickness values determined from the intensity of the corresponding O 1s spectra and with thickness values resulting from ellipsometric analysis. The sensitivity of the reconstruction procedure with regard to film thickness...

  12. A multiplex network analysis of the Mexican banking system: link persistence, overlap, and waiting times

    NARCIS (Netherlands)

    Molina-Borboa, J.L.; Martínez-Jaramillo, S.; López-Gallo, F.; van der Leij, M.

    2015-01-01

    This paper analyzes the persistence and overlap of relationships between banks in a multiplex decomposition of the exposures network. Our analysis may be useful for researchers designing stress tests or models in which the behavior of banks is modeled explicitly. This has not been looked at previous

  13. 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.

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

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    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.

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

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    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.

  16. 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...... 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......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...

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

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    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.

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

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    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

  19. GeneAnalytics Pathway Analysis and Genetic Overlap among Autism Spectrum Disorder, Bipolar Disorder and Schizophrenia

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    Naveen S. Khanzada

    2017-02-01

    Full Text Available Bipolar disorder (BPD and schizophrenia (SCH show similar neuropsychiatric behavioral disturbances, including impaired social interaction and communication, seen in autism spectrum disorder (ASD with multiple overlapping genetic and environmental influences implicated in risk and course of illness. GeneAnalytics software was used for pathway analysis and genetic profiling to characterize common susceptibility genes obtained from published lists for ASD (792 genes, BPD (290 genes and SCH (560 genes. Rank scores were derived from the number and nature of overlapping genes, gene-disease association, tissue specificity and gene functions subdivided into categories (e.g., diseases, tissues or functional pathways. Twenty-three genes were common to all three disorders and mapped to nine biological Superpathways including Circadian entrainment (10 genes, score = 37.0, Amphetamine addiction (five genes, score = 24.2, and Sudden infant death syndrome (six genes, score = 24.1. Brain tissues included the medulla oblongata (11 genes, score = 2.1, thalamus (10 genes, score = 2.0 and hypothalamus (nine genes, score = 2.0 with six common genes (BDNF, DRD2, CHRNA7, HTR2A, SLC6A3, and TPH2. Overlapping genes impacted dopamine and serotonin homeostasis and signal transduction pathways, impacting mood, behavior and physical activity level. Converging effects on pathways governing circadian rhythms support a core etiological relationship between neuropsychiatric illnesses and sleep disruption with hypoxia and central brain stem dysfunction.

  20. 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...

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

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    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.

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

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    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.

  3. A tutorial on structural equation modeling for analysis of overlapping symptoms in co-occurring conditions using MPlus.

    Science.gov (United States)

    Gunzler, Douglas D; Morris, Nathan

    2015-10-30

    Structural equation modeling (SEM) is a very general approach to analyzing data in the presence of measurement error and complex causal relationships. In this tutorial, we describe SEM, with special attention to exploratory factor analysis, confirmatory factor analysis, and multiple indicator multiple cause modeling. The tutorial is motivated by a problem of symptom overlap routinely faced by clinicians and researchers, in which symptoms or test results are common to two or more co-occurring conditions. As a result of such overlap, diagnoses, treatment decisions, and inferences about the effectiveness of treatments for these conditions can be biased. This problem is further complicated by increasing reliance on patient-reported outcomes, which introduces systematic error based on an individual's interpretation of a test questionnaire. SEM provides flexibility in handling this type of differential item functioning and disentangling the overlap. Scales and scoring approaches can be revised to be free of this overlap, leading to better care. This tutorial uses an example of depression screening in multiple sclerosis patients in which depressive symptoms overlap with other symptoms, such as fatigue, cognitive impairment, and functional impairment. Details of how MPlus (Muthén & Muthén, Los Angeles, CA, USA) software can be used to address the symptom overlap problem, including data requirements, code and output are described in this tutorial.

  4. Non-overlapped random decrement technique for parameter identification in operational modal analysis

    Science.gov (United States)

    Zhang, Y.; Song, H. W.

    2016-03-01

    The random decrement technique (RDT) is used to estimate free vibration response from output data generated by Gaussian white noise. The principle is to decay the excitation via averaging of segments in output data. With RDT, the triggering condition for determining the initial points of segments causes overlap during averaging; the consequence is a residual excitation, peaking at the first natural frequency. This paper presents a modified RDT with non-overlapped segments to eliminate this peak. Numerical comparison between non-overlapped RDT (NRDT) and RDT shows the accuracy improvement of damping. However, time history data is sometimes not long enough in NRDT, which results in an inevitable overlap. In order to keep the accuracy of NRDT, the first natural period is viewed as the critical length between adjacent initial points to distinguish the inevitable overlap from that in RDT.

  5. A method for identification and analysis of non-overlapping myeloid immunophenotypes in humans.

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    Michael P Gustafson

    Full Text Available The development of flow cytometric biomarkers in human studies and clinical trials has been slowed by inconsistent sample processing, use of cell surface markers, and reporting of immunophenotypes. Additionally, the function(s of distinct cell types as biomarkers cannot be accurately defined without the proper identification of homogeneous populations. As such, we developed a method for the identification and analysis of human leukocyte populations by the use of eight 10-color flow cytometric protocols in combination with novel software analyses. This method utilizes un-manipulated biological sample preparation that allows for the direct quantitation of leukocytes and non-overlapping immunophenotypes. We specifically designed myeloid protocols that enable us to define distinct phenotypes that include mature monocytes, granulocytes, circulating dendritic cells, immature myeloid cells, and myeloid derived suppressor cells (MDSCs. We also identified CD123 as an additional distinguishing marker for the phenotypic characterization of immature LIN-CD33+HLA-DR- MDSCs. Our approach permits the comprehensive analysis of all peripheral blood leukocytes and yields data that is highly amenable for standardization across inter-laboratory comparisons for human studies.

  6. Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

    Science.gov (United States)

    Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

    2017-01-25

    This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

  7. 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.

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

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    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.

  9. 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.)

  10. 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.

  11. Compare Analysis between Chinese and Indonesian Phonetics and teaching suggestions

    Directory of Open Access Journals (Sweden)

    Lydia Anggreani

    2014-05-01

    Full Text Available With further development of friendly relations between China and Indonesia, coupled with a growing number of Indonesian Chinese, learning Chinese language is getting more important. Article compared Chinese and Indonesian voice and showed the voice of the Chinese language. Moreover, article provided ideas for Chinese phonetics teaching and for Indonesian students in learning Chinese pronunciation. In addition, article puts forward suggestions in order to improve foreign language teaching.

  12. 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...

  13. 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.

  14. Sleep overlap syndrome

    Directory of Open Access Journals (Sweden)

    Fariba Rezaeetalab

    2016-12-01

    Full Text Available Overlap syndrome, which is known as the coexistence of chronic obstructive pulmonary disease (COPD and obstructive sleep apnea (OSA, was first defined by Flenley. Although it can refer to concomitant occurrence of any of the pulmonary diseases and OSA, overlap syndrome is commonly considered as the coexistence of OSA and COPD. This disease has unique adverse health consequences distinct from either condition alone. Given the high prevalence of each solitary disease, overlap syndrome is also likely to be common and clinically relevant. Despite the fact that overlap syndrome has been described in the literature for nearly 30 years, paucity of evaluations and studies limited the discussion on diagnosis, prevalence, pathophysiology, treatment, and outcomes of this disease. This review article addresses these issues by reviewing several recent studies conducted in Iran or other countries. This review suggests that overlap syndrome has worse outcomes than either disease alone. Our findings accentuated the urgent need for further studies on overlap syndrome and all overlaps between OSA and chronic pulmonary disease to provide a deeper insight into diagnosis and non-invasive treatments of this disease.

  15. 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.

  16. 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.

  17. Analysis of steel-concrete composite structure with overlap slab of Xingguang bridge

    Institute of Scientific and Technical Information of China (English)

    YE Mei-xin; HUANG Qiong; WU Qin-qin

    2007-01-01

    Finire element modeling methods of steel-concrete composire structure with overlap slab were investigated.A two-step finite element method wag presented.It was applied to analyze an extra long span composite bridge.The conversion of structure system and the mechanical behavior of the bridge were analyzed with two different construction methods.The stresses of steel beams, precast slabs and in-situ-place concrete under the total load were compared. The results show that steel-concrete composite structure with overlap slab has many advantages, the construction method that the top in-situ concrete and the concrete in construction joints are cast respectively is rather reasonable than the one that the top in-situ concrete and the concrete in construction joints are cast at the same time, and the two-step finite element method is affective to such large-scale structures.

  18. 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

    and a composite material is created, which has the same magnetization characteristic. The benefit of this technique is that it allows a designer to perform design and optimization of magnetic cores with overlapped laminations using a 2-D FE model rather than a 3-D FE model, which saves modeling and simulation...... time. The modeling technique is verified experimentally by creating a composite material of a lap joint with a 3-mm overlapping region and using it in a 2-D FE model of a ring sample made up of a stack of 20 laminations. The B-H curve of the simulated ring sample is compared with the B-H curve obtained...

  19. 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

  20. Comparative transcriptomic analysis reveals the roles of overlapping heat-/drought-responsive genes in poplars exposed to high temperature and drought

    Science.gov (United States)

    Jia, Jingbo; Zhou, Jing; Shi, Wenguang; Cao, Xu; Luo, Jie; Polle, Andrea; Luo, Zhi-Bin

    2017-01-01

    High temperature (HT) and drought are both critical factors that constrain tree growth and survival under global climate change, but it is surprising that the transcriptomic reprogramming and physiological relays involved in the response to HT and/or drought remain unknown in woody plants. Thus, Populus simonii saplings were exposed to either ambient temperature or HT combined with sufficient watering or drought. RNA-sequencing analysis showed that a large number of genes were differentially expressed in poplar roots and leaves in response to HT and/or desiccation, but only a small number of these genes were identified as overlapping heat-/drought-responsive genes that are mainly involved in RNA regulation, transport, hormone metabolism, and stress. Furthermore, the overlapping heat-/drought-responsive genes were co-expressed and formed hierarchical genetic regulatory networks under each condition compared. HT-/drought-induced transcriptomic reprogramming is linked to physiological relays in poplar roots and leaves. For instance, HT- and/or drought-induced abscisic acid accumulation and decreases in auxin and other phytohormones corresponded well with the differential expression of a few genes involved in hormone metabolism. These results suggest that overlapping heat-/drought-responsive genes will play key roles in the transcriptional and physiological reconfiguration of poplars to HT and/or drought under future climatic scenarios. PMID:28233854

  1. Overlap of PIV syndrome, VACTERL and Pallister-Hall syndrome: clinical and molecular analysis.

    Science.gov (United States)

    Killoran, C E; Abbott, M; McKusick, V A; Biesecker, L G

    2000-07-01

    The polydactyly, imperforate anus, vertebral anomalies syndrome (PIV, OMIM 174100) was determined as a distinct syndrome by Say and Gerald in 1968 (Say B, Gerald PS. Lancet 1968: 2: 688). We noted that the features of PIV overlap with the VATER association and Pallister-Hall syndrome (PHS, OMIM 146510), which includes polydactyly, (central or postaxial), shortened fingers, hypoplastic nails, renal anomalies, imperforate anus, and hypothalamic hamartoma. Truncation mutations in GL13, a zinc finger transcription factor gene, have been shown to cause PHS. We performed a molecular evaluation on a patient diagnosed with PIV, whose mother, grandfather, and maternal aunt had similar malformations. We sequenced the GLI3 gene in the patient to determine if she had a mutation. The patient was found to have a deletion in nucleotides 2188-2207 causing a frameshift mutation that predicts a truncated protein product of the gene. Later clinical studies demonstrated that the patient also has a hypothalamic hamartoma, a finding in PHS. We concluded that this family had atypical PHS and not PIV. This result has prompted us to re-evaluate the PIV literature to see if PIV is a valid entity. Based on these data and our examination of the literature, we conclude that PIV is not a valid diagnostic entity. We conclude that patients diagnosed with PIV should be reclassified as having VACTERL, or PHS, or another syndrome with overlapping malformations.

  2. Analysis of the stress-strain state in single overlap joints using piezo-ceramic actuators

    Science.gov (United States)

    Pǎltânea, Veronica; Pǎltânea, Gheorghe; Popovici, Dorina; Jiga, Gabriel; Papanicolaou, George

    2014-05-01

    In this paper is presented a 2D approach to finite element modeling and an analytical calculus of a single lap bonded joint. As adherent material were selected a sheet of wood, aluminum and titanium. For adhesive part were selected Bison Super Wood D3 in case of the wood single lap joint and an epoxy resin type DGEBA-TETA for gluing together aluminum and titanium parts. In the article is described a combined method, which consists in the placement of the piezoelectric actuator inside of the adhesive part, in order to determine the tensile stress in the overlap joint. A comparison between the analytical and numerical results has been achieved through a multiphysics modeling - electrical and mechanical coupled problem. The technique used to calculate the mechanical parameters (First Principal Stress, displacements) was the three-point bending test, where different forces were applied in the mid-span of the structure, in order to maintain a constant displacement rate. The length of the overlap joint was modified from 20 to 50 mm.

  3. 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.

  4. 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.

  5. Global transcriptional analysis of Bacillus licheniformis reveals an overlap between heat shock and iron limitation stimulon.

    Science.gov (United States)

    Nielsen, Allan K; Breüner, Anne; Krzystanek, Marcin; Andersen, Jens T; Poulsen, Thomas A; Olsen, Peter B; Mijakovic, Ivan; Rasmussen, Michael D

    2010-01-01

    In this study, we characterized the heat shock stimulon of the important industrial microorganism Bacillus licheniformis using DNA microarrays. While sharing a high degree of homology with the closely related model organism Bacillus subtilis, the heat shock stimulon of B. licheniformis exhibited several novel and unexpected features. Most notably, heat shock in B. licheniformis resulted in decreased amounts of mRNA from the ytrABCEF operon, encoding a putative acetoin uptake system, and stimulated the transcription of purine biosynthesis and iron uptake genes. Unexpectedly, deletion of the ytrEF genes did not affect acetoin uptake, but increased heat sensitivity. To investigate the connection between heat stress and iron uptake further, we analyzed the iron limitation response of B. licheniformis by DNA microarrays and concluded that the response mostly involves the genes related to iron uptake and metabolism, while the only heat shock gene affected by iron limitation was clpE. We also attempted to delete the fur gene (encoding the ferric uptake repressor), but unexpectedly found it to be essential in B. licheniformis. Using the fluorescent protein-encoding reporter gene under control of the dhb promoter, which responded to both heat shock and iron-starvation, we confirmed the overlap between these responses.

  6. 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.

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tokunaga, Ken, E-mail: tokunaga@cc.kogakuin.ac.jp [Division of Liberal Arts, Kogakuin University, Nakano machi 2665-1, Hachioji, Tokyo 192-0015 (Japan); Ohmori, Shigekazu [Venture Business Laboratory, Kyoto University, Yoshida honmachi, Sakyo-ku, Kyoto, Kyoto 615-8510 (Japan); Kawabata, Hiroshi [Young Researchers Education Center, Hiroshima University, Kagamiyama 1-1-1, Higashi hiroshima, Hiroshima 739-8512 (Japan)

    2014-03-03

    Through-space electron transfer between the benzene rings of [3{sub n}]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.

  9. [Analysis of diet composition and overlap in four species of the genus Diplectrum (Perciformes: Serranidae) in the Mexican Central Pacific].

    Science.gov (United States)

    Aguilar Palomino, Bernabé; González Sansón, Gaspar

    2010-12-01

    Analysis of diet composition and overlap in four species of the genus Diplectrum (Perciformes: Serranidae) in the Mexican Central Pacific. The information of trophic interactions among species is essential to understand ecosystem function. To assess this in four Diplectrum species, we analyzed the stomach contents of 397 individuals caught using shrimp trawling nets off the coasts of Jalisco and Colima, Mexico. Main food component of D. eumelum were fish of the Order Pleuronectiformes, followed by shrimps (Metapenaeopsis spp). D. euryplectrum feeds mainly on crustaceans, with stomatopods (Squilla mantoidea) as main food items followed by shrimps and brachyurans. Fish and polychaetes had a low representation in the diet of this species. D. labarum feeds mainly on crustaceans, mollusks and fish. The stomatopod Eurysquilla veleronis contributed to with a high diet percentage by weight, followed by shrimps (mostly Solenoceraflorae) and brachyurans, as well as the squid Lolliguncula diomedae. Fishes (Ophidion spp.) were also an important component of the diet of this species. The most common preys of D. rostrum were crustaceans, mollusks, polychaetes and fish. The squid Lolliguncula diomedae and fishes of genus Ophidion were also well represented in the diet. Diet breadth index yielded significant differences between species. The number of diet items varied from 16 in D. euryplectrum to 6 in D. eumelum. The average value of overlap (0.247) was not significantly different (p = 0.118) from the expected one for a null model (0.174). The observed variance of the overlap index (0.071) was significantly higher (V = 0.025, p = 0.0004) than the value expected for a null model.

  10. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

    Directory of Open Access Journals (Sweden)

    Henriette O'Geen

    2007-06-01

    Full Text Available We performed a genome-scale chromatin immunoprecipitation (ChIP-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27] of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C2H2 ZNFs, especially those containing Krüppel-associated box (KRAB domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is

  11. 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.

  12. 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

  13. Assessing the Collective Wealth of Australian Research Libraries: Measuring Overlap Using "Worldcat Collection Analysis"

    Science.gov (United States)

    Genoni, Paul; Wright, Jannette

    2010-01-01

    This paper reports the results of recent research examining the holdings of Australian research library collections recorded in the WorldCat database using OCLC WorldCat Collection Analysis software. The objectives of the research are: 1. To better understand the distribution of printed monographs amongst Australian research collections in order…

  14. Is Five Percent Too Small? Analysis of the Overlaps between Disorder, Coiled Coil and Collagen Predictions in Complete Proteomes

    Directory of Open Access Journals (Sweden)

    Zoltán Gáspári

    2014-02-01

    Full Text Available Identification of intrinsic disorder in proteins and proteomes has revealed important novel aspects of protein function and interactions. However, it has been pointed out that several oligomeric fibrillar protein motifs such as coiled coils and collagen triple helical segments can also identified as intrinsically disordered. This feature has not yet been investigated in more detail at the proteome level. The present work aims at the identification and quantification of such overlaps in full proteomes to assess their significance in large-scale studies of protein disorder. It was found that the percentage of cross-predicted residues is around 5% in the human proteome and is generally near that value in other metazoan ones but shows remarkable variation in different organisms. In particular, smaller proteomes are increasingly prone to such cross-predictions, thus, especially the analysis of viral proteomes requires the use of specific prediction tools.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. A Coordinate-Based Meta-Analysis of Overlaps in Regional Specialization and Functional Connectivity across Subjective Value and Default Mode Networks

    Science.gov (United States)

    Acikalin, M. Yavuz; Gorgolewski, Krzysztof J.; Poldrack, Russell A.

    2017-01-01

    Previous research has provided qualitative evidence for overlap in a number of brain regions across the subjective value network (SVN) and the default mode network (DMN). In order to quantitatively assess this overlap, we conducted a series of coordinate-based meta-analyses (CBMA) of results from 466 functional magnetic resonance imaging experiments on task-negative or subjective value-related activations in the human brain. In these analyses, we first identified significant overlaps and dissociations across activation foci related to SVN and DMN. Second, we investigated whether these overlapping subregions also showed similar patterns of functional connectivity, suggesting a shared functional subnetwork. We find considerable overlap between SVN and DMN in subregions of central ventromedial prefrontal cortex (cVMPFC) and dorsal posterior cingulate cortex (dPCC). Further, our findings show that similar patterns of bidirectional functional connectivity between cVMPFC and dPCC are present in both networks. We discuss ways in which our understanding of how subjective value (SV) is computed and represented in the brain can be synthesized with what we know about the DMN, mind-wandering, and self-referential processing in light of our findings. PMID:28154520

  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. Independent vector analysis based on overlapped cliques of variable width for frequency-domain blind signal separation

    Science.gov (United States)

    Lee, Intae; Jang, Gil-Jin

    2012-12-01

    A novel method is proposed to improve the performance of independent vector analysis (IVA) for blind signal separation of acoustic mixtures. IVA is a frequency-domain approach that successfully resolves the well-known permutation problem by applying a spherical dependency model to all pairs of frequency bins. The dependency model of IVA is equivalent to a single clique in an undirected graph; a clique in graph theory is defined as a subset of vertices in which any pair of vertices is connected by an undirected edge. Therefore, IVA imposes the same amount of statistical dependency on every pair of frequency bins, which may not match the characteristics of real-world signals. The proposed method allows variable amounts of statistical dependencies according to the correlation coefficients observed in real acoustic signals and, hence, enables more accurate modeling of statistical dependencies. A number of cliques constitutes the new dependency graph so that neighboring frequency bins are assigned to the same clique, while distant bins are assigned to different cliques. The permutation ambiguity is resolved by overlapped frequency bins between neighboring cliques. For speech signals, we observed especially strong correlations across neighboring frequency bins and a decrease in these correlations with an increase in the distance between bins. The clique sizes are either fixed, or determined by the reciprocal of the mel-frequency scale to impose a wider dependency on low-frequency components. Experimental results showed improved performances over conventional IVA. The signal-to-interference ratio improved from 15.5 to 18.8 dB on average for seven different source locations. When we varied the clique sizes according to the observed correlations, the stability of the proposed method increased with a large number of cliques.

  4. 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...

  5. 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

  6. Intelligence, previous convictions and interrogative suggestibility: a path analysis of alleged false-confession cases.

    Science.gov (United States)

    Sharrock, R; Gudjonsson, G H

    1993-05-01

    The main purpose of this study was to investigate the relationship between interrogative suggestibility and previous convictions among 108 defendants in criminal trials, using a path analysis technique. It was hypothesized that previous convictions, which may provide defendants with interrogative experiences, would correlate negatively with 'shift' as measured by the Gudjonsson Suggestibility Scale (Gudjonsson, 1984a), after intelligence and memory had been controlled for. The hypothesis was partially confirmed and the theoretical and practical implications of the findings are discussed.

  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. 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.

  9. 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.

  10. 基于 TEN 的三维空间叠置分析%3D Spacial Overlap Analysis Based on TEN

    Institute of Scientific and Technical Information of China (English)

    蔡振锋; 史云飞; 邵长江; 林黎明

    2016-01-01

    3D spatial analysis is an important sign for the maturity of 3D GIS,and it is also a hot in the cur-rent industry overlap analys as the most commonly used and the most basic function,and its implementa-tion has important practical significance.The paper discusses 3D overlap analysis based on TEN and propo-ses the overlap analysis method by point and body,line and body,surface and body,body and body.The method decomposes complex body into TEN firstly,then carries out overlap analysis between various fea-tures with body,which has certain innovation.%三维空间分析是3D GIS 成熟的一个重要标志,也是当前业界的研究热点之一。叠置分析作为空间分析的一种最常用、最基本的功能,其实现具有重要的现实意义。通过探讨基于 TEN 的三维叠置分析,分别给出了点与体、线与体、面与体、体与体的叠置分析方法。该方法实现了将复杂的体先分解为 TEN,然后再将各类实体与 TEN 进行叠置分析。

  11. Topological susceptibility from the overlap

    CERN Document Server

    Del Debbio, L; Debbio, Luigi Del; Pica, Claudio

    2004-01-01

    The chiral symmetry at finite lattice spacing of Ginsparg-Wilson fermionic actions constrains the renormalization of the lattice operators; in particular, the topological susceptibility does not require any renormalization, when using a fermionic estimator to define the topological charge. Therefore, the overlap formalism appears as an appealing candidate to study the continuum limit of the topological susceptibility while keeping the systematic errors under theoretical control. We present results for the SU(3) pure gauge theory using the index of the overlap Dirac operator to study the topology of the gauge configurations. The topological charge is obtained from the zero modes of the overlap and using a new algorithm for the spectral flow analysis. A detailed comparison with cooling techniques is presented. Particular care is taken in assessing the systematic errors. Relatively high statistics (500 to 1000 independent configurations) yield an extrapolated continuum limit with errors that are comparable with ...

  12. 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.

  13. Exome sequence analysis suggests genetic burden contributes to phenotypic variability and complex neuropathy

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Harel, Tamar; Gambin, Tomasz; Kousi, Maria; Griffin, Laurie B.; Francescatto, Ludmila; Ozes, Burcak; Karaca, Ender; Jhangiani, Shalini; Bainbridge, Matthew N.; Lawson, Kim S.; Pehlivan, Davut; Okamoto, Yuji; Withers, Marjorie; Mancias, Pedro; Slavotinek, Anne; Reitnauer, Pamela J; Goksungur, Meryem T.; Shy, Michael; Crawford, Thomas O.; Koenig, Michel; Willer, Jason; Flores, Brittany N.; Pediaditrakis, Igor; Us, Onder; Wiszniewski, Wojciech; Parman, Yesim; Antonellis, Anthony; Muzny, Donna M.; Katsanis, Nicholas; Battaloglu, Esra; Boerwinkle, Eric; Gibbs, Richard A.; Lupski, James R.

    2015-01-01

    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 mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HMPVs) 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. PMID:26257172

  14. 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.

  15. 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

  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. Overlap maximum matching ratio (OMMR):a new measure to evaluate overlaps of essential modules

    Institute of Scientific and Technical Information of China (English)

    Xiao-xia ZHANG; Qiang-hua XIAO; Bin LI; Sai HU; Hui-jun XIONG; Bi-hai ZHAO

    2015-01-01

    Protein complexes are the basic units of macro-molecular organizations and help us to understand the cell’s mechanism. The development of the yeast two-hybrid, tandem affinity purification, and mass spectrometry high-throughput proteomic techniques supplies a large amount of protein-protein interaction data, which make it possible to predict overlapping complexes through computational methods. Research shows that overlapping complexes can contribute to identifying essential proteins, which are necessary for the organism to survive and reproduce, and for life’s activities. Scholars pay more attention to the evaluation of protein complexes. However, few of them focus on predicted overlaps. In this paper, an evaluation criterion called overlap maximum matching ratio (OMMR) is proposed to analyze the similarity between the identified overlaps and the benchmark overlap modules. Comparison of essential proteins and gene ontology (GO) analysis are also used to assess the quality of overlaps. We perform a comprehensive comparison of serveral overlapping complexes prediction approaches, using three yeast protein-protein interaction (PPI) networks. We focus on the analysis of overlaps identified by these algorithms. Experimental results indicate the important of overlaps and reveal the relationship between overlaps and identification of essential proteins.

  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.

  19. 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.

  20. Genomic survey, gene expression analysis and structural modeling suggest diverse roles of DNA methyltransferases in legumes.

    Science.gov (United States)

    Garg, Rohini; Kumari, Romika; Tiwari, Sneha; Goyal, Shweta

    2014-01-01

    DNA methylation plays a crucial role in development through inheritable gene silencing. Plants possess three types of DNA methyltransferases (MTases), namely Methyltransferase (MET), Chromomethylase (CMT) and Domains Rearranged Methyltransferase (DRM), which maintain methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far. Here, we report the identification and analysis of putative DNA MTases in five legumes, including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2) subfamilies based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2 represents a transfer RNA (tRNA) MTase. Structural comparison of all the MTases in plants with known MTases in mammalian and plant systems have been reported to assign structural features in context of biological functions of these proteins. The structure analysis clearly specified regions crucial for protein-protein interactions and regions important for nucleosome binding in various domains of CMT and MET proteins. In addition, structural model of DRM suggested that circular permutation of motifs does not have any effect on overall structure of DNA methyltransferase domain. These results provide valuable insights into role of various domains in molecular recognition and should facilitate mechanistic understanding of their function in mediating specific methylation patterns. Further, the comprehensive gene expression analyses of MTases in legumes provided evidence of their role in various developmental processes throughout the plant life cycle and response to various abiotic stresses. Overall, our study will be very helpful in establishing the specific functions of DNA MTases in legumes.

  1. 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.

  2. Meta-analysis of phenotypic selection on flowering phenology suggests that early flowering plants are favoured.

    Science.gov (United States)

    Munguía-Rosas, Miguel A; Ollerton, Jeff; Parra-Tabla, Victor; De-Nova, J Arturo

    2011-05-01

    Flowering times of plants are important life-history components and it has previously been hypothesized that flowering phenologies may be currently subject to natural selection or be selectively neutral. In this study we reviewed the evidence for phenotypic selection acting on flowering phenology using ordinary and phylogenetic meta-analysis. Phenotypic selection exists when a phenotypic trait co-varies with fitness; therefore, we looked for studies reporting an association between two components of flowering phenology (flowering time or flowering synchrony) with fitness. Data sets comprising 87 and 18 plant species were then used to assess the incidence and strength of phenotypic selection on flowering time and flowering synchrony, respectively. The influence of dependence on pollinators, the duration of the reproductive event, latitude and plant longevity as moderators of selection were also explored. Our results suggest that selection favours early flowering plants, but the strength of selection is influenced by latitude, with selection being stronger in temperate environments. However, there is no consistent pattern of selection on flowering synchrony. Our study demonstrates that phenotypic selection on flowering time is consistent and relatively strong, in contrast to previous hypotheses of selective neutrality, and has implications for the evolution of temperate floras under global climate change.

  3. 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.

  4. Overlap among Environmental Databases.

    Science.gov (United States)

    Miller, Betty

    1981-01-01

    Describes the methodology and results of a study comparing the overlap of Enviroline, Pollution, and the Environmental Periodicals Bibliography files through searches on acid rain, asbestos and water, diesel, glass recycling, Lake Erie, Concorde, reverse osmosis wastewater treatment cost, and Calspan. Nine tables are provided. (RBF)

  5. Neural overlap in processing music and speech.

    Science.gov (United States)

    Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L

    2015-03-19

    Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing.

  6. 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.

  7. 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.

  8. 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.

  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. 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

  11. A Suggested Stress Analysis Procedure For Nozzle To Head Shell Element Model – A Case Study

    Directory of Open Access Journals (Sweden)

    Sanket S. Chaudhari

    2012-08-01

    Full Text Available Stress analysis of pressure vessel has been always a serious and a critical analysis. The paper performs a standard procedure of pressure vessel analysis and validation based on previous papers. It also demonstrates the most critical part and how it affects entire structure. Relevant ASME (ASME, 2004, ASME Boiler and Pressure Vessel Code, Section VIII, Division 2, American Society of Mechanical Engineers, New York norms are produced to explain analysis procedure. WRC (Welding research council methodology is explained to validate finite element analysis work

  12. Offshoring and Firm Overlap

    OpenAIRE

    Schmerer, Hans-Jörg; Capuano, Stella; Egger, Hartmut; Koch, Michael

    2015-01-01

    We set up a model of offshoring with heterogeneous producers that captures two empirical regularities on offshoring firms: larger, more productive firms are more likely to make use of the offshoring opportunity; the fraction of firms that engages in offshoring is positive and smaller than one in any size or revenue category. These patterns generate an overlap of offshoring and non-offshoring firms, which is non-monotonic in the costs of offshoring. In an empirical exercise, we employ firm-lev...

  13. 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

  14. Generation of stable overlaps between antiparallel filaments

    CERN Document Server

    Johann, D; Kruse, K

    2015-01-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of bipolarity, but the underlying mechanisms are poorly understood. Using a particle-based stochastic model, we find that the interplay of motors and passive cross linkers can robustly generate partial overlaps between antiparallel filaments. Our analysis shows that motors reduce the overlap in a length-dependent manner, whereas passive cross linkers increase it independently of the length. In addition to maintaining structural integrity, passive cross linkers can thus also have a dynamic role for size regulation.

  15. 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.

  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. Post-Foundational Discourse Analysis: A Suggestion for a Research Program

    Directory of Open Access Journals (Sweden)

    Tomas Marttila

    2015-08-01

    Full Text Available Post-foundational discourse analysis, also labeled as Essex School in Discourse Analysis, has been observed to suffer from a considerable methodological deficit that limits its applicability in empirical research. The principal aim of this article is to overcome this methodological deficit by constructing the research program of the post-foundational discourse analysis that facilitates its operationalization in empirical research. In accordance with Imre LAKATOS (1970 and David HOWARTH (2004a, a research program is referred to an internally consistent and openly scrutinizable system of theoretical, methodological and phenomenal concepts that opens up the possibility to distinguish between the "negative" and the "positive" heuristics of empirical research. The first three sections develop the positive heuristics of the post-foundational discourse analysis by elucidating its theoretical foundations, methodological position and phenomenal framework. The concluding fourth section draws on the presented positive heuristics to outline the analytical stages and strategies of the post-foundational discourse analysis and discusses suitable methods for sampling and interpreting empirical data. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs150319

  19. 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.

  20. 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.

  1. 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.…

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

    NARCIS (Netherlands)

    Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger; Schulz, Herbert; de Kovel, Carolien G.; Trenite, Dorothee Kasteleijn-Nolst; 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; Moller, Rikke S.; Hjalgrim, Helle; De Jonghe, Peter; Suls, Arvid; Lieb, Wolfgang; Franke, Andre; Strauch, Konstantin; Gieger, Christian; Schurmann, Claudia; Schminke, Ulf; Nuernberg, 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 (= 200

  3. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

    Science.gov (United States)

    Ravcheev, Dmitry A.; Thiele, Ines

    2016-01-01

    Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM. PMID:26904004

  4. 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…

  5. Widespread kelp-derived carbon in pelagic and benthic nearshore fishes suggested by stable isotope analysis

    Science.gov (United States)

    von Biela, Vanessa R.; Newsome, Seth D.; Bodkin, James L.; Kruse, Gordon H.; Zimmerman, Christian E.

    2016-11-01

    Kelp forests provide habitat for diverse and abundant fish assemblages, but the extent to which kelp provides a source of energy to fish and other predators is unclear. To examine the use of kelp-derived energy by fishes we estimated the contribution of kelp- and phytoplankton-derived carbon using carbon (δ13C) and nitrogen (δ15N) isotopes measured in muscle tissue. Benthic-foraging kelp greenling (Hexagrammos decagrammus) and pelagic-foraging black rockfish (Sebastes melanops) were collected at eight sites spanning ∼35 to 60°N from the California Current (upwelling) to Alaska Coastal Current (downwelling) in the northeast Pacific Ocean. Muscle δ13C values were expected to be higher for fish tissue primarily derived from kelp, a benthic macroalgae, and lower for tissue primarily derived from phytoplankton, pelagic microalgae. Muscle δ13C values were higher in benthic-feeding kelp greenling than in pelagic-feeding black rockfish at seven of eight sites, indicating more kelp-derived carbon in greenling as expected. Estimates of kelp carbon contributions ranged from 36 to 89% in kelp greenling and 32 to 65% in black rockfish using carbon isotope mixing models. Isotopic evidence suggests that these two nearshore fishes routinely derive energy from kelp and phytoplankton, across coastal upwelling and downwelling systems. Thus, the foraging mode of nearshore predators has a small influence on their ultimate energy source as energy produced by benthic macroalgae and pelagic microalgae were incorporated in fish tissue regardless of feeding mode and suggest strong and widespread benthic-pelagic coupling. Widespread kelp contributions to benthic- and pelagic-feeding fishes suggests that kelp energy provides a benefit to nearshore fishes and highlights the potential for kelp and fish production to be linked.

  6. 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.

  7. Multiple pathways for steel regulation suggested by genomic and sequence analysis of the murine Steel gene

    Energy Technology Data Exchange (ETDEWEB)

    Bedell, M.A.; Copeland, N.G.; Jenkins, N.A. [NCI-Frederick Cancer Research and Development Center, Frederick, MD (United States)

    1996-03-01

    The Steel (Sl) locus encodes mast cell growth factor (Mgf) that is required for the development of germ cells, hematopoietic cells and melanocytes. Although the expression patterns of the Mgf gene are well characterized, little is known of the factors which regulate its expression. Here, we describe the cloning and sequence of the full-length transcription unit and the 5{prime} flanking region of the murine Mgf gene. The full-length Mgf mRNA consists of a short 5{prime} untranslated region (UTR), a 0.8-kb ORF and a long 3{prime} UTR. A single transcription initiation site is used in a number of mouse tissues and is located just downstream of binding sites for several known transcription factors. In the 5{prime} UTR, two ATGs were found upstream of the initiator methionine and are conserved among different species, suggesting that Mgf may be translationally regulated. At least two Mgf mRNAs are produced by alternative use of polyadenylation sites, but numerous other potential polyadenylation sites were found in the 3{prime} UTR. In addition, the 3{prime} UTR contains numerous sequence motifs that may regulate Mgf mRNA stability. These studies suggest multiple ways in which expression of Mgf may be regulated. 39 refs., 4 figs.

  8. 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.

  9. DNA microarray analysis suggests that zinc pyrithione causes iron starvation to the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Yasokawa, Daisuke; Murata, Satomi; Iwahashi, Yumiko; Kitagawa, Emiko; Kishi, Katsuyuki; Okumura, Yukihiro; Iwahashi, Hitoshi

    2010-05-01

    Zinc pyrithione has been used in anti-dandruff shampoos and in anti-fouling paint on ships. However, little is known of its mode of action. We characterized the effects of sub-lethal concentrations of zinc pyrithione (Zpt) on Saccharomyces cerevisiae using DNA microarrays. The majority of the strongly upregulated genes are related to iron transport, and many of the strongly downregulated genes are related to the biosynthesis of cytochrome (heme). These data suggest that Zpt induces severe iron starvation. To confirm the DNA microarray data, we supplemented cultures containing Zpt with iron, and the growth of the yeast was restored significantly. From these results, we propose that the principal toxicity of zinc pyrithione arises from iron starvation.

  10. The Vindija Neanderthal scapular glenoid fossa: comparative shape analysis suggests evo-devo changes among Neanderthals.

    Science.gov (United States)

    Di Vincenzo, Fabio; Churchill, Steven E; Manzi, Giorgio

    2012-02-01

    Although the shape of the scapular glenoid fossa (SGF) may be influenced by epigenetic and developmental factors, there appears to be strong genetic control over its overall form, such that variation within and between hominin taxa in SGF shape may contain information about their evolutionary histories. Here we present the results of a geometric morphometric study of the SGF of the Neanderthal Vi-209 from Vindjia Cave (Croatia), relative to samples of Plio-Pleistocene, later Pleistocene, and recent hominins. Variation in overall SGF shape follows a chronological trend from the plesiomorphic condition seen in Australopithecus to modern humans, with pre-modern species of the genus Homo exhibiting intermediate morphologies. Change in body size across this temporal series is not linearly directional, which argues against static allometry as an explanation. However, life history and developmental rates change directionally across the series, suggesting an ontogenetic effect on the observed changes in shape (ontogenetic allometry). Within this framework, the morphospace occupied by the Neanderthals exhibits a discontinuous distribution. The Vindija SGF and those of the later Near Eastern Neanderthals (Kebara and Shanidar) approach the modern condition and are somewhat segregated from both northwestern European (Neandertal and La Ferrassie) and early Mediterranean Neanderthals (Krapina and Tabun). Although more than one scenario may account for the pattern seen in the Neanderthals, the data is consistent with palaeogenetic evidence suggesting low levels of gene flow between Neanderthals and modern humans in the Near East after ca. 120-100 ka (thousands of years ago) (with subsequent introgression of modern human alleles into eastern and central Europe). Thus, in keeping with previous analyses that document some modern human features in the Vindija Neanderthals, the Vindija G(3) sample should not be seen as representative of 'classic'--that is, unadmixed, pre

  11. Molecular Network Analysis Suggests Aberrant CREB-Mediated Gene Regulation in the Alzheimer Disease Hippocampus

    Directory of Open Access Journals (Sweden)

    Jun-ichi Satoh

    2009-01-01

    Full Text Available The pathogenesis of Alzheimer disease (AD involves the complex interaction between genetic and environmental factors affecting multiple cellular pathways. Recent advances in systems biology provide a system-level understanding of AD by elucidating the genome-wide molecular interactions. By using KeyMolnet, a bioinformatics tool for analyzing molecular interactions on the curated knowledgebase, we characterized molecular network of 2,883 all stages of AD-related genes (ADGs and 559 incipient AD-related genes (IADGs identified by global gene expression profiling of the hippocampal CA1 region of AD brains in terms of significant clinical and pathological correlations (Blalock et al., Proc Natl Acad Sci USA 101: 2173-2178, 2004. By the common upstream search, KeyMolnet identified cAMP-response element-binding protein (CREB as the principal transcription factor exhibiting the most significant relevance to molecular networks of both ADGs and IADGs. The CREB-regulated transcriptional network included upregulated and downregulated sets of ADGs and IADGs, suggesting an involvement of generalized deregulation of the CREB signaling pathway in the pathophysiology of AD, beginning at the early stage of the disease. To verify the in silico observations in vivo, we conducted immunohistochemical studies of 11 AD and 13 age-matched control brains by using anti-phoshorylated CREB (pCREB antibody. An abnormal accumulation of pCREB imunoreactivity was identified in granules of granulovacuolar degeneration (GVD in the hippocampal neurons of AD brains. These observations suggest that aberrant CREB-mediated gene regulation serves as a molecular biomarker of AD-related pathological processes, and support the hypothesis that sequestration of pCREB in GVD granules is in part responsible for deregulation of CREB-mediated gene expression in AD hippocampus.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions.

    Science.gov (United States)

    Weinert, Brian T; Moustafa, Tarek; Iesmantavicius, Vytautas; Zechner, Rudolf; Choudhary, Chunaram

    2015-11-03

    Acetylation is frequently detected on mitochondrial enzymes, and the sirtuin deacetylase SIRT3 is thought to regulate metabolism by deacetylating mitochondrial proteins. However, the stoichiometry of acetylation has not been studied and is important for understanding whether SIRT3 regulates or suppresses acetylation. Using quantitative mass spectrometry, we measured acetylation stoichiometry in mouse liver tissue and found that SIRT3 suppressed acetylation to a very low stoichiometry at its target sites. By examining acetylation changes in the liver, heart, brain, and brown adipose tissue of fasted mice, we found that SIRT3-targeted sites were mostly unaffected by fasting, a dietary manipulation that is thought to regulate metabolism through SIRT3-dependent deacetylation. Globally increased mitochondrial acetylation in fasted liver tissue, higher stoichiometry at mitochondrial acetylation sites, and greater sensitivity of SIRT3-targeted sites to chemical acetylation in vitro and fasting-induced acetylation in vivo, suggest a nonenzymatic mechanism of acetylation. Our data indicate that most mitochondrial acetylation occurs as a low-level nonenzymatic protein lesion and that SIRT3 functions as a protein repair factor that removes acetylation lesions from lysine residues.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

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

    Science.gov (United States)

    Anderson, R. Ernest; Beard, 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.

  6. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.

    Directory of Open Access Journals (Sweden)

    Alessia Galgano

    Full Text Available Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3'-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3'-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs.

  7. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.

    Science.gov (United States)

    Galgano, Alessia; Forrer, Michael; Jaskiewicz, Lukasz; Kanitz, Alexander; Zavolan, Mihaela; Gerber, André P

    2008-09-08

    Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3'-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3'-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs.

  8. The FLIC Overlap Quark Propagator

    CERN Document Server

    Kamleh, W; Leinweber, D B; Williams, A G; Zhang, J; Kamleh, Waseem; Bowman, Patrick O.; Leinweber, Derek B.; Williams, Anthony G.; Zhang, Jianbo

    2004-01-01

    FLIC overlap fermions are a variant of the standard (Wilson) overlap action, with the FLIC (Fat Link Irrelevant Clover) action as the overlap kernel rather than the Wilson action. The structure of the FLIC overlap fermion propagator in momentum space is studied, and a comparison against previous studies of the Wilson overlap propagator in quenched QCD is performed. To explore the scaling properties of the propagator for the two actions, numerical calculations are performed in Landau Gauge across three lattices with different lattice spacing $a$ and similar physical volumes. We find that at light quark masses the acti ons agree in both the infrared and the ultraviolet, but at heavier masses some disagreement in the ultraviolet appears. This is attributed to the two action s having different discretisation errors with the FLIC overlap providing superior performance in this regime. Both actions scale reasonably, but some scaling violations are observed.

  9. 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

  10. Outcome of overlapping heterogenous drug-eluting stents and of overlapping drug-eluting and bare metal stents.

    Science.gov (United States)

    Burzotta, Francesco; Siviglia, Massimo; Altamura, Luca; Trani, Carlo; Leone, Antonio Maria; Romagnoli, Enrico; Mazzari, Mario Attilio; Mongiardo, Rocco; Niccoli, Giampaolo; Brancati, Marta; Biondi-Zoccai, Giuseppe; Rebuzzi, Antonio Giuseppe; Schiavoni, Giovanni; Crea, Filippo

    2007-02-01

    Overlapping homogenous drug-eluting stents (DESs) may be used instead of overlapping bare metal stents (BMSs) to treat coronary lesions longer than available stents. Yet, no data are available on patients treated with overlapping heterogenous DESs or DESs and BMSs. We prospectively assessed 9-month clinical outcome and 6-month angiographic late loss (evaluated at 5 different lesion segments) in a consecutive series of 40 patients who received overlapping homogenous DESs (sirolimus-eluting stent [SES] or paclitaxel-eluting stent [PES]), heterogenous DESs (SES + PES), or overlapping DESs and BMSs. In 8 patients (7 with angiographic follow-up) with overlapping heterogenous DESs, no angiographic or clinical adverse event was observed. Moreover, in-segment late loss was similar to that of patients who received homogenous DESs. In 8 patients (7 with angiographic follow-up) with overlapping DESs and BMSs, there was a higher incidence of major adverse events (3 repeat percutaneous coronary interventions and 1 death, 50% adverse event rate) and worse in-segment binary restenosis rate compared with patients treated with homogenous or heterogenous DESs (p = 0.02 and 0.012, respectively). Late lumen loss at the site of stent overlap showed significant differences according to type of overlapped stent (1.00 +/- 0.76 mm in DES-BMS overlap, 0.32 +/- 0.55 mm in PES-PES overlap, 0.13 +/- 0.11 in SES-PES overlap, and 0.08 +/- 0.10 mm in SES-SES overlap, p = 0.005). In conclusion, the present study suggests that overlap of DESs and BMSs should be avoided because the antirestenotic effect of DESs is skewed by contiguous BMS implantation. Overlap between SESs and PESs in this very preliminary report was associated with no specific adverse event.

  11. 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.

  12. 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.

  13. Analysis of origin and protein-protein interaction maps suggests distinct oncogenic role of nuclear EGFR during cancer evolution

    Science.gov (United States)

    Sharip, Ainur; Abdukhakimova, Diyora; Wang, Xiao; Kim, Alexey; Kim, Yevgeniy; Sharip, Aigul; Orakov, Askarbek; Miao, Lixia; Sun, Qinglei; Chen, Yue; Chen, Zhenbang; Xie, Yingqiu

    2017-01-01

    Receptor tyrosine kinase EGFR usually is localized on plasma membrane to induce progression of many cancers including cancers in children (Bodey et al. In Vivo. 2005, 19:931-41), but it contains a nuclear localization signal (NLS) that mediates EGFR nuclear translocation (Lin et al. Nat Cell Biol. 2001, 3:802-8). Here we report that NLS of EGFR has its old evolutionary origin. Protein-protein interaction maps suggests that nEGFR pathways are different from membrane EGFR and EGF is not found in nEGFR network while androgen receptor (AR) is found, which suggests the evolution of prostate cancer, a well-known AR driven cancer, through changes in androgen- or EGF-dependence. Database analysis suggests that nEGFR correlates with the tumor grades especially in prostate cancer patients. Structural predication analysis suggests that NLS can compromise the differential protein binding to EGFR through stretch linkers with evolutionary mutation from N to V. In experiment, elevation of nEGFR but not membrane EGFR was found in castration resistant prostate cancer cells. Finally, systems analysis of NLS and transmembrane domain (TM) suggests that NLS has old origin while NLS neighboring domain of TM has been undergone accelerated evolution. Thus nEGFR has an old origin resembling the cancer evolution but TM may interfere with NLS driven signaling for natural selection of survival to evade NLS induced aggressive cancers. Our data suggest NLS is a dynamic inducer of EGFR oncogenesis during evolution for advanced cancers. Our model provides novel insights into the evolutionary role of NLS of oncogenic kinases in cancers.

  14. Asthma–COPD overlap syndrome in the US: a prospective population-based analysis of patient-reported outcomes and health care utilization

    Science.gov (United States)

    Vaz Fragoso, Carlos A; Murphy, Terrence E; Agogo, George O; Allore, Heather G; McAvay, Gail J

    2017-01-01

    Background Prior work suggests that asthma–COPD overlap syndrome (ACOS) has a greater health burden than asthma alone or COPD alone. In the current study, we have further evaluated the health burden of ACOS in a nationally representative sample of the US population, focusing on patient-reported outcomes and health care utilization and on comparisons with asthma alone and COPD alone. Patient-reported outcomes are especially meaningful, as these include functional activities that are highly valued by patients and are the basis for patient-centered care. Methods Using data from the Medical Expenditure Panel Survey (MEPS), we evaluated patient-reported outcomes and health care utilization among participants who were aged 40–85 years and had self-reported, physician-diagnosed asthma or COPD. MEPS administered five rounds of interviews, at baseline and approximately every 6 months over 2.5 years. Patient-reported outcomes included activities of daily living (ADLs), mobility, social/recreational activities, disability days in bed, and health status (Short Form 12, Version 2). Health care utilization included outpatient and emergency department (ED) visits, and hospitalization. Results Of 3,486 participants with asthma or COPD, 1,585 (45.4%) had asthma alone, 1,294 (37.1%) had COPD alone, and 607 (17.4%) had ACOS. Relative to asthma alone, ACOS was significantly associated with higher odds of prevalent disability in ADLs and limitations in mobility and social/recreational activities (adjusted odds ratios [adjORs]: 1.91–3.98), as well as with higher odds of incident limitations in mobility and social/recreational activities, disability days in bed, and respiratory-based outpatient and ED visits, and hospitalization (adjORs: 1.86–2.35). In addition, ACOS had significantly worse physical and mental health scores than asthma alone (P-values social/recreational activities (adjORs: 1.68–2.06), as well as with higher odds of incident disability days in bed and

  15. Vertical overlap of probability density functions of cloud and precipitation hydrometeors: CLOUD AND PRECIPITATION PDF OVERLAP

    Energy Technology Data Exchange (ETDEWEB)

    Ovchinnikov, Mikhail [Pacific Northwest National Laboratory, Richland Washington USA; Lim, Kyo-Sun Sunny [Pacific Northwest National Laboratory, Richland Washington USA; Korea Atomic Energy Research Institute, Daejeon Republic of Korea; Larson, Vincent E. [Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee Wisconsin USA; Wong, May [Pacific Northwest National Laboratory, Richland Washington USA; National Center for Atmospheric Research, Boulder Colorado USA; Thayer-Calder, Katherine [National Center for Atmospheric Research, Boulder Colorado USA; Ghan, Steven J. [Pacific Northwest National Laboratory, Richland Washington USA

    2016-11-05

    Coarse-resolution climate models increasingly rely on probability density functions (PDFs) to represent subgrid-scale variability of prognostic variables. While PDFs characterize the horizontal variability, a separate treatment is needed to account for the vertical structure of clouds and precipitation. When sub-columns are drawn from these PDFs for microphysics or radiation parameterizations, appropriate vertical correlations must be enforced via PDF overlap specifications. This study evaluates the representation of PDF overlap in the Subgrid Importance Latin Hypercube Sampler (SILHS) employed in the assumed PDF turbulence and cloud scheme called the Cloud Layers Unified By Binormals (CLUBB). PDF overlap in CLUBB-SILHS simulations of continental and tropical oceanic deep convection is compared with overlap of PDF of various microphysics variables in cloud-resolving model (CRM) simulations of the same cases that explicitly predict the 3D structure of cloud and precipitation fields. CRM results show that PDF overlap varies significantly between different hydrometeor types, as well as between PDFs of mass and number mixing ratios for each species, - a distinction that the current SILHS implementation does not make. In CRM simulations that explicitly resolve cloud and precipitation structures, faster falling species, such as rain and graupel, exhibit significantly higher coherence in their vertical distributions than slow falling cloud liquid and ice. These results suggest that to improve the overlap treatment in the sub-column generator, the PDF correlations need to depend on hydrometeor properties, such as fall speeds, in addition to the currently implemented dependency on the turbulent convective length scale.

  16. An Exposition of Fischer's Model of Overlapping Contracts.

    Science.gov (United States)

    Fields, T. Windsor; Hart, William R.

    1992-01-01

    Suggests how the classic model of overlapping contracts can be incorporated into the contract wage model of aggregate supply. Illustrates dynamics of macroeconomic adjustment following a shock to aggregate demand. Concludes that overlapping contracts do not prolong the adjustment process; rather, the longest remaining contract determines the time…

  17. 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.

  18. Pitfalls in the analysis of volatile breath biomarkers: suggested solutions and SIFT-MS quantification of single metabolites.

    Science.gov (United States)

    Smith, David; Spanel, Patrik

    2015-04-01

    The experimental challenges presented by the analysis of trace volatile organic compounds (VOCs) in exhaled breath with the objective of identifying reliable biomarkers are brought into focus. It is stressed that positive identification and accurate quantification of the VOCs are imperative if they are to be considered as discreet biomarkers. Breath sampling procedures are discussed and it is suggested that for accurate quantification on-line real time sampling and analysis is desirable. Whilst recognizing such real time analysis is not always possible and sample collection is often required, objective recognition of the pitfalls involved in this is essential. It is also emphasized that mouth-exhaled breath is always contaminated to some degree by orally generated compounds and so, when possible, analysis of nose-exhaled breath should be performed. Some difficulties in breath analysis are mitigated by the choice of analytical instrumentation used, but no single instrument can provide solutions to all the analytical challenges. Analysis and interpretation of breath analysis data, however acquired, needs to be treated circumspectly. In particular, the excessive use of statistics to treat imperfect mass spectrometry/mobility spectra should be avoided, since it can result in unjustifiable conclusions. It is should be understood that recognition of combinations of VOCs in breath that, for example, apparently describe particular cancer states, will not be taken seriously until they are replicated in other laboratories and clinics. Finally, the inhibiting notion that single biomarkers of infection and disease will not be identified and utilized clinically should be dispelled by the exemplary and widely used single biomarkers NO and H2 and now, as indicated by recent selected ion flow tube mass spectroscopy (SIFT-MS) results, triatomic hydrogen cyanide and perhaps pentane and acetic acid. Hopefully, these discoveries will provide encouragement to research workers to be

  19. Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis

    Directory of Open Access Journals (Sweden)

    Amrutraj eZade

    2015-09-01

    Full Text Available Rab GTPases are the key regulators of intracellular membrane trafficking in eukaryotes. Many viruses and intracellular bacterial pathogens have evolved to hijack the host Rab GTPase functions, mainly through activators and effector proteins, for their benefit. Acanthamoeba polyphaga mimivirus (APMV is one of the largest viruses and belongs to the monophyletic clade of nucleo-cytoplasmic large DNA viruses (NCLDV. The inner membrane lining is integral to the APMV virion structure. APMV assembly involves extensive host membrane modifications, like vesicle budding and fusion, leading to the formation of a membrane sheet that is incorporated into the virion. Intriguingly, APMV and all group I members of the Mimiviridae family code for a putative Rab GTPase protein. APMV is the first reported virus to code for a Rab GTPase (encoded by R214 gene. Our thorough in silico analysis of the subfamily specific (SF region of Mimiviridae Rab GTPase sequences suggests that they are related to Rab5, a member of the group II Rab GTPases, of lower eukaryotes. Because of their high divergence from the existing three isoforms, A, B and C of the Rab5-family, we suggest that Mimiviridae Rabs constitute a new isoform, Rab5D. Phylogenetic analysis indicated probable horizontal acquisition from a lower eukaryotic ancestor followed by selection and divergence. Furthermore, interaction network analysis suggests that vps34 (a Class III P13K homolog, coded by APMV L615, Atg-8 and dynamin (host proteins are recruited by APMV Rab GTPase during capsid assembly. Based on these observations, we hypothesize that APMV Rab plays a role in the acquisition of inner membrane during virion assembly.

  20. 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.

  1. Asthma–COPD overlap syndrome in the US: a prospective population-based analysis of patient-reported outcomes and health care utilization

    Directory of Open Access Journals (Sweden)

    Vaz Fragoso CA

    2017-02-01

    Full Text Available Carlos A Vaz Fragoso,1,2 Terrence E Murphy,1 George O Agogo,1 Heather G Allore,1,3 Gail J McAvay1 1Department of Medicine, Yale School of Medicine, New Haven, 2Veterans Affairs Clinical Epidemiology Research Center, West Haven, 3Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA Background: Prior work suggests that asthma–COPD overlap syndrome (ACOS has a greater health burden than asthma alone or COPD alone. In the current study, we have further evaluated the health burden of ACOS in a nationally representative sample of the US population, focusing on patient-reported outcomes and health care utilization and on comparisons with asthma alone and COPD alone. Patient-reported outcomes are especially meaningful, as these include functional activities that are highly valued by patients and are the basis for patient-centered care.Methods: Using data from the Medical Expenditure Panel Survey (MEPS, we evaluated patient-reported outcomes and health care utilization among participants who were aged 40–85 years and had self-reported, physician-diagnosed asthma or COPD. MEPS administered five rounds of interviews, at baseline and approximately every 6 months over 2.5 years. Patient-reported outcomes included activities of daily living (ADLs, mobility, social/recreational activities, disability days in bed, and health status (Short Form 12, Version 2. Health care utilization included outpatient and emergency department (ED visits, and hospitalization.Results: Of 3,486 participants with asthma or COPD, 1,585 (45.4% had asthma alone, 1,294 (37.1% had COPD alone, and 607 (17.4% had ACOS. Relative to asthma alone, ACOS was significantly associated with higher odds of prevalent disability in ADLs and limitations in mobility and social/recreational activities (adjusted odds ratios [adjORs]: 1.91–3.98, as well as with higher odds of incident limitations in mobility and social/recreational activities, disability days in bed, and

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Analysis of the influence of the overlapping factor in the laser transformation hardening of extended surfaces of steel; Analisis de la influencia del factor de solapamiento en el tratamiento termico de superficies extensas de aceros por laser

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Beltran, A.; Marin, L. F.; Ocana, J. L.

    2007-07-01

    On the basis of numerical models developed by the authors for the predictive analysis of transformation hardening of extended steel surfaces, the difficulties existing for the treatment of extended surfaces by overlapping cycles of laser heating are analyzed from a computational point of view. In this analysis, thermal and physical properties of the material are considered along with their temperature dependence. Some optimization for the irradiation parameters (including modification of the spatial distribution of the laser bean energy) are determined in order to obtain both the adequate material transformed depth and the required hardness profiles. (Author)

  9. 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.

  10. Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa.

    Directory of Open Access Journals (Sweden)

    Babi Ramesh Reddy Nallamilli

    Full Text Available Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa. We identified 60 lysine acetylated sites on 44 proteins of diverse biological functions. Immunoblot studies further validated the presence of a large number of acetylated non-histone proteins. Examination of the amino acid composition revealed substantial amino acid bias around the acetylation sites and the amino acid preference is conserved among different organisms. Gene ontology analysis demonstrates that lysine acetylation occurs in diverse cytoplasmic, chloroplast and mitochondrial proteins in addition to the histone modifications. Our results suggest that lysine acetylation might constitute a regulatory mechanism for many proteins, including both histones and non-histone proteins of diverse biological functions.

  11. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

    Science.gov (United States)

    Chartier, Matthieu; Gaudreault, Francis; Najmanovich, Rafael

    2012-01-01

    Motivation: An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output. Results: Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. Availability: The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca Contact: rafael.najmanovich@usherbrooke.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22467916

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum

    Science.gov (United States)

    Vilela, Mariane de Mendonça; Del Bem, Luiz Eduardo; Van Sluys, Marie-Anne; de Setta, Nathalia; Kitajima, João Paulo; Cruz, Guilherme Marcelo Queiroga; Sforça, Danilo Augusto; de Souza, Anete Pereira; Ferreira, Paulo Cavalcanti Gomes; Grativol, Clícia; Cardoso-Silva, Claudio Benicio; Vicentini, Renato

    2017-01-01

    Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum. PMID:28082603

  17. Overlapping constraint for variational surface reconstruction

    DEFF Research Database (Denmark)

    Aanæs, Henrik; Solem, J.E.

    2005-01-01

    In this paper a counter example, illustrating a shortcoming in most variational formulations for 3D surface estimation, is presented. The nature of this shortcoming is a lack of an overlapping constraint. A remedy for this shortcoming is presented in the form of a penalty function with an analysis...... of the effects of this function on surface motion. For practical purposes, this will only have minor influence on current methods. However, the insight provided in the analysis is likely to influence future developments in the field of variational surface reconstruction....

  18. 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.

  19. 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.

  20. 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...

  1. 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.

  2. Planktonic foraminiferal oxygen isotope analysis by ion microprobe technique suggests warm tropical sea surface temperatures during the Early Paleogene

    Science.gov (United States)

    Kozdon, Reinhard; Kelly, D. Clay; Kita, Noriko T.; Fournelle, John H.; Valley, John W.

    2011-09-01

    Cool tropical sea surface temperatures (SSTs) are reported for warm Paleogene greenhouse climates based on the δ18O of planktonic foraminiferal tests. These results are difficult to reconcile with models of greenhouse gas-forced climate. It has been suggested that this "cool tropics paradox" arises from postdepositional alteration of foraminiferal calcite, yielding erroneously high δ18O values. Recrystallization of foraminiferal tests is cryptic and difficult to quantify, and the compilation of robust δ18O records from moderately altered material remains challenging. Scanning electron microscopy of planktonic foraminiferal chamber-wall cross sections reveals that the basal area of muricae, pustular outgrowths on the chamber walls of species belonging to the genus Morozovella, contain no mural pores and may be less susceptible to postdepositional alteration. We analyzed the δ18O in muricae bases of morozovellids from the central Pacific (Ocean Drilling Program Site 865) by ion microprobe using 10 μm pits with an analytical reproducibility of ±0.34‰ (2 standard deviations). In situ measurements of δ18O in these domains yield consistently lower values than those published for conventional multispecimen analyses. Assuming that the original δ18O is largely preserved in the basal areas of muricae, this new δ18O record indicates Early Paleogene (˜49-56 Ma) tropical SSTs in the central Pacific were 4°-8°C higher than inferred from the previously published δ18O record and that SSTs reached at least ˜33°C during the Paleocene-Eocene thermal maximum. This study demonstrates the utility of ion microprobe analysis for generating more reliable paleoclimate records from moderately altered foraminiferal tests preserved in deep-sea sediments.

  3. Differential proteomic analysis of platelets suggested possible signal cascades network in platelets treated with salvianolic acid B.

    Directory of Open Access Journals (Sweden)

    Chao Ma

    Full Text Available BACKGROUND: Salvianolic acid B (SB is an active component isolated from Danshen, a traditional Chinese medicine widely used for the treatment of cardiovascular disorders. Previous study suggested that SB might inhibit adhesion as well as aggregation of platelets by a mechanism involving the integrin α2β1. But, the signal cascades in platelets after SB binding are still not clear. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, a differential proteomic analysis (two-dimensional electrophoresis was conducted to check the protein expression profiles of rat platelets with or without treatment of SB. Proteins altered in level after SB exposure were identified by MALDI-TOF MS/MS. Treatment of SB caused regulation of 20 proteins such as heat shock-related 70 kDa protein 2 (hsp70, LIM domain protein CLP-36, copine I, peroxiredoxin-2, coronin-1 B and cytoplasmic dynein intermediate chain 2C. The regulation of SB on protein levels was confirmed by Western blotting. The signal cascades network induced by SB after its binding with integrin α2β1 was predicted. To certify the predicted network, binding affinity of SB to integrin α2β1 was checked in vitro and ex vivo in platelets. Furthermore, the effects of SB on protein levels of hsp70, coronin-1B and intracellular levels of Ca²+ and reactive oxygen species (ROS were checked with or without pre-treatment of platelets using antibody against integrin α2β1. Electron microscopy study confirmed that SB affected cytoskeleton structure of platelets. CONCLUSIONS/SIGNIFICANCE: Integrin α2β1 might be one of the direct target proteins of SB in platelets. The signal cascades network of SB after binding with integrin α2β1 might include regulation of intracellular Ca²+ level, cytoskeleton-related proteins such as coronin-1B and cytoskeleton structure of platelets.

  4. Differential Proteomic Analysis of Platelets Suggested Possible Signal Cascades Network in Platelets Treated with Salvianolic Acid B

    Science.gov (United States)

    Ma, Chao; Yao, Yan; Yue, Qing-Xi; Zhou, Xin-Wen; Yang, Peng-Yuan; Wu, Wan-Ying; Guan, Shu-Hong; Jiang, Bao-Hong; Yang, Min; Liu, Xuan; Guo, De-An

    2011-01-01

    Background Salvianolic acid B (SB) is an active component isolated from Danshen, a traditional Chinese medicine widely used for the treatment of cardiovascular disorders. Previous study suggested that SB might inhibit adhesion as well as aggregation of platelets by a mechanism involving the integrin α2β1. But, the signal cascades in platelets after SB binding are still not clear. Methodology/Principal Findings In the present study, a differential proteomic analysis (two-dimensional electrophoresis) was conducted to check the protein expression profiles of rat platelets with or without treatment of SB. Proteins altered in level after SB exposure were identified by MALDI-TOF MS/MS. Treatment of SB caused regulation of 20 proteins such as heat shock-related 70 kDa protein 2 (hsp70), LIM domain protein CLP-36, copine I, peroxiredoxin-2, coronin-1 B and cytoplasmic dynein intermediate chain 2C. The regulation of SB on protein levels was confirmed by Western blotting. The signal cascades network induced by SB after its binding with integrin α2β1 was predicted. To certify the predicted network, binding affinity of SB to integrin α2β1 was checked in vitro and ex vivo in platelets. Furthermore, the effects of SB on protein levels of hsp70, coronin-1B and intracellular levels of Ca(2+) and reactive oxygen species (ROS) were checked with or without pre-treatment of platelets using antibody against integrin α2β1. Electron microscopy study confirmed that SB affected cytoskeleton structure of platelets. Conclusions/Significance Integrin α2β1 might be one of the direct target proteins of SB in platelets. The signal cascades network of SB after binding with integrin α2β1 might include regulation of intracellular Ca(2+) level, cytoskeleton-related proteins such as coronin-1B and cytoskeleton structure of platelets. PMID:21379382

  5. Clique graphs and overlapping communities

    Science.gov (United States)

    Evans, T. S.

    2010-12-01

    It is shown how to construct a clique graph in which properties of cliques of a fixed order in a given graph are represented by vertices in a weighted graph. Various definitions and motivations for these weights are given. The detection of communities or clusters is used to illustrate how a clique graph may be exploited. In particular a benchmark network is shown where clique graphs find the overlapping communities accurately while vertex partition methods fail.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Spectroscopic (FT-IR, (1)H, (13)C NMR, UV), DOS and orbital overlap population analysis of copper complex of (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine by density functional theory.

    Science.gov (United States)

    Diwaker

    2015-02-05

    The geometric parameters, chemical shifts, FTIR, NMR and orbital overlap population along with DOS (density of states) to know different kinds of interactions for binding of copper atom with (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine to form its copper complex has been reported by DFT methods. The theoretically predicted values for structural parameters are in agreement with the experimentally reported values. NMR chemical shifts calculated using B3LYP/DFT/GIAO level of theory gives information about binding of copper atom with three nitrogen atoms namely N (3, 8 and 11). Orbital overlap population analysis using DFT/B3LYP/SDD level of theory is used to study the kind of interactions involved in binding of copper with the three nitrogen atoms. DOS studies are done to know about the contribution of alpha, beta electrons to the valence and conduction band. IR spectroscopy investigations gave the absorption bands for the formation of title compound. Electronic spectrum along with HOMO-LUMO energies of the title compound has been investigated using Time-dependent (TD-DFT) approach.

  8. 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...... towards a smaller trapping region, which is the intersection over the family. All these trapping regions are compact sets, and thus, practical weak persistence is guaranteed. We conclude our analysis by proposing 4 novel treatment strategies: increasing the phagocytic ability of resting macrophages...

  9. 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

    . Individual larval growth rates, averaged over the 30 days prior to capture, were estimated for 200 larval otoliths from four different years using a model‐based analysis of the ring widths. The otolith measurements were complemented with additional information derived from hydrographic backtracking models (e...... stock productivity) as taking place during the larval overwintering phase: however, the underlying mechanism remains elusive. In this study we analysed archived larval samples captured both before and after the onset of the reduced survival to test the hypothesis of a reduction in the larval growth rate...... demonstrates how coupling two different techniques (otolith microstructure analysis and hydrographic modelling) can yield unique insights into fish ecology...

  10. Molecular and biochemical analysis of rainbow trout LCK suggests a conserved mechanism for T-cell signaling in gnathostomes

    Science.gov (United States)

    Laing, K.J.; Dutton, S.; Hansen, J.D.

    2007-01-01

    Two genes were identified in rainbow trout that display high sequence identity to vertebrate Lck. Both of the trout Lck transcripts are associated with lymphoid tissues and were found to be highly expressed in IgM-negative lymphocytes. In vitro analysis of trout lymphocytes indicates that trout Lck mRNA is up-regulated by T-cell mitogens, supporting an evolutionarily conserved function for Lck in the signaling pathways of T-lymphocytes. Here, we describe the generation and characterization of a specific monoclonal antibody raised against the N-terminal domains of recombinant trout Lck that can recognize Lck protein(s) from trout thymocyte lysates that are similar in size (???57 kDa) to mammalian Lck. This antibody also reacted with permeabilized lymphocytes during FACS analysis, indicating its potential usage for cellular analyses of trout lymphocytes, thus representing an important tool for investigations of salmonid T-cell function.

  11. On Multigrid for Overlapping Grids

    Energy Technology Data Exchange (ETDEWEB)

    Henshaw, W

    2004-01-13

    The solution of elliptic partial differential equations on composite overlapping grids using multigrid is discussed. An approach is described that provides a fast and memory efficient scheme for the solution of boundary value problems in complex geometries. The key aspects of the new scheme are an automatic coarse grid generation algorithm, an adaptive smoothing technique for adjusting residuals on different component grids, and the use of local smoothing near interpolation boundaries. Other important features include optimizations for Cartesian component grids, the use of over-relaxed Red-Black smoothers and the generation of coarse grid operators through Galerkin averaging. Numerical results in two and three dimensions show that very good multigrid convergence rates can be obtained for both Dirichlet and Neumann/mixed boundary conditions. A comparison to Krylov based solvers shows that the multigrid solver can be much faster and require significantly less memory.

  12. Suggestions for automatic quantitation of endoscopic image analysis to improve detection of small intestinal pathology in celiac disease patients.

    Science.gov (United States)

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-10-01

    Although many groups have attempted to develop an automated computerized method to detect pathology of the small intestinal mucosa caused by celiac disease, the efforts have thus far failed. This is due in part to the occult presence of the disease. When pathological evidence of celiac disease exists in the small bowel it is visually often patchy and subtle. Due to presence of extraneous substances such as air bubbles and opaque fluids, the use of computerized automation methods have only been partially successful in detecting the hallmarks of the disease in the small intestine-villous atrophy, fissuring, and a mottled appearance. By using a variety of computerized techniques and assigning a weight or vote to each technique, it is possible to improve the detection of abnormal regions which are indicative of celiac disease, and of treatment progress in diagnosed patients. Herein a paradigm is suggested for improving the efficacy of automated methods for measuring celiac disease manifestation in the small intestinal mucosa. The suggestions are applicable to both standard and videocapsule endoscopic imaging, since both methods could potentially benefit from computerized quantitation to improve celiac disease diagnosis.

  13. Genetic Overlap Between Affective Disorders: An Association Analysis of M18 and M23 SNPs of DAOA/G72 Gene With Schizophrenia and Bipolar Disorder

    OpenAIRE

    Leila Ahmadi; Seyyed Reza Kazeminezhad; Niloufar Khajehdin; Mehdi Pourmehdi-Boroujeni; Parisima Behbahani

    2015-01-01

    Background: Schizophrenia and bipolar disorder are common and often destructive brain disorders. It has generally been assumed that dozens of genes, along with environmental factors, contribute to the development of these diseases. Schizophrenia and bipolar mood disorder affect many families simultaneously. This theme suggests that these disorders have a shared genetic etiology at least to some extent. The DAOA/G72 gene is one of the common loci shared both by schizophrenia and bipolar disord...

  14. Haplotype transmission analysis provides evidence of association for DISC1 to schizophrenia and suggests sex-dependent effects.

    Science.gov (United States)

    Hennah, William; Varilo, Teppo; Kestilä, Marjo; Paunio, Tiina; Arajärvi, Ritva; Haukka, Jari; Parker, Alex; Martin, Rory; Levitzky, Steve; Partonen, Timo; Meyer, Joanne; Lönnqvist, Jouko; Peltonen, Leena; Ekelund, Jesper

    2003-12-01

    We have previously reported a linkage peak on 1q42 in a Finnish schizophrenia sample. In this study we genotyped 28 single nucleotide polymorphisms (SNPs) from 1q42 covering the three candidate genes TRAX, DISC1 and DISC2, using a study sample of 458 Finnish families ascertained for schizophrenia. Two-point and haplotype association analysis revealed a significant region of interest within the DISC1 gene. A common haplotype (HEP3) was observed to be significantly under-transmitted to affected individuals (P=0.0031). HEP3 represents a two SNP haplotype spanning from intron 1 to exon 2 of DISC1. This haplotype also displayed sex differences in transmission distortion, the under-transmission being significant only to affected females (P=0.00024). Three other regions of interest were observed in the TRAX and DISC genes. However, analysis of only those families with complete genotype information specifically highlights the HEP3 haplotype as a true observation. The finding of a common under-transmitted SNP haplotype might imply that this particular allele offers some protection from the development of schizophrenia. Analysis of component-traits of schizophrenia, derived from the Operational Criteria Checklist of Psychotic Illness (OCCPI), displayed association of HEP3 to features of the general phenotype of schizophrenia, including traits representing delusions, hallucinations and negative symptoms. This study provides further evidence for the hypothesis that the DISC1 gene is involved in the aetiology of schizophrenia, and implies a putative sex difference for the effect of the gene. Our findings would also encourage more detailed analyses of the effect of DISC1 on the component-traits of schizophrenia.

  15. 中国化肥消费分析及建议%Analysis and Suggestion on Fertilizers Usage in China

    Institute of Scientific and Technical Information of China (English)

    代瑞熙; 郝晓燕

    2015-01-01

    通过对中国化肥的生产和消费情况进行分析,指出中国化肥供求中存在的主要问题,并总结和借鉴发达国家减施化肥的政策经验,提出促进中国化肥减施和产业发展的建议。%Through analyzing the present conditions of fertilizers consumption and production in China, the authors pointed out the problems existing in the supply and demand of China's fertilizers, summarized and borrowed from developed countries in policies and experience about reducing fertilizing, and put forward some suggestions to promote the reduce of fertilizing and the development of fertilizer industry in China.

  16. 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.

  17. 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...... 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......, raising questions about the mechanism of the causal SNP on atherosclerosis....

  18. 基于简化SIFT算法的无人机影像重叠度分析%Overlapping degree analysis of images from an unmanned aerial vehicle based on a reduced scale-invariant feature transform (SIFT) algorithm

    Institute of Scientific and Technical Information of China (English)

    邢诚

    2012-01-01

    Compared with traditional images, high-resolution images obtained by unmanned aerial vehicles ( UAV) are superior in many aspects such as low cost, rapidness and convenience. However, the attitude of unmanned aerial vehicles cannot be determined accurately, which leads to a decrease in accuracy and efficiency of automatic matching. There are several ascendant characteristics of a SIFT operator such as invariance to scale, rotation, and lightness, and these characteristics are very useful in increasing the matching accuracy of UAV images; however, the traditional SIFT algorithm is complex and requires a long time for image processing. In this paper, a reduced SIFT method was described and some comparisons were made. The overlap analysis of UAV images were processed based on a reduced SIFT and the random sample consensus ( RANSAC ) algorithm, and the steps of overlap analysis were described. Finally, satisfactory results were obtained.%利用无人机进行低空摄影获取地面高分辨率影像,具有成本低、方便、快捷等优点,但由于无人机飞行姿态不稳定,会导致影像自动匹配效率及准确程度降低.SIFT算子具有良好的尺度、旋转、光照等不变特性,但传统SIFT算法复杂度较高,处理影像时间较长,使数据处理工作效率降低.介绍了一种简化的SIFT算法,并与原SIFT算法做出了对比.说明了影像重叠度分析的主要步骤,将简化的SIFT算法RANSAC算法相结合应用到序列影像重叠度分析中,通过实验证明了可行性.

  19. 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.)

  20. Overlapping Structures in Sensory-Motor Mappings

    Science.gov (United States)

    Earland, Kevin; Lee, Mark; Shaw, Patricia; Law, James

    2014-01-01

    This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots. PMID:24392118

  1. Analysis of educational research at a medical faculty in Germany and suggestions for strategic development - a case study.

    Science.gov (United States)

    Prediger, Sarah; Harendza, Sigrid

    2016-01-01

    Background: Evidence-based medical education is playing an increasingly important role in the choice of didactic methods and the development of medical curricula and assessments. In Germany, a growing number of educational research projects has accompanied an ongoing change in the medical education process. The aim of this project was to assess medical education research activities at one medical faculty to develop procedural recommendations for the support and development of best evidence medical education. Methods: Using a newly developed online questionnaire, the 65 institutes and departments of the medical faculty of Hamburg University at Hamburg University Medical-Center (UKE) were asked to report their medical education research and service projects, medical education publications, medical education theses, financial support for educational projects, and supportive structures that they would consider helpful in the future. The data were grouped, and a SWOT analysis was performed. Results: In total, 60 scientists who were involved in 112 medical education research publications between 1998 and 2014 were identified at the UKE. Twenty-five of them had published at least one manuscript as first or last author. Thirty-three UKE institutions were involved in educational service or research projects at the time of the study, and 75.8% of them received internal or external funding. Regular educational research meetings and the acquisition of co-operation partners were mentioned most frequently as beneficial supportive structures for the future. Conclusion: An analysis to define the status quo of medical education research at a medical faculty seems to be a helpful first step for the development of a strategy and structure to further support researchers in medical education.

  2. 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.

  3. Analysis of the beta-tubulin gene and morphological changes of the microsporidium Anncaliia algerae both suggest albendazole sensitivity.

    Science.gov (United States)

    Santiana, Marianita; Pau, Cyrilla; Takvorian, Peter M; Cali, Ann

    2015-01-01

    The Microsporidium, Anncaliia algerae, an obligate intracellular parasite, has been identified as an opportunistic human pathogen, but treatment has not been evaluated for infections with this organism. Albendazole, an antitubulin polymerization drug used against parasitic worm infections, has been the medication of choice used to treat some microsporidial infections affecting humans, with varying results ranging from clearing infection (Encephalitozoon) to resistance (Enterocytozoon). This study illustrates the effect of albendazole treatment on A. algerae infection in Rabbit Kidney (RK13) cells and Human Fetal Lung (HFL-1) fibroblasts. Albendazole appears to have an attenuating effect on A. algerae infection and albendazole's IC50 in RK13 cells is 0.1 μg/ml. Long-term treatment inhibits up to 98% of spore production, but interrupting treatment reestablishes the infection without new exposure to the parasite as supported by microscopic observations. The parasite's beta-tubulin gene was purified, cloned, and sequenced. Five of the six specific amino acids, associated with benzimidazole sensitivity, are conserved in A. algerae. These findings suggest that A. algerae is sensitive to albendazole; however, the organism is not completely cleared from cultures.

  4. Beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids.

    Science.gov (United States)

    Hewitt, R; Krause, A; Goldman, A; Campbell, G; Jenkins, T

    1996-06-01

    The origins of the inhabitants of Madagascar have not been fully resolved. Anthropological studies and preliminary genetic data point to two main sources of ancestry of the Malagasy, namely, Indonesian and African, with additional contributions from India and Arabia. The sickle-cell (beta s) mutation is found in populations of African and Indian origin. The frequency of the beta s-globin gene, derived from 1,425 Malagasy individuals, varies from 0 in some highland populations to .25 in some coastal populations. The beta s mutation is thought to have arisen at least five times, on the basis of the presence of five distinct beta s-associated haplotypes, each found in a separate geographic area. Twenty-five of the 35 Malagasy beta s haplotypes were of the typical "Bantu" type, 1 "Senegal" haplotype was found, and 2 rare or atypical haplotypes were observed; the remaining 7 haplotypes were consistent with the Bantu haplotype. The Bantu beta s mutation is thought to have been introduced into Madagascar by Bantu-speaking immigrants (colonists or slaves) from central or east Africa. The Senegal beta s mutation may have been introduced to the island via Portuguese naval explorers. This study provides the first definitive biological evidence that a major component of Malagasy ancestry is derived from African populations, in particular, Bantu-speaking Negroids. beta A haplotypes are also consistent with the claim for a significant African contribution to Malagasy ancestry but are also suggestive of Asian/Oceanic and Caucasoid admixture within the Malagasy population.

  5. Analysis and modeling of heat-labile enterotoxins of Escherichia coli suggests a novel space with insights into receptor preference.

    Science.gov (United States)

    Krishna Raja, M; Ghosh, Asit Ranjan; Vino, S; Sajitha Lulu, S

    2015-01-01

    Features of heat-labile enterotoxins of Escherichia coli which make them fit to use as novel receptors for antidiarrheals are not completely explored. Data-set of 14 different serovars of enterotoxigenic Escherichia coli producing heat-labile toxins were taken from NCBI Genbank database and used in the study. Sequence analysis showed mutations in different subunits and also at their interface residues. As these toxins lack crystallography structures, homology modeling using Modeller 9.11 led to the structural approximation for the E. coli producing heat-labile toxins. Interaction of modeled toxin subunits with proanthocyanidin, an antidiarrheal showed several strong hydrogen bonding interactions at the cost of minimized energy. The hits were subsequently characterized by molecular dynamics simulation studies to monitor their binding stabilities. This study looks into novel space where the ligand can choose the receptor preference not as a whole but as an individual subunit. Mutation at interface residues and interaction among subunits along with the binding of ligand to individual subunits would help to design a non-toxic labile toxin and also to improve the therapeutics.

  6. 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.

  7. Gene network interconnectedness and the generalized topological overlap measure

    Directory of Open Access Journals (Sweden)

    Horvath Steve

    2007-01-01

    Full Text Available Abstract Background Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. 1 can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness. Results We generalize the topological overlap measure from m = 1 step neighborhoods to m ≥ 2 step neighborhoods. This allows us to define the m-th order generalized topological overlap measure (GTOM by (i counting the number of m-step neighbors that a pair of nodes share and (ii normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis. Conclusion Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The m-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules.

  8. Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis.

    Science.gov (United States)

    Alanazi, Ibrahim; Ebrahimie, Esmaeil; Hoffmann, Peter; Adelson, David L

    2013-11-01

    A431 cells, derived from epidermoid carcinoma, overexpress the epidermal growth factor receptor (EGFR) and when treated with a high dose of EGF will undergo apoptosis. We exploited microarray and proteomics techniques and network prediction to study the regulatory mechanisms of EGF-induced apoptosis in A431 cells. We observed significant changes in gene expression in 162 genes, approximately evenly split between pro-apoptotic and anti-apoptotic genes and identified 30 proteins from the proteomic data that had either pro or anti-apoptotic annotation. Our correlation analysis of gene expression and proteome modeled a number of distinct sub-networks that are associated with the onset of apoptosis, allowing us to identify specific pathways and components. These include components of the interferon signalling pathway, and down stream components, including cytokines and suppressors of cytokine signalling. A central component of almost all gene expression sub-networks identified was TP53, which is mutated in A431 cells, and was down regulated. This down regulation of TP53 appeared to be correlated with proteomic sub-networks of cytoskeletal or cell adhesion components that might induce apoptosis by triggering cytochrome C release. Of the only three genes also differentially expressed as proteins, only serpinb1 had a known association with apoptosis. We confirmed that up regulation and cleavage of serpinb1 into L-DNAaseII was correlated with the induction of apoptosis. It is unlikely that a single pathway, but more likely a combination of pathways is needed to trigger EGF induced apoptosis in A431cells.

  9. 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.

  10. 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.

  11. Recombining overlapping BACs into single large BACs.

    Science.gov (United States)

    Kotzamanis, George; Kotsinas, Athanassios

    2015-01-01

    BAC clones containing the entire genomic region of a gene including the long-range regulatory elements are very useful for gene functional analysis. However, large genes often span more than the insert of a BAC clone, and single BACs covering the entire region of interest are not available. Here, we describe a general system for linking two or more overlapping BACs into a single clone. Two rounds of homologous recombination are used. In the first, the BAC inserts are subcloned into the pBACLink vectors. In the second, the two BACs are combined together. Multiple BACs in a contig can be combined by alternating use of the pBACLInk vectors, resulting in several BAC clones containing as much of the genomic region of a gene as required. Such BACs can then be used in gene expression studies and/or gene therapy applications.

  12. Solving Partial Differential Equations on Overlapping Grids

    Energy Technology Data Exchange (ETDEWEB)

    Henshaw, W D

    2008-09-22

    We discuss the solution of partial differential equations (PDEs) on overlapping grids. This is a powerful technique for efficiently solving problems in complex, possibly moving, geometry. An overlapping grid consists of a set of structured grids that overlap and cover the computational domain. By allowing the grids to overlap, grids for complex geometries can be more easily constructed. The overlapping grid approach can also be used to remove coordinate singularities by, for example, covering a sphere with two or more patches. We describe the application of the overlapping grid approach to a variety of different problems. These include the solution of incompressible fluid flows with moving and deforming geometry, the solution of high-speed compressible reactive flow with rigid bodies using adaptive mesh refinement (AMR), and the solution of the time-domain Maxwell's equations of electromagnetism.

  13. 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.

  14. 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.

  15. 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.

  16. Finding overlapping communities using seed set

    Science.gov (United States)

    Yang, Jin-Xuan; Zhang, Xiao-Dong

    2017-02-01

    The local optimization algorithm using seed set to find overlapping communities has become more and more a significant method, but it is a great challenge how to choose a good seed set. In this paper, a new method is proposed to achieve the choice of candidate seed sets, and yields a new algorithm to find overlapping communities in complex networks. By testing in real world networks and synthetic networks, this method can successfully detect overlapping communities and outperform other state-of-the-art overlapping community detection methods.

  17. Market positioning: the shifting effects of niche overlap

    NARCIS (Netherlands)

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

    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

  18. 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…

  19. Neurofibromatosis type 1 with overlap Turner syndrome and Klinefelter syndrome.

    Science.gov (United States)

    Hatipoglu, Nihal; Kurtoglu, Selim; Kendirci, Mustafa; Keskin, Mehmet; Per, Hüseyin

    2010-02-01

    Turner's syndrome is a sex chromosome disorder. Klinefelter's syndrome is one of the most severe genetic diseases. Neurofibromatosis is an autosomal dominant disorder characterized by cafe-au-lait spots and fibromatous tumors of the skin. In this article, we report the overlap of neurofibromatosis-1 with Turner and Klinefelter syndromes. Thus, these disorders might overlap within the same patient. Due to these cases, we suggest that each patient with Turner-like symptoms or Klinefelter's-like syndrome, be carefully examined for café au lait macules before the initiation of hormone replacement treatment.

  20. 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

  1. Presentation of dynamically overlapping auditory messages in user interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Papp, III, Albert Louis [Univ. of California, Davis, CA (United States)

    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

  2. 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.

  3. 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.

  4. 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.

  5. Piles, Tabs and Overlaps in Navigation among Documents

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Rønne; Hornbæk, Kasper Anders Søren

    2010-01-01

    documents worked well for tasks that involved visual features of the documents, but the utility of recency or stable ordering of documents was task dependent. Based on the results, we discuss the effects of spatial arrangement, visibility, and task-dependency, and suggest areas for future research......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...

  6. 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.

  7. Overlapping Community Detection by Online Cluster Aggregation

    CERN Document Server

    Kozdoba, Mark

    2015-01-01

    We present a new online algorithm for detecting overlapping communities. The main ingredients are a modification of an online k-means algorithm and a new approach to modelling overlap in communities. An evaluation on large benchmark graphs shows that the quality of discovered communities compares favorably to several methods in the recent literature, while the running time is significantly improved.

  8. Australia's National Research Collection: Overlap, Uniqueness, and Distribution

    Science.gov (United States)

    Genoni, Paul; Wright, Janette

    2011-01-01

    This paper reports on the results of an overlap study of Australian research library collections. The study used OCLC's WorldCat Collection Analysis software to mine data recording Australian holdings on the WorldCat database. The data is analysed according to the results obtained for six "groups" which represent various coalitions of…

  9. Quality Assurance in the Determination of Overlapping Peak Areas

    DEFF Research Database (Denmark)

    Christensen, L.H.; Heydorn, K.

    1987-01-01

    The ability of different computer programs to yield accurate peak areas in statistical control in the case of partially overlapping photopeaks has been tested by the Analysis of Precision. A modified Covell method, two commercially available peak-fitting programs from Nuclear Data and Ortec, and ...

  10. 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.

  11. 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.

  12. 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...

  13. Overlapping community detection in weighted networks via a Bayesian approach

    Science.gov (United States)

    Chen, Yi; Wang, Xiaolong; Xiang, Xin; Tang, Buzhou; Chen, Qingcai; Fan, Shixi; Bu, Junzhao

    2017-02-01

    Complex networks as a powerful way to represent complex systems have been widely studied during the past several years. One of the most important tasks of complex network analysis is to detect communities embedded in networks. In the real world, weighted networks are very common and may contain overlapping communities where a node is allowed to belong to multiple communities. In this paper, we propose a novel Bayesian approach, called the Bayesian mixture network (BMN) model, to detect overlapping communities in weighted networks. The advantages of our method are (i) providing soft-partition solutions in weighted networks; (ii) providing soft memberships, which quantify 'how strongly' a node belongs to a community. Experiments on a large number of real and synthetic networks show that our model has the ability in detecting overlapping communities in weighted networks and is competitive with other state-of-the-art models at shedding light on community partition.

  14. Toxic epidermal necrolysis, DRESS, AGEP: Do overlap cases exist?

    Directory of Open Access Journals (Sweden)

    Bouvresse Sophie

    2012-09-01

    Full Text Available Abstract Background Severe cutaneous adverse reactions to drugs (SCARs include acute generalized exanthematous pustulosis (AGEP, drug reaction with eosinophilia and systemic symptoms (DRESS and epidermal necrolysis (Stevens-Johnson syndrome–toxic epidermal necrolysis [SJS-TEN]. Because of the varied initial presentation of such adverse drug reactions, diagnosis may be difficult and suggests overlap among SCARs. Overlapping SCARs are defined as cases fulfilling the criteria for definite or probable diagnosis of at least 2 ADRs according to scoring systems for AGEP, DRESS and SJS-TEN. We aimed to evaluate the prevalence of overlap among SCARs among cases in the referral hospital in France. Methods We retrospectively analyzed data for 216 patients hospitalized in the referral centre over 7 years with a discharge diagnosis of AGEP (n = 45, DRESS (n = 47, SJS-TEN (n = 80 or “drug rash” (n = 44. Each case with detailed clinical data and a skin biopsy specimen was scored for AGEP, DRESS and SJS-TEN by use of diagnostic scores elaborated by the RegiSCAR group. Results In total, 45 of 216 cases (21% had at least 2 possible diagnoses: 35 had a single predominant diagnosis (definite or probable, 7 had several possible diagnoses and 3 (2.1% of 145 confirmed SCARs were overlap SCARs. Conclusions Despite ambiguities among SCARs, confirmed overlap cases are rare. This study did not avoid pitfalls linked to its retrospective nature and selection bias. In the acute stage of disease, early identification of severe ADRs can be difficult because of clinical or biologic overlapping features and missing data on histology, biology and evolution. Retrospectively analyzing cases by use of diagnostic algorithms can lead to reliable discrimination among AGEP, DRESS and SJS-TEN.

  15. 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)

  16. 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 ...

  17. 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.

  18. Resequencing and association analysis of coding regions at twenty candidate genes suggest a role for rare risk variation at AKAP9 and protective variation at NRXN1 in schizophrenia susceptibility.

    Science.gov (United States)

    Suárez-Rama, José Javier; Arrojo, Manuel; Sobrino, Beatriz; Amigo, Jorge; Brenlla, Julio; Agra, Santiago; Paz, Eduardo; Brión, María; Carracedo, Ángel; Páramo, Mario; Costas, Javier

    2015-01-01

    A fraction of genetic risk to develop schizophrenia may be due to low-frequency variants. This multistep study attempted to find low-frequency variants of high effect at coding regions of eleven schizophrenia susceptibility genes supported by genome-wide association studies (GWAS) and nine genes for the DISC1 interactome, a susceptibility gene-set. During the discovery step, a total of 125 kb per sample were resequenced in 153 schizophrenia patients and 153 controls from Galicia (NW Spain), and the cumulative role of low-frequency variants at a gene or at the DISC1 gene-set were analyzed by burden and variance-based tests. Relevant results were meta-analyzed when appropriate data were available. In addition, case-only putative damaging variants were genotyped in a further 419 cases and 398 controls. The discovery step revealed a protective effect of rare missense variants at NRXN1, a result supported by meta-analysis (OR = 0.67, 95% CI: 0.47-0.94, P = 0.021, based on 3848 patients and 3896 controls from six studies). The follow-up step based on case-only putative damaging variants revealed a promising risk variant at AKAP9. This variant, K873R, reached nominal significance after inclusion of 240 additional Spanish controls from databases. The variant, located in an ADCY2 binding region, is absent from large public databases. Interestingly, GWAS revealed an association between common ADCY2 variants and bipolar disorder, a disorder with considerable genetic overlap with schizophrenia. These data suggest a role of rare missense variants at NRXN1 and AKAP9 in schizophrenia susceptibility, probably related to alteration of the excitatory/inhibitory synaptic balance, deserving further investigation.

  19. 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.

  20. 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...

  1. Theories of Suggestion.

    Science.gov (United States)

    Brown, W

    1928-02-01

    The word "suggestion" has been used in educational, scientific and medical literature in slightly different senses. In psychological medicine the use of suggestion has developed out of the earlier use of hypnotic influence.Charcot defined hypnosis as an artificial hysteria, Bernheim as an artificially increased suggestibility. The two definitions need to be combined to give an adequate account of hypnosis. Moreover, due allowance should be made for the factors of dissociation and of rapport in hypnotic phenomena.The relationships between dissociation, suggestibility, and hypnotizability.Theories of suggestion propounded by Pierre Janet, Freud, McDougall, Pawlow and others. Ernest Jones's theory of the nature of auto-suggestion. Janet explains suggestion in terms of ideo-motor action in which the suggested idea, because of the inactivity of competing ideas, produces its maximum effect. Freud explains rapport in terms of the sex instinct "inhibited in its aim" (transference) and brings in his distinction of "ego" and "ego-ideal" (or "super-ego") to supplement the theory. Jones explains auto-suggestion in terms of narcissism. McDougall explains hypnotic suggestion in terms of the instinct of self-abasement. But different instincts may supply the driving power to produce suggestion-effects in different circumstances. Such instincts as those of self-preservation (fear) and gregariousness may play their part. Auto-suggestion as a therapeutic factor is badly named. It supplements, but does not supplant the will, and makes complete volition possible.

  2. 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.

  3. Overlapping networks engaged during spoken language production and its cognitive control.

    Science.gov (United States)

    Geranmayeh, Fatemeh; Wise, Richard J S; Mehta, Amrish; Leech, Robert

    2014-06-25

    Spoken language production is a complex brain function that relies on large-scale networks. These include domain-specific networks that mediate language-specific processes, as well as domain-general networks mediating top-down and bottom-up attentional control. Language control is thought to involve a left-lateralized fronto-temporal-parietal (FTP) system. However, these regions do not always activate for language tasks and similar regions have been implicated in nonlinguistic cognitive processes. These inconsistent findings suggest that either the left FTP is involved in multidomain cognitive control or that there are multiple spatially overlapping FTP systems. We present evidence from an fMRI study using multivariate analysis to identify spatiotemporal networks involved in spoken language production in humans. We compared spoken language production (Speech) with multiple baselines, counting (Count), nonverbal decision (Decision), and "rest," to pull apart the multiple partially overlapping networks that are involved in speech production. A left-lateralized FTP network was activated during Speech and deactivated during Count and nonverbal Decision trials, implicating it in cognitive control specific to sentential spoken language production. A mirror right-lateralized FTP network was activated in the Count and Decision trials, but not Speech. Importantly, a second overlapping left FTP network showed relative deactivation in Speech. These three networks, with distinct time courses, overlapped in the left parietal lobe. Contrary to the standard model of the left FTP as being dominant for speech, we revealed a more complex pattern within the left FTP, including at least two left FTP networks with competing functional roles, only one of which was activated in speech production.

  4. Sterol content analysis suggests altered eburicol 14alpha-demethylase (CYP51) activity in isolates of Mycosphaerella graminicola adapted to azole fungicides.

    Science.gov (United States)

    Bean, Tim P; Cools, Hans J; Lucas, John A; Hawkins, Nathaniel D; Ward, Jane L; Shaw, Michael W; Fraaije, Bart A

    2009-06-01

    The recent decline in the effectiveness of some azole fungicides in controlling the wheat pathogen Mycosphaerella graminicola has been associated with mutations in the CYP51 gene encoding the azole target, the eburicol 14alpha-demethylase (CYP51), an essential enzyme of the ergosterol biosynthesis pathway. In this study, analysis of the sterol content of M. graminicola isolates carrying different variants of the CYP51 gene has revealed quantitative differences in sterol intermediates, particularly the CYP51 substrate eburicol. Together with CYP51 gene expression studies, these data suggest that mutations in the CYP51 gene impact on the activity of the CYP51 protein.

  5. 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

    Background: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated...... colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n = 8), quiescent UC (n = 9), and with irritable bowel...... 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...

  6. Analysis of a herpetofaunal community from an altered marshy area in Sicily; with special remarks on habitat use (niche breadth and overlap), relative abundance of lizards and snakes, and the correlation between predator abundance and tail loss in lizards

    NARCIS (Netherlands)

    Luiselli, L.; Angelici, F.M.; Di Vittorio, M.; Spinnato, A.; Politano, E.

    2005-01-01

    A field survey was conducted in a highly degraded barren environment in Sicily in order to investigate herpetofaunal community composition and structure, habitat use (niche breadth and overlap) and relative abundance of a snake predator and two species of lizard prey. The site was chosen because it

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance.

    Science.gov (United States)

    Zhou, Tao; Liu, Shikai; Geng, Xin; Jin, Yulin; Jiang, Chen; Bao, Lisui; Yao, Jun; Zhang, Yu; Zhang, Jiaren; Sun, Luyang; Wang, Xiaozhu; Li, Ning; Tan, Suxu; Liu, Zhanjiang

    2017-02-01

    Disease problems cause major economic losses for the aquaculture industries. In catfish, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem, causing tens of millions of dollars of annual economic losses. In this study, we conducted a genome-wide association study to determine quantitative trait loci (QTL) for resistance against ESC using an interspecific hybrid system. Five hundred fish were used in the analysis and 192 phenotypic extremes were used for genotyping with the catfish 250K SNP arrays. A genomic region on linkage group (LG) 1 was found significantly associated with ESC disease resistance. In addition, two suggestively associated QTL for ESC resistance were identified on LG 12 and LG 16. The nlrc3 duplicates were identified within all the three QTL, suggesting their importance in association with the QTL. Within the significant QTL on LG 1, 16 genes with known functions in immunity were identified. Of particular interest is the nck1 gene nearby the most significantly associated SNP. Nck1 was known to function as an adaptor to facilitating the pathogenesis of enteropathogenic Escherichia coli (EPEC) in humans. E. ictaluri and EPEC pathogens belong to the same bacterial family and share many common characteristics. The fact that nck1 is mapped in the QTL and that it was significantly upregulated in channel catfish intestine after ESC challenge suggested its candidacy of being involved in resistance/susceptibility of ESC.

  12. 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

  13. 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

  14. Schwinger model simulations with dynamical overlap fermions

    CERN Document Server

    Bietenholz, W; Volkholz, J

    2007-01-01

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate Sigma vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain -- for the very light fermion masses -- values for $\\Sigma$ that follow closely the analytical predictions in the continuum.

  15. Schwinger model simulations with dynamical overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Bietenholz, W. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Shcheredin, S. [Bielefeld Univ. (Germany). Fakultaet fuer Physik; Volkholz, J. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik

    2007-11-15

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate {sigma} vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain - for the very light fermion masses - values for {sigma} that follow closely the analytical predictions in the continuum. (orig.)

  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. 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...

  19. 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.

  20. Using character overlap to improve language transformation

    NARCIS (Netherlands)

    Wubben, S.; Krahmer, E.; Bosch, A.P.J. van den

    2013-01-01

    Language transformation can be defined as translating between diachronically distinct language variants. We investigate the transformation of Middle Dutch into Modern Dutch by means of machine translation. We demonstrate that by using character overlap the performance of the machine translation proce

  1. 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.

  2. Current status of Dynamical Overlap project

    CERN Document Server

    Cundy, N

    2006-01-01

    We discuss the adaptation of the Hybrid Monte Carlo algorithm to overlap fermions. We derive a method which can be used to account for the delta function in the fermionic force caused by the differential of the sign function. We discuss the algoritmic difficulties that have been overcome, and mention those that still need to be solved.

  3. Chromosome Segregation: Organizing Overlap at the Midzone

    NARCIS (Netherlands)

    Janson, M.E.; Tran, P.T.

    2008-01-01

    Sets of overlapping microtubules support the segregation of chromosomes by linking the poles of mitotic spindles. Recent work examines the effect of putting these linkages under pressure by the activation of dicentric chromosomes and sheds new light on the structural role of several well-known spind

  4. 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.

  5. 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…

  6. Multilocus sequence analysis of the marine bacterial genus Tenacibaculum suggests parallel evolution of fish pathogenicity and endemic colonization of aquaculture systems.

    Science.gov (United States)

    Habib, Christophe; Houel, Armel; Lunazzi, Aurélie; Bernardet, Jean-François; Olsen, Anne Berit; Nilsen, Hanne; Toranzo, Alicia E; Castro, Nuria; Nicolas, Pierre; Duchaud, Eric

    2014-09-01

    The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the species T. maritimum constitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoring Tenacibaculum infections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related to T. dicentrarchi, a recently described species.

  7. Some Suggestions to Rock and Mineral Analysis (the 4th Edition)%对岩石矿物分析第四版一书的建议

    Institute of Scientific and Technical Information of China (English)

    郑大中; 赵芳芳; 陈琳玲; 郑若锋

    2013-01-01

    对书中一些特殊样品的制备方法提出建议;对切乔特经验缩分公式的科学性提出质疑,建议吐故纳新;指出HF-HCIO4法测二氧化硅存在严重的缺陷,建议用HF、H2SO4-V2O5法代替;指出酸溶-亚铁容量法测钒主要反应式不当,建议更正;在稀王水、稀盐酸介质中,活性炭吸附的金是单质金(为还原吸附),而不是AuCl4-,建议改正。%This paper makes some suggestions to Rock and Mineral Analysis (the 4th Edition). Query the Qeqott formula. Make a suggestion on determination of SiO2 by HF and H2SO4-V2O5 other than HF-HCIO4. The main chemical reaction formula for determination of Vanadium by acid pasting and ferrous ammonium sulfate volumetry should be changed. Au adsorbed by activated carbon in dilute hydrochloric acid and dilute aqua regia is Au as simple substance other than AuCl4-.

  8. 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.

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

    Science.gov (United States)

    Das, Palashpriya; Yang, Xin-Ping; Ma, Luyan Z

    2014-01-01

    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 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 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 affected the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In line with this finding, rhamnolipids of IMP67 also reduced the MIC of some antibiotics against bacteria, suggesting their synergistic role with the antibiotics.

  10. 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.

  11. 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-

  12. Genome-wide gene expression analysis suggests an important role of hypoxia in the pathogenesis of endemic osteochondropathy Kashin-Beck disease.

    Directory of Open Access Journals (Sweden)

    Feng Zhang

    Full Text Available Kashin-Beck Disease (KBD is an endemic osteochondropathy, the pathogenesis of which remains unclear now. In this study, we compared gene expression profiles of articular cartilage derived respectively from KBD patients and normal controls. Total RNA were isolated, amplified, labeled and hybridized to Agilent human 1A 22 k whole genome microarray chip. qRT-PCR was conducted to validate our microarray data. We detected 57 up-regulated genes (ratios ≥2.0 and 24 down-regulated genes (ratios ≤0.5 in KBD cartilage. To further identify the key genes involved in the pathogenesis of KBD, Bayesian analysis of variance for microarrays (BAM software was applied and identified 12 potential key genes with an average ratio 6.64, involved in apoptosis, metabolism, cytokine & growth factor and cytoskeleton & cell movement. Gene Set Enrichment Analysis (GSEA software was used to identify differently expressed gene ontology categories and pathways. GSEA found that a set of apoptosis, hypoxia and mitochondrial function related gene ontology categories and pathways were significantly up-regulated in KBD compared to normal controls. Based on the results of this study, we suggest that chronic hypoxia-induced mitochondrial damage and apoptosis might play an important role in the pathogenesis of KBD. Our efforts may help to understand the pathogenesis of KBD as well as other osteoarthrosis with similar articular cartilage lesions.

  13. 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.

  14. 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.

  15. A Genome-Wide SNP Linkage Analysis Suggests a Susceptibility Locus on 6p21 for Ankylosing Spondylitis and Inflammatory Back Pain Trait

    Science.gov (United States)

    Zhang, Yanli; Liao, Zetao; Wei, Qiujing; Pan, Yunfeng; Wang, Xinwei; Cao, Shuangyan; Guo, Zishi; Wu, Yuqiong; Rong, Ju; Jin, Ou; Xu, Manlong; Gu, Jieruo

    2016-01-01

    Objectives To screen susceptibility loci for ankylosing spondylitis (AS) using an affected-only linkage analysis based on high-density single nucleotide polymorphisms (SNPs) in a genome-wide manner. Patients and Methods AS patients from ten families with Cantonese origin of China were enrolled in the study. Blood samples were genotyped using genomic DNA derived from peripheral blood leukocytes by Illumina HumanHap 610-Quad SNP Chip. Genotype data were generated using the Illumina BeadStudio 3.2 software. PLINK package was used to remove non-autosomal SNPs and to further eliminate markers of typing errors. An affected-only linkage analysis was carried out using both non-parametric and parametric linkage analyses, as implemented in MERLIN. Result Seventy-eight AS patients (48 males and 30 females, mean age: 39±16 years) were enrolled in the study. The mean age of onset was 23±10 years and mean duration of disease was 16.7±12.2 years. Iritis (2/76, 2.86%), dactylitis (5/78, 6.41%), hip joint involvement (9/78, 11.54%), peripheral arthritis (22/78, 28.21%), inflammatory back pain (IBP) (69/78, 88.46%) and HLA-B27 positivity (70/78, 89.74%) were observed in these patients. Using non-parameter linkage analysis, we found one susceptibility locus for AS, IBP and HLA-B27 in 6p21 respectively, spanning about 13.5Mb, 20.9Mb and 21.2Mb, respectively No significant results were found in the other clinical trait groups including dactylitis, hip involved and arthritis. The identical susceptibility locus region spanning above 9.44Mb was detected in AS IBP and HLA-B27 by the parametric linkage analysis. Conclusion Our genome-wide SNP linkage analysis in ten families with ankylosing spondylitis suggests a susceptibility locus on 6p21 in AS, which is a risk locus for IBP in AS patients. PMID:27973620

  16. 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.

  17. 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.

  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. 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 .

  1. 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

  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. Securely measuring the overlap between private datasets with cryptosets.

    Science.gov (United States)

    Swamidass, S Joshua; Matlock, Matthew; Rozenblit, Leon

    2015-01-01

    Many scientific questions are best approached by sharing data--collected by different groups or across large collaborative networks--into a combined analysis. Unfortunately, some of the most interesting and powerful datasets--like health records, genetic data, and drug discovery data--cannot be freely shared because they contain sensitive information. In many situations, knowing if private datasets overlap determines if it is worthwhile to navigate the institutional, ethical, and legal barriers that govern access to sensitive, private data. We report the first method of publicly measuring the overlap between private datasets that is secure under a malicious model without relying on private protocols or message passing. This method uses a publicly shareable summary of a dataset's contents, its cryptoset, to estimate its overlap with other datasets. Cryptosets approach "information-theoretic" security, the strongest type of security possible in cryptography, which is not even crackable with infinite computing power. We empirically and theoretically assess both the accuracy of these estimates and the security of the approach, demonstrating that cryptosets are informative, with a stable accuracy, and secure.

  4. 基于上海市嘉定区交通事故的小偏置碰撞特征分析%Characteristic analysis of small overlap crash based on road trafifc accidents in Jiading district of Shanghai city

    Institute of Scientific and Technical Information of China (English)

    王宏雁; 贾志功; 陈君毅; 何宇桐

    2014-01-01

    总结了小偏置碰撞在这些事故中的基本特征。从上海市嘉定区的交通事故统计集合中,采集了其中45辆小偏置事故车辆和车上57名前排乘员的信息,分析了事故的实际道路交通状况、车损情况、乘员伤情和运动响应4个方面。结果表明:87%的事故车辆并未明显侵入到座舱;88%的乘员未伤或轻伤;碰撞后车辆的爆胎和旋转响应对乘员伤情有显著影响。这可为将来制定与车辆小偏置碰撞相关的中国试验规范和中国评估标准提供数据支持。%The main characteristics of smal overlap crash were summarized with the trafifc accident data colected from the statistics in Jiading District of Shanghai. 45 vehicles in smal overlap crashes and 57 injured occupants in front-row seats were analyzed based on trafifc environments, vehicle damages, occupant injuries and motion responses. The results show that 87% of vehicle intrusions does not obviously come into driving space with 88% of occupants lightly injured or not injured, and with tire-punctures and vehicle-rotations obviously affecting occupant injuries after colisions. Therefore, these results provide support to the test speciifcations and the evaluation criteria for smal overlap crash in China.

  5. 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...

  6. 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.

  7. FISH and array-CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions.

    Science.gov (United States)

    Dijkhuizen, Trijnie; van Essen, Ton; van der Vlies, Pieter; Verheij, Joke B G M; Sikkema-Raddatz, Birgit; van der Veen, Anneke Y; Gerssen-Schoorl, Klasien B J; Buys, Charles H C M; Kok, Klaas

    2006-11-15

    Imbalances of 3p telomeric sequences cause 3p- and trisomy 3p syndrome, respectively, showing distinct, but also shared clinical features. No causative genes have been identified in trisomy 3p patients, but for the 3p- syndrome, there is growing evidence that monosomy for one or more of four genes at 3pter, CHL1, CNTN4, CRBN, and MEGAP/srGAP3, may play a causative role. We describe here an analysis of a complex chromosome 3p aberration in a severely mentally retarded patient that revealed two adjacent segments with different copy number gains and a distal deletion. The deletion in this patient included the loci for CHL1, CNTN4, and CRBN, and narrowed the critical segment associated with the 3p- syndrome to 1.5 Mb, including the loci for CNTN4 and CRBN. We speculate that the deletion contributes more to this patient's phenotype than the gains that were observed. We suggest that 3p- syndrome associated features are primarily caused by loss of CNTN4 and CRBN, with loss of CHL1 probably having an additional detrimental effect on the cognitive functioning of the present patient.

  8. Overlap Removal Methods for Data Projection Algorithms

    OpenAIRE

    Spicker, Marc

    2011-01-01

    Projection algorithms map high dimensional data points to lower dimensions. However, when adding arbitrary shaped objects as representatives for these data points, they may intersect. The positions of these representatives have to be modi ed in order to remove existing overlaps. There are multiple algorithms designed to deal with this layout adjustment problem, which lead to very di erent results. These adjustment strategies are evaluated according to di erent measures for comparison: euclide...

  9. 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.

  10. Analysis of Transformation Mechanism and Gear Ratio on Overlap-Connect Combinational Gear Train%迭连组合轮系的转化机构及传动比分析

    Institute of Scientific and Technical Information of China (English)

    张冬梅

    2013-01-01

    迭连组合轮系是将附加的行星式轮系或组合轮系以迭连方式装置在基础轮系上,构成迭连组合轮系。本文分析以2KH-WN型行星轮系为基础轮系,分别以单一周转轮系、并联轮系、反馈轮系作为迭连子轮系组成迭连组合轮系。其转化机构有串联式、并联式、反馈式,组合轮系的传动比以行星轮系为基础计算。%The Overlap-Connect combinational gear train is fixed on the base gear train, which connect attached Epicylic Gear Train or combined each other. In this paper,the base gear train is 2KH-WN Epicylic Gear Train. This Overlap-Connect combinational gear train take single turenover gear train or parallel gear train or feedback gear train as son gear train. The form of transformation mechanism is series, parallel or feedback. The calculation of combinational gear ratio is based on Epicylic Gear Train.

  11. 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.

  12. Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria.

    Science.gov (United States)

    Krupovic, Mart; Forterre, Patrick; Bamford, Dennis H

    2010-03-19

    Tailed double-stranded DNA viruses (order Caudovirales) represent the dominant morphotype among viruses infecting bacteria. Analysis and comparison of complete genome sequences of tailed bacterial viruses provided insights into their origin and evolution. Structural and genomic studies have unexpectedly revealed that tailed bacterial viruses are evolutionarily related to eukaryotic herpesviruses. Organisms from the third domain of life, Archaea, are also infected by viruses that, in their overall morphology, resemble tailed viruses of bacteria. However, high-resolution structural information is currently unavailable for any of these viruses, and only a few complete genomes have been sequenced so far. Here we identified nine proviruses that are clearly related to tailed bacterial viruses and integrated into chromosomes of species belonging to four different taxonomic orders of the Archaea. This more than doubled the number of genome sequences available for comparative studies. Our analyses indicate that highly mosaic tailed archaeal virus genomes evolve by homologous and illegitimate recombination with genomes of other viruses, by diversification, and by acquisition of cellular genes. Comparative genomics of these viruses and related proviruses revealed a set of conserved genes encoding putative proteins similar to virion assembly and maturation, as well as genome packaging proteins of tailed bacterial viruses and herpesviruses. Furthermore, fold prediction and structural modeling experiments suggest that the major capsid proteins of tailed archaeal viruses adopt the same topology as the corresponding proteins of tailed bacterial viruses and eukaryotic herpesviruses. Data presented in this study strongly support the hypothesis that tailed viruses infecting archaea share a common ancestry with tailed bacterial viruses and herpesviruses.

  13. Comparative analysis of protocadherin-11 X-linked expression among postnatal rodents, non-human primates, and songbirds suggests its possible involvement in brain evolution.

    Directory of Open Access Journals (Sweden)

    Eiji Matsunaga

    Full Text Available BACKGROUND: Protocadherin-11 is a cell adhesion molecule of the cadherin superfamily. Since, only in humans, its paralog is found on the Y chromosome, it is expected that protocadherin-11X/Y plays some role in human brain evolution or sex differences. Recently, a genetic mutation of protocadherin-11X/Y was reported to be associated with a language development disorder. Here, we compared the expression of protocadherin-11 X-linked in developing postnatal brains of mouse (rodent and common marmoset (non-human primate to explore its possible involvement in mammalian brain evolution. We also investigated its expression in the Bengalese finch (songbird to explore a possible function in animal vocalization and human language faculties. METHODOLOGY/PRINCIPAL FINDINGS: Protocadherin-11 X-linked was strongly expressed in the cerebral cortex, hippocampus, amygdala and brainstem. Comparative analysis between mice and marmosets revealed that in certain areas of marmoset brain, the expression was clearly enriched. In Bengalese finches, protocadherin-11 X-linked was expressed not only in nuclei of regions of the vocal production pathway and the tracheosyringeal hypoglossal nucleus, but also in areas homologous to the mammalian amygdala and hippocampus. In both marmosets and Bengalese finches, its expression in pallial vocal control areas was developmentally regulated, and no clear expression was seen in the dorsal striatum, indicating a similarity between songbirds and non-human primates. CONCLUSIONS/SIGNIFICANCE: Our results suggest that the enriched expression of protocadherin-11 X-linked is involved in primate brain evolution and that some similarity exists between songbirds and primates regarding the neural basis for vocalization.

  14. 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.

  15. Scalar condensate and light quark masses from overlap fermions

    OpenAIRE

    Hernandez, Pilar; Jansen, Karl; Lellouch, Laurent; Wittig, Hartmut

    2001-01-01

    We have studied pseudoscalar correlation functions computed using the overlap operator. Within the accuracy of our calculation we find that the quark mass dependence agrees with the prediction of lowest-order Chiral Perturbation Theory (ChPT) for quark masses in the range of m ~ m_s/2-2m_s. We present the results of an analysis which assumes lowest-order ChPT to be valid to extract the low-energy constants Sigma and f_P, as well as the strange quark mass. Non-perturbative renormalization is i...

  16. Cumulative overlap distribution function in realistic spin glasses

    Science.gov (United States)

    Billoire, A.; Maiorano, A.; Marinari, E.; Martin-Mayor, V.; Yllanes, D.

    2014-09-01

    We use a sample-dependent analysis, based on medians and quantiles, to analyze the behavior of the overlap probability distribution of the Sherrington-Kirkpatrick and 3D Edwards-Anderson models of Ising spin glasses. We find that this approach is an effective tool to distinguish between replica symmetry breaking-like and droplet-like behavior of the spin-glass phase. Our results are in agreement with a replica symmetry breaking-like behavior for the 3D Edwards-Anderson model.

  17. 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.

  18. 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

  19. 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.

  20. 抗疟疾中药专利申请现状分析和建议%Analysis and Suggestions of Patent TCM for Anti-malaria

    Institute of Scientific and Technical Information of China (English)

    吕茂平; 刘瑞华

    2016-01-01

    This article concluded application number of patent TCM, law condition, applicant distribution, patent types, authorized patent condition and covered TCM types by searching patent applications about patent TCM for anti-malaria in Chinese patent retrieval system. By means of general analysis on patent applications about patent TCM for anti-malaria, this article believed that some problems existed in the application, such as small quantity of application because of lack of attention, poor-quality application (few authorized patent), weak basic research foundation for anti-malaria TCM, and few profound research. Therefore, it proposed the suggestions of enhancing patent portfolio, improving innovation ability and strengthening material basis research, with a purpose to promote the development and research of anti-malaria TCM.%本文通过检索中国专利检索系统公开的抗疟疾中药发明专利申请,总结了我国目前抗疟疾中药专利申请的数量、法律状态、申请人分布、专利类型、授权专利状况以及涉及的中药种类。通过对抗疟疾中药专利申请的总体分析认为,抗疟疾中药专利申请存在由于关注度不够因而申请数量少、专利申请质量低,尤其表现为授权专利少以及对抗疟疾中药基础研究缺乏、深入研究不足等问题,相应从加强专利布局、提高创新能力和加强物质基础研究方面提出了促进我国的抗疟疾中药研发的建议。

  1. Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

    Directory of Open Access Journals (Sweden)

    Casey R Richardson

    Full Text Available BACKGROUND: MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery. PRINCIPAL FINDINGS: We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes. CONCLUSIONS: Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non

  2. 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

  3. 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.

  4. 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.

  5. THE PHASE-OFFSET OVERLAPPED WAVE TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    Liang Dequn; Liang Weihua; Sun Changnian

    2003-01-01

    A new digital communication technology based on the Phase-Offset Overlapped Waves (POOW) has been introduced in this letter. The waves can be considered as a special multicarrier different from traditional ones. The sub-waves in a coded word's period of the POOW are sine waves and have the same frequencies, but different starting phases. The most important characteristic is that these sub-waves are the piecewise functions and not orthogonal in a code word period. The decoding can be implemented by solving a linear equation group.This code has very high efficiency and thus the data transmission rate is increased greatly.

  6. Recombining overlapping BACs into a single larger BAC

    Directory of Open Access Journals (Sweden)

    Huxley Clare

    2004-01-01

    Full Text Available Abstract Background BAC clones containing entire mammalian genes including all the transcribed region and long range controlling elements are very useful for functional analysis. Sequenced BACs are available for most of the human and mouse genomes and in many cases these contain intact genes. However, large genes often span more than one BAC, and single BACs covering the entire region of interest are not available. Here we describe a system for linking two or more overlapping BACs into a single clone by homologous recombination. Results The method was used to link a 61-kb insert carrying the final 5 exons of the human CFTR gene onto a 160-kb BAC carrying the first 22 exons. Two rounds of homologous recombination were carried out in the EL350 strain of bacteria which can be induced for the Red genes. In the first round, the inserts of the two overlapping BACs were subcloned into modified BAC vectors using homologous recombination. In the second round, the BAC to be added was linearised with the very rare-cutting enzyme I-PpoI and electroporated into recombination efficient EL350 bacteria carrying the other BAC. Recombined BACs were identified by antibiotic selection and PCR screening and 10% of clones contained the correctly recombined 220-kb BAC. Conclusion The system can be used to link the inserts from any overlapping BAC or PAC clones. The original orientation of the inserts is not important and desired regions of the inserts can be selected. The size limit for the fragments recombined may be larger than the 61 kb used here and multiple BACs in a contig could be combined by alternating use of the two pBACLink vectors. This system should be of use to many investigators wishing to carry out functional analysis on large mammalian genes which are not available in single BAC clones.

  7. 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.

  8. Heterogeneity of asthma–COPD overlap syndrome

    Science.gov (United States)

    Joo, Hyonsoo; Han, Deokjae; Lee, Jae Ha; Rhee, Chin Kook

    2017-01-01

    Many patients suffering from asthma or COPD have overlapping features of both diseases. However, a phenotypical approach for evaluating asthma–COPD overlap syndrome (ACOS) has not been established. In this report, we examined the phenotypes in patients with ACOS. Patients diagnosed with ACOS between 2011 and 2015 were identified and classified into four phenotype groups. Group A was composed of patients who smoked <10 pack years and had blood eosinophil counts ≥300. Group B was composed of patients who smoked <10 pack years and had blood eosinophil counts <300. Group C was composed of patients who smoked ≥10 pack years and had blood eosinophil counts ≥300. Group D was composed of patients who smoked <10 pack years and had blood eosinophil counts <300. Clinical characteristics were analyzed and compared among groups. Comparisons were made among 103 ACOS patients. Patients in group D were oldest, while patients in group A were youngest. There were relatively more female patients in groups A and B; the majority of patients in groups C and D were male. The degree of airflow obstruction was most severe in group C. The rate of being free of severe exacerbation was significantly lower in group C than in the other groups. In this study, each ACOS phenotype showed different characteristics. The proportion of patients free of severe exacerbation differed significantly among groups. At this time, further studies on the phenotypes of ACOS are required.

  9. Adaptive overlapped sub-blocks contrast enhancement

    Science.gov (United States)

    Chen, Anqiu; Yuan, Fei; Liu, Jing; Liu, Siqi; Li, An; Zheng, Zhenrong

    2016-09-01

    In this paper, an overlapped sub-block gray-level average method for contrast enhancement is presented. The digital image correction of uneven illumination under microscope transmittance is a problem in image processing, also sometimes the image in the dark place need to correct the uneven problem. A new correction method was proposed based on the mask method and sub-blocks gray-level average method because Traditional mask method and background fitting method are restricted due to application scenarios, and the corrected image brightness is low by using background fitting method, so it has some limitations of the application. In this paper, we introduce a new method called AOSCE for image contrast enhancement. The image is divided into many sub-blocks which are overlapped, calculate the average gray-level of the whole image as M and the calculate the average gray-level of each one as mi, next for each block it can get d = mi - m, each block minus d to get a new image, and then get the minimum gray-level of each block into a matrix DD to get the background, and use bilinearity to get the same scale of the image. over fitting the image in matlab in order to get smoother image, then minus the background to get the contrast enhancement image.

  10. 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.

  11. Distinct and Overlapping Sarcoma Subtypes Initiated from Muscle Stem and Progenitor Cells

    Directory of Open Access Journals (Sweden)

    Jordan M. Blum

    2013-11-01

    Full Text Available Rhabdomyosarcoma (RMS is the most common soft tissue sarcoma in children, whereas undifferentiated pleomorphic sarcoma (UPS is one of the most common soft tissue sarcomas diagnosed in adults. To investigate the myogenic cell(s of origin of these sarcomas, we used Pax7-CreER and MyoD-CreER mice to transform Pax7+ and MyoD+ myogenic progenitors by expressing oncogenic KrasG12D and deleting Trp53 in vivo. Pax7-CreER mice developed RMS and UPS, whereas MyoD-CreER mice developed UPS. Using gene set enrichment analysis, RMS and UPS each clustered specifically within their human counterparts. These results suggest that RMS and UPS have distinct and overlapping cells of origin within the muscle lineage. Taking them together, we have established mouse models of soft tissue sarcoma from muscle stem and progenitor cells.

  12. 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

  13. Spatial overlap in a solitary carnivore: support for the land tenure, kinship or resource dispersion hypotheses?

    Science.gov (United States)

    Elbroch, L Mark; Lendrum, Patrick E; Quigley, Howard; Caragiulo, Anthony

    2016-03-01

    There are several alternative hypotheses about the effects of territoriality, kinship and prey availability on individual carnivore distributions within populations. The first is the land-tenure hypothesis, which predicts that carnivores regulate their density through territoriality and temporal avoidance. The second is the kinship hypothesis, which predicts related individuals will be clumped within populations, and the third is the resource dispersion hypothesis, which suggests that resource richness may explain variable sociality, spatial overlap or temporary aggregations of conspecifics. Research on the socio-spatial organization of animals is essential in understanding territoriality, intra- and interspecific competition, and contact rates that influence diverse ecology, including disease transmission between conspecifics and courtship behaviours. We explored these hypotheses with data collected on a solitary carnivore, the cougar (Puma concolor), from 2005 to 2012 in the Southern Yellowstone Ecosystem, Wyoming, USA. We employed 27 annual home ranges for 13 cougars to test whether home range overlap was better explained by land tenure, kinship, resource dispersion or some combination of the three. We found support for both the land tenure and resource dispersion hypotheses, but not for kinship. Cougar sex was the primary driver explaining variation in home range overlap. Males overlapped significantly with females, whereas the remaining dyads (F-F, M-M) overlapped significantly less. In support for the resource dispersion hypothesis, hunting opportunity (the probability of a cougar killing prey in a given location) was often higher in overlapping than in non-overlapping portions of cougar home ranges. In particular, winter hunt opportunity rather than summer hunt opportunity was higher in overlapping portions of female-female and male-female home ranges. Our results may indicate that solitary carnivores are more tolerant of sharing key resources with unrelated

  14. 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.

  15. 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。

  16. Omega: an Overlap-graph de novo Assembler for Meta-genomics

    Energy Technology Data Exchange (ETDEWEB)

    Haider, Bahlul [ORNL; Ahn, Tae-Hyuk [ORNL; Bushnell, Brian [U.S. Department of Energy, Joint Genome Institute; Chai, JJ [ORNL; Copeland, Alex [U.S. Department of Energy, Joint Genome Institute; Pan, Chongle [ORNL

    2014-01-01

    Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.

  17. Transgenic analysis of sugar beet xyloglucan endo-transglucosylase/hydrolase Bv-XTH1 and Bv-XTH2 promoters reveals overlapping tissue-specific and wound-inducible expression profiles.

    Science.gov (United States)

    Dimmer, Emily; Roden, Laura; Cai, Daguang; Kingsnorth, Crawford; Mutasa-Göttgens, Effie

    2004-03-01

    The identification and analysis of tissue-specific gene regulatory elements will improve our knowledge of the molecular mechanisms that control the growth and development of different plant tissues and offer potentially useful tools for the genetic engineering of plants. A polymerase chain reaction (PCR)-based 5'-genome walk from sequences of an isolated sugar beet xyloglucan endo-transglucosylase hydrolase (XTH) gene led to the isolation of two independent upstream fragments. They were 1332 and 2163 base pairs upstream of the XTH ATG start site, respectively. In vivo transgenic assays in sugar beet hairy roots and Arabidopsis thaliana revealed that both fragments had promoter function and, in A. thaliana, directed expression in vascular tissues within the root, leaves and petals. Promoter activity was also observed in the leaf trichomes and within rapidly expanding stem internodes. Expression driven by both promoters was found to be wound inducible. Overall, the spatial and temporal expression pattern of these promoters suggested that the corresponding Bv-XTH genes (designated Bv-XTH1 and Bv-XTH2) may be involved in secondary cell wall formation. This work provides new insights on molecular mechanisms that could be exploited for the genetic engineering of sugar beet crops.

  18. 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

  19. 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.

  20. Generation of non-overlapping fiber architecture

    DEFF Research Database (Denmark)

    Chapelle, Lucie; Lévesque, M.; Brøndsted, Povl;

    2015-01-01

    Numerical models generating actual fiber architecture by including parameters such as the fiber geometry and arrangement are a powerful tool to explore the relation between the fiber architecture and mechanical properties. The generation of virtual architectures of fibrous materials is the first...... step toward the computation of their physical properties. In this work, a realistic 3D model is developed to describe the architecture of a complex fiber structure. The domain of application of the model could include natural fibers composites, wood fibers materials, papers, mineral and steel wools...... and polymer networks. The model takes into account the complex geometry of the fiber arrangement in which a fiber can be modeled with a certain degree of bending while keeping a main fiber orientation. The model is built in two steps. First, fibers are generated as a chain of overlapping spheres or as a chain...

  1. 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.

  2. [Syndrome overlap: autoimmune hepatitis and autoimmune cholangitis].

    Science.gov (United States)

    Guerra Montero, Luis; Ortega Alvarez, Félix; Marquez Teves, Maguin; Asato Higa, Carmen; Sumire Umeres, Julia

    2016-01-01

    Autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis and autoimmune cholangitis are chronic autoimmune liver disease, usually present separate, the cases where characteristics of two of the above is observed liver disease is commonly referred to as Overlap Syndromes (OS). Although there is no consensus on specific criteria for the diagnosis of OS identification of this association is important for initiating appropriate treatment and prevent its progression to cirrhosis or at least the complications of cirrhosis and death. We report the case of awoman aged 22 cirrhotic which debuted are edematous ascites, severe asthenia and jaundice compliant diagnostics SS criteria and initially present any response to treatment with ursodeoxycholic acid and oral corticosteroids, but ultimately finished performing a transplant orthotopic liver.

  3. Syntactic priming without lexical overlap in reading comprehension.

    Science.gov (United States)

    Kim, Christina S; Carbary, Kathleen M; Tanenhaus, Michael K

    2014-06-01

    Syntactic priming without lexical overlap is well-documented in language production. In contrast, reading-time comprehension studies, which typically use locally ambiguous sentences, generally find syntactic priming only with lexical overlap. This asymmetry has led some researchers to propose that distinct mechanisms underlie the comprehension and production of syntactic structure. Instead, we propose that methodological differences in how priming is assessed are largely responsible for the asymmetry: in comprehension, lexical biases in a locally ambiguous target sentence may overwhelm the influence of syntactic priming effects on a reader's interpretation. We addressed these issues in a self-paced reading study by (1) using target sentences containing global attachment ambiguities, (2) examining a syntactic structure which does not involve an argument of the verb, and (3) factoring out the unavoidable lexical biases associated with the target sentences in a mixed-effects regression model. Under these conditions, syntactic priming affected how ambiguous sentences were parsed, and facilitated reading times when target sentences were parsed using the primed structure. This resolves discrepancies among previous findings, and suggests that the same mechanism underlies syntactic priming in comprehension and production.

  4. 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.

  5. Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b▿

    Science.gov (United States)

    Hübschen, Judith M.; Mihneva, Zefira; Mentis, Andreas F.; Schneider, François; Aboudy, Yair; Grossman, Zehava; Rudich, Hagit; Kasymbekova, Kalia; Sarv, Inna; Nedeljkovic, Jasminka; Tahita, Marc C.; Tarnagda, Zekiba; Ouedraogo, Jean-Bosco; Gerasimova, A. G.; Moskaleva, T. N.; Tikhonova, Nina T.; Chitadze, Nazibrola; Forbi, J. C.; Faneye, Adedayo O.; Otegbayo, Jesse A.; Charpentier, Emilie; Muller, Claude P.

    2009-01-01

    Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa. PMID:19741071

  6. Meta-analysis of gene expression patterns in animal models of prenatal alcohol exposure suggests role for protein synthesis inhibition and chromatin remodeling

    Science.gov (United States)

    Rogic, Sanja; Wong, Albertina; Pavlidis, Paul

    2017-01-01

    Background Prenatal alcohol exposure (PAE) can result in an array of morphological, behavioural and neurobiological deficits that can range in their severity. Despite extensive research in the field and a significant progress made, especially in understanding the range of possible malformations and neurobehavioral abnormalities, the molecular mechanisms of alcohol responses in development are still not well understood. There have been multiple transcriptomic studies looking at the changes in gene expression after PAE in animal models, however there is a limited apparent consensus among the reported findings. In an effort to address this issue, we performed a comprehensive re-analysis and meta-analysis of all suitable, publically available expression data sets. Methods We assembled ten microarray data sets of gene expression after PAE in mouse and rat models consisting of samples from a total of 63 ethanol-exposed and 80 control animals. We re-analyzed each data set for differential expression and then used the results to perform meta-analyses considering all data sets together or grouping them by time or duration of exposure (pre- and post-natal, acute and chronic, respectively). We performed network and Gene Ontology enrichment analysis to further characterize the identified signatures. Results For each sub-analysis we identified signatures of differential expressed genes that show support from multiple studies. Overall, the changes in gene expression were more extensive after acute ethanol treatment during prenatal development than in other models. Considering the analysis of all the data together, we identified a robust core signature of 104 genes down-regulated after PAE, with no up-regulated genes. Functional analysis reveals over-representation of genes involved in protein synthesis, mRNA splicing and chromatin organization. Conclusions Our meta-analysis shows that existing studies, despite superficial dissimilarity in findings, share features that allow us

  7. Content patterns in topic-based overlapping communities.

    Science.gov (United States)

    Ríos, Sebastián A; Muñoz, Ricardo

    2014-01-01

    Understanding the underlying community structure is an important challenge in social network analysis. Most state-of-the-art algorithms only consider structural properties to detect disjoint subcommunities and do not include the fact that people can belong to more than one community and also ignore the information contained in posts that users have made. To tackle this problem, we developed a novel methodology to detect overlapping subcommunities in online social networks and a method to analyze the content patterns for each subcommunities using topic models. This paper presents our main contribution, a hybrid algorithm which combines two different overlapping sub-community detection approaches: the first one considers the graph structure of the network (topology-based subcommunities detection approach) and the second one takes the textual information of the network nodes into consideration (topic-based subcommunities detection approach). Additionally we provide a method to analyze and compare the content generated. Tests on real-world virtual communities show that our algorithm outperforms other methods.

  8. First evidence of overlaps between HIV-Associated Dementia (HAD and non-viral neurodegenerative diseases: proteomic analysis of the frontal cortex from HIV+ patients with and without dementia

    Directory of Open Access Journals (Sweden)

    Kapur Amit

    2010-06-01

    Full Text Available Abstract Background The pathogenesis of HIV-associated dementia (HAD is poorly understood. To date, detailed proteomic fingerprinting directly from autopsied brain tissues of HAD and HIV non-dementia patients has not been performed. Result Here, we have analyzed total proteins from the frontal cortex of 9 HAD and 5 HIV non-dementia patients. Using 2-Dimensional differential in-gel electrophoresis (2-DIGE to analyze the brain tissue proteome, 76 differentially expressed proteins (p 1.25 were identified between HAD and HIV non-dementia patients, of which 36 protein spots (based on 3D appearance of spots on the images were chosen for the mass spectrometry analysis. The large majority of identified proteins were represented in the energy metabolic (mitochondria and signal transduction pathways. Furthermore, over 90% of the protein candidates are common to both HAD and other non-viral neurodegenerative disease, such as Alzheimer's disease. The data was further validated using specific antibodies to 4 proteins (CA2, GS, CKMT and CRMP2 by western blot (WB in the same samples used for 2D-DIGE, with additional confirmation by immunohistochemitsry (IHC using frontal lobe tissue from different HAD and HIV+ non-dementia patients. The validation for all 4 antibodies by WB and IHC was in concordance with the DIGE results, lending further credence to the current findings. Conclusion These results suggest not only convergent pathogenetic pathways for the two diseases but also the possibility of increased Alzheimer's disease (AD susceptibility in HAD patients whose life expectancy has been significantly increased by highly active antiretroviral therapy.

  9. Y chromosome analysis of dingoes and southeast asian village dogs suggests a neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals.

    Science.gov (United States)

    Sacks, Benjamin N; Brown, Sarah K; Stephens, Danielle; Pedersen, Niels C; Wu, Jui-Te; Berry, Oliver

    2013-05-01

    Dogs originated more than 14,000 BP, but the location(s) where they first arose is uncertain. The earliest archeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5-7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 single-nucleotide polymorphism (SNPs) and 5 single tandem repeats (STRs), from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia

  10. 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

  11. 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.

  12. 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.

  13. Analysis of the ACTN3 heterozygous genotype suggests that α-actinin-3 controls sarcomeric composition and muscle function in a dose-dependent fashion.

    Science.gov (United States)

    Hogarth, Marshall W; Garton, Fleur C; Houweling, Peter J; Tukiainen, Taru; Lek, Monkol; Macarthur, Daniel G; Seto, Jane T; Quinlan, Kate G R; Yang, Nan; Head, Stewart I; North, Kathryn N

    2016-03-01

    A common null polymorphism (R577X) in ACTN3 causes α-actinin-3 deficiency in ∼ 18% of the global population. There is no associated disease phenotype, but α-actinin-3 deficiency is detrimental to sprint and power performance in both elite athletes and the general population. However, despite considerable investigation to date, the functional consequences of heterozygosity for ACTN3 are unclear. A subset of studies have shown an intermediate phenotype in 577RX individuals, suggesting dose-dependency of α-actinin-3, while others have shown no difference between 577RR and RX genotypes. Here, we investigate the effects of α-actinin-3 expression level by comparing the muscle phenotypes of Actn3(+/-) (HET) mice to Actn3(+/+) [wild-type (WT)] and Actn3(-/-) [knockout (KO)] littermates. We show reduction in α-actinin-3 mRNA and protein in HET muscle compared with WT, which is associated with dose-dependent up-regulation of α-actinin-2, z-band alternatively spliced PDZ-motif and myotilin at the Z-line, and an incremental shift towards oxidative metabolism. While there is no difference in force generation, HET mice have an intermediate endurance capacity compared with WT and KO. The R577X polymorphism is associated with changes in ACTN3 expression consistent with an additive model in the human genotype-tissue expression cohort, but does not influence any other muscle transcripts, including ACTN2. Overall, ACTN3 influences sarcomeric composition in a dose-dependent fashion in mouse skeletal muscle, which translates directly to function. Variance in fibre type between biopsies likely masks this phenomenon in human skeletal muscle, but we suggest that an additive model is the most appropriate for use in testing ACTN3 genotype associations.

  14. 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。

  15. 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...... 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...

  16. 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

  17. Gene expression analysis of overwintering mountain pine beetle larvae suggests multiple systems involved in overwintering stress, cold hardiness, and preparation for spring development

    Directory of Open Access Journals (Sweden)

    Jeanne A. Robert

    2016-07-01

    Full Text Available Cold-induced mortality has historically been a key aspect of mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae, population control, but little is known about the molecular basis for cold tolerance in this insect. We used RNA-seq analysis to monitor gene expression patterns of mountain pine beetle larvae at four time points during their overwintering period—early-autumn, late-autumn, early-spring, and late-spring. Changing transcript profiles over the winter indicates a multipronged physiological response from larvae that is broadly characterized by gene transcripts involved in insect immune responses and detoxification during the autumn. In the spring, although transcripts associated with developmental process are present, there was no particular biological process dominating the transcriptome.

  18. 浅析食品监测中数据的信息管理和建议%Analysis of Data Informatics Management and Suggestions in Food Supervision

    Institute of Scientific and Technical Information of China (English)

    曹进; 张庆生; 李晓瑜

    2015-01-01

    The data analysis of food supervision needs to reflect the integration of food safety and possible trend based on the fun-damental test data of stressed foods and their products. With the assessment and analysis on potential resources of hazard elements, the integrate management support of food safety could be achieved. The data management could be organized and evaluated through plan, collection, treatment and display, which might be assisted to establish data-link with process mining to enforce the prospect of food safety background and trend and to provide the support of food safety management.%食品监测数据分析是通过对重点食品进行针对性检测获取基础数据结果的基础上,反映出食品整体的安全状态和可能的发展走势,并通过潜在危害因子来源的预测和分析,实现对食品安全的整体管理支持. 其数据管理需要通过计划、采集、处理和呈现等步骤进行管理和评估,通过过程剖析的方式进行数据链的建立,从而实现对食品安全本底和走势的预测,为食品安全监管提供技术支撑.

  19. Mucopolysaccharidosis type I in 21 Czech and Slovak patients: Mutation analysis suggests a functional importance of C-terminus of the IDUA protein

    Science.gov (United States)

    Vazna, Alzbeta; Beesley, Clare; Berna, Linda; Stolnaja, Larisa; Myskova, Helena; Bouckova, Michaela; Vlaskova, Hana; Poupetova, Helena; Zeman, Jiri; Magner, Martin; Hlavata, Anna; Winchester, Bryan; Hrebicek, Martin; Dvorakova, Lenka

    2009-01-01

    Abstract Mucopolysaccharidosis type I (MPS I) is an autosomal recessive lysosomal storage disorder that is caused by a deficiency of the enzyme α-l-iduronidase (IDUA). Of the 21 Czech and Slovak patients who have been diagnosed with MPS I in the last 30 years, 16 have a severe clinical presentation (Hurler syndrome), 2 less severe manifestations (Scheie syndrome), and 3 an intermediate severity (Hurler/Scheie phenotype). Mutation analysis was performed in 20 MPS I patients and 39 mutant alleles were identified. There was a high prevalence of the null mutations p.W402X (12 alleles) and p.Q70X (7 alleles) in this cohort. Four of the 13 different mutations were novel: p.V620F (3 alleles), p.W626X (1 allele), c.1727 + 2T > G (1 allele) and c.1918_1927del (2 alleles). The pathogenicity of the novel mutations was verified by transient expression studies in Chinese hamster ovary cells. Seven haplotypes were observed in the patient alleles using 13 intragenic polymorphisms. One of the two haplotypes associated with the mutation p.Q70X was not found in any of the controls. Haplotype analysis showed, that mutations p.Q70X, p.V620F, and p.D315Y probably have more than one ancestor. Missense mutations localized predominantly in the hydrophobic core of the enzyme are associated with the severe phenotype, whereas missense mutations localized to the surface of the enzyme are usually associated with the attenuated phenotypes. Mutations in the 130 C-terminal amino acids lead to clinical manifestations, which indicates a functional importance of the C-terminus of the IDUA protein. © 2009 Wiley-Liss, Inc. PMID:19396826

  20. Strange quark momentum fraction from overlap fermion

    CERN Document Server

    Sun, Mingyang; Liu, Keh-Fei; Gong, Ming

    2015-01-01

    We present a calculation of $\\langle x \\rangle_s$ for the strange quark in the nucleon. We also report the ratio of the strange $\\langle x \\rangle$ to that of $u/d$ in the disconnected insertion which will be useful in constraining the global fit of parton distribution functions at small $x$. We adopt overlap fermion action on $2 + 1$ flavor domain-wall fermion configurations on the $24^3 \\times 64$ lattice with a light sea quark mass which corresponds to $m_{\\pi}=330$ MeV. Smeared grid $Z_3$ sources are deployed to calculate the nucleon propagator with low-mode substitution. Even-odd grid sources and time-dilution technique with stochastic noises are used to calculate the high mode contribution to the quark loop. Low mode averaging (LMA) for the quark loop is applied to reduce the statistical error of the disconnected insertion calculation. We find the ratio $\\langle x \\rangle_s/\\langle x \\rangle_{u/d}^{\\mathrm{DI}}= 0.78(3)$ in this study.

  1. 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.

  2. Analysis of transcriptional regulation and tissue-specific expression of Avicennia marina Plasma Membrane Protein 3 suggests it contributes to Na(+) transport and homoeostasis in A. marina.

    Science.gov (United States)

    Chidambaram, Rajalakshmi; Venkataraman, Gayatri; Parida, Ajay

    2015-07-01

    Plasma membrane proteins (PMP3) play a role in cation homoeostasis. The 5' flanking sequence of stress inducible, Avicennia marina PMP3 (AmPMP3prom) was transcriptionally fused to (a) GUS or (b) GFP-AmPMP3 and analyzed in transgenic tobacco. Tissue-histochemical GUS and GFP:AmPMP3 localization are co-incident under basal and stress conditions. AmPMP3prom directed GUS activity is highest in roots. Basal transcription is conferred by a 388bp segment upstream of the translation start site. A 463bp distal enhancer in the AmPMP3prom confers enhanced expression under salinity in all tissues and also responds to increases in salinity. The effect of a central, stem-specific negative regulatory region is suppressed by the distal enhancer. The A. marina rhizosphere encounters dynamic changes in salinity at the inter-tidal interface. The complex, tissue-specific transcriptional responsiveness of AmPMP3 to salinity appears to have evolved in response to these changes. Under salinity, guard cell and phloem-specific expression of GFP:AmPMP3 is highly enhanced. Mesophyll, trichomes, bundle sheath, parenchymatous cortex and xylem parenchyma also show GFP:AmPMP3 expression. Cis-elements conferring stress, root and vascular-specific expression are enriched in the AmPMP3 promoter. Pronounced vascular-specific AmPMP3 expression suggests a role in salinity induced Na(+) transport, storage, and secretion in A. marina.

  3. Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins.

    Science.gov (United States)

    Dan, Adi; Ofran, Yanay; Kliger, Yossef

    2010-02-01

    Conformational changes in proteins often involve secondary structure transitions. Such transitions can be divided into two types: disorder-to-order changes, in which a disordered segment acquires an ordered secondary structure (e.g., disorder to alpha-helix, disorder to beta-strand), and order-to-order changes, where a segment switches from one ordered secondary structure to another (e.g., alpha-helix to beta-strand, alpha-helix to turn). In this study, we explore the distribution of these transitions in the proteome. Using a comprehensive, yet highly conservative method, we compared solved three-dimensional structures of identical protein sequences, looking for differences in the secondary structures with which they were assigned. Protein chains in which such secondary structure transitions were detected, were classified into two sets according to the type of transition that is involved (disorder-to-order or order-to-order), allowing us to characterize each set by examining enrichment of gene ontology terms. The results reveal that the disorder-to-order set is significantly enriched with nucleotide binding proteins, whereas the order-to-order set is more diverse. Remarkably, further examination reveals that >22% of the purine nucleotide binding proteins include segments which undergo disorder-to-order transitions, suggesting that such transitions play an important role in this process.

  4. 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.

  5. 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。

  6. Isolation and functional analysis of CONSTANS-LIKE genes suggests that a central role for CONSTANS in flowering time control is not evolutionarily conserved in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Albert eWong

    2014-09-01

    Full Text Available The zinc finger transcription factor CONSTANS has a well-established central role in the mechanism for photoperiod sensing in Arabidopsis, integrating light and circadian clock signals to upregulate the florigen gene FT under long-day but not short-day conditions. Although CONSTANS-like (COL genes in other species have also been shown to regulate flowering time, it is not clear how widely this central role in photoperiod sensing is conserved.Legumes are a major plant group and various legume species show significant natural variation for photoperiod responsive flowering. Orthologs of several Arabidopsis genes have been shown to participate in photoperiodic flowering in legumes, but the possible function of COL genes as integrators of the photoperiod response has not yet been examined in detail. Here we characterize the COL family in the temperate long-day legume Medicago truncatula, using expression analyses, reverse genetics, transient activation assays and Arabidopsis transformation. Our results provide several lines of evidence suggesting that COL genes are unlikely to have a central role in the photoperiod response mechanism in this species.

  7. 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.

  8. Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the order lagomorpha.

    Directory of Open Access Journals (Sweden)

    Katie Leach

    Full Text Available Climate change during the past five decades has impacted significantly on natural ecosystems, and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs have been used widely to project changes in species' bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical, and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed 'modellable' within our framework were projected under future climate scenarios (58 species. Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares, and jackrabbits likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov's Pika (Ochotona koslowi. Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of

  9. 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.

  10. 影响食品安全包装因素的分析与建议%Analysis and suggestion of package factors on food safety

    Institute of Scientific and Technical Information of China (English)

    鲁奇林; 王月华; 徐方旭; 马蓉; 冯叙桥

    2014-01-01

    In recent years, the issue of food safety has increasingly aroused the attention of all circles of the society. The issue of food safety relates, to a large extent, to food package, and is one of the factors that cause the food safety issue, so it is put widely attention by the researchers both at home and abroad. This paper introduced the present situation of food packaging at home and abroad, focusing on the effect of package mate-rials, package structure and package printing on food safety. Package factors were analyzed in this review paper. New technologies of food package related to food safety were also summarized and some suggestions to assure food safety provided.%近几年,食品安全问题越来越引起社会各界的广泛关注,而食品包装的安全性与食品安全问题息息相关,也是引起食品安全问题的因素之一,因此受到国内外研究者的广泛关注。本文介绍了国内外食品包装安全现状,主要从影响食品安全的相关包装因素入手,分析了包装材料、包装结构和包装印刷对食品安全的影响,归纳总结了食品包装技术,并提出了一些保证食品包装安全的建议。

  11. 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.

  12. 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

  13. Simultaneous Combined Myositis, Inflammatory Polyneuropathy, and Overlap Myasthenic Syndrome

    Directory of Open Access Journals (Sweden)

    Stéphane Mathis

    2016-01-01

    Full Text Available Immune-mediated neuromuscular disorders include pathologies of the peripheral nervous system, neuromuscular junction, and muscles. If overlap syndromes (or the association of almost two autoimmune disorders are recognized, the simultaneous occurrence of several autoimmune neuromuscular disorders is rare. We describe two patients presenting the simultaneous occurrence of inflammatory neuropathy, myositis, and myasthenia gravis (with positive acetylcholine receptor antibodies. For each patient, we carried out a pathological analysis (nerve and muscle and an electrophysiological study (and follow-up. To our knowledge, this is the first description of such a triple immune-mediated neuromuscular syndrome. We compared our observations with a few other cases of simultaneous diagnosis of two inflammatory neuromuscular disorders.

  14. 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.

  15. Segmentation of Telugu Touching Conjunct Consonants Using Overlapping Bounding Boxes

    Directory of Open Access Journals (Sweden)

    J. Bharathi

    2013-06-01

    Full Text Available Telugu is an ancient historic language. It is spoken by about 84.6 million people of Andhra Pradesh. The script has circular orthography with few horizontal and slant strokes. Huge literature exists for this language in printed form which needs to be preserved by scanning and converting it into editable form. Segmentation of touching characters is a major issue in any OCR system. Segmenting the wordsinto individual glyphs by Connected Component Analysis yields poor results due to touching characters. Touching conjunct consonants is the major component which needs to be properly addressed for improving the accuracy of an OCR system. In this paper an overlapping bounding box approach is presented for segmenting the conjunct consonants along with an algorithm for identifying the correcttouching location. An accuracy rate of 91.27% is achieved.

  16. 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.

  17. 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.

  18. A Detailed Analysis of the BR1 Locus Suggests a New Mechanism for Bolting after Winter in Sugar Beet (Beta vulgaris L.).

    Science.gov (United States)

    Tränkner, Conny; Lemnian, Ioana M; Emrani, Nazgol; Pfeiffer, Nina; Tiwari, Surya P; Kopisch-Obuch, Friedrich J; Vogt, Sebastian H; Müller, Andreas E; Schilhabel, Markus; Jung, Christian; Grosse, Ivo

    2016-01-01

    Sugar beet (Beta vulgaris ssp. vulgaris) is a biennial, sucrose-storing plant, which is mainly cultivated as a spring crop and harvested in the vegetative stage before winter. For increasing beet yield, over-winter cultivation would be advantageous. However, bolting is induced after winter and drastically reduces yield. Thus, post-winter bolting control is essential for winter beet cultivation. To identify genetic factors controlling bolting after winter, a F2 population was previously developed by crossing the sugar beet accessions BETA 1773 with reduced bolting tendency and 93161P with complete bolting after winter. For a mapping-by-sequencing analysis, pools of 26 bolting-resistant and 297 bolting F2 plants were used. Thereby, a single continuous homozygous region of 103 kb was co-localized to the previously published BR1 QTL for post-winter bolting resistance (Pfeiffer et al., 2014). The BR1 locus was narrowed down to 11 candidate genes from which a homolog of the Arabidopsis CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I (CPSF73-I) was identified as the most promising candidate. A 2 bp deletion within the BETA 1773 allele of BvCPSF73-Ia results in a truncated protein. However, the null allele of BvCPSF73-Ia might partially be compensated by a second BvCPSF73-Ib gene. This gene is located 954 bp upstream of BvCPSF73-Ia and could be responsible for the incomplete penetrance of the post-winter bolting resistance allele of BETA 1773. This result is an important milestone for breeding winter beets with complete bolting resistance after winter.

  19. 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

  20. 中国铋供需形势分析及对策建议%The analysis and suggestions of the bismuth' s supply and demand in China

    Institute of Scientific and Technical Information of China (English)

    龙涛; 陈其慎; 于汶加; 余倩; 张艳松

    2016-01-01

    Bismuth is a kind of "green metal"which can be used safely .This fact is now acknowledged widely in the world . At present , bismuth is widely applied in bismuth oxide industry , pharmaceutical industry ,bismuth alloy ,solder and metallurgical additive ,etc .Although China is now the largest bismuth resources keeper , producer , consumer and exporter , it is not a powerful bismuth industry country . Therefore ,recognizing timely the supply and demand situation of bismuth is the basement of the country and the enterprises to develop strategies . This paper which is based on the global view firstly took a comprehensive analysis about bismuth resources ,production ,supply ,demand ,trade and other status .And then by combining with the development trend of bismuth in China ,it made a judgment that is the demand of bismuth in China will peak to 18000t around 2030 .Considering the prominent problems bismuth industry faced ,this paper finally putted forward several measures and advices respectively from resource development ,resource recovery ,technology improvement and reducing international market risks to ensure the healthy development of bismuth industry in China .%铋(Bismuth)是全球公认的一种可安全使用的"绿色金属".目前,铋广泛应用于氧化铋行业、医药行业、铋合金及焊料和冶金添加剂等领域.中国是全球最大的铋资源国、生产国、消费国和出口国,但不是铋产业强国,因此及时认清当前中国铋的供需形势,是国家和企业制定发展战略的基础.本文在全球视野下,首先对中国铋的资源状况、生产供应、需求现状、贸易等进行综合分析,然后结合中国铋未来发展趋势,作出了2030年左右中国铋的需求量将达到峰值18000 t的判断.文章最后针对中国铋产业面临的突出问题,分别从资源开发、资源回收、技术提高和降低国际市场风险等方面提出了中国铋产业健康发展的对策建议.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    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......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...... compare our qualitative predictions with recent measurements of the wave function overlap and find good agreement....

  2. 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.

  3. Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes.

    Science.gov (United States)

    Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya

    2013-11-15

    Up to 15% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression.

  4. 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.

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. Shake for Sigma, Pray for Pi: Classroom Orbital Overlap Analogies

    Science.gov (United States)

    Dicks, Andrew P.

    2011-01-01

    An introductory organic classroom demonstration is discussed where analogies are made between common societal hand contact and covalent bond formation. A handshake signifies creation of a [sigma] bond ("head-on" orbital overlap), whereas the action of praying illustrates "sideways" overlap and generation of a [pi] bond. The nature of orbital and…

  10. Influence of line isolation overlappings on formation of lightning overvoltages

    Directory of Open Access Journals (Sweden)

    Antropov I. M.

    2015-12-01

    Full Text Available The model of substation protection against lightning waves with considered multiple overlappings of line isolation has been presented. Influence of multiple overlapping of isolation on line support on formation of lightning overvoltages has been shown. Ambiguity of determination of lightning current dangerous parameters at the fixed length of its front has been revealed

  11. Distribution and content of dust in overlapping galaxy systems

    CERN Document Server

    White, R E; Conselice, C J; White, Raymond E; Keel, William C; Conselice, Christopher J

    1996-01-01

    Partially overlapping galaxies are used to directly determine the effective absorption in spiral galaxy disks. The non-overlapping parts of the galaxies and symmetry considerations are used to reconstruct, via differential photometry, how much background galaxy light is lost in passing through the foreground disks.

  12. 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.

  13. 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.

  14. Microfluidic platform with four orthogonal and overlapping gradients for soluble compound screening in regenerative medicine research

    NARCIS (Netherlands)

    Harink, Björn; Le Gac, Séverine; Barata, David; Blitterswijk, van Clemens; Habibovic, Pamela

    2015-01-01

    We present here a screening method based on a microfluidic platform, which can generate four orthogonal and overlapping concentration gradients of soluble compounds over a monolayer of cells, in combination with automated and in situ image analysis, for use in regenerative medicine research. The dev

  15. Multi-segment and multi-ply overlapping process of multi coupled activities based on valid information evolution

    Science.gov (United States)

    Wang, Zhiliang; Wang, Yunxia; Qiu, Shenghai

    2013-01-01

    increment caused by all overlapping process. And then, based on overlapping degree analysis of these planning models, by the VIE degree function, the four lemmas theory proofs are represented, and two propositions are finally proved: (1) The multi-ply overlapping of the multi coupled activities will weaken the basic overlapping effect on the development cycle time reduction (2) Overlapping the multi coupled activities will decrease product development cycle, but increase product development cost. And there is trade-off between development time and cost. And so, two methods are given to slacken and eliminate multi-ply overlapping effects. At last, an example about a vehicle upper subsystem design illustrates the application of the proposed models; compared with a sequential execution pattern, the decreasing of development cycle (22%) and the increasing of development cost (3%) show the validity of the method in the example. The proposed research not only lays a theoretical foundation for correctly planning complex product development process, but also provides specific and effective operation methods for overlapping multi coupled activities.

  16. 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.

  17. Impossible spaces: maximizing natural walking in virtual environments with self-overlapping architecture.

    Science.gov (United States)

    Suma, Evan A; Lipps, Zachary; Finkelstein, Samantha; Krum, David M; Bolas, Mark

    2012-04-01

    Walking is only possible within immersive virtual environments that fit inside the boundaries of the user's physical workspace. To reduce the severity of the restrictions imposed by limited physical area, we introduce "impossible spaces," a new design mechanic for virtual environments that wish to maximize the size of the virtual environment that can be explored with natural locomotion. Such environments make use of self-overlapping architectural layouts, effectively compressing comparatively large interior environments into smaller physical areas. We conducted two formal user studies to explore the perception and experience of impossible spaces. In the first experiment, we showed that reasonably small virtual rooms may overlap by as much as 56% before users begin to detect that they are in an impossible space, and that the larger virtual rooms that expanded to maximally fill our available 9.14 m x 9.14 m workspace may overlap by up to 31%. Our results also demonstrate that users perceive distances to objects in adjacent overlapping rooms as if the overall space was uncompressed, even at overlap levels that were overtly noticeable. In our second experiment, we combined several well-known redirection techniques to string together a chain of impossible spaces in an expansive outdoor scene. We then conducted an exploratory analysis of users' verbal feedback during exploration, which indicated that impossible spaces provide an even more powerful illusion when users are naive to the manipulation.

  18. Compression of flow can reveal overlapping modular organization in networks

    CERN Document Server

    Esquivel, Alcides Viamontes

    2011-01-01

    To better understand the overlapping modular organization of large networks with respect to flow, here we introduce the map equation for overlapping modules. In this information-theoretic framework, we use the correspondence between compression and regularity detection. The generalized map equation measures how well we can compress a description of flow in the network when we partition it into modules with possible overlaps. When we minimize the generalized map equation over overlapping network partitions, we detect modules that capture flow and determine which nodes at the boundaries between modules should be classified in multiple modules and to what degree. With a novel greedy search algorithm, we find that some networks, for example, the neural network of C. Elegans, are best described by modules dominated by hard boundaries, but that others, for example, the sparse road network of California, have a highly overlapping modular organization. To compare our approach with other clustering algorithms, we sugg...

  19. 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.

  20. Segmentation of Overlapping Shapes using Test Ray Intersections

    DEFF Research Database (Denmark)

    Rasmusson, Allan

    be a major task, but in bioimaging and tissue quantification it is often complicated further by the need for segmenting images of overlapping particles, for instance neurons. One approach to segmenting overlapping particles is to oversegment the image into many small regions which are then combined...... into the correct shapes in a postprocessing step. The postprocessing step is unfortunately often both difficult and computationally expensive. Another approach is to incorporate descriptions of the overlapping shapes into a segmentation algorithm which normally only segments the union of all particle profiles....... This may, however, quickly lead to the implementation of complex descriptions of any possible configuration the overlapping shapes may appear in. Presented here is a new approach to segment overlapping shapes which utilizes information gained from probing the image with test rays. Test rays intersections...

  1. 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.

  2. 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.

  3. 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.

  4. An extension to artifact-free projection overlaps

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jianyu, E-mail: jianyulin@hotmail.com [Department of Electrical and Computer Engineering, Curtin University, GPO Box U1987, Perth, Western Australia 6845 (Australia)

    2015-05-15

    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

  5. 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

    2016-04-05

    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 (P<0.05), anti-hypertensive (P<0.05), anti-diabetic drug use (men P<0.05, women P=0.06) and waist circumference for the male cohort (P<0.05), after adjusting for age. Subjects with ABA had spatially extensive gray matter loss in the frontal, parietal and temporal lobes (false-discovery-rate-corrected q<0.001). ABA patterns 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.

  6. 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

  7. Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation

    DEFF Research Database (Denmark)

    Salas, A; Rasmussen, Erik Michael; Lareu, M V

    2001-01-01

    of mtDNA sequencing implies a great lab effort when a high number of samples must be analyzed.The present work introduces a novel and reliable method for the screening of mtDNA variation in the first and second hypervariables (HV1 and HV2) regions which we have denominated fluorescent single strand...... conformation polymorphism (SSCP) of overlapping fragments (FSSCP-OF). FSSCP-OF is based on the basic theory of SSCP analysis and combines two complementary strategies: the use of PCR amplified overlapping fragments and fluorescent detection technology. The overlap region contains a high percentage (50......%) of the d-loop mtDNA variation and for this reason, the probability to detect a polymorphic position by SSCP analysis is clearly increased in comparison to conventional SSCP methods due to the fact that the same polymorphic position is usually placed in a different "relative" position in the two overlapped...

  8. Computation of overlap integrals over STOs with mathematica

    Science.gov (United States)

    Yükçü, S. A.; Yükçü, N.

    2017-02-01

    Overlap integrals which encountered in molecular structure calculations are the most basic of molecular integrals. Also, other molecular integrals can be expressed in terms of these integrals. Overlap integrals can be calculated by using Slater Type Orbitals (STOs). In this work, we develop algorithms for two-center overlap integrals which are calculated over the STOs in ellipsoidal coordinates and some auxiliary functions by S. M. Mekelleche's group. During the computation of this paper, Mathematica programming language has been used to produce algorithms. Numerical results for some quantum numbers are presented in the tables. Finally, our numerical results and others are compared, then some details of evaluation method are discussed.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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...... of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes...

  14. Lichen planus and lupus erythematosus overlap syndrome

    Directory of Open Access Journals (Sweden)

    Chopra Adarsh

    1996-01-01

    Full Text Available A 45-year-old woman with livid plaques showing central atrophy and erythematous vesicular borders over both dorsa of feet and buttocks, and follicular and papular lesions over buttocks and lumbar area, was difficult to diagnose as either lichen planus (LP or lupus erythematosus (LE. The histological studies from two places showed features of both LE and LP. Laboratory findings were within normal limits first, but follow up studies for two years showed persistent albuminurea, leucopenia, arthritis and erythema over the exposed areas with same histology suggesting that eruption may be an unusual variant of LE.

  15. The overlapping host responses to bacterial cyclic dinucleotides.

    Science.gov (United States)

    Abdul-Sater, Ali A; Grajkowski, Andrzej; Erdjument-Bromage, Hediye; Plumlee, Courtney; Levi, Assaf; Schreiber, Michael T; Lee, Carolyn; Shuman, Howard; Beaucage, Serge L; Schindler, Christian

    2012-02-01

    Macrophages respond to infection with Legionella pneumophila by the induction of inflammatory mediators, including type I Interferons (IFN-Is). To explore whether the bacterial second messenger cyclic 3'-5' diguanylate (c-diGMP) activates some of these mediators, macrophages were infected with L. pneumophila strains in which the levels of bacterial c-diGMP had been altered. Intriguingly, there was a positive correlation between c-diGMP levels and IFN-I expression. Subsequent studies with synthetic derivatives of c-diGMP, and newly described cyclic 3'-5' diadenylate (c-diAMP), determined that these molecules activate overlapping inflammatory responses in human and murine macrophages. Moreover, UV crosslinking studies determined that both dinucleotides physically associate with a shared set of host proteins. Fractionation of macrophage extracts on a biotin-c-diGMP affinity matrix led to the identification of a set of candidate host binding proteins. These studies suggest that mammalian macrophages can sense and mount a specific inflammatory response to bacterial dinucleotides.

  16. 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.

  17. Evidence for partial overlap of male olfactory cues in lampreys

    Science.gov (United States)

    Buchinger, Tyler J.; Li, Ke; Huertas, Mar; Baker, Cindy F.; Jia, Liang; Hayes, Michael C.; Li, Weiming; Johnson, Nicholas S.

    2016-01-01

    Animals rely on a mosaic of complex information to find and evaluate mates. Pheromones, often comprised of multiple components, are considered to be particularly important for species-recognition in many species. While the evolution of species-specific pheromone blends is well-described in many insects, very few vertebrate pheromones have been studied in a macro-evolutionary context. Here, we report a phylogenetic comparison of multi-component male odours that guide reproduction in lampreys. Chemical profiling of sexually mature males from eleven species of lamprey, representing six of ten genera and two of three families, indicated the chemical profiles of sexually mature male odours are partially shared among species. Behavioural assays conducted with four species sympatric in the Laurentian Great Lakes indicated asymmetric female responses to heterospecific odours, where Petromyzon marinus were attracted to male odour collected from all species tested but other species generally preferred only the odour of conspecifics. Electro-olfactogram recordings from P. marinusindicated that although P. marinus exhibited behavioural responses to odours from males of all species, at least some of the compounds that elicited olfactory responses were different in conspecific male odours compared to heterospecific male odours. We conclude that some of the compounds released by sexually mature males are shared among species and elicit olfactory and behavioural responses in P. marinus, and suggest that our results provide evidence for partial overlap of male olfactory cues among lampreys. Further characterization of the chemical identities of odour components is needed to confirm shared pheromones among species.

  18. Notes on the Polynomial Identities in Random Overlap Structures

    Science.gov (United States)

    Sollich, Peter; Barra, Adriano

    2012-04-01

    In these notes we review first in some detail the concept of random overlap structure (ROSt) applied to fully connected and diluted spin glasses. We then sketch how to write down the general term of the expansion of the energy part from the Boltzmann ROSt (for the Sherrington-Kirkpatrick model) and the corresponding term from the RaMOSt, which is the diluted extension suitable for the Viana-Bray model. From the ROSt energy term, a set of polynomial identities (often known as Aizenman-Contucci or AC relations) is shown to hold rigorously at every order because of a recursive structure of these polynomials that we prove. We show also, however, that this set is smaller than the full set of AC identities that is already known. Furthermore, when investigating the RaMOSt energy for the diluted counterpart, at higher orders, combinations of such AC identities appear, ultimately suggesting a crucial role for the entropy in generating these constraints in spin glasses.

  19. 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.

  20. 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.

  1. Overlapping Modularity at the Critical Point of k-Clique Percolation

    Science.gov (United States)

    Tóth, Bálint; Vicsek, Tamás; Palla, Gergely

    2013-05-01

    One of the most remarkable social phenomena is the formation of communities in social networks corresponding to families, friendship circles, work teams, etc. Since people usually belong to several different communities at the same time, the induced overlaps result in an extremely complicated web of the communities themselves. Thus, uncovering the intricate community structure of social networks is a non-trivial task with great potential for practical applications, gaining a notable interest in the recent years. The Clique Percolation Method (CPM) is one of the earliest overlapping community finding methods, which was already used in the analysis of several different social networks. In this approach the communities correspond to k-clique percolation clusters, and the general heuristic for setting the parameters of the method is to tune the system just below the critical point of k-clique percolation. However, this rule is based on simple physical principles and its validity was never subject to quantitative analysis. Here we examine the quality of the partitioning in the vicinity of the critical point using recently introduced overlapping modularity measures. According to our results on real social and other networks, the overlapping modularities show a maximum close to the critical point, justifying the original criteria for the optimal parameter settings.

  2. 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.  

  3. Overlap Dirac Operator, Eigenvalues and Random Matrix Theory

    OpenAIRE

    Edwards, Robert G.; Heller, Urs M.; Kiskis, Joe; Narayanan, Rajamani

    1999-01-01

    The properties of the spectrum of the overlap Dirac operator and their relation to random matrix theory are studied. In particular, the predictions from chiral random matrix theory in topologically non-trivial gauge field sectors are tested.

  4. 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

  5. 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.

  6. 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.

  7. A fuzzy approach to the Weighted Overlap Dominance model

    DEFF Research Database (Denmark)

    Franco de los Rios, Camilo Andres; Hougaard, Jens Leth; Nielsen, Kurt

    2013-01-01

    Decision support models are required to handle the various aspects of multi-criteria decision problems in order to help the individual understand its possible solutions. In this sense, such models have to be capable of aggregating and exploiting different types of measurements and evaluations in ...... is presented for ordering and identifying the best alternatives under an interactive procedure that takes into account the natural imprecision and relevance of information....... in an interactive way, where input data can take the form of uniquely-graded or interval-valued information. Here we explore the Weighted Overlap Dominance (WOD) model from a fuzzy perspective and its outranking approach to decision support and multidimensional interval analysis. Firstly, imprecision measures...... are introduced for characterizing the type of uncertainty being expressed by intervals, examining at the same time how the WOD model handles both non-interval as well as interval data, and secondly, relevance degrees are proposed for obtaining a ranking over the alternatives. Hence, a complete methodology...

  8. Advanced UXO discrimination: resolving multiple targets and overlapping EMI signals

    Science.gov (United States)

    Shubitidze, Fridon; Barrowes, Benjamin E.; Shamatava, Irma; Fernandez, Juan Pablo; Bijamov, Alex; O'Neill, Kevin

    2011-06-01

    In this paper we employ advanced electromagnetic induction models to resolve multiple targets with overlapping EMI signals-i.e. to discriminate objects of interest, such as unexploded ordnance (UXO), from innocuous items. The models include a) a joint diagonalization (JD) technique that takes data from next-generation EMI sensors and uses the eigenvalues of the multistatic response matrix to estimate the number of potential targets, and b) the orthonormalized volume magnetic source (ONVMS) model, a physically complete, fast, and accurate forward model whose representation of a target's intrinsic EMI response is used to extract classification parameters. In the given approach the overall EMI inversion and classification problem proceeds as follows: first, the JD is applied to the data and the number of targets is estimated; once this is known, the ONVMS is combined with an optimization technique to yield the location and orientation of each buried object, as well as the amplitude of its ONVMS. Finally, a total ONVMS is calculated for each object and used as a discriminant to distinguish between UXO and non-UXO items and between different kinds of UXO. We illustrate the applicability of our multi-target analysis technique by using it on several teststand and live-site datasets collected with the TEMTADS sensor array. We end by demonstrating the superior performance of the ONVMS by applying it to multi-target blind-test data compiled at the Aberdeen Proving Ground test-stand facility.

  9. Topological summation of observables measured with dynamical overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Bietenholz, W. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Hip, I. [Zagreb Univ. (Croatia). Faculty of Geothechnical Engineering

    2008-10-15

    HMC histories for light dynamical overlap fermions tend to stay in a fixed topological sector for many trajectories, so that the different sectors are not sampled properly. Therefore the suitable summation of observables, which have been measured in separate sectors, is a major challenge. We explore several techniques for this issue, based on data for the chiral condensate and the (analogue of the) pion mass in the 2-flavour Schwinger model with dynamical overlap-hypercube fermions. (orig.)

  10. Topological Summation of Observables Measured with Dynamical Overlap Fermions

    OpenAIRE

    2008-01-01

    HMC histories for light dynamical overlap fermions tend to stay in a fixed topological sector for many trajectories, so that the different sectors are not sampled properly. Therefore the suitable summation of observables, which have been measured in separate sectors, is a major challenge. We explore several techniques for this issue, based on data for the chiral condensate and the (analogue of the) pion mass in the 2-flavour Schwinger model with dynamical overlap-hypercube fermions.

  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. Characterizing Computation-Communication Overlap in Message-Passing Systems

    Energy Technology Data Exchange (ETDEWEB)

    David E. Bernholdt; Jarek Nieplocha; P. Sadayappan; Aniruddha G. Shet; Vinod Tipparaju

    2008-01-31

    Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this report, we describe an instrumentation framework developed for messagepassing systems to characterize the degree of overlap of communication with computation in the execution of parallel applications. The inability to obtain precise time-stamps for pertinent communication events is a significant problem, and is addressed by generation of minimum and maximum bounds on achieved overlap. The overlap measures can aid application developers and system designers in investigating scalability issues. The approach has been used to instrument two MPI implementations as well as the ARMCI system. The implementation resides entirely within the communication library and thus integrates well with existing approaches that operate outside the library. The utility of the framework is demonstrated by analyzing communication-computation overlap for micro-benchmarks and the NAS benchmarks, and the insights obtained are used to modify the NAS SP benchmark, resulting in improved overlap.

  13. Characterizing Computation-Communication Overlap in Message-Passing Systems

    Energy Technology Data Exchange (ETDEWEB)

    David E. Bernholdt; Jarek Nieplocha; P. Sadayappan; Aniruddha G. Shet; Vinod Tipparaju

    2008-01-31

    Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this report, we describe an instrumentation framework developed for message-passing systems to characterize the degree of overlap of communication with computation in the execution of parallel applications. The inability to obtain precise time-stamps for pertinent communication events is a significant problem, and is addressed by generation of minimum and maximum bounds on achieved overlap. The overlap measures can aid application developers and system designers in investigating scalability issues. The approach has been used to instrument two MPI implementations as well as the ARMCI system. The implementation resides entirely within the communication library and thus integrates well with existing approaches that operate outside the library. The utility of the framework is demonstrated by analyzing communication-computation overlap for micro-benchmarks and the NAS benchmarks, and the insights obtained are used to modify the NAS SP benchmark, resulting in improved overlap.

  14. 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.

  15. 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.

  16. 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.

  17. Overlapped optics induced perfect coherent effects

    Science.gov (United States)

    Li, Jian Jie; Zang, Xiao Fei; Mao, Jun Fa; Tang, Min; Zhu, Yi Ming; Zhuang, Song Lin

    2013-12-01

    For traditional coherent effects, two separated identical point sources can be interfered with each other only when the optical path difference is integer number of wavelengths, leading to alternate dark and bright fringes for different optical path difference. For hundreds of years, such a perfect coherent condition seems insurmountable. However, in this paper, based on transformation optics, two separated in-phase identical point sources can induce perfect interference with each other without satisfying the traditional coherent condition. This shifting illusion media is realized by inductor-capacitor transmission line network. Theoretical analysis, numerical simulations and experimental results are performed to confirm such a kind of perfect coherent effect and it is found that the total radiation power of multiple elements system can be greatly enhanced. Our investigation may be applicable to National Ignition Facility (NIF), Inertial Confined Fusion (ICF) of China, LED lighting technology, terahertz communication, and so on.

  18. 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.

  19. 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.

  20. 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.

  1. Stevens Johnson syndrome, toxic epidermal necrolysis and SJS-TEN overlap: A retrospective study of causative drugs and clinical outcome

    Directory of Open Access Journals (Sweden)

    Sharma Vinod

    2008-01-01

    Full Text Available Background and Aims: Stevens Johnson syndrome (SJS, toxic epidermal necrolysis (TEN and SJS-TEN overlap are serious adverse cutaneous drug reactions. Drugs are often implicated in these reactions. Methods: A retrospective analysis of inpatients′ data with these dermatological diagnoses were carried out for three years, to study the causative drugs, clinical outcome, and mortality in these conditions. Results: Thirty patients (15 TEN, nine SJS-TEN overlap, and six SJS were admitted. In 21 cases, multiple drugs were implicated whereas single drugs were responsible in nine. Anticonvulsants (35.08% were the most commonly implicated drugs followed by antibiotics (33.33% and NSAIDS (24.56%. Twenty-five patients recovered whereas five died (four TEN, one SJS-TEN overlap. Conclusion: Anticonvulsants, antibiotics and NSAIDs were the most frequently implicated drugs. TEN causes higher mortality than both SJS and SJS-TEN overlap.

  2. 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.

  3. [Suggestion and hypnosis in hysteria].

    Science.gov (United States)

    Berner, P

    1995-12-15

    Suggestive influences allow to resolve ambiguities. Normally they are only accepted if they correspond with the knowledge and believes of the subject. Under hypnosis or under the impact of serious psychic perturbations one may take up reality constructions which are not in conformity with these criteria. The restriction of consciousness and the ignoring of certain functions permitting this are the common basis of hypnosis and hysteria. But suggestions do not cause the later; they may only shape the symptomatology. Hypnosis can create a terrain facilitating the resolution of the problems underlying hysteria but it does not represent the treatment of hysteria.

  4. 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.

  5. 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.

  6. 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.

  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.

  8. 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 evalua...

  9. Extraction of pure components from overlapped signals in gas chromatography-mass spectrometry (GC-MS

    Directory of Open Access Journals (Sweden)

    Likić Vladimir A

    2009-10-01

    Full Text Available Abstract Gas chromatography-mass spectrometry (GC-MS is a widely used analytical technique for the identification and quantification of trace chemicals in complex mixtures. When complex samples are analyzed by GC-MS it is common to observe co-elution of two or more components, resulting in an overlap of signal peaks observed in the total ion chromatogram. In such situations manual signal analysis is often the most reliable means for the extraction of pure component signals; however, a systematic manual analysis over a number of samples is both tedious and prone to error. In the past 30 years a number of computational approaches were proposed to assist in the process of the extraction of pure signals from co-eluting GC-MS components. This includes empirical methods, comparison with library spectra, eigenvalue analysis, regression and others. However, to date no approach has been recognized as best, nor accepted as standard. This situation hampers general GC-MS capabilities, and in particular has implications for the development of robust, high-throughput GC-MS analytical protocols required in metabolic profiling and biomarker discovery. Here we first discuss the nature of GC-MS data, and then review some of the approaches proposed for the extraction of pure signals from co-eluting components. We summarize and classify different approaches to this problem, and examine why so many approaches proposed in the past have failed to live up to their full promise. Finally, we give some thoughts on the future developments in this field, and suggest that the progress in general computing capabilities attained in the past two decades has opened new horizons for tackling this important problem.

  10. 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.

  11. Victimization and Violent Offending: An Assessment of the Victim-Offender Overlap Among Native American Adolescents and Young Adults.

    Science.gov (United States)

    Reingle, Jennifer M; Maldonado-Molina, Mildred M

    2012-06-01

    The purpose of this article is to evaluate the victim-offender overlap among a nationally representative sample of Native American adolescents and young adults. Data for this study were obtained from 338 Native American youth who participated in the National Longitudinal Study of Adolescent Health (Add Health) Waves I-IV. Group-based trajectory modeling was used to estimate trajectories of violence and victimization separately. Bivariate tests were used to assess the overlap between victimization and violent trajectory groups. Multinomial regression procedures were used to assess the predictors of victimization, offending, and the overlap category of both victimization and offending. Three trajectory groups were found for violence (nonviolent, escalators, and desistors) and victimization (nonvictim, decreasing victimization, and increasing victimization). We found substantial evidence of an overlap between victimization and offending among Native Americans, as 27.5% of the sample reported both victimization and offending. Those in the overlap group had greater number of risk factors present at baseline. These results suggest that the victim-offender overlap is present in Native American adolescents. Explanations and implications are discussed.

  12. 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...

  13. 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.

  14. 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.

  15. 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...

  16. Genetic architecture of sporadic frontotemporal dementia and overlap with Alzheimer’s and Parkinson’s diseases

    Science.gov (United States)

    Ferrari, Raffaele; Wang, Yunpeng; Vandrovcova, Jana; Guelfi, Sebastian; Witeolar, Aree; Karch, Celeste M; Schork, Andrew J; Fan, Chun C; Brewer, James B; Schellenberg, Gerard S; Dillon, William P; Sugrue, Leo P; Hess, Christopher P; Yokoyama, Jennifer S; Bonham, Luke W; Rabinovici, Gil D; Miller, Bruce L; Andreassen, Ole A; Dale, Anders M; Hardy, John; Desikan, Rahul S

    2016-01-01

    Background Clinical, pathological and genetic overlap between sporadic frontotemporal dementia (FTD), Alzheimer’s disease (AD) and Parkinson’s disease (PD) has been suggested; however, the relationship between these disorders is still not well understood. Here we evaluated genetic overlap between FTD, AD and PD to assess shared pathobiology and identify novel genetic variants associated with increased risk for FTD. Methods Summary statistics were obtained from the International FTD Genomics Consortium, International PD Genetics Consortium and International Genomics of AD Project (n>75 000 cases and controls). We used conjunction false discovery rate (FDR) to evaluate genetic pleiotropy and conditional FDR to identify novel FTD-associated SNPs. Relevant variants were further evaluated for expression quantitative loci. Results We observed SNPs within the HLA, MAPT and APOE regions jointly contributing to increased risk for FTD and AD or PD. By conditioning on polymorphisms associated with PD and AD, we found 11 loci associated with increased risk for FTD. Meta-analysis across two independent FTD cohorts revealed a genome-wide signal within the APOE region (rs6857, 3′-UTR=PVRL2, p=2.21×10−12), and a suggestive signal for rs1358071 within the MAPT region (intronic=CRHR1, p=4.91×10−7) with the effect allele tagging the H1 haplotype. Pleiotropic SNPs at the HLA and MAPT loci associated with expression changes in cis-genes supporting involvement of intracellular vesicular trafficking, immune response and endo/lysosomal processes. Conclusions Our findings demonstrate genetic pleiotropy in these neurodegenerative diseases and indicate that sporadic FTD is a polygenic disorder where multiple pleiotropic loci with small effects contribute to increased disease risk. PMID:27899424

  17. 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.

  18. 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.)

  19. Overlap syndromes of autoimmune hepatitis: an open question.

    Science.gov (United States)

    Durazzo, Marilena; Premoli, Alberto; Paschetta, Elena; Belci, Paola; Spandre, Maurizio; Bo, Simona

    2013-02-01

    The headword "overlap syndromes" of liver diseases includes the coexistence of autoimmune hepatitis, primary biliary cirrhosis, and primary sclerosing cholangitis. These syndromes often represent a diagnostic and therapeutic challenge for hepatologists; it remains unclear whether these overlap syndromes form distinct entities or they are only variants of the major autoimmune liver diseases. The most frequent reported association occurs between autoimmune hepatitis and primary biliary cirrhosis, whereas the overlap between autoimmune hepatitis and primary sclerosing cholangitis is less frequent, typically at young age and often attendant with an inflammatory bowel disease. The choice therapy is based on ursodeoxycholic acid and immunosuppressive drugs, used at the same time or consecutively, according to the course of disease. The diagnostic scores for autoimmune hepatitis can help for diagnosis, even though their definitive soundness is lacking.

  20. 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...

  1. 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

  2. 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.

  3. Overlapping illusions by transformation optics without any negative refraction material

    Science.gov (United States)

    Sun, Fei; He, Sailing

    2016-01-01

    A novel method to achieve an overlapping illusion without any negative refraction index material is introduced with the help of the optic-null medium (ONM) designed by an extremely stretching spatial transformation. Unlike the previous methods to achieve such an optical illusion by transformation optics (TO), our method can achieve a power combination and reshape the radiation pattern at the same time. Unlike the overlapping illusion with some negative refraction index material, our method is not sensitive to the loss of the materials. Other advantages over existing methods are discussed. Numerical simulations are given to verify the performance of the proposed devices.

  4. Experimental characterization of Raman overlaps between mode-groups

    DEFF Research Database (Denmark)

    Christensen, Erik Nicolai; Koefoed, Jacob Gade; Friis, Søren Michael Mørk;

    2016-01-01

    -equalized gain. In this paper, we present an experimental characterization of the intermodal Raman intensity overlaps of a few-mode fiber using backward-pumped Raman amplification. By varying the input pump power and the degree of higher order mode-excitation for the pump and the signal in a 10km long two......-mode fiber, we are able to characterize all intermodal Raman intensity overlaps. Using these results, we perform a Raman amplification measurement and demonstrate a mode-differential gain of only 0.25dB per 10dB overall gain. This is, to the best of our knowledge, the lowest mode differential gain achieved...

  5. 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.

  6. 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.

  7. A note on Zolotarev optimal rational approximation for the overlap Dirac operator

    CERN Document Server

    Chiu, T W; Huang, C H; Huang, T R; Chiu, Ting-Wai; Hsieh, Tung-Han; Huang, Chao-Hsi; Huang, Tsung-Ren

    2002-01-01

    We discuss the salient features of Zolotarev optimal rational approximation for the inverse square root function, in particular, for its applications in lattice QCD with overlap Dirac quark. The theoretical error bound for the matrix-vector multiplication $ H_w (H_w^2)^{-1/2}Y $ is derived. We check that the error bound is always satisfied amply, for any QCD gauge configurations we have tested. An empirical formula for the error bound is determined, together with its numerical values (by evaluating elliptic functions) listed in Table 2 as well as plotted in Figure 3. Our results suggest that with Zolotarev approximation to $ (H_w^2)^{-1/2} $, one can practically preserve the exact chiral symmetry of the overlap Dirac operator to very high precision, for any gauge configurations on a finite lattice.

  8. 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.

  9. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs.

    Science.gov (United States)

    Swanson, A K; Stoltzfus, C M

    1998-12-18

    Alternative splicing is used to generate more than 30 human immunodeficiency virus type 1 (HIV-1) spliced and unspliced mRNAs from a single primary transcript. The abundance of HIV-1 mRNAs is determined by the efficiencies with which its different 5' and 3' splice sites are used. Three splice sites (A4c, A4a, and A4b) are upstream of the rev initiator AUG. RNAs spliced at A4c, A4a, and A4b are used as mRNAs for Rev. Another 3' splice site (A5) is immediately downstream of the rev initiator. RNAs spliced at A5 are used as mRNAs for Env and Nef. In this report, primer extension analysis of splicing intermediates was used to show that there are eight branch points in this region, all of which map to adenosine residues. In addition, cis elements recognized by the cellular splicing machinery overlap; the two most 3' branch points overlap with the AG dinucleotides at rev 3' splice sites A4a and A4b. Competition of the overlapping cis sites for different splicing factors may play a role in maintaining the appropriate balance of mRNAs in HIV-1-infected cells. In support of this possibility, mutations at rev 3' splice site A4b AG dinucleotide dramatically increased splicing of the env/nef 3' splice site A5. This correlated with increased usage of the four most 3' branch points, which include those within the rev 3' splice site AG dinucleotides. Consistent with these results, analysis of a mutant in which three of the four env/nef branch points were inactivated indicated that use of splice site A5 was inhibited and splicing was shifted predominantly to the most 5' rev 3' splice site A4c with preferential use of the two most 5' branch points. Our results suggest that spliceosomes formed at rev A4a-4b, rev A4c, and env/nef A5 3' splice sites each recognize different subsets of the eight branch point sequences.

  10. The geography and ecology of plant speciation: range overlap and niche divergence in sister species.

    Science.gov (United States)

    Anacker, Brian L; Strauss, Sharon Y

    2014-03-07

    A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under 'budding' speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister-non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.

  11. Segregation analysis of the testis-determining autosomal trait, Tda, that differs between the C57Bl/6J and DBA/2J mouse strains suggests a multigenic threshold model.

    Science.gov (United States)

    Eisner, J R; Eales, B A; Biddle, F G

    1996-04-01

    The testis-determining autosomal trait (Tda) of the mouse was uncovered when the Y chromosome of the poschiavinus variety of Mus musculus domesticus was introduced into the C57BL/6J laboratory strain background. Testis development is normal in the F1 generation but, in the backcross and subsequent crosses to C57BL/6J females, XY individuals with the poschiavinus Y chromosome expressed bilateral ovaries or various combinations of an ovotestis with a contralateral ovary or testis or bilateral ovotestes and few had testes bilaterally. In other strain backgrounds, such as DBA/2J, XY individuals with the poschiavinus Y chromosome always expressed normal testes bilaterally. The first breeding analysis of this difference in the interaction of strain background with the poschiavinus Y chromosome suggested that the Tda trait was due to a single gene, but attempts to map it failed. We constructed two strains of C57BL/6J and DBA/2J that are consomic for the poschiavinus Y chromosome in order to conduct a segregation analysis of the Tda trait. In the C57BL/6J.Y-POS consomic strain, liability to express incomplete testis development is normally distributed and thresholds in development specify the probability of different classes of ovary, ovotestis, and testis combinations. Testis development is complete in the DBA/2J.Y-POS consomic strain. We demonstrated previously that the Tda trait of C57BL/6J is recessive to that of DBA/2J and the segregating first backcross generation of embryos rejected the single-gene model. We have extended our analysis to a F2 generation of embryos that also rejects a single-gene model. We also report a test mating analysis of the first backcross generation. It was initiated to provide an independent assessment of the single-gene model, but the analysis of the distribution of test mating results suggests that the difference in the Tda trait between C57BL/6J and DBA/2J may be due to a small number of loci, possibly four or five, and that the

  12. 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.

  13. Correlation functions at small quark masses with overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Giusti, L. [CNRS Luminy, Marseille (France). Centre de Physique Theorique; Hernandez, P. [Edificio Institutos Investigacion, Valencia (Spain). Dpto. Fisica Teorica and IFIC; Laine, M. [Bielefeld Univ. (Germany). Fakultaet fuer Physik; Pena, C.; Wennekers, J.; Wittig, H.; Weisz, P. [Max-Planck-Institut fuer Physik, Muenchen (Germany)

    2004-09-01

    We report on recent work on the determination of low-energy constants describing {delta}S = 1 weak transitions, in order to investigate the origins of the {delta}I = 1/2 rule. We focus on numerical techniques designed to enhance the statistical signal in three-point correlation functions computed with overlap fermions near the chiral limit. (orig.)

  14. Correlation functions at small quark masses with overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Giusti, L. [Centre de Physique Theorique, CNRS Luminy, F-13288 Marseille Cedex 9 (France); Hernandez, P. [Dpto. Fisica Teorica and IFIC, Edificio Institutos Investigacion, E-46071 Valencia (Spain); Laine, M. [Faculty of Physics, University of Bielefeld, D-33501 Bielefeld (Germany); Pena, C. [Deutsches Elektronen-Synchrotron, DESY, Notkestr. 85, D-22603 Hamburg (Germany); Weisz, P. [Max-Planck-Institut fuer Physik, Foehringer Ring 6, D-80805 Munich (Germany); Wennekers, J. [Deutsches Elektronen-Synchrotron, DESY, Notkestr. 85, D-22603 Hamburg (Germany); Wittig, H. [Deutsches Elektronen-Synchrotron, DESY, Notkestr. 85, D-22603 Hamburg (Germany)

    2005-03-15

    We report on recent work on the determination of low-energy constants describing {delta}S=1 weak transitions, in order to investigate the origins of the {delta}I=1/2 rule. We focus on numerical techniques designed to enhance the statistical signal in three-point correlation functions computed with overlap fermions near the chiral limit.

  15. Correlation functions at small quark masses with overlap fermions

    CERN Document Server

    Giusti, Leonardo; Laine, Mikko; Peña, C; Weisz, P; Wennekers, J; Wittig, H

    2005-01-01

    We report on recent work on the determination of low-energy constants describing Delta{S}=1 weak transitions, in order to investigate the origins of the Delta{I}=1/2 rule. We focus on numerical techniques designed to enhance the statistical signal in three-point correlation functions computed with overlap fermions near the chiral limit.

  16. Handover Incentives for Self-Interested WLANs with Overlapping Coverage

    DEFF Research Database (Denmark)

    Fafoutis, Xenofon; Siris, Vasilios A.

    2012-01-01

    We consider an environment where self-interested IEEE 802.11 Wireless Local Area Networks (WLANs) have overlapping coverage, and investigate the incentives that can trigger handovers between the WLANs. Our focus is on the incentives for supporting handovers due solely to the improved performance ...

  17. THE ROLE OF PREPARATION IN OVERLAPPING-TASK PERFORMANCE

    NARCIS (Netherlands)

    de Jong, Robert (Rob)

    1995-01-01

    We examined how performance of two overlapping discrete tasks is organized and controlled. Experiment 1 showed that when stimuli were presented in an unexpected order, expectations rather than actual presentation order determined the order in which the two stimuli were processed. In Experiment 2, wh

  18. Room acoustic transition time based on reflection overlap

    DEFF Research Database (Denmark)

    Jeong, Cheol-Ho; Brunskog, Jonas; Jacobsen, Finn

    2010-01-01

    at time t, which is mainly controlled by the absorption characteristics of the boundary surfaces of the room. Scattering, diffuse reflections, and diffraction, which facilitate the overlapping process, have not been taken into account. Measured impulse responses show that the transition occurs earlier...... in a room with nonuniform absorption and furniture than in a room that satisfies the underlying assumptions....

  19. Room acoustic transition time based on reflection overlap

    DEFF Research Database (Denmark)

    Jeong, Cheol-Ho; Brunskog, Jonas; Jacobsen, Finn

    2013-01-01

    at time t, which is mainly controlled by the absorption characteristics of the boundary surfaces of the room. Scattering, diffuse reflections, and diffraction, which facilitate the overlapping process, have not been taken into account. Measured impulse responses show that the transition occurs earlier...... in a room with nonuniform absorption and furniture than in a room that satisfies the underlying assumptions....

  20. Interference management with partial uplink/downlink spectrum overlap

    KAUST Repository

    Randrianantenaina, Itsikiantsoa

    2016-07-26

    Simultaneous reuse of spectral resources by uplink and downlink, denoted as in-band full duplex (FD) communication, is promoted to double the spectral efficiency when compared to its half-duplex (HD) counterpart. Interference management, however, remains challenging in FD cellular networks, especially when high disparity between uplink and downlink transmission powers exists. The uplink performance can be particularly deteriorated when operating on channels that are simultaneously occupied with downlink transmission. This paper considers a cellular wireless system with partial spectrum overlap between the downlink and uplink. The performance of the system becomes, therefore, a function of the overlap fraction, as well as the power levels of both the uplink and downlink transmissions. The paper considers the problem of maximizing an overall network utility to find the uplink/downlink transmission powers and the spectrum overlap fraction between the uplink and downlink spectrum in each cell, and proposes solving the problem using interior point method. Simulations results confirm the vulnerability of the uplink performance to the FD operation, and show the superiority of the proposed scheme over the FD and HD schemes. The results further show that explicit uplink and downlink performance should be considered for efficient design of cellular networks with overlapping uplink/downlink resources. © 2016 IEEE.

  1. Two Efficient Techniques to Find Approximate Overlaps between Sequences

    Science.gov (United States)

    2017-01-01

    The next-generation sequencing (NGS) technology outputs a huge number of sequences (reads) that require further processing. After applying prefiltering techniques in order to eliminate redundancy and to correct erroneous reads, an overlap-based assembler typically finds the longest exact suffix-prefix match between each ordered pair of the input reads. However, another trend has been evolving for the purpose of solving an approximate version of the overlap problem. The main benefit of this direction is the ability to skip time-consuming error-detecting techniques which are applied in the prefiltering stage. In this work, we present and compare two techniques to solve the approximate overlap problem. The first adapts a compact prefix tree to efficiently solve the approximate all-pairs suffix-prefix problem, while the other utilizes a well-known principle, namely, the pigeonhole principle, to identify a potential overlap match in order to ultimately solve the same problem. Our results show that our solution using the pigeonhole principle has better space and time consumption over an FM-based solution, while our solution based on prefix tree has the best space consumption between all three solutions. The number of mismatches (hamming distance) is used to define the approximate matching between strings in our work.

  2. 9 CFR 121.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-01-01

    ... OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS POSSESSION, USE...; Hendra virus; Nipah virus; Rift Valley fever virus; Venezuelan equine encephalitis virus. (c) Genetic... infectious forms of any of the overlap select agent viruses listed in paragraph (b) of this section. 4 4...

  3. 42 CFR 73.4 - Overlap select agents and toxins.

    Science.gov (United States)

    2010-10-01

    ... pseudomallei (formerly Pseudomonas pseudomallei) Hendra virus Nipah virus Rift Valley fever virus Venezuelan Equine Encephalitis virus (c) Genetic Elements, Recombinant Nucleic Acids, and Recombinant Organisms: (1) Nucleic acids that can produce infectious forms of any of the overlap select agent viruses listed...

  4. On the geometry of coating layers formed by overlap

    NARCIS (Netherlands)

    Ocelik, V.; Nenadl, O.; Palavra, A.; De Hosson, J. Th. M.

    2014-01-01

    A recursive model is presented for the prediction of the profile of a coating layer formed by single track overlap. A known shape of single track is assumed and on the base of simple physical assumptions the recursive sequence is deduced to construct an entire profile of such coatings. Calculations

  5. On-the-fly Overlapping of Sparse Generations

    DEFF Research Database (Denmark)

    Sørensen, Chres Wiant; Roetter, Daniel Enrique Lucani; Fitzek, Frank

    2014-01-01

    performance and complexity as well as providing measurements in commercial devices to support our conclusions. Our results show that a judicious choice of the overlapping of the generations provides close-to-optimal delay performance, while reducing the decoding complexity by up to an order of magnitude...

  6. 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.

  7. 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.

  8. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds.

    Science.gov (United States)

    Alvarez-Martínez, Estela R; Valverde, Angel; Ramírez-Bahena, Martha Helena; García-Fraile, Paula; Tejedor, Carmen; Mateos, Pedro F; Santillana, Nery; Zúñiga, Doris; Peix, Alvaro; Velázquez, Encarna

    2009-08-01

    In this work, we analysed the core and symbiotic genes of rhizobial strains isolated from Vicia sativa in three soils from the Northwest of Spain, and compared them with other Vicia endosymbionts isolated in other geographical locations. The analysis of rrs, recA and atpD genes and 16S-23S rRNA intergenic spacer showed that the Spanish strains nodulating V. sativa are phylogenetically close to those isolated from V. sativa and V. faba in different European, American and Asian countries forming a group related to Rhizobium leguminosarum. The analysis of the nodC gene of strains nodulating V. sativa and V. faba in different continents showed they belong to a phylogenetically compact group indicating that these legumes are restrictive hosts. The results of the nodC gene analysis allow the delineation of the biovar viciae showing a common phylogenetic origin of V. sativa and V. faba endosymbionts in several continents. Since these two legume species are indigenous from Europe, our results suggest a world distribution of strains from R. leguminosarum together with the V. sativa and V. faba seeds and a close coevolution among chromosome, symbiotic genes and legume host in this Rhizobium-Vicia symbiosis.

  9. Peak overlaps and corresponding solutions in the X-ray photoelectron spectroscopic study of hydrodesulfurization catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Qiu Limei [Research Institute of Petroleum Processing, SINOPEC, 18 Xue Yuan Road, 100083 Beijing (China); Xu Guangtong, E-mail: gtxu@sina.com [Research Institute of Petroleum Processing, SINOPEC, 18 Xue Yuan Road, 100083 Beijing (China)

    2010-03-15

    Al{sub 2}O{sub 3}-SiO{sub 2}-based Co(Ni)-Mo(W)-S catalysts are widely investigated hydrodesulfurization (HDS) catalysts in recent decades. XPS is a suitable technique to detect the surface properties of HDS catalysts. Typical overlapping spectra in the XPS analysis of HDS catalysts, such as Mo3d and S2s, Si2p and bremsstrahlung-induced Al KL{sub 23}L{sub 23} using nonmonochromatic AlK{alpha} source, W4f and W5p{sub 3/2}, as well as the disturbance of Auger lines on Ni2p and Co2p, are carefully studied in the present paper. Besides, effective methods to overcome the influence of peak overlaps are illustrated. These results would provide basic and important information in interpreting XPS results of HDS catalysts.

  10. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    AlAmmouri, Ahmad

    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.

  11. Overlapping modularity at the critical point of k-clique percolation

    CERN Document Server

    Toth, Balint; Palla, Gergely

    2013-01-01

    One of the most remarkable social phenomena is the formation of communities in social networks corresponding to families, friendship circles, work teams, etc. Since people usually belong to several different communities at the same time, the induced overlaps result in an extremely complicated web of the communities themselves. Thus, uncovering the intricate community structure of social networks is a non-trivial task with great potential for practical applications, gaining a notable interest in the recent years. The Clique Percolation Method (CPM) is one of the earliest overlapping community finding methods, which was already used in the analysis of several different social networks. In this approach the communities correspond to k-clique percolation clusters, and the general heuristic for setting the parameters of the method is to tune the system just below the critical point of k-clique percolation. However, this rule is based on simple physical principles and its validity was never subject to quantitative ...

  12. 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

  13. Foraging behavior of lactating South American sea lions (Otaria flavescens) and spatial-temporal resource overlap with the Uruguayan fisheries

    Science.gov (United States)

    Riet-Sapriza, Federico G.; Costa, Daniel P.; Franco-Trecu, Valentina; Marín, Yamandú; Chocca, Julio; González, Bernardo; Beathyate, Gastón; Louise Chilvers, B.; Hückstadt, Luis A.

    2013-04-01

    Resource competition between fisheries and marine mammal continue to raise concern worldwide. Understanding this complex conflict requires data on spatial and dietary overlap of marine mammal and fisheries. In Uruguay the South American sea lions population has been dramatically declining over the past decade. The reasons for this population decline are unknown but may include the following: (1) direct harvesting; (2) reduced prey availability and distribution as a consequence of environmental change; or (3) biological interaction with fisheries. This study aims to determine resource overlap and competition between South American sea lions (SASL, Otaria flavescens, n=10) and the artisanal fisheries (AF), and the coastal bottom trawl fisheries (CBTF). We integrated data on sea lions diet (scat analysis), spatial and annual consumption estimates; and foraging behavior-satellite-tracking data from lactating SASL with data on fishing effort areas and fisheries landings. We found that lactating SASL are benthic divers and forage in shallow water within the continental shelf. SASL's foraging areas overlapped with CBTF and AF fisheries operational areas. Dietary analysis indicated a high degree of overlap between the diet of SASL and the AF and CBTF fisheries catch. The results of our work show differing degrees of spatial resource overlap with AF and CBTF, highlighting that there are differences in potential impact from each fishery; and that different management/conservation approaches may need to be taken to solve the fisheries-SASL conflict.

  14. 浅析火电工程监理现场工作问题与建议%Analysis on Problem of the Supervisor Works on the Thermal Power Engineering Scene and Suggestion

    Institute of Scientific and Technical Information of China (English)

    焦体华

    2013-01-01

      通过对火电工程建设过程中监理现场工作问题的分析,结合业主的职责和定位,对监理的管理工作提出建议,保障监理的责、权、利,提高监理的队伍素质,充分发挥工程监理的作用。%Pass the analysis of the problem of the supervisor works on the thermal power engineering scene, combine the owners of the responsibilities and position, put forward a suggestion to the supervisor’s management work, security supervisor’s responsibilities, rights, interests, improve the supervision team quality, give full play to the role of Engineering supervision.

  15. 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.

  16. Application of a Hierarchical Linear Model to the Study of Adolescent Deviance in an Overlapping Cohort Design.

    Science.gov (United States)

    Raudenbush, Stephen W.; Chan, Wing-Shing

    1993-01-01

    Used data on attitudes toward deviance during adolescence to illustrate assessment of psychometric properties of instrument for studying change, compare adequacy of linear and curvilinear growth models, control for time invariant and time-varying covariates, and link overlapping data cohorts. Findings suggest that prodeviant attitudes increased…

  17. Meta-Analysis of Genome-Wide Association Studies and Network Analysis-Based Integration with Gene Expression Data Identify New Suggestive Loci and Unravel a Wnt-Centric Network Associated with Dupuytren’s Disease

    Science.gov (United States)

    Becker, Kerstin; Siegert, Sabine; Toliat, Mohammad Reza; Du, Juanjiangmeng; Casper, Ramona; Dolmans, Guido H.; Werker, Paul M.; Tinschert, Sigrid; Franke, Andre; Gieger, Christian; Strauch, Konstantin; Nothnagel, Michael; Nürnberg, Peter; Hennies, Hans Christian

    2016-01-01

    Dupuytren´s disease, a fibromatosis of the connective tissue in the palm, is a common complex disease with a strong genetic component. Up to date nine genetic loci have been found to be associated with the disease. Six of these loci contain genes that code for Wnt signalling proteins. In spite of this striking first insight into the genetic factors in Dupuytren´s disease, much of the inherited risk in Dupuytren´s disease still needs to be discovered. The already identified loci jointly explain ~1% of the heritability in this disease. To further elucidate the genetic basis of Dupuytren´s disease, we performed a genome-wide meta-analysis combining three genome-wide association study (GWAS) data sets, comprising 1,580 cases and 4,480 controls. We corroborated all nine previously identified loci, six of these with genome-wide significance (p-value Dupuytren´s disease. PMID:27467239

  18. ASSESSMENT OF RELIABILITY OF OVERLAPPINGS IN THE COURSE OF THE WAREHOUSE RECONSTRUCTION

    Directory of Open Access Journals (Sweden)

    Dolganov Andrey Ivanovich

    2012-07-01

    As a result of a specialized analysis, the authors have identified that the probability of compliance of the steel beams with the requirements of the first group of limit states, with account for the identified damages, is equal to 5σ. The analysis of the structure of the overlapping and the columns demonstrates that their bearing capacity and rigidity are sufficient to resist the principal combinations of load, including the loads that come from the two allied loaded loaders of Doosan series (48B AC that represent a short term load.

  19. Stereo transparency in ambiguous stereograms generated by overlapping two identical dot patterns.

    Science.gov (United States)

    Watanabe, Osamu

    2009-11-30

    In binocular vision, observers can perceive transparent surfaces by fusing a stereogram composed of two overlapping patterns with different disparities. When dot patterns of two surfaces are identical, the stereogram has potential matches leading to both transparency and non-transparency (or unitary surface) perceptions. However, these two matching candidates are exclusive if the uniqueness assumption holds. This stereogram can be regarded as a random-dot version of the double-nail illusion and a stereo version of the locally paired-dot stimulus that was used to investigate the neural mechanism for motion transparency. Which surface is perceived in this ambiguous stereogram would reflect the property of the transparency detection mechanism in human stereopsis. Here we perform a parametric study to examine the perceptual property in this ambiguous stereogram. The result showed that the ability in transparency detection from this stereogram is determined by the contrast reversal ratio between overlapping patterns within small regions the width of which was about 0.4 deg. The width was similar to the receptive field sizes of neurons in striate cortex. The result suggests that the contrast reversal between two identical patterns would modulate activities of binocular neurons, and this modification gives a crucial effect on the neural representation for overlapping disparities.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. Burnout and depression: Label-related stigma, help-seeking, and syndrome overlap.

    Science.gov (United States)

    Bianchi, Renzo; Verkuilen, Jay; Brisson, Romain; Schonfeld, Irvin Sam; Laurent, Eric

    2016-11-30

    We investigated whether burnout and depression differed in terms of public stigma and help-seeking attitudes and behaviors. Secondarily, we examined the overlap of burnout and depressive symptoms. A total of 1046 French schoolteachers responded to an Internet survey in November-December 2015. The survey included measures of public stigma, help-seeking attitudes and behaviors, burnout and depressive symptoms, self-rated health, neuroticism, extraversion, history of anxiety or depressive disorder, social desirability, and socio-demographic variables. The burnout label appeared to be less stigmatizing than the depression label. In either case, however, fewer than 1% of the participants exhibited stigma scores signaling agreement with the proposed stigmatizing statements. Help-seeking attitudes and behaviors did not differ between burnout and depression. Participants considered burnout and depression similarly worth-treating. A huge overlap was observed between the self-report, time-standardized measures of burnout and depressive symptoms (disattenuated correlation: .91). The overlap was further evidenced in a confirmatory factor analysis. Thus, while burnout and depression as syndromes are unlikely to be distinct, how burnout and depression are socially represented may differ. To our knowledge, this study is the first to compare burnout- and depression-related stigma and help-seeking in the French context. Cross-national, multi-occupational studies examining different facets of stigma are needed.

  5. 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.

  6. 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.

  7. 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.

  8. 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...

  9. Overlapping coalition formation games in wireless communication networks

    CERN Document Server

    Wang, Tianyu; Saad, Walid; Han, Zhu

    2017-01-01

    This brief introduces overlapping coalition formation games (OCF games), a novel mathematical framework from cooperative game theory that can be used to model, design and analyze cooperative scenarios in future wireless communication networks. The concepts of OCF games are explained, and several algorithmic aspects are studied. In addition, several major application scenarios are discussed. These applications are drawn from a variety of fields that include radio resource allocation in dense wireless networks, cooperative spectrum sensing for cognitive radio networks, and resource management for crowd sourcing. For each application, the use of OCF games is discussed in detail in order to show how this framework can be used to solve relevant wireless networking problems. Overlapping Coalition Formation Games in Wireless Communication Networks provides researchers, students and practitioners with a concise overview of existing works in this emerging area, exploring the relevant fundamental theories, key techniqu...

  10. Functional overlap of the Arabidopsis leaf and root microbiota.

    Science.gov (United States)

    Bai, Yang; Müller, Daniel B; Srinivas, Girish; Garrido-Oter, Ruben; Potthoff, Eva; Rott, Matthias; Dombrowski, Nina; Münch, Philipp C; Spaepen, Stijn; Remus-Emsermann, Mitja; Hüttel, Bruno; McHardy, Alice C; Vorholt, Julia A; Schulze-Lefert, Paul

    2015-12-17

    Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.

  11. 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.

  12. 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.

  13. 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

  14. Overlapping Domain Decomposition Methods with FreeFem++

    OpenAIRE

    Jolivet, Pierre; Hecht, Frédéric; Nataf, Frédéric; Prud'Homme, Christophe

    2012-01-01

    International audience; In this note, the performances of a framework for two-level overlapping domain decomposition methods are assessed. Numerical experiments are run on Curie, a Tier-0 system for PRACE, for two second order elliptic PDE with highly heterogeneous coefficients: a scalar equation of diffusivity and the system of linear elasticity. Those experiments yield systems with up to ten billion unknowns in 2D and one billion unknowns in 3D, solved on few thousands cores.

  15. Random matrix theory and the spectra of overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Shcheredin, S.; Bietenholz, W.; Chiarappa, T.; Jansen, K.; Nagai, K.-I

    2004-03-01

    The application of Random Matrix Theory to the Dirac operator of QCD yields predictions for the probability distributions of the lowest eigenvalues. We measured Dirac operator spectra using massless overlap fermions in quenched QCD at topological charge {nu} = 0, {+-} 1 and {+-}2, and found agreement with those predictions -- at least for the first non-zero eigenvalue -- if the volume exceeds about (1.2 fm){sup 4}.

  16. 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.

  17. 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.

  18. Managing overlapping federal FMLA and state leave regulations.

    Science.gov (United States)

    Grebowski, Lucinda S

    2002-03-01

    The overlap between the Family and Medical Leave Act and state leave laws can create complications. Employers, particularly those with multistate operations, may wish to consider an outsourced absence management system, which can remove the burden of day-to-day administration and the need to stay abreast of changing state regulations. However, employers cannot outsource the responsibility to set broad policy toward absence management.

  19. Bilateral coxitis in scleroderma-polymyositis overlap syndrome

    Science.gov (United States)

    Berrada, Khadija; Abourazzak, Fatima Ezzahra; Houssaini, Ghita Sqalli; Kadi, Nadira; Tahiri, Latifa; Amrani, Kawthar; Khammar, Zineb; Lahlou, Meriam; Berrady, Rhizlane; Rabhi, Samira; Tizniti, Siham; Bono, Wafaa; Harzy, Taoufik

    2014-01-01

    Joint manifestations in scleroderma (Scl) and polymyositis (PM) are dominated by inflammatory arthralgia. Arthritis is less common and preferentially affects the hands, wrists, knees, and ankles. Involvement of the hip has been rarely reported in the literature. We report a case of coxitis diagnosed in a patient suffering from scleroderma-polymyositis overlap syndrome successfully treated by ultrasound-guided infiltration of triamcinolone hexacetonide PMID:27708891

  20. 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.

  1. 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.

  2. Asthma, chronic obstructive pulmonary disease (COPD), and the overlap syndrome.

    Science.gov (United States)

    Nakawah, Mohammad Obadah; Hawkins, Clare; Barbandi, Farouk

    2013-01-01

    Asthma and chronic obstructive pulmonary disease (COPD) are highly prevalent chronic diseases in the general population. Both are characterized by heterogeneous chronic airway inflammation and airway obstruction. In both conditions, chronic inflammation affects the whole respiratory tract, from central to peripheral airways, with different inflammatory cells recruited, different mediators produced, and thus differing responses to therapy. Airway obstruction is typically intermittent and reversible in asthma but is progressive and largely irreversible in COPD. However, there is a considerable pathologic and functional overlap between these 2 heterogeneous disorders, particularly among the elderly, who may have components of both diseases (asthma-COPD overlap syndrome). The definitions for asthma and COPD recommended by current guidelines are useful but limited because they do not illustrate the full spectrum of obstructive airway diseases that is encountered in clinical practice. Defining asthma and COPD as separate entities neglects a considerable proportion of patients with overlapping features and is largely based on expert opinion rather than on the best current evidence. The presence of different phenotypes or components of obstructive airway diseases, therefore, needs to be addressed to individualize and optimize treatment to achieve the best effect with the fewest side effects for the patient. Although specific interventions vary by disease, the treatment goals of obstructive airway diseases are similar and driven primarily by the need to control symptoms, optimize health status, and prevent exacerbations.

  3. Statistically validated network of portfolio overlaps and systemic risk.

    Science.gov (United States)

    Gualdi, Stanislao; Cimini, Giulio; Primicerio, Kevin; Di Clemente, Riccardo; Challet, Damien

    2016-12-21

    Common asset holding by financial institutions (portfolio overlap) is nowadays regarded as an important channel for financial contagion with the potential to trigger fire sales and severe losses at the systemic level. We propose a method to assess the statistical significance of the overlap between heterogeneously diversified portfolios, which we use to build a validated network of financial institutions where links indicate potential contagion channels. The method is implemented on a historical database of institutional holdings ranging from 1999 to the end of 2013, but can be applied to any bipartite network. We find that the proportion of validated links (i.e. of significant overlaps) increased steadily before the 2007-2008 financial crisis and reached a maximum when the crisis occurred. We argue that the nature of this measure implies that systemic risk from fire sales liquidation was maximal at that time. After a sharp drop in 2008, systemic risk resumed its growth in 2009, with a notable acceleration in 2013. We finally show that market trends tend to be amplified in the portfolios identified by the algorithm, such that it is possible to have an informative signal about institutions that are about to suffer (enjoy) the most significant losses (gains).

  4. 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

  5. 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.

  6. The Evaluation of Diastolic Hypertention in Sleep Overlap Syndrome

    Directory of Open Access Journals (Sweden)

    Fariba Rezaeetalab

    2015-01-01

    Full Text Available Introduction: The overlap syndrome, consisting ofobstructive sleep apnea hypopnea syndrome (OSAHS and chronic obstructvie pulmonary disease (COPD is a major problem in COPD patients. OSHAS corresponds to the likelihood of systemic hypertension.The present study was aimed to evaluate the association between apnea-hypopnea index and diastolic blood presssure (DBP in overlap  patients. Materials and Methods: We conducted a cross-sectional study involving overnight polysomnography after measurment of resting diastolic blood pressure (DBP in patients with overlap syndrome in Sleep Laboartory of Imam Reza Hospital, Mashhad, Iran from October 2011 to December 2012. Participants were divided into four subgroups regarding to their Apnea-Hypopnea Index (AHI (AHI 30.Descriptive statistics included age, body mass index (BMI, OSA, Apnea-Hypopnea Index (AHI, DBP, and neck circumference. Results: Sixty participants ranged between from 46 to 82 years old were entered into this study. There was statistically significant difference in mean DBP among different AHI subgroups (80±0.50, 95±0.60, and 105±0.65, respectively (p

  7. STITCHER 2.0: primer design for overlapping PCR applications.

    Science.gov (United States)

    O'Halloran, Damien M; Uriagereka-Herburger, Isabel; Bode, Katrin

    2017-03-30

    Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to 'stitch' individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user's input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.

  8. STITCHER 2.0: primer design for overlapping PCR applications

    Science.gov (United States)

    O’Halloran, Damien M.; Uriagereka-Herburger, Isabel; Bode, Katrin

    2017-01-01

    Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to ‘stitch’ individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user’s input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html. PMID:28358011

  9. QM/MM analysis suggests that Alkaline Phosphatase (AP) and Nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily

    Science.gov (United States)

    Hou, Guanhua

    2011-01-01

    Several members of the Alkaline Phosphatase (AP) superfamily exhibit a high level of catalytic proficiency and promiscuity in structurally similar active sites. A thorough characterization of the nature of transition state for different substrates in these enzymes is crucial for understanding the molecular mechanisms that govern those remarkable catalytic properties. In this work, we study the hydrolysis of a phosphate diester, MpNPP−, in solution, two experimentally well-characterized variants of AP (R166S AP, R166S/E322Y AP) and wild type Nucleotide pyrophosphatase/phosphodiesterase (NPP) by QM/MM calculations in which the QM method is an approximate density functional theory previously parameterized for phosphate hydrolysis (SCC-DFTBPR). The general agreements found between these calculations and available experimental data for both solution and enzymes support the use of SCC-DFTBPR/MM for a semi-quantitative analysis of the catalytic mechanism and nature of transition state in AP and NPP. Although phosphate diesters are cognate substrates for NPP but promiscuous substrates for AP, the calculations suggest that their hydrolysis reactions catalyzed by AP and NPP feature similar synchronous transition states that are slightly tighter in nature compared to that in solution, due in part to the geometry of the bimetallic zinc motif. Therefore, this study provides the first direct computational support to the hypothesis that enzymes in the AP superfamily catalyze cognate and promiscuous substrates via similar transition states to those in solution. Our calculations do not support the finding of recent QM/MM studies by López-Canut and coworkers, who suggested that the same diester substrate goes through a much looser transition state in NPP/AP than in solution, a result likely biased by the large structural distortion of the bimetallic zinc site in their simulations. Finally, our calculations for different phosphate diester orientations and phosphorothioate diesters

  10. 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

    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 Leu......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...... inhibition of dopamine transport by cocaine....

  11. 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.

  12. 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.

  13. 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.

  14. A novel approach for efficient extrication of overlapping chromosomes in automated karyotyping.

    Science.gov (United States)

    Munot, Mousami V; Mukherjee, Jayanta; Joshi, Madhuri

    2013-12-01

    Since the introduction of the automated karyotyping systems, segmentation and classification of touching and overlapping chromosomes in the metaphase images are major challenges. The earlier reported techniques for disentangling the chromosome overlaps have limited success and use only color information in case of multispectral imaging. Most of them are restricted to separation of single overlap of two chromosomes. This paper introduces a novel algorithm to extricate overlapping chromosomes in a metaphase image. The proposed technique uses Delaunay triangulation to automatically identify the number of overlaps in a cluster followed by the detection of the appropriate cut-points. The banding information on the overlapped region further resolves the set of overlapping chromosomes with the identified cut-points. The proposed algorithm has been tested with four data sets of 60 overlapping cases, obtained from publically available databases and private genetic labs. The experimental results provide an overall accuracy of 75–100 % for resolving the cluster of 1–6 overlaps.

  15. 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.

  16. 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.

  17. 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.

  18. The cumulative overlap distribution function in spin glasses: mean field vs. three dimensions

    Science.gov (United States)

    Yllanes, David; Billoire, Alain; Maiorano, Andrea; Marinari, Enzo; Martin-Mayor, Victor

    2015-03-01

    We use a sample-dependent analysis, based on medians and quantiles, to analyze the behavior of the overlap probability distribution in spin glasses. Using analytical and numerical mean-field results for the Sherrington-Kirkpatrick model, as well as data from toy models, we show that this approach is an effective tool to distinguish the low-temperature behavior of replica symmmetry breaking systems from that expected in the droplet picture. An application of the method to the three-dimensional Edwards-Anderson models shows agreement with the replica symmetry breaking predictions. Supported by ERC Grant No. 247328 and from MINECO (Spain), Contract No. FIS2012-35719-C02.

  19. 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.

  20. 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.