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Sample records for composite transcriptional signature

  1. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

    Science.gov (United States)

    Le Billan, Florian; Amazit, Larbi; Bleakley, Kevin; Xue, Qiong-Yao; Pussard, Eric; Lhadj, Christophe; Kolkhof, Peter; Viengchareun, Say; Fagart, Jérôme; Lombès, Marc

    2018-05-07

    Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldosterone and cortisol and GR essentially activated by cortisol. Their coexpression and ability to bind similar DNA motifs highlight the need to investigate their respective contributions to overall corticosteroid signaling. Here, we decipher the transcriptional regulatory mechanisms that underlie selective effects of MRs and GRs on shared genomic targets in a human renal cellular model. Kinetic, serial, and sequential chromatin immunoprecipitation approaches were performed on the period circadian protein 1 ( PER1) target gene, providing evidence that both receptors dynamically and cyclically interact at the same target promoter in a specific and distinct transcriptional signature. During this process, both receptors regulate PER1 gene by binding as homo- or heterodimers to the same promoter region. Our results suggest a novel level of MR-GR target gene regulation, which should be considered for a better and integrated understanding of corticosteroid-related pathophysiology.-Le Billan, F., Amazit, L., Bleakley, K., Xue, Q.-Y., Pussard, E., Lhadj, C., Kolkhof, P., Viengchareun, S., Fagart, J., Lombès, M. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

  2. First Exon Length Controls Active Chromatin Signatures and Transcription

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    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  3. Strong signatures of right-handed compositeness

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    Redi, Michele [INFN, Sesto Fiorentino, Firenze (Italy); Sanz, Veronica [York Univ., Toronto, ON (Canada). Dept. of Physics and Astronomy; Sussex Univ., Brighton (United Kingdom). Dept. of Physics and Astronomy; Vries, Maikel de; Weiler, Andreas [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-05-15

    Right-handed light quarks could be significantly composite, yet compatible with experimental searches at the LHC and precision tests on Standard Model couplings. In these scenarios, that are motivated by flavor physics, one expects large cross sections for the production of new resonances coupled to light quarks. We study experimental strong signatures of right-handed compositeness at the LHC, and constrain the parameter space of these models with recent results by ATLAS and CMS. We show that the LHC sensitivity could be significantly improved if dedicated searches were performed, in particular in multi-jet signals.

  4. Can specific transcriptional regulators assemble a universal cancer signature?

    Science.gov (United States)

    Roy, Janine; Isik, Zerrin; Pilarsky, Christian; Schroeder, Michael

    2013-10-01

    Recently, there is a lot of interest in using biomarker signatures derived from gene expression data to predict cancer progression. We assembled signatures of 25 published datasets covering 13 types of cancers. How do these signatures compare with each other? On one hand signatures answering the same biological question should overlap, whereas signatures predicting different cancer types should differ. On the other hand, there could also be a Universal Cancer Signature that is predictive independently of the cancer type. Initially, we generate signatures for all datasets using classical approaches such as t-test and fold change and then, we explore signatures resulting from a network-based method, that applies the random surfer model of Google's PageRank algorithm. We show that the signatures as published by the authors and the signatures generated with classical methods do not overlap - not even for the same cancer type - whereas the network-based signatures strongly overlap. Selecting 10 out of 37 universal cancer genes gives the optimal prediction for all cancers thus taking a first step towards a Universal Cancer Signature. We furthermore analyze and discuss the involved genes in terms of the Hallmarks of cancer and in particular single out SP1, JUN/FOS and NFKB1 and examine their specific role in cancer progression.

  5. Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers.

    Science.gov (United States)

    Bloom, Chloe I; Graham, Christine M; Berry, Matthew P R; Rozakeas, Fotini; Redford, Paul S; Wang, Yuanyuan; Xu, Zhaohui; Wilkinson, Katalin A; Wilkinson, Robert J; Kendrick, Yvonne; Devouassoux, Gilles; Ferry, Tristan; Miyara, Makoto; Bouvry, Diane; Valeyre, Dominique; Dominique, Valeyre; Gorochov, Guy; Blankenship, Derek; Saadatian, Mitra; Vanhems, Phillip; Beynon, Huw; Vancheeswaran, Rama; Wickremasinghe, Melissa; Chaussabel, Damien; Banchereau, Jacques; Pascual, Virginia; Ho, Ling-Pei; Lipman, Marc; O'Garra, Anne

    2013-01-01

    New approaches to define factors underlying the immunopathogenesis of pulmonary diseases including sarcoidosis and tuberculosis are needed to develop new treatments and biomarkers. Comparing the blood transcriptional response of tuberculosis to other similar pulmonary diseases will advance knowledge of disease pathways and help distinguish diseases with similar clinical presentations. To determine the factors underlying the immunopathogenesis of the granulomatous diseases, sarcoidosis and tuberculosis, by comparing the blood transcriptional responses in these and other pulmonary diseases. We compared whole blood genome-wide transcriptional profiles in pulmonary sarcoidosis, pulmonary tuberculosis, to community acquired pneumonia and primary lung cancer and healthy controls, before and after treatment, and in purified leucocyte populations. An Interferon-inducible neutrophil-driven blood transcriptional signature was present in both sarcoidosis and tuberculosis, with a higher abundance and expression in tuberculosis. Heterogeneity of the sarcoidosis signature correlated significantly with disease activity. Transcriptional profiles in pneumonia and lung cancer revealed an over-abundance of inflammatory transcripts. After successful treatment the transcriptional activity in tuberculosis and pneumonia patients was significantly reduced. However the glucocorticoid-responsive sarcoidosis patients showed a significant increase in transcriptional activity. 144-blood transcripts were able to distinguish tuberculosis from other lung diseases and controls. Tuberculosis and sarcoidosis revealed similar blood transcriptional profiles, dominated by interferon-inducible transcripts, while pneumonia and lung cancer showed distinct signatures, dominated by inflammatory genes. There were also significant differences between tuberculosis and sarcoidosis in the degree of their transcriptional activity, the heterogeneity of their profiles and their transcriptional response to treatment.

  6. Identification of a transcriptional signature for the wound healing continuum

    OpenAIRE

    Peake, Matthew A; Caley, Mathew; Giles, Peter J; Wall, Ivan; Enoch, Stuart; Davies, Lindsay C; Kipling, David; Thomas, David W; Stephens, Phil

    2014-01-01

    There is a spectrum/continuum of adult human wound healing outcomes ranging from the enhanced (nearly scarless) healing observed in oral mucosa to scarring within skin and the nonhealing of chronic skin wounds. Central to these outcomes is the role of the fibroblast. Global gene expression profiling utilizing microarrays is starting to give insight into the role of such cells during the healing process, but no studies to date have produced a gene signature for this wound healing continuum. Mi...

  7. Identification of a transcriptional signature for the wound healing continuum

    Science.gov (United States)

    Peake, Matthew A; Caley, Mathew; Giles, Peter J; Wall, Ivan; Enoch, Stuart; Davies, Lindsay C; Kipling, David; Thomas, David W; Stephens, Phil

    2014-01-01

    There is a spectrum/continuum of adult human wound healing outcomes ranging from the enhanced (nearly scarless) healing observed in oral mucosa to scarring within skin and the nonhealing of chronic skin wounds. Central to these outcomes is the role of the fibroblast. Global gene expression profiling utilizing microarrays is starting to give insight into the role of such cells during the healing process, but no studies to date have produced a gene signature for this wound healing continuum. Microarray analysis of adult oral mucosal fibroblast (OMF), normal skin fibroblast (NF), and chronic wound fibroblast (CWF) at 0 and 6 hours post-serum stimulation was performed. Genes whose expression increases following serum exposure in the order OMF healing phenotype (the dysfunctional healing group), whereas genes with the converse pattern are potentially associated with a positive/preferential healing phenotype (the enhanced healing group). Sixty-six genes in the enhanced healing group and 38 genes in the dysfunctional healing group were identified. Overrepresentation analysis revealed pathways directly and indirectly associated with wound healing and aging and additional categories associated with differentiation, development, and morphogenesis. Knowledge of this wound healing continuum gene signature may in turn assist in the therapeutic assessment/treatment of a patient's wounds. PMID:24844339

  8. Identification of a transcriptional signature for the wound healing continuum.

    Science.gov (United States)

    Peake, Matthew A; Caley, Mathew; Giles, Peter J; Wall, Ivan; Enoch, Stuart; Davies, Lindsay C; Kipling, David; Thomas, David W; Stephens, Phil

    2014-01-01

    There is a spectrum/continuum of adult human wound healing outcomes ranging from the enhanced (nearly scarless) healing observed in oral mucosa to scarring within skin and the nonhealing of chronic skin wounds. Central to these outcomes is the role of the fibroblast. Global gene expression profiling utilizing microarrays is starting to give insight into the role of such cells during the healing process, but no studies to date have produced a gene signature for this wound healing continuum. Microarray analysis of adult oral mucosal fibroblast (OMF), normal skin fibroblast (NF), and chronic wound fibroblast (CWF) at 0 and 6 hours post-serum stimulation was performed. Genes whose expression increases following serum exposure in the order OMF healing phenotype (the dysfunctional healing group), whereas genes with the converse pattern are potentially associated with a positive/preferential healing phenotype (the enhanced healing group). Sixty-six genes in the enhanced healing group and 38 genes in the dysfunctional healing group were identified. Overrepresentation analysis revealed pathways directly and indirectly associated with wound healing and aging and additional categories associated with differentiation, development, and morphogenesis. Knowledge of this wound healing continuum gene signature may in turn assist in the therapeutic assessment/treatment of a patient's wounds. © 2014 The Authors. Wound Repair and Regeneration published by Wiley Periodicals, Inc. on behalf of Wound Healing Society.

  9. Molecular signatures define alopecia areata subtypes and transcriptional biomarkers

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    Ali Jabbari

    2016-05-01

    Full Text Available Alopecia areata (AA is an autoimmune disease typified by nonscarring hair loss with a variable clinical course. In this study, we conducted whole genome gene expression analysis of 96 human scalp skin biopsy specimens from AA or normal control subjects. Based on gene expression profiling, samples formed distinct clusters based on the presence or absence of disease as well as disease phenotype (patchy disease compared with alopecia totalis or universalis. Differential gene expression analysis allowed us to robustly demonstrate graded immune activity in samples of increasing phenotypic severity and generate a quantitative gene expression scoring system that classified samples based on interferon and cytotoxic T lymphocyte immune signatures critical for disease pathogenesis.

  10. Signatures of DNA target selectivity by ETS transcription factors.

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    Poon, Gregory M K; Kim, Hye Mi

    2017-05-27

    The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.

  11. Novel transcriptional signatures for sputum-independent diagnostics of tuberculosis in children

    DEFF Research Database (Denmark)

    Gjøen, John Espen; Jenum, Synne; Sivakumaran, Dhanasekaran

    2017-01-01

    Pediatric tuberculosis (TB) is challenging to diagnose, confirmed by growth of Mycobacterium tuberculosis at best in 40% of cases. The WHO has assigned high priority to the development of non-sputum diagnostic tools. We therefore sought to identify transcriptional signatures in whole blood...

  12. Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing

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    Anderson Donald M

    2006-04-01

    Full Text Available Abstract Background Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS. Results Data from the two MPSS libraries showed that the number of unique signatures found in A. fundyense cells is similar to that of humans and Arabidopsis thaliana, two eukaryotes that have been extensively analyzed using this method. The general distribution, abundance and expression patterns of the A. fundyense signatures were also quite similar to other eukaryotes, and at least 10% of the A. fundyense signatures were differentially expressed between the two conditions. RACE amplification and sequencing of a subset of signatures showed that multiple signatures arose from sequence variants of a single gene. Single signatures also mapped to different sequence variants of the same gene. Conclusion The MPSS data presented here provide a quantitative view of the transcriptome and its regulation in these unusual single-celled eukaryotes. The observed signature abundance and distribution in Alexandrium is similar to that of other eukaryotes that have been analyzed using MPSS. Results of signature mapping via RACE indicate that many signatures result from sequence variants of individual genes. These data add to the growing body of evidence for widespread gene

  13. A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.

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    Francesco Iorio

    Full Text Available We present a novel strategy to identify drug-repositioning opportunities. The starting point of our method is the generation of a signature summarising the consensual transcriptional response of multiple human cell lines to a compound of interest (namely the seed compound. This signature can be derived from data in existing databases, such as the connectivity-map, and it is used at first instance to query a network interlinking all the connectivity-map compounds, based on the similarity of their transcriptional responses. This provides a drug neighbourhood, composed of compounds predicted to share some effects with the seed one. The original signature is then refined by systematically reducing its overlap with the transcriptional responses induced by drugs in this neighbourhood that are known to share a secondary effect with the seed compound. Finally, the drug network is queried again with the resulting refined signatures and the whole process is carried on for a number of iterations. Drugs in the final refined neighbourhood are then predicted to exert the principal mode of action of the seed compound. We illustrate our approach using paclitaxel (a microtubule stabilising agent as seed compound. Our method predicts that glipizide and splitomicin perturb microtubule function in human cells: a result that could not be obtained through standard signature matching methods. In agreement, we find that glipizide and splitomicin reduce interphase microtubule growth rates and transiently increase the percentage of mitotic cells-consistent with our prediction. Finally, we validated the refined signatures of paclitaxel response by mining a large drug screening dataset, showing that human cancer cell lines whose basal transcriptional profile is anti-correlated to them are significantly more sensitive to paclitaxel and docetaxel.

  14. The Transcriptional Signature of Active Tuberculosis Reflects Symptom Status in Extra-Pulmonary and Pulmonary Tuberculosis.

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    Simon Blankley

    Full Text Available Mycobacterium tuberculosis infection is a leading cause of infectious death worldwide. Gene-expression microarray studies profiling the blood transcriptional response of tuberculosis (TB patients have been undertaken in order to better understand the host immune response as well as to identify potential biomarkers of disease. To date most of these studies have focused on pulmonary TB patients with gene-expression profiles of extra-pulmonary TB patients yet to be compared to those of patients with pulmonary TB or sarcoidosis.A novel cohort of patients with extra-pulmonary TB and sarcoidosis was recruited and the transcriptional response of these patients compared to those with pulmonary TB using a variety of transcriptomic approaches including testing a previously defined 380 gene meta-signature of active TB.The 380 meta-signature broadly differentiated active TB from healthy controls in this new dataset consisting of pulmonary and extra-pulmonary TB. The top 15 genes from this meta-signature had a lower sensitivity for differentiating extra-pulmonary TB from healthy controls as compared to pulmonary TB. We found the blood transcriptional responses in pulmonary and extra-pulmonary TB to be heterogeneous and to reflect the extent of symptoms of disease.The transcriptional signature in extra-pulmonary TB demonstrated heterogeneity of gene expression reflective of symptom status, while the signature of pulmonary TB was distinct, based on a higher proportion of symptomatic individuals. These findings are of importance for the rational design and implementation of mRNA based TB diagnostics.

  15. Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis

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    Michał Korostyński

    2017-01-01

    Full Text Available Biomarkers of osteoarthritis (OA that can accurately diagnose the disease at the earliest stage would significantly support efforts to develop treatments for prevention and early intervention. We have sought to determine the time course of alterations in peripheral blood gene expression profile associated with the development of OA. Blood samples were collected from a tail vein of individual rats with monosodium iodoacetate- (MIA- induced OA (2, 14, 21, and 28 days after the treatment. We used whole-genome microarrays to reveal OA-related transcriptional alterations of 72 transcripts. Three main groups of coexpressed genes revealed diverse time-dependent profiles of up- and downregulation. Functional links that connect expression of the gradually downregulated genes to the G13 signaling pathway were indicated. The mRNA abundance levels of the identified transcripts were further analyzed in publicly available gene expression dataset obtained from a GARP study cohort of OA patients. We revealed three-gene signature differentially expressed in both rat and human blood (TNK2, KCTD2, and WDR37. The alterations in expression of the selected transcripts in peripheral blood samples of the patients indicate heterogeneity of the OA profiles potentially related to disease progress and severity of clinical symptoms. Our study identifies several potential stage-specific biomarkers of OA progression.

  16. Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4+ T Cells in Early Human Pregnancy

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    Weihong Zeng

    2017-06-01

    Full Text Available Decidual CD4+ T (dCD4 T cells are crucial for the maternal-fetal immune tolerance required for a healthy pregnancy outcome. However, their molecular and functional characteristics are not well elucidated. In this study, we performed the first analysis of transcriptional and alternative splicing (AS landscapes for paired decidual and peripheral blood CD4+ T (pCD4 T cells in human early pregnancy using high throughput mRNA sequencing. Our data showed that dCD4 T cells are endowed with a unique transcriptional signature when compared to pCD4 T cells: dCD4 T cells upregulate 1,695 genes enriched in immune system process whereas downregulate 1,011 genes mainly related to mRNA catabolic process and the ribosome. Moreover, dCD4 T cells were observed to be at M phase, and show increased activation, proliferation, and cytokine production, as well as display an effector-memory phenotype and a heterogenous nature containing Th1, Th17, and Treg cell subsets. However, dCD4 T cells undergo a comparable number of upregulated and downregulated AS events, both of which are enriched in the genes related to cellular metabolic process. And the changes at the AS event level do not reflect measurable differences at the gene expression level in dCD4 T cells. Collectively, our findings provide a comprehensive portrait of the unique transcriptional signature and AS profile of CD4+ T cells in human decidua and help us gain more understanding of the functional characteristic of these cells during early pregnancy.

  17. Di-boson signatures as standard candles for partial compositeness

    Energy Technology Data Exchange (ETDEWEB)

    Belyaev, Alexander [School of Physics & Astronomy, University of Southampton,Southampton (United Kingdom); Particle Physics Department, Rutherford Appleton Laboratory,Chilton, Didcot, Oxon OX11 0QX (United Kingdom); Cacciapaglia, Giacomo; Cai, Haiying [Univerity of Lyon, Université Lyon 1,CNRS/IN2P3, IPNL, F-69622, Villeurbanne (France); Ferretti, Gabriele [Department of Physics, Chalmers University of Technology,Fysikgården, 41296 Göteborg (Sweden); Flacke, Thomas [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS),Daejeon, 34051 (Korea, Republic of); Department of Physics, Korea University,Seoul 136-713 (Korea, Republic of); Parolini, Alberto [Department of Physics, Korea University,Seoul 136-713 (Korea, Republic of); Serodio, Hugo [Department of Physics, Korea University,Seoul 136-713 (Korea, Republic of); Department of Astronomy and Theoretical Physics,Lund University, SE-223 62 Lund (Sweden)

    2017-01-23

    Composite Higgs Models are often constructed including fermionic top partners with a mass around the TeV scale, with the top partners playing the role of stabilizing the Higgs potential and enforcing partial compositeness for the top quark. A class of models of this kind can be formulated in terms of fermionic strongly coupled gauge theories. A common feature they all share is the presence of specific additional scalar resonances, namely two neutral singlets and a colored octet, described by a simple effective Lagrangian. We study the phenomenology of these scalars, both in a model independent and model dependent way, including the bounds from all the available searches in the relevant channels with di-boson and di-top final states. We develop a generic framework which can be used to constrain any model containing pseudo-scalar singlets or octets. Using it, we find that such signatures provide strong bounds on the compositeness scale complementary to the traditional EWPT and Higgs couplings deviations. In many cases a relatively light scalar can be on the verge of discovery as a first sign of new physics.

  18. Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes

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    Lang Thierry

    2009-03-01

    Full Text Available Abstract Background Mammal macrophages (MΦ display a wide range of functions which contribute to surveying and maintaining tissue integrity. One such function is phagocytosis, a process known to be subverted by parasites like Leishmania (L. Indeed, the intracellular development of L. amazonensis amastigote relies on the biogenesis and dynamic remodelling of a phagolysosome, termed the parasitophorous vacuole, primarily within dermal MΦ. Results Using BALB/c mouse bone marrow-derived MΦ loaded or not with amastigotes, we analyzed the transcriptional signatures of MΦ 24 h later, when the amastigote population was growing. Total RNA from MΦ cultures were processed and hybridized onto Affymetrix Mouse430_2 GeneChips®, and some transcripts were also analyzed by Real-Time quantitative PCR (RTQPCR. A total of 1,248 probe-sets showed significant differential expression. Comparable fold-change values were obtained between the Affymetrix technology and the RTQPCR method. Ingenuity Pathway Analysis software® pinpointed the up-regulation of the sterol biosynthesis pathway (p-value = 1.31e-02 involving several genes (1.95 to 4.30 fold change values, and the modulation of various genes involved in polyamine synthesis and in pro/counter-inflammatory signalling. Conclusion Our findings suggest that the amastigote growth relies on early coordinated gene expression of the MΦ lipid and polyamine pathways. Moreover, these MΦ hosting multiplying L. amazonensis amastigotes display a transcriptional profile biased towards parasite-and host tissue-protective processes.

  19. Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.

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    Enge, Martin; Arda, H Efsun; Mignardi, Marco; Beausang, John; Bottino, Rita; Kim, Seung K; Quake, Stephen R

    2017-10-05

    As organisms age, cells accumulate genetic and epigenetic errors that eventually lead to impaired organ function or catastrophic transformation such as cancer. Because aging reflects a stochastic process of increasing disorder, cells in an organ will be individually affected in different ways, thus rendering bulk analyses of postmitotic adult cells difficult to interpret. Here, we directly measure the effects of aging in human tissue by performing single-cell transcriptome analysis of 2,544 human pancreas cells from eight donors spanning six decades of life. We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift. By determining the mutational history of individual cells, we uncover a novel mutational signature in healthy aging endocrine cells. Our results demonstrate the feasibility of using single-cell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. TEXT WRITING IN SMALL CHILDREN: RELATIONSHIP BETWEEN TRANSCRIPTION AND COMPOSITION

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    BEATRIZ DIUK

    2007-11-01

    Full Text Available The work studies the relationship between word writing and text production skills in children of 1st year of BasicGeneral Education. In the frame of the cognitive psychology, the differences observed between performance inthese tasks are attributed to the difficulties in both the composition and the transcription processes. These processeswere assessed by oral and written retelling of a story test. The results showed that children performance was worsein the text production task than in the word- writing task. This difference can no be attributed to the compositionprocess, since the children evidenced good discursive skills in the oral task. The transcription skills could explain thedifferent performance in these tasks.

  1. A Resource for the Transcriptional Signature of Bona Fide Trophoblast Stem Cells and Analysis of Their Embryonic Persistence

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    Georg Kuales

    2015-01-01

    Full Text Available Trophoblast stem cells (TSCs represent the multipotent progenitors that give rise to the different cells of the embryonic portion of the placenta. Here, we analysed the expression of key TSC transcription factors Cdx2, Eomes, and Elf5 in the early developing placenta of mouse embryos and in cultured TSCs and reveal surprising heterogeneity in protein levels. We analysed persistence of TSCs in the early placenta and find that TSCs remain in the chorionic hinge until E9.5 and are lost shortly afterwards. To define the transcriptional signature of bona fide TSCs, we used inducible gain- and loss-of-function alleles of Eomes or Cdx2, and EomesGFP, to manipulate and monitor the core maintenance factors of TSCs, followed by genome-wide expression profiling. Combinatorial analysis of resulting expression profiles allowed for defining novel TSC marker genes that might functionally contribute to the maintenance of the TSC state. Analyses by qRT-PCR and in situ hybridisation validated novel TSC- and chorion-specific marker genes, such as Bok/Mtd, Cldn26, Duox2, Duoxa2, Nr0b1, and Sox21. Thus, these expression data provide a valuable resource for the transcriptional signature of bona fide and early differentiating TSCs and may contribute to an increased understanding of the transcriptional circuitries that maintain and/or establish stemness of TSCs.

  2. Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.

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    Herberg, Jethro A; Kaforou, Myrsini; Wright, Victoria J; Shailes, Hannah; Eleftherohorinou, Hariklia; Hoggart, Clive J; Cebey-López, Miriam; Carter, Michael J; Janes, Victoria A; Gormley, Stuart; Shimizu, Chisato; Tremoulet, Adriana H; Barendregt, Anouk M; Salas, Antonio; Kanegaye, John; Pollard, Andrew J; Faust, Saul N; Patel, Sanjay; Kuijpers, Taco; Martinón-Torres, Federico; Burns, Jane C; Coin, Lachlan J M; Levin, Michael

    Because clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment, while bacterial infection is missed in others. To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children. Febrile children presenting to participating hospitals in the United Kingdom, Spain, the Netherlands, and the United States between 2009-2013 were prospectively recruited, comprising a discovery group and validation group. Each group was classified after microbiological investigation as having definite bacterial infection, definite viral infection, or indeterminate infection. RNA expression signatures distinguishing definite bacterial from viral infection were identified in the discovery group and diagnostic performance assessed in the validation group. Additional validation was undertaken in separate studies of children with meningococcal disease (n = 24) and inflammatory diseases (n = 48) and on published gene expression datasets. A 2-transcript RNA expression signature distinguishing bacterial infection from viral infection was evaluated against clinical and microbiological diagnosis. Definite bacterial and viral infection was confirmed by culture or molecular detection of the pathogens. Performance of the RNA signature was evaluated in the definite bacterial and viral group and in the indeterminate infection group. The discovery group of 240 children (median age, 19 months; 62% male) included 52 with definite bacterial infection, of whom 36 (69%) required intensive care, and 92 with definite viral infection, of whom 32 (35%) required intensive care. Ninety-six children had indeterminate infection. Analysis of RNA expression data identified a 38-transcript signature distinguishing bacterial from viral infection. A smaller (2-transcript) signature (FAM89A and IFI44L) was identified by removing highly correlated transcripts. When this 2-transcript

  3. Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness.

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    Bogeas, Alexandra; Morvan-Dubois, Ghislaine; El-Habr, Elias A; Lejeune, François-Xavier; Defrance, Matthieu; Narayanan, Ashwin; Kuranda, Klaudia; Burel-Vandenbos, Fanny; Sayd, Salwa; Delaunay, Virgile; Dubois, Luiz G; Parrinello, Hugues; Rialle, Stéphanie; Fabrega, Sylvie; Idbaih, Ahmed; Haiech, Jacques; Bièche, Ivan; Virolle, Thierry; Goodhardt, Michele; Chneiweiss, Hervé; Junier, Marie-Pierre

    2018-02-01

    Although a growing body of evidence indicates that phenotypic plasticity exhibited by glioblastoma cells plays a central role in tumor development and post-therapy recurrence, the master drivers of their aggressiveness remain elusive. Here we mapped the changes in active (H3K4me3) and repressive (H3K27me3) histone modifications accompanying the repression of glioblastoma stem-like cells tumorigenicity. Genes with changing histone marks delineated a network of transcription factors related to cancerous behavior, stem state, and neural development, highlighting a previously unsuspected association between repression of ARNT2 and loss of cell tumorigenicity. Immunohistochemistry confirmed ARNT2 expression in cell sub-populations within proliferative zones of patients' glioblastoma. Decreased ARNT2 expression was consistently observed in non-tumorigenic glioblastoma cells, compared to tumorigenic cells. Moreover, ARNT2 expression correlated with a tumorigenic molecular signature at both the tissue level within the tumor core and at the single cell level in the patients' tumors. We found that ARNT2 knockdown decreased the expression of SOX9, POU3F2 and OLIG2, transcription factors implicated in glioblastoma cell tumorigenicity, and repressed glioblastoma stem-like cell tumorigenic properties in vivo. Our results reveal ARNT2 as a pivotal component of the glioblastoma cell tumorigenic signature, located at a node of a transcription factor network controlling glioblastoma cell aggressiveness.

  4. Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

    DEFF Research Database (Denmark)

    Zelezniak, Aleksej; Pers, Tune Hannes; Pinho Soares, Simao Pedro

    2010-01-01

    mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challenging task due to the complexity of transcriptional regulation and the highly interconnected nature of the metabolic network. In this study we integrate skeletal muscle gene expression datasets...... with human metabolic network reconstructions to identify key metabolic regulatory features of T2DM. These features include reporter metabolites—metabolites with significant collective transcriptional response in the associated enzyme-coding genes, and transcription factors with significant enrichment...... factor regulatory network connecting several parts of metabolism. The identified transcription factors include members of the CREB, NRF1 and PPAR family, among others, and represent regulatory targets for further experimental analysis. Overall, our results provide a holistic picture of key metabolic...

  5. Mediator Undergoes a Compositional Change during Transcriptional Activation.

    Science.gov (United States)

    Petrenko, Natalia; Jin, Yi; Wong, Koon Ho; Struhl, Kevin

    2016-11-03

    Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC). We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements. However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase. Severing the kinase module from Mediator by removing the connecting subunit Med13 does not affect Mediator association at the core promoter but increases occupancy at enhancers. Thus, Mediator undergoes a compositional change in which the kinase module, recruited via Mediator to the enhancer, dissociates from Mediator to permit association with Pol II and the PIC. As such, Mediator acts as a dynamic bridge between the enhancer and core promoter. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Identification of upstream transcription factors (TFs) for expression signature genes in breast cancer.

    Science.gov (United States)

    Zang, Hongyan; Li, Ning; Pan, Yuling; Hao, Jingguang

    2017-03-01

    Breast cancer is a common malignancy among women with a rising incidence. Our intention was to detect transcription factors (TFs) for deeper understanding of the underlying mechanisms of breast cancer. Integrated analysis of gene expression datasets of breast cancer was performed. Then, functional annotation of differentially expressed genes (DEGs) was conducted, including Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, TFs were identified and a global transcriptional regulatory network was constructed. Seven publically available GEO datasets were obtained, and a set of 1196 DEGs were identified (460 up-regulated and 736 down-regulated). Functional annotation results showed that cell cycle was the most significantly enriched pathway, which was consistent with the fact that cell cycle is closely related to various tumors. Fifty-three differentially expressed TFs were identified, and the regulatory networks consisted of 817 TF-target interactions between 46 TFs and 602 DEGs in the context of breast cancer. Top 10 TFs covering the most downstream DEGs were SOX10, NFATC2, ZNF354C, ARID3A, BRCA1, FOXO3, GATA3, ZEB1, HOXA5 and EGR1. The transcriptional regulatory networks could enable a better understanding of regulatory mechanisms of breast cancer pathology and provide an opportunity for the development of potential therapy.

  7. Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae).

    Science.gov (United States)

    Chanderbali, André S; Albert, Victor A; Leebens-Mack, Jim; Altman, Naomi S; Soltis, Douglas E; Soltis, Pamela S

    2009-06-02

    The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, male and female reproductive organs surrounded by a sterile perianth of sepals and petals constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure of floral organs, whereas the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. Here we show that broadly overlapping transcriptional programs characterize the floral transcriptome of the basal angiosperm Persea americana (avocado), whereas floral gene expression domains are considerably more organ specific in the model eudicot Arabidopsis thaliana. Our findings therefore support the "fading borders" model for organ identity determination in basal angiosperm flowers and extend it from the action of regulatory genes to downstream transcriptional programs. Furthermore, the declining expression of components of the staminal transcriptome in central and peripheral regions of Persea flowers concurs with elements of a previous hypothesis for developmental regulation in a gymnosperm "floral progenitor." Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.

  8. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Science.gov (United States)

    2010-01-01

    Background The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph) and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs) were identified as unique to the axolotl (n = 76) and tiger salamander (n = 292) than were identified as shared (n = 108). All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome-wide reduction in mRNA abundance

  9. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Directory of Open Access Journals (Sweden)

    Putta Srikrishna

    2010-06-01

    Full Text Available Abstract Background The Mexican axolotl (Ambystoma mexicanum is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs were identified as unique to the axolotl (n = 76 and tiger salamander (n = 292 than were identified as shared (n = 108. All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome

  10. Transcriptional profiling of primary endometrial epithelial cells following acute HIV-1 exposure reveals gene signatures related to innate immunity.

    Science.gov (United States)

    Zahoor, Muhammad Atif; Woods, Matthew William; Dizzell, Sara; Nazli, Aisha; Mueller, Kristen M; Nguyen, Philip V; Verschoor, Chris P; Kaushic, Charu

    2018-04-01

    Genital epithelial cells (GECs) line the mucosal surface of the female genital tract (FGT) and are the first cells that interface with both commensal microbiota and sexually transmitted pathogens. Despite the protective barrier formed by GECs, the FGT is a major site of HIV-1 infection. This highlights the importance of studying the interaction of HIV-1 and GECs. Using microarray analysis, we characterized the transcriptional profile of primary endometrial GECs grown in the presence or absence of physiological levels of E2 (10 -9  mol/L) or P4 (10 -7  mol/L) following acute exposure to HIV-1 for 6 hours. Acute exposure of primary endometrial GECs to HIV-1 resulted in the expression of genes related to inflammation, plasminogen activation, adhesion and diapedesis and interferon response. Interestingly, exposure to HIV-1 in the presence of E2 and P4 resulted in differential transcriptional profiles, suggesting that the response of primary endometrial GECs to HIV-1 exposure is modulated by female sex hormones. The gene expression signature of endometrial GECs indicates that the response of these cells may be key to determining host susceptibility to HIV-1 and that sex hormones modulate these interactions. This study allows us to explore possible mechanisms that explain the hormone-mediated fluctuation of HIV-1 susceptibility in women. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

    Science.gov (United States)

    Kim, Jong Wook; Abudayyeh, Omar O; Yeerna, Huwate; Yeang, Chen-Hsiang; Stewart, Michelle; Jenkins, Russell W; Kitajima, Shunsuke; Konieczkowski, David J; Medetgul-Ernar, Kate; Cavazos, Taylor; Mah, Clarence; Ting, Stephanie; Van Allen, Eliezer M; Cohen, Ofir; Mcdermott, John; Damato, Emily; Aguirre, Andrew J; Liang, Jonathan; Liberzon, Arthur; Alexe, Gabriella; Doench, John; Ghandi, Mahmoud; Vazquez, Francisca; Weir, Barbara A; Tsherniak, Aviad; Subramanian, Aravind; Meneses-Cime, Karina; Park, Jason; Clemons, Paul; Garraway, Levi A; Thomas, David; Boehm, Jesse S; Barbie, David A; Hahn, William C; Mesirov, Jill P; Tamayo, Pablo

    2017-08-23

    The systematic sequencing of the cancer genome has led to the identification of numerous genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states. We applied the methodology to the RAS pathway and identified nine distinct components that reflect transcriptional activities downstream of RAS and defined several functional states associated with patterns of transcriptional component activation that associates with genomic hallmarks and response to genetic and pharmacological perturbations. These results show that the Onco-GPS is an effective approach to explore the complex landscape of oncogenic cellular states across cancers, and an analytic framework to summarize knowledge, establish relationships, and generate more effective disease models for research or as part of individualized precision medicine paradigms. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Expression profiling feline peripheral blood monocytes identifies a transcriptional signature associated with type two diabetes mellitus.

    Science.gov (United States)

    O'Leary, Caroline A; Sedhom, Mamdouh; Reeve-Johnson, Mia; Mallyon, John; Irvine, Katharine M

    2017-04-01

    Diabetes mellitus is a common disease of cats and is similar to type 2 diabetes (T2D) in humans, especially with respect to the role of obesity-induced insulin resistance, glucose toxicity, decreased number of pancreatic β-cells and pancreatic amyloid deposition. Cats have thus been proposed as a valuable translational model of T2D. In humans, inflammation associated with adipose tissue is believed to be central to T2D development, and peripheral blood monocytes (PBM) are important in the inflammatory cascade which leads to insulin resistance and β-cell failure. PBM may thus provide a useful window to study the pathogenesis of diabetes mellitus in cats, however feline monocytes are poorly characterised. In this study, we used the Affymetrix Feline 1.0ST array to profile peripheral blood monocytes from 3 domestic cats with T2D and 3 cats with normal glucose tolerance. Feline monocytes were enriched for genes expressed in human monocytes, and, despite heterogeneous gene expression, we identified a T2D-associated expression signature associated with cell cycle perturbations, DNA repair and the unfolded protein response, oxidative phosphorylation and inflammatory responses. Our data provide novel insights into the feline monocyte transcriptome, and support the hypothesis that inflammatory monocytes contribute to T2D pathogenesis in cats as well as in humans. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility

    Directory of Open Access Journals (Sweden)

    Naessens Jan

    2009-05-01

    Full Text Available Abstract Background African animal trypanosomiasis (AAT caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course. Results Trypanotolerant N'Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post-infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in response to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle. Conclusion This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N'Dama cattle respond more rapidly and with a

  14. A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice.

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    Michela Riba

    Full Text Available Control of systemic iron homeostasis is interconnected with the inflammatory response through the key iron regulator, the antimicrobial peptide hepcidin. We have previously shown that mice with iron deficiency anemia (IDA-low hepcidin show a pro-inflammatory response that is blunted in iron deficient-high hepcidin Tmprss6 KO mice. The transcriptional response associated with chronic hepcidin overexpression due to genetic inactivation of Tmprss6 is unknown. By using whole genome transcription profiling of the liver and analysis of spleen immune-related genes we identified several functional pathways differentially expressed in Tmprss6 KO mice, compared to IDA animals and thus irrespective of the iron status. In the effort of defining genes potentially targets of Tmprss6 we analyzed liver gene expression changes according to the genotype and independently of treatment. Tmprss6 inactivation causes down-regulation of liver pathways connected to immune and inflammatory response as well as spleen genes related to macrophage activation and inflammatory cytokines production. The anti-inflammatory status of Tmprss6 KO animals was confirmed by the down-regulation of pathways related to immunity, stress response and intracellular signaling in both liver and spleen after LPS treatment. Opposite to Tmprss6 KO mice, Hfe(-/- mice are characterized by iron overload with inappropriately low hepcidin levels. Liver expression profiling of Hfe(-/- deficient versus iron loaded mice show the opposite expression of some of the genes modulated by the loss of Tmprss6. Altogether our results confirm the anti-inflammatory status of Tmprss6 KO mice and identify new potential target pathways/genes of Tmprss6.

  15. Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection

    Science.gov (United States)

    Pandey, Rajesh; Bhattacharya, Aniket; Bhardwaj, Vivek; Jha, Vineet; Mandal, Amit K.; Mukerji, Mitali

    2016-09-01

    Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H  2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges.

  16. A transcriptional signature of "exercise resistance" in skeletal muscle of individuals with type 2 diabetes mellitus.

    Science.gov (United States)

    Stephens, Natalie A; Xie, Hui; Johannsen, Neil M; Church, Timothy S; Smith, Steven R; Sparks, Lauren M

    2015-09-01

    Exercise benefits most, but not all, individuals with type 2 diabetes mellitus (T2DM). The aim of this study was to determine whether a proportion of individuals with T2DM would fail to demonstrate exercise-induced metabolic improvements. We hypothesized that this lack of response would be related to their skeletal muscle transcriptional profile. 42 participants with T2DM from the previously reported HART-D study underwent a 9-month supervised exercise intervention. We performed a principal components analysis to distinguish Responders from Non-Responders (n=9 each) based on: decreases in (1) HbA1c, (2) %fat (3) BMI and (4) increase in skeletal muscle mtDNA. mRNA expression patterns in muscle tissue at baseline were assessed by microarray and qRT-PCR analysis in both groups. Of 186 genes identified by microarray analysis, 70% were up-regulated in Responders and down-regulated in Non-Responders. Several genes involved in substrate metabolism and mitochondrial biogenesis were significantly different (fold-change>1.5, pexercise response in metabolic outcomes, thus allowing exercise interventions to be targeted to these individuals and aid in the identification of novel approaches to treat Non-Responders in the future. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

    Science.gov (United States)

    Cheung, Iris; Bharadwaj, Rahul; Chou, Hsin-Jung; Houston, Isaac B.; Peter, Cyril J.; Mitchell, Amanda C.; Yao, Wei-Dong; Myers, Richard H.; Chen, Jiang-fan; Preuss, Todd M.; Rogaev, Evgeny I.; Jensen, Jeffrey D.; Weng, Zhiping; Akbarian, Schahram

    2012-01-01

    Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5–1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans. PMID:23185133

  18. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling

    Science.gov (United States)

    Potempa, Krzysztof; Graham, Christine M.; Moreira-Teixeira, Lucia; McNab, Finlay W.; Howes, Ashleigh; Stavropoulos, Evangelos; Pascual, Virginia; Banchereau, Jacques; Chaussabel, Damien; O’Garra, Anne

    2016-01-01

    Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes. PMID:26918359

  19. Thermoelectric Transport Signatures of Dirac Composite Fermions in the Half-Filled Landau Level

    Science.gov (United States)

    Potter, Andrew C.; Serbyn, Maksym; Vishwanath, Ashvin

    2016-07-01

    The half-filled Landau level is expected to be approximately particle-hole symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of the compressible state observed at this filling. Recent work indicates that, when particle-hole symmetry is preserved, the composite fermions experience a quantized π -Berry phase upon winding around the composite Fermi surface, analogous to Dirac fermions at the surface of a 3D topological insulator. In contrast, the effective low-energy theory of the composite fermion liquid originally proposed by HLR lacks particle-hole symmetry and has vanishing Berry phase. In this paper, we explain how thermoelectric transport measurements can be used to test the Dirac nature of the composite fermions by quantitatively extracting this Berry phase. First, we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because of the unusual nature of particle-hole symmetry in this context and is not sensitive to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst effect) is directly related to the topological structure of the composite Fermi surface, vanishing for zero Berry phase and taking its maximal value for π Berry phase. In contrast, in purely electrical transport signatures, the Berry phase contributions appear as small corrections to a large background signal, making the Nernst effect a promising diagnostic of the Dirac nature of composite fermions.

  20. Simultaneous estimation of diet composition and calibration coefficients with fatty acid signature data

    Science.gov (United States)

    Bromaghin, Jeffrey F.; Budge, Suzanne M.; Thiemann, Gregory W.; Rode, Karyn D.

    2017-01-01

    Knowledge of animal diets provides essential insights into their life history and ecology, although diet estimation is challenging and remains an active area of research. Quantitative fatty acid signature analysis (QFASA) has become a popular method of estimating diet composition, especially for marine species. A primary assumption of QFASA is that constants called calibration coefficients, which account for the differential metabolism of individual fatty acids, are known. In practice, however, calibration coefficients are not known, but rather have been estimated in feeding trials with captive animals of a limited number of model species. The impossibility of verifying the accuracy of feeding trial derived calibration coefficients to estimate the diets of wild animals is a foundational problem with QFASA that has generated considerable criticism. We present a new model that allows simultaneous estimation of diet composition and calibration coefficients based only on fatty acid signature samples from wild predators and potential prey. Our model performed almost flawlessly in four tests with constructed examples, estimating both diet proportions and calibration coefficients with essentially no error. We also applied the model to data from Chukchi Sea polar bears, obtaining diet estimates that were more diverse than estimates conditioned on feeding trial calibration coefficients. Our model avoids bias in diet estimates caused by conditioning on inaccurate calibration coefficients, invalidates the primary criticism of QFASA, eliminates the need to conduct feeding trials solely for diet estimation, and consequently expands the utility of fatty acid data to investigate aspects of ecology linked to animal diets.

  1. A compatible interaction of Alternaria brassicicola with Arabidopsis thaliana ecotype DiG: evidence for a specific transcriptional signature

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    Gepstein Shimon

    2009-03-01

    Full Text Available Abstract Background The interaction of Arabidopsis with Alternaria brassicicola provides a model for disease caused by necrotrophs, but a drawback has been the lack of a compatible pathosystem. Infection of most ecotypes, including the widely-studied line Col-0, with this pathogen generally leads to a lesion that does not expand beyond the inoculated area. This study examines an ecotype, Dijon G (DiG, which is considered sensitive to A. brassicicola. Results We show that the interaction has the characteristics of a compatible one, with expanding rather than limited lesions. To ask whether DiG is merely more sensitive to the pathogen or, rather, interacts in distinct manner, we identified genes whose regulation differs between Col-0 and DiG challenged with A. brassicicola. Suppression subtractive hybridization was used to identify differentially expressed genes, and their expression was verified using semi-quantitative PCR. We also tested a set of known defense-related genes for differential regulation in the two plant-pathogen interactions. Several known pathogenesis-related (PR genes are up-regulated in both interactions. PR1, and a monooxygenase gene identified in this study, MO1, are preferentially up-regulated in the compatible interaction. In contrast, GLIP1, which encodes a secreted lipase, and DIOX1, a pathogen-response related dioxygenase, are preferentially up-regulated in the incompatible interaction. Conclusion The results show that DiG is not only more susceptible, but demonstrate that its interaction with A. brassicicola has a specific transcriptional signature.

  2. Transcriptional Profiling of Whole Blood Identifies a Unique 5-Gene Signature for Myelofibrosis and Imminent Myelofibrosis Transformation

    DEFF Research Database (Denmark)

    Hasselbalch, Hans Carl; Skov, Vibe; Stauffer Larsen, Thomas

    2014-01-01

    Identifying a distinct gene signature for myelofibrosis may yield novel information of the genes, which are responsible for progression of essential thrombocythemia and polycythemia vera towards myelofibrosis. We aimed at identifying a simple gene signature - composed of a few genes - which were...

  3. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and brassica napus

    Science.gov (United States)

    In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide co...

  4. Evolution of proteomes: fundamental signatures and global trends in amino acid compositions

    Directory of Open Access Journals (Sweden)

    Yeramian Edouard

    2006-12-01

    Full Text Available Abstract Background The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level. Results In this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment. Conclusion A simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.

  5. Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.

    Science.gov (United States)

    Goettel, Wolfgang; Xia, Eric; Upchurch, Robert; Wang, Ming-Li; Chen, Pengyin; An, Yong-Qiang Charles

    2014-04-23

    Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.

  6. Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    William W. Lau

    2016-12-01

    Full Text Available Background: The proliferation of publicly accessible large-scale biological data together with increasing availability of bioinformatics tools have the potential to transform biomedical research. Here we report a crowdsourcing Jamboree that explored whether a team of volunteer biologists without formal bioinformatics training could use OMiCC, a crowdsourcing web platform that facilitates the reuse and (meta- analysis of public gene expression data, to compile and annotate gene expression data, and design comparisons between disease and control sample groups. Methods: The Jamboree focused on several common human autoimmune diseases, including systemic lupus erythematosus (SLE, multiple sclerosis (MS, type I diabetes (DM1, and rheumatoid arthritis (RA, and the corresponding mouse models. Meta-analyses were performed in OMiCC using comparisons constructed by the participants to identify 1 gene expression signatures for each disease (disease versus healthy controls at the gene expression and biological pathway levels, 2 conserved signatures across all diseases within each species (pan-disease signatures, and 3 conserved signatures between species for each disease and across all diseases (cross-species signatures. Results: A large number of differentially expressed genes were identified for each disease based on meta-analysis, with observed overlap among diseases both within and across species. Gene set/pathway enrichment of upregulated genes suggested conserved signatures (e.g., interferon across all human and mouse conditions. Conclusions: Our Jamboree exercise provides evidence that when enabled by appropriate tools, a "crowd" of biologists can work together to accelerate the pace by which the increasingly large amounts of public data can be reused and meta-analyzed for generating and testing hypotheses. Our encouraging experience suggests that a similar crowdsourcing approach can be used to explore other biological questions.

  7. Transcriptional profiling of whole blood identifies a unique 5-gene signature for myelofibrosis and imminent myelofibrosis transformation.

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    Hans Carl Hasselbalch

    Full Text Available Identifying a distinct gene signature for myelofibrosis may yield novel information of the genes, which are responsible for progression of essential thrombocythemia and polycythemia vera towards myelofibrosis. We aimed at identifying a simple gene signature - composed of a few genes - which were selectively and highly deregulated in myelofibrosis patients. Gene expression microarray studies have been performed on whole blood from 69 patients with myeloproliferative neoplasms. Amongst the top-20 of the most upregulated genes in PMF compared to controls, we identified 5 genes (DEFA4, ELA2, OLFM4, CTSG, and AZU1, which were highly significantly deregulated in PMF only. None of these genes were significantly regulated in ET and PV patients. However, hierarchical cluster analysis showed that these genes were also highly expressed in a subset of patients with ET (n = 1 and PV (n = 4 transforming towards myelofibrosis and/or being featured by an aggressive phenotype. We have identified a simple 5-gene signature, which is uniquely and highly significantly deregulated in patients in transitional stages of ET and PV towards myelofibrosis and in patients with PMF only. Some of these genes are considered to be responsible for the derangement of bone marrow stroma in myelofibrosis. Accordingly, this gene-signature may reflect key processes in the pathogenesis and pathophysiology of myelofibrosis development.

  8. Transcriptional signatures in leaves of adult European beech trees (Fagus sylvatica L.) in an experimentally enhanced free air ozone setting

    Energy Technology Data Exchange (ETDEWEB)

    Olbrich, Maren, E-mail: maren.olbrich@helmholtz-muenchen.d [Institute of Biochemical Plant Pathology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, 85764 Neuherberg (Germany); Gerstner, Elke; Bahnweg, Guenther [Institute of Biochemical Plant Pathology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, 85764 Neuherberg (Germany); Haeberle, Karl-Heinz; Matyssek, Rainer [Technische Universitaet Muenchen, Ecophysiology of Plants, Am Hochanger 13, 85354 Freising (Germany); Welzl, Gerhard [Institute of Developmental Genetics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, 85764 Neuherberg (Germany); Heller, Werner; Ernst, Dieter [Institute of Biochemical Plant Pathology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, 85764 Neuherberg (Germany)

    2010-04-15

    Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavaria). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two other transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees. - At the transcriptional level, leaves of mature beech trees barely react to double ambient ozone concentrations; differences are detected primarily between sun/shade leaves and between different growing seasons.

  9. Transcriptional signatures in leaves of adult European beech trees (Fagus sylvatica L.) in an experimentally enhanced free air ozone setting

    International Nuclear Information System (INIS)

    Olbrich, Maren; Gerstner, Elke; Bahnweg, Guenther; Haeberle, Karl-Heinz; Matyssek, Rainer; Welzl, Gerhard; Heller, Werner; Ernst, Dieter

    2010-01-01

    Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavaria). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two other transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees. - At the transcriptional level, leaves of mature beech trees barely react to double ambient ozone concentrations; differences are detected primarily between sun/shade leaves and between different growing seasons.

  10. Auxin-dependent compositional change in Mediator in ARF7- and ARF19-mediated transcription.

    Science.gov (United States)

    Ito, Jun; Fukaki, Hidehiro; Onoda, Makoto; Li, Lin; Li, Chuanyou; Tasaka, Masao; Furutani, Masahiko

    2016-06-07

    Mediator is a multiprotein complex that integrates the signals from transcription factors binding to the promoter and transmits them to achieve gene transcription. The subunits of Mediator complex reside in four modules: the head, middle, tail, and dissociable CDK8 kinase module (CKM). The head, middle, and tail modules form the core Mediator complex, and the association of CKM can modify the function of Mediator in transcription. Here, we show genetic and biochemical evidence that CKM-associated Mediator transmits auxin-dependent transcriptional repression in lateral root (LR) formation. The AUXIN/INDOLE 3-ACETIC ACID 14 (Aux/IAA14) transcriptional repressor inhibits the transcriptional activity of its binding partners AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 by making a complex with the CKM-associated Mediator. In addition, TOPLESS (TPL), a transcriptional corepressor, forms a bridge between IAA14 and the CKM component MED13 through the physical interaction. ChIP assays show that auxin induces the dissociation of MED13 but not the tail module component MED25 from the ARF7 binding region upstream of its target gene. These findings indicate that auxin-induced degradation of IAA14 changes the module composition of Mediator interacting with ARF7 and ARF19 in the upstream region of their target genes involved in LR formation. We suggest that this regulation leads to a quick switch of signal transmission from ARFs to target gene expression in response to auxin.

  11. Whole genome transcript profiling of drug induced steatosis in rats reveals a gene signature predictive of outcome.

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    Nishika Sahini

    Full Text Available Drug induced steatosis (DIS is characterised by excess triglyceride accumulation in the form of lipid droplets (LD in liver cells. To explore mechanisms underlying DIS we interrogated the publically available microarray data from the Japanese Toxicogenomics Project (TGP to study comprehensively whole genome gene expression changes in the liver of treated rats. For this purpose a total of 17 and 12 drugs which are diverse in molecular structure and mode of action were considered based on their ability to cause either steatosis or phospholipidosis, respectively, while 7 drugs served as negative controls. In our efforts we focused on 200 genes which are considered to be mechanistically relevant in the process of lipid droplet biogenesis in hepatocytes as recently published (Sahini and Borlak, 2014. Based on mechanistic considerations we identified 19 genes which displayed dose dependent responses while 10 genes showed time dependency. Importantly, the present study defined 9 genes (ANGPTL4, FABP7, FADS1, FGF21, GOT1, LDLR, GK, STAT3, and PKLR as signature genes to predict DIS. Moreover, cross tabulation revealed 9 genes to be regulated ≥10 times amongst the various conditions and included genes linked to glucose metabolism, lipid transport and lipogenesis as well as signalling events. Additionally, a comparison between drugs causing phospholipidosis and/or steatosis revealed 26 genes to be regulated in common including 4 signature genes to predict DIS (PKLR, GK, FABP7 and FADS1. Furthermore, a comparison between in vivo single dose (3, 6, 9 and 24 h and findings from rat hepatocyte studies (2 h, 8 h, 24 h identified 10 genes which are regulated in common and contained 2 DIS signature genes (FABP7, FGF21. Altogether, our studies provide comprehensive information on mechanistically linked gene expression changes of a range of drugs causing steatosis and phospholipidosis and encourage the screening of DIS signature genes at the preclinical stage.

  12. Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy

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    Weihong Zeng

    2018-05-01

    Full Text Available Decidual CD8+ (dCD8 T cells have been proposed to play important roles in immune protection against the invading pathogens and in tolerance toward the growing semi-allogeneic fetus during early pregnancy. However, their phenotypic and functional characteristics remain poorly defined. Here, we performed the first analysis of the transcriptional and alternative splicing (AS signatures for human first-trimester dCD8 T cells using high-throughput mRNA sequencing. Our data revealed that dCD8 T cells have distinct transcriptional and AS landscapes when compared with their autologous peripheral blood CD8+ (pCD8 T counterparts. Furthermore, human dCD8 T cells were observed to contain CD8-Treg and effector-memory T-cell subsets, and display enhanced functionality in terms of degranulation and cytokine production on a per-cell basis. Additionally, we have identified the novel splice junctions that use a high ratio of the non-canonical splicing motif GC-AG and found that AS is not a major contributor to the gene expression-level changes between paired pCD8 and dCD8 T cells. Together, our findings not only provide a comprehensive framework of the transcriptional and AS landscapes but also reveal the functional feature of human dCD8 T cells, which are of great importance in understanding the biology of these cells and the physiology of human healthy pregnancy.

  13. A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2.

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    Christopher W Woods

    Full Text Available There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and limitations of traditional pathogen-based testing for suspected upper respiratory viral infection. We inoculated human volunteers with either influenza A (A/Brisbane/59/2007 (H1N1 or A/Wisconsin/67/2005 (H3N2, and assayed the peripheral blood transcriptome every 8 hours for 7 days. Of 41 inoculated volunteers, 18 (44% developed symptomatic infection. Using unbiased sparse latent factor regression analysis, we generated a gene signature (or factor for symptomatic influenza capable of detecting 94% of infected cases. This gene signature is detectable as early as 29 hours post-exposure and achieves maximal accuracy on average 43 hours (p = 0.003, H1N1 and 38 hours (p-value = 0.005, H3N2 before peak clinical symptoms. In order to test the relevance of these findings in naturally acquired disease, a composite influenza A signature built from these challenge studies was applied to Emergency Department patients where it discriminates between swine-origin influenza A/H1N1 (2009 infected and non-infected individuals with 92% accuracy. The host genomic response to Influenza infection is robust and may provide the means for detection before typical clinical symptoms are apparent.

  14. Computational Tools and Approaches for Design and Control of Coating and Composite Color, Appearance, and Electromagnetic Signature

    Directory of Open Access Journals (Sweden)

    Erik D. Sapper

    2013-04-01

    Full Text Available The transport behavior of electromagnetic radiation through a polymeric coating or composite is the basis for the material color, appearance, and overall electromagnetic signature. As multifunctional materials become more advanced and next generation in-service applications become more demanding, a need for predictive design of electromagnetic signature is desired. This paper presents various components developed and used in a computational suite for the study and design of electromagnetic radiation transport properties in polymeric coatings and composites. Focus is given to the treatment of the forward or direct scattering problem on surfaces and in bulk matrices of polymeric materials. The suite consists of surface and bulk light scattering simulation modules that may be coupled together to produce a multiscale model for predicting the electromagnetic signature of various material systems. Geometric optics ray tracing is used to predict surface scattering behavior of realistically rough surfaces, while a coupled ray tracing-finite element approach is used to predict bulk scattering behavior of material matrices consisting of microscale and nanoscale fillers, pigments, fibers, air voids, and other inclusions. Extension of the suite to color change and appearance metamerism is addressed, as well as the differences between discrete versus statistical material modeling.

  15. Identification of contemporary selection signatures using composite log likelihood and their associations with marbling score in Korean cattle.

    Science.gov (United States)

    Ryu, Jihye; Lee, Chaeyoung

    2014-12-01

    Positive selection not only increases beneficial allele frequency but also causes augmentation of allele frequencies of sequence variants in close proximity. Signals for positive selection were detected by the statistical differences in subsequent allele frequencies. To identify selection signatures in Korean cattle, we applied a composite log-likelihood (CLL)-based method, which calculates a composite likelihood of the allelic frequencies observed across sliding windows of five adjacent loci and compares the value with the critical statistic estimated by 50,000 permutations. Data for a total of 11,799 nucleotide polymorphisms were used with 71 Korean cattle and 209 foreign beef cattle. As a result, 147 signals were identified for Korean cattle based on CLL estimates (P selected. Further genetic association analysis with 41 intragenic variants in the selection signatures with the greatest CLL for each chromosome revealed that marbling score was associated with five variants. Intensive association studies with all the selection signatures identified in this study are required to exclude signals associated with other phenotypes or signals falsely detected and thus to identify genetic markers for meat quality. © 2014 Stichting International Foundation for Animal Genetics.

  16. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

    Science.gov (United States)

    Vignali, Marissa; Armour, Christopher D.; Chen, Jingyang; Morrison, Robert; Castle, John C.; Biery, Matthew C.; Bouzek, Heather; Moon, Wonjong; Babak, Tomas; Fried, Michal; Raymond, Christopher K.; Duffy, Patrick E.

    2011-01-01

    Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a preponderance of host RNA in clinical samples. We report here the application of RNA sequencing to clinical isolates of P. falciparum, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for parasite transcripts. Using NSR-seq, we confirmed earlier microarray studies showing upregulation of a distinct subset of genes in parasites infecting pregnant women, including that encoding the well-established pregnancy malaria vaccine candidate var2csa. We also describe a subset of parasite transcripts that distinguished parasites infecting children from those infecting pregnant women and confirmed this observation using quantitative real-time PCR and mass spectrometry proteomic analyses. Based on their putative functional properties, we propose that these proteins could have a role in childhood malaria pathogenesis. Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases. PMID:21317536

  17. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.

    Science.gov (United States)

    Vignali, Marissa; Armour, Christopher D; Chen, Jingyang; Morrison, Robert; Castle, John C; Biery, Matthew C; Bouzek, Heather; Moon, Wonjong; Babak, Tomas; Fried, Michal; Raymond, Christopher K; Duffy, Patrick E

    2011-03-01

    Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a preponderance of host RNA in clinical samples. We report here the application of RNA sequencing to clinical isolates of P. falciparum, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for parasite transcripts. Using NSR-seq, we confirmed earlier microarray studies showing upregulation of a distinct subset of genes in parasites infecting pregnant women, including that encoding the well-established pregnancy malaria vaccine candidate var2csa. We also describe a subset of parasite transcripts that distinguished parasites infecting children from those infecting pregnant women and confirmed this observation using quantitative real-time PCR and mass spectrometry proteomic analyses. Based on their putative functional properties, we propose that these proteins could have a role in childhood malaria pathogenesis. Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases.

  18. Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

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    Xu Fuyu

    2012-09-01

    Full Text Available Abstract Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa formed ten clusters of orthologous groups (COG with genes from the monocot sorghum (Sorghum bicolor and dicot Arabidopsis (Arabidopsis thaliana. The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in

  19. Tissue-specific signatures in the transcriptional response to Anaplasma phagocytophilum infection of Ixodes scapularis and Ixodes ricinus tick cell lines

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    Pilar eAlberdi

    2016-02-01

    Full Text Available Anaplasma phagocytophilum are transmitted by Ixodes spp. ticks and have become one of the most common and relevant tick-borne pathogens due to their impact on human and animal health. Recent results have increased our understanding of the molecular interactions between Ixodes scapularis and A. phagocytophilum through the demonstration of tissue-specific molecular pathways that ensure pathogen infection, development and transmission by ticks. However, little is known about the Ixodes ricinus genes and proteins involved in the response to A. phagocytophilum infection. The tick species I. scapularis and I. ricinus are evolutionarily closely related and therefore similar responses are expected in A. phagocytophilum-infected cells. However, differences may exist between I. scapularis ISE6 and I. ricinus IRE/CTVM20 tick cells associated with tissue-specific signatures of these cell lines. To address this hypothesis, the transcriptional response to A. phagocytophilum infection was characterized by RNA sequencing and compared between I. scapularis ISE6 and I. ricinus IRE/CTVM20 tick cell lines. The transcriptional response to infection of I. scapularis ISE6 cells resembled that of tick hemocytes while the response in I. ricinus IRE/CTVM20 cells was more closely related to that reported previously in infected tick midguts. The inhibition of cell apoptosis by A. phagocytophilum appears to be a key adaptation mechanism to facilitate infection of both vertebrate and tick cells and was used to investigate further the tissue-specific response of tick cell lines to pathogen infection. The results supported a role for the intrinsic pathway in the inhibition of cell apoptosis by A. phagocytophilum infection of I. scapularis ISE6 cells. In contrast, the results in I. ricinus IRE/CTVM20 cells were similar to those obtained in tick midguts and suggested a role for the JAK/STAT pathway in the inhibition of apoptosis in tick cells infected with A. phagocytophilum

  20. RNA-Sequencing Reveals Unique Transcriptional Signatures of Running and Running-Independent Environmental Enrichment in the Adult Mouse Dentate Gyrus

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    Catherine-Alexandra Grégoire

    2018-04-01

    Full Text Available Environmental enrichment (EE is a powerful stimulus of brain plasticity and is among the most accessible treatment options for brain disease. In rodents, EE is modeled using multi-factorial environments that include running, social interactions, and/or complex surroundings. Here, we show that running and running-independent EE differentially affect the hippocampal dentate gyrus (DG, a brain region critical for learning and memory. Outbred male CD1 mice housed individually with a voluntary running disk showed improved spatial memory in the radial arm maze compared to individually- or socially-housed mice with a locked disk. We therefore used RNA sequencing to perform an unbiased interrogation of DG gene expression in mice exposed to either a voluntary running disk (RUN, a locked disk (LD, or a locked disk plus social enrichment and tunnels [i.e., a running-independent complex environment (CE]. RNA sequencing revealed that RUN and CE mice showed distinct, non-overlapping patterns of transcriptomic changes versus the LD control. Bio-informatics uncovered that the RUN and CE environments modulate separate transcriptional networks, biological processes, cellular compartments and molecular pathways, with RUN preferentially regulating synaptic and growth-related pathways and CE altering extracellular matrix-related functions. Within the RUN group, high-distance runners also showed selective stress pathway alterations that correlated with a drastic decline in overall transcriptional changes, suggesting that excess running causes a stress-induced suppression of running’s genetic effects. Our findings reveal stimulus-dependent transcriptional signatures of EE on the DG, and provide a resource for generating unbiased, data-driven hypotheses for novel mediators of EE-induced cognitive changes.

  1. RNA-Sequencing Reveals Unique Transcriptional Signatures of Running and Running-Independent Environmental Enrichment in the Adult Mouse Dentate Gyrus.

    Science.gov (United States)

    Grégoire, Catherine-Alexandra; Tobin, Stephanie; Goldenstein, Brianna L; Samarut, Éric; Leclerc, Andréanne; Aumont, Anne; Drapeau, Pierre; Fulton, Stephanie; Fernandes, Karl J L

    2018-01-01

    Environmental enrichment (EE) is a powerful stimulus of brain plasticity and is among the most accessible treatment options for brain disease. In rodents, EE is modeled using multi-factorial environments that include running, social interactions, and/or complex surroundings. Here, we show that running and running-independent EE differentially affect the hippocampal dentate gyrus (DG), a brain region critical for learning and memory. Outbred male CD1 mice housed individually with a voluntary running disk showed improved spatial memory in the radial arm maze compared to individually- or socially-housed mice with a locked disk. We therefore used RNA sequencing to perform an unbiased interrogation of DG gene expression in mice exposed to either a voluntary running disk (RUN), a locked disk (LD), or a locked disk plus social enrichment and tunnels [i.e., a running-independent complex environment (CE)]. RNA sequencing revealed that RUN and CE mice showed distinct, non-overlapping patterns of transcriptomic changes versus the LD control. Bio-informatics uncovered that the RUN and CE environments modulate separate transcriptional networks, biological processes, cellular compartments and molecular pathways, with RUN preferentially regulating synaptic and growth-related pathways and CE altering extracellular matrix-related functions. Within the RUN group, high-distance runners also showed selective stress pathway alterations that correlated with a drastic decline in overall transcriptional changes, suggesting that excess running causes a stress-induced suppression of running's genetic effects. Our findings reveal stimulus-dependent transcriptional signatures of EE on the DG, and provide a resource for generating unbiased, data-driven hypotheses for novel mediators of EE-induced cognitive changes.

  2. Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

    Science.gov (United States)

    Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

    2013-01-01

    The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

  3. Contribution of Oral Language Skills, Linguistic Skills, and Transcription Skills to Chinese Written Composition among Fourth-Grade Students

    Science.gov (United States)

    Yeung, Pui-sze; Ho, Connie Suk-han; Chan, David Wai-ock; Chung, Kevin Kien-hoa

    2013-01-01

    The present study aimed to investigate the contribution of oral language skills, linguistic skills, and transcription skills to Chinese written composition among Grade 4 students in Hong Kong. Measures assessing verbal working memory, oral language skills, linguistic skills (i.e., syntactic skills and discourse skills), transcription skills (i.e.,…

  4. Type 2 diabetes alters metabolic and transcriptional signatures of glucose and amino acid metabolism during exercise and recovery

    DEFF Research Database (Denmark)

    Hansen, Jakob S; Zhao, Xinjie; Irmler, Martin

    2015-01-01

    AIMS/HYPOTHESIS: The therapeutic benefit of physical activity to prevent and treat type 2 diabetes is commonly accepted. However, the impact of the disease on the acute metabolic response is less clear. To this end, we investigated the effect of type 2 diabetes on exercise-induced plasma metabolite...... changes and the muscular transcriptional response using a complementary metabolomics/transcriptomics approach. METHODS: We analysed 139 plasma metabolites and hormones at nine time points, and whole genome expression in skeletal muscle at three time points, during a 60 min bicycle ergometer exercise...... and a 180 min recovery phase in type 2 diabetic patients and healthy controls matched for age, percentage body fat and maximal oxygen consumption (VO2). RESULTS: Pathway analysis of differentially regulated genes upon exercise revealed upregulation of regulators of GLUT4 (SLC2A4RG, FLOT1, EXOC7, RAB13...

  5. Transcriptional signature of human adipose tissue-derived stem cells (hASCs) preconditioned for chondrogenesis in hypoxic conditions

    International Nuclear Information System (INIS)

    Pilgaard, L.; Lund, P.; Duroux, M.; Lockstone, H.; Taylor, J.; Emmersen, J.; Fink, T.; Ragoussis, J.; Zachar, V.

    2009-01-01

    Hypoxia is an important factor involved in the control of stem cells. To obtain a better insight into the phenotypical changes brought about by hypoxic preconditioning prior to chondrogenic differentiation; we have investigated growth, colony-forming and chondrogenic capacity, and global transcriptional responses of six adipose tissue-derived stem cell lines expanded at oxygen concentrations ranging from ambient to 1%. The assessment of cell proliferation and colony-forming potential revealed that the hypoxic conditions corresponding to 1% oxygen played a major role. The chondrogenic inducibility, examined by high-density pellet model, however, did not improve on hypoxic preconditioning. While the microarray analysis revealed a distinctive inter-donor variability, the exposure to 1% hypoxia superseded the biological variability and produced a specific expression profile with 2581 significantly regulated genes and substantial functional enrichment in the pathways of cell proliferation and apoptosis. Additionally, exposure to 1% oxygen resulted in upregulation of factors related to angiogenesis and cell growth. In particular, leptin (LEP), the key regulator of body weight and food intake was found to be highly upregulated. In conclusion, the results of this investigation demonstrate the significance of donor demographics and the importance of further studies into the use of regulated oxygen tension as a tool for preparation of ASCs in order to exploit their full potential.

  6. Dietary alleviation of maternal obesity and diabetes: increased resistance to diet-induced obesity transcriptional and epigenetic signatures.

    Science.gov (United States)

    Attig, Linda; Vigé, Alexandre; Gabory, Anne; Karimi, Moshen; Beauger, Aurore; Gross, Marie-Sylvie; Athias, Anne; Gallou-Kabani, Catherine; Gambert, Philippe; Ekstrom, Tomas J; Jais, Jean-Philippe; Junien, Claudine

    2013-01-01

    According to the developmental origins of health and diseases (DOHaD), and in line with the findings of many studies, obesity during pregnancy is clearly a threat to the health and well-being of the offspring, later in adulthood. We previously showed that 20% of male and female inbred mice can cope with the obesogenic effects of a high-fat diet (HFD) for 20 weeks after weaning, remaining lean. However the feeding of a control diet (CD) to DIO mice during the periconceptional/gestation/lactation period led to a pronounced sex-specific shift (17% to 43%) from susceptibility to resistance to HFD, in the female offspring only. Our aim in this study was to determine how, in the context of maternal obesity and T2D, a CD could increase resistance on female fetuses. Transcriptional analyses were carried out with a custom-built mouse liver microarray and by quantitative RT-PCR for muscle and adipose tissue. Both global DNA methylation and levels of pertinent histone marks were assessed by LUMA and western blotting, and the expression of 15 relevant genes encoding chromatin-modifying enzymes was analyzed in tissues presenting global epigenetic changes. Resistance was associated with an enhancement of hepatic pathways protecting against steatosis, the unexpected upregulation of neurotransmission-related genes and the modulation of a vast imprinted gene network. Adipose tissue displayed a pronounced dysregulation of gene expression, with an upregulation of genes involved in lipid storage and adipocyte hypertrophy or hyperplasia in obese mice born to lean and obese mothers, respectively. Global DNA methylation, several histone marks and key epigenetic regulators were also altered. Whether they were themselves lean (resistant) or obese (sensitive), the offspring of lean and obese mice clearly differed in terms of several metabolic features and epigenetic marks suggesting that the effects of a HFD depend on the leanness or obesity of the mother.

  7. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  8. Beyond temperature: Clumped isotope signatures in dissolved inorganic carbon species and the influence of solution chemistry on carbonate mineral composition

    Science.gov (United States)

    Tripati, Aradhna K.; Hill, Pamela S.; Eagle, Robert A.; Mosenfelder, Jed L.; Tang, Jianwu; Schauble, Edwin A.; Eiler, John M.; Zeebe, Richard E.; Uchikawa, Joji; Coplen, Tyler B.; Ries, Justin B.; Henry, Drew

    2015-01-01

    “Clumped-isotope” thermometry is an emerging tool to probe the temperature history of surface and subsurface environments based on measurements of the proportion of 13C and 18O isotopes bound to each other within carbonate minerals in 13C18O16O22- groups (heavy isotope “clumps”). Although most clumped isotope geothermometry implicitly presumes carbonate crystals have attained lattice equilibrium (i.e., thermodynamic equilibrium for a mineral, which is independent of solution chemistry), several factors other than temperature, including dissolved inorganic carbon (DIC) speciation may influence mineral isotopic signatures. Therefore we used a combination of approaches to understand the potential influence of different variables on the clumped isotope (and oxygen isotope) composition of minerals.We conducted witherite precipitation experiments at a single temperature and at varied pH to empirically determine 13C-18O bond ordering (Δ47) and δ18O of CO32- and HCO3- molecules at a 25 °C equilibrium. Ab initio cluster models based on density functional theory were used to predict equilibrium 13C-18O bond abundances and δ18O of different DIC species and minerals as a function of temperature. Experiments and theory indicate Δ47 and δ18O compositions of CO32- and HCO3- ions are significantly different from each other. Experiments constrain the Δ47-δ18O slope for a pH effect (0.011 ± 0.001; 12 ⩾ pH ⩾ 7). Rapidly-growing temperate corals exhibit disequilibrium mineral isotopic signatures with a Δ47-δ18O slope of 0.011 ± 0.003, consistent with a pH effect.Our theoretical calculations for carbonate minerals indicate equilibrium lattice calcite values for Δ47 and δ18O are intermediate between HCO3− and CO32−. We analyzed synthetic calcites grown at temperatures ranging from 0.5 to 50 °C with and without the enzyme carbonic anhydrase present. This enzyme catalyzes oxygen isotopic exchange between DIC species and is present in many

  9. Beyond temperature: Clumped isotope signatures in dissolved inorganic carbon species and the influence of solution chemistry on carbonate mineral composition

    Science.gov (United States)

    Tripati, Aradhna K.; Hill, Pamela S.; Eagle, Robert A.; Mosenfelder, Jed L.; Tang, Jianwu; Schauble, Edwin A.; Eiler, John M.; Zeebe, Richard E.; Uchikawa, Joji; Coplen, Tyler B.; Ries, Justin B.; Henry, Drew

    2015-10-01

    ;Clumped-isotope; thermometry is an emerging tool to probe the temperature history of surface and subsurface environments based on measurements of the proportion of 13C and 18O isotopes bound to each other within carbonate minerals in 13C18O16O22- groups (heavy isotope ;clumps;). Although most clumped isotope geothermometry implicitly presumes carbonate crystals have attained lattice equilibrium (i.e., thermodynamic equilibrium for a mineral, which is independent of solution chemistry), several factors other than temperature, including dissolved inorganic carbon (DIC) speciation may influence mineral isotopic signatures. Therefore we used a combination of approaches to understand the potential influence of different variables on the clumped isotope (and oxygen isotope) composition of minerals. We conducted witherite precipitation experiments at a single temperature and at varied pH to empirically determine 13C-18O bond ordering (Δ47) and δ18O of CO32- and HCO3- molecules at a 25 °C equilibrium. Ab initio cluster models based on density functional theory were used to predict equilibrium 13C-18O bond abundances and δ18O of different DIC species and minerals as a function of temperature. Experiments and theory indicate Δ47 and δ18O compositions of CO32- and HCO3- ions are significantly different from each other. Experiments constrain the Δ47-δ18O slope for a pH effect (0.011 ± 0.001; 12 ⩾ pH ⩾ 7). Rapidly-growing temperate corals exhibit disequilibrium mineral isotopic signatures with a Δ47-δ18O slope of 0.011 ± 0.003, consistent with a pH effect. Our theoretical calculations for carbonate minerals indicate equilibrium lattice calcite values for Δ47 and δ18O are intermediate between HCO3- and CO32-. We analyzed synthetic calcites grown at temperatures ranging from 0.5 to 50 °C with and without the enzyme carbonic anhydrase present. This enzyme catalyzes oxygen isotopic exchange between DIC species and is present in many natural systems. The two

  10. Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

    DEFF Research Database (Denmark)

    Olsen, Anders Krüger; Boyd, Mette; Danielsen, Erik Thomas

    2012-01-01

    Upon developmental or environmental cues, the composition of transcription factors in a transcriptional regulatory network is deeply implicated in controlling the signature of the gene expression and thereby specifies the cell or tissue type. Novel methods including ChIP-chip and ChIP-Seq have been...

  11. Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

    DEFF Research Database (Denmark)

    Olsen, Anders Krûger; Boyd, Mette; Danielsen, Erik Thomas

    2012-01-01

    Upon developmental or environmental cues, the composition of transcription factors in a transcriptional regulatory network is deeply implicated in controlling the signature of the gene expression and thereby specifies the cell- or tissue-type. Novel methods including ChIP-chip and ChIP-Seq have...

  12. Robust Real-Time Music Transcription with a Compositional Hierarchical Model.

    Science.gov (United States)

    Pesek, Matevž; Leonardis, Aleš; Marolt, Matija

    2017-01-01

    The paper presents a new compositional hierarchical model for robust music transcription. Its main features are unsupervised learning of a hierarchical representation of input data, transparency, which enables insights into the learned representation, as well as robustness and speed which make it suitable for real-world and real-time use. The model consists of multiple layers, each composed of a number of parts. The hierarchical nature of the model corresponds well to hierarchical structures in music. The parts in lower layers correspond to low-level concepts (e.g. tone partials), while the parts in higher layers combine lower-level representations into more complex concepts (tones, chords). The layers are learned in an unsupervised manner from music signals. Parts in each layer are compositions of parts from previous layers based on statistical co-occurrences as the driving force of the learning process. In the paper, we present the model's structure and compare it to other hierarchical approaches in the field of music information retrieval. We evaluate the model's performance for the multiple fundamental frequency estimation. Finally, we elaborate on extensions of the model towards other music information retrieval tasks.

  13. AN ANOMALOUS COMPOSITION IN SLOW SOLAR WIND AS A SIGNATURE OF MAGNETIC RECONNECTION IN ITS SOURCE REGION

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, L.; Landi, E.; Lepri, S. T.; Kocher, M.; Zurbuchen, T. H.; Fisk, L. A.; Raines, J. M., E-mail: lzh@umich.edu [Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)

    2017-01-01

    In this paper, we study a subset of slow solar winds characterized by an anomalous charge state composition and ion temperatures compared to average solar wind distributions, and thus referred to as an “Outlier” wind. We find that although this wind is slower and denser than normal slow wind, it is accelerated from the same source regions (active regions and quiet-Sun regions) as the latter and its occurrence rate depends on the solar cycle. The defining property of the Outlier wind is that its charge state composition is the same as that of normal slow wind, with the only exception being a very large decrease in the abundance of fully charged species (He{sup 2+}, C{sup 6+}, N{sup 7+}, O{sup 8+}, Mg{sup 12+}), resulting in a significant depletion of the He and C element abundances. Based on these observations, we suggest three possible scenarios for the origin of this wind: (1) local magnetic waves preferentially accelerating non-fully stripped ions over fully stripped ions from a loop opened by reconnection; (2) depleted fully stripped ions already contained in the corona magnetic loops before they are opened up by reconnection; or (3) fully stripped ions depleted by Coulomb collision after magnetic reconnection in the solar corona. If any one of these three scenarios is confirmed, the Outlier wind represents a direct signature of slow wind release through magnetic reconnection.

  14. Impact of ejecta morphology and composition on the electromagnetic signatures of neutron star mergers

    Science.gov (United States)

    Wollaeger, Ryan T.; Korobkin, Oleg; Fontes, Christopher J.; Rosswog, Stephan K.; Even, Wesley P.; Fryer, Christopher L.; Sollerman, Jesper; Hungerford, Aimee L.; van Rossum, Daniel R.; Wollaber, Allan B.

    2018-04-01

    The electromagnetic transients accompanying compact binary mergers (γ-ray bursts, afterglows and 'macronovae') are crucial to pinpoint the sky location of gravitational wave sources. Macronovae are caused by the radioactivity from freshly synthesised heavy elements, e.g. from dynamic ejecta and various types of winds. We study macronova signatures by using multi-dimensional radiative transfer calculations. We employ the radiative transfer code SuperNu and state-of-the art LTE opacities for a few representative elements from the wind and dynamical ejecta (Cr, Pd, Se, Te, Br, Zr, Sm, Ce, Nd, U) to calculate synthetic light curves and spectra for a range of ejecta morphologies. The radioactive power of the resulting macronova is calculated with the detailed input of decay products. We assess the detection prospects for our most complex models, based on the portion of viewing angles that are sufficiently bright, at different cosmological redshifts (z). The brighter emission from the wind is unobscured by the lanthanides (or actinides) in some of the models, permitting non-zero detection probabilities for redshifts up to z = 0.07. We also find the nuclear mass model and the resulting radioactive heating rate are crucial for the detectability. While for the most pessimistic heating rate (from the FRDM model) no reasonable increase in the ejecta mass or velocity, or wind mass or velocity, can possibly make the light curves agree with the observed nIR excess after GRB130603B, a more optimistic heating rate (from the Duflo-Zuker model) leads to good agreement. We conclude that future reliable macronova observations would constrain nuclear heating rates, and consequently help constrain nuclear mass models.

  15. Compositional Signatures in Acoustic Backscatter Over Vegetated and Unvegetated Mixed Sand-Gravel Riverbeds

    Science.gov (United States)

    Buscombe, D.; Grams, P. E.; Kaplinski, M. A.

    2017-10-01

    Multibeam acoustic backscatter has considerable utility for remote characterization of spatially heterogeneous bed sediment composition over vegetated and unvegetated riverbeds of mixed sand and gravel. However, the use of high-frequency, decimeter-resolution acoustic backscatter for sediment classification in shallow water is hampered by significant topographic contamination of the signal. In mixed sand-gravel riverbeds, changes in the abiotic composition of sediment (such as homogeneous sand to homogeneous gravel) tend to occur over larger spatial scales than is characteristic of small-scale bedform topography (ripples, dunes, and bars) or biota (such as vascular plants and periphyton). A two-stage method is proposed to filter out the morphological contributions to acoustic backscatter. First, the residual supragrain-scale topographic effects in acoustic backscatter with small instantaneous insonified areas, caused by ambiguity in the local (beam-to-beam) bed-sonar geometry, are removed. Then, coherent scales between high-resolution topography and backscatter are identified using cospectra, which are used to design a frequency domain filter that decomposes backscatter into the (unwanted) high-pass component associated with bedform topography (ripples, dunes, and sand waves) and vegetation, and the (desired) low-frequency component associated with the composition of sediment patches superimposed on the topography. This process strengthens relationships between backscatter and sediment composition. A probabilistic framework is presented for classifying vegetated and unvegetated substrates based on acoustic backscatter at decimeter resolution. This capability is demonstrated using data collected from diverse settings within a 386 km reach of a canyon river whose bed varies among sand, gravel, cobbles, boulders, and submerged vegetation.

  16. Compositional signatures in acoustic backscatter over vegetated and unvegetated mixed sand-gravel riverbeds

    Science.gov (United States)

    Buscombe, Daniel; Grams, Paul E.; Kaplinski, Matt A.

    2017-01-01

    Multibeam acoustic backscatter has considerable utility for remote characterization of spatially heterogeneous bed sediment composition over vegetated and unvegetated riverbeds of mixed sand and gravel. However, the use of high-frequency, decimeter-resolution acoustic backscatter for sediment classification in shallow water is hampered by significant topographic contamination of the signal. In mixed sand-gravel riverbeds, changes in the abiotic composition of sediment (such as homogeneous sand to homogeneous gravel) tend to occur over larger spatial scales than is characteristic of small-scale bedform topography (ripples, dunes, and bars) or biota (such as vascular plants and periphyton). A two-stage method is proposed to filter out the morphological contributions to acoustic backscatter. First, the residual supragrain-scale topographic effects in acoustic backscatter with small instantaneous insonified areas, caused by ambiguity in the local (beam-to-beam) bed-sonar geometry, are removed. Then, coherent scales between high-resolution topography and backscatter are identified using cospectra, which are used to design a frequency domain filter that decomposes backscatter into the (unwanted) high-pass component associated with bedform topography (ripples, dunes, and sand waves) and vegetation, and the (desired) low-frequency component associated with the composition of sediment patches superimposed on the topography. This process strengthens relationships between backscatter and sediment composition. A probabilistic framework is presented for classifying vegetated and unvegetated substrates based on acoustic backscatter at decimeter resolution. This capability is demonstrated using data collected from diverse settings within a 386 km reach of a canyon river whose bed varies among sand, gravel, cobbles, boulders, and submerged vegetation.

  17. Electroweak symmetry breaking and collider signatures in the next-to-minimal composite Higgs model

    Science.gov (United States)

    Niehoff, Christoph; Stangl, Peter; Straub, David M.

    2017-04-01

    We conduct a detailed numerical analysis of the composite pseudo-Nambu-Goldstone Higgs model based on the next-to-minimal coset SO(6)/SO(5) ≅ SU(4)/Sp(4), featuring an additional SM singlet scalar in the spectrum, which we allow to mix with the Higgs boson. We identify regions in parameter space compatible with all current exper-imental constraints, including radiative electroweak symmetry breaking, flavour physics, and direct searches at colliders. We find the additional scalar, with a mass predicted to be below a TeV, to be virtually unconstrained by current LHC data, but potentially in reach of run 2 searches. Promising indirect searches include rare semi-leptonic B decays, CP violation in B s mixing, and the electric dipole moment of the neutron.

  18. Electroweak symmetry breaking and collider signatures in the next-to-minimal composite Higgs model

    Energy Technology Data Exchange (ETDEWEB)

    Niehoff, Christoph; Stangl, Peter; Straub, David M. [Excellence Cluster Universe, TUM,Boltzmannstr. 2, 85748 Garching (Germany)

    2017-04-20

    We conduct a detailed numerical analysis of the composite pseudo-Nambu-Goldstone Higgs model based on the next-to-minimal coset SO(6)/SO(5)≅SU(4)/Sp(4), featuring an additional SM singlet scalar in the spectrum, which we allow to mix with the Higgs boson. We identify regions in parameter space compatible with all current experimental constraints, including radiative electroweak symmetry breaking, flavour physics, and direct searches at colliders. We find the additional scalar, with a mass predicted to be below a TeV, to be virtually unconstrained by current LHC data, but potentially in reach of run 2 searches. Promising indirect searches include rare semi-leptonic B decays, C P violation in B{sub s} mixing, and the electric dipole moment of the neutron.

  19. An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships.

    Directory of Open Access Journals (Sweden)

    Daniel Vaiman

    Full Text Available Preeclampsia (PE is a pregnancy disorder defined by hypertension and proteinuria. This disease remains a major cause of maternal and fetal morbidity and mortality. Defective placentation is generally described as being at the root of the disease. The characterization of the transcriptome signature of the preeclamptic placenta has allowed to identify differentially expressed genes (DEGs. However, we still lack a detailed knowledge on how these DEGs impact the function of the placenta. The tools of network biology offer a methodology to explore complex diseases at a systems level. In this study we performed a cross-platform meta-analysis of seven publically available gene expression datasets comparing non-pathological and preeclamptic placentas. Using the rank product algorithm we identified a total of 369 DEGs consistently modified in PE. The DEGs were used as seeds to build both an extended physical protein-protein interactions network and a transcription factors regulatory network. Topological and clustering analysis was conducted to analyze the connectivity properties of the networks. Finally both networks were merged into a composite network which presents an integrated view of the regulatory pathways involved in preeclampsia and the crosstalk between them. This network is a useful tool to explore the relationship between the DEGs and enable hypothesis generation for functional experimentation.

  20. Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

    Science.gov (United States)

    Jahnke, Linda L.; Edger, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; DesMarais, David J.; Cady, Sherry; Hope, Janet M.; Summons, Roger E.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarkers and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber. "Thermocrinis sp. HI", Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyls. The fatty acids of all cultured organisms were dominated by a very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as CIS() monoethers with the expection of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known 'pink-streamers community' (PSC), siliceous filaments of a microbial consortia growing in the upper outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic Aquificales n-C-20:1 and cy-C-21, and in addition, a series of iso-branched fatty acids from i-C-15:0 to i-C-21:0, With i-C-17:0 dominant in the PSC and i-C-19:0 in the biofilm, suggesting the presence of two major bacterial groups. Bacteriohopanepolyols were absent and the minute quantities of archaeol detected showed that Archaea were only minor constituents. Carbon isotopic compositions of the PSC yielded information about community structure and likely physiology. Biomass was C-13-depleted (10.9%) relative to available

  1. Genotypic variation in the sulfur assimilation and metabolism of onion (Allium cepa L.) I. Plant composition and transcript accumulation

    KAUST Repository

    McCallum, John A.

    2011-06-01

    Organosulfur compounds are major sinks for assimilated sulfate in onion (Allium cepa L.) and accumulation varies widely due to plant genotype and sulfur nutrition. In order to better characterise sulfur metabolism phenotypes and identify potential control points we compared plant composition and transcript accumulation of the primary sulfur assimilation pathway in the high pungency genotype \\'W202A\\' and the low pungency genotype \\'Texas Grano 438\\' grown hydroponically under S deficient (S-) and S-sufficient (S+) conditions. Accumulation of total S and alk(en)yl cysteine sulfoxide flavour precursors was significantly higher under S+ conditions and in \\'W202A\\' in agreement with previous studies. Leaf sulfate and cysteine levels were significantly higher in \\'W202A\\' and under S+. Glutathione levels were reduced by S- treatment but were not affected by genotype, suggesting that thiol pool sizes are regulated differently in mild and pungent onions. The only significant treatment effect observed on transcript accumulation in leaves was an elevated accumulation of O-acetyl serine thiol-lyase under S-. By contrast, transcript accumulation of all genes in roots was influenced by one or more treatments. APS reductase transcript level was not affected by genotype but was strongly increased by S-. Significant genotype × S treatment effects were observed in a root high affinity-sulfur transporter and ferredoxin-sulfite reductase. ATP sulfurylase transcript levels were significantly higher under S+ and in \\'W202A\\'. © 2011 Elsevier Ltd. All rights reserved.

  2. A Host Transcriptional Signature for Presymptomatic Detection of Infection in Humans Exposed to Influenza H1N1 or H3N2

    Science.gov (United States)

    2013-01-09

    intensity [6]. Although previous studies with dengue, melioidosis, tuberculosis, candidiasis , and sepsis have focused on diagnosis in patients as they...the quarantine. All subjects received oral oseltamivir (Roche Pharmaceuticals) 75 mg by mouth twice daily as treatment or prophylaxis at day 6...Lucas J, Perfect JR, Ginsburg GS (2010) Blood gene expression signatures predict invasive candidiasis . Sci Transl Med 2: 21ra17. 8. Berry MP, Graham

  3. Signature Balancing

    NARCIS (Netherlands)

    Noordkamp, H.W.; Brink, M. van den

    2006-01-01

    Signatures are an important part of the design of a ship. In an ideal situation, signatures must be as low as possible. However, due to budget constraints it is most unlikely to reach this ideal situation. The arising question is which levels of signatures are optimal given the different scenarios

  4. How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota.

    Science.gov (United States)

    Bost, Alyssa; Franzenburg, Soeren; Adair, Karen L; Martinson, Vincent G; Loeb, Greg; Douglas, Angela E

    2018-04-01

    Despite evidence from laboratory experiments that perturbation of the gut microbiota affects many traits of the animal host, our understanding of the effect of variation in microbiota composition on animals in natural populations is very limited. The core purpose of this study on the fruit fly Drosophila melanogaster was to identify the impact of natural variation in the taxonomic composition of gut bacterial communities on host traits, with the gut transcriptome as a molecular index of microbiota-responsive host traits. Use of the gut transcriptome was validated by demonstrating significant transcriptional differences between the guts of laboratory flies colonized with bacteria and maintained under axenic conditions. Wild Drosophila from six field collections made over two years had gut bacterial communities of diverse composition, dominated to varying extents by Acetobacteraceae and Enterobacteriaceae. The gut transcriptomes also varied among collections and differed markedly from those of laboratory flies. However, no overall relationship between variation in the wild fly transcriptome and taxonomic composition of the gut microbiota was evident at all taxonomic scales of bacteria tested for both individual fly genes and functional categories in Gene Ontology. We conclude that the interaction between microbiota composition and host functional traits may be confounded by uncontrolled variation in both ecological circumstance and host traits (e.g., genotype, age physiological condition) under natural conditions, and that microbiota effects on host traits identified in the laboratory should, therefore, be extrapolated to field population with great caution. © 2017 John Wiley & Sons Ltd.

  5. Construction and characterization of a forward subtracted library of blue mussels Mytilus edulis for the identification of gene transcription signatures and biomarkers of styrene exposure

    International Nuclear Information System (INIS)

    Diaz de Cerio, O.; Hands, E.; Humble, J.; Cajaraville, M.P.; Craft, J.A.; Cancio, I.

    2013-01-01

    Highlights: ► Transcription responses in blue mussels exposed to styrene have been studied by SSH. ► 1440 Clones were obtained from which 287 were sequenced. ► Immune system, cancer-related and ribosomal genes identified as upregulated genes. ► Chitin and β-1-3-glucan metabolism genes highly represented in subtracted library. -- Abstract: Transcriptional profiling can elucidate adaptive/toxicity pathways participating in achieving homeostasis or leading to pathogenesis in marine biota exposed to chemical substances. With the aim of analyzing transcriptional responses in the mussel Mytilus edulis exposed to the corrosive and putatively carcinogenic hydrocarbon styrene (3–5 ppm, 3 days), a forward subtracted (SSH) cDNA library was produced. Female mussels were selected and digestive gland mRNA was isolated. A library with 1440 clones was produced and a total of 287 clones were sequenced, 53% being identified through BlastN analysis against Mytibase and DeepSeaVent databases. Those genes included GO terms such as ‘response to drugs’, ‘immune defense’ and ‘cell proliferation’. Furthermore, sequences related to chitin and beta-1-3-glucan metabolism were also up-regulated by styrene. Many of the obtained sequences could not be annotated constituting new mussel sequences. In conclusion, this SSH study reveals novel sequences useful to generate molecular biomarkers of styrene exposure in mussels

  6. Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures – linking genome-wide transcriptional changes to cellular physiology

    Science.gov (United States)

    Pócsi, István; Miskei, Márton; Karányi, Zsolt; Emri, Tamás; Ayoubi, Patricia; Pusztahelyi, Tünde; Balla, György; Prade, Rolf A

    2005-01-01

    Background In addition to their cytotoxic nature, reactive oxygen species (ROS) are also signal molecules in diverse cellular processes in eukaryotic organisms. Linking genome-wide transcriptional changes to cellular physiology in oxidative stress-exposed Aspergillus nidulans cultures provides the opportunity to estimate the sizes of peroxide (O22-), superoxide (O2•-) and glutathione/glutathione disulphide (GSH/GSSG) redox imbalance responses. Results Genome-wide transcriptional changes triggered by diamide, H2O2 and menadione in A. nidulans vegetative tissues were recorded using DNA microarrays containing 3533 unique PCR-amplified probes. Evaluation of LOESS-normalized data indicated that 2499 gene probes were affected by at least one stress-inducing agent. The stress induced by diamide and H2O2 were pulse-like, with recovery after 1 h exposure time while no recovery was observed with menadione. The distribution of stress-responsive gene probes among major physiological functional categories was approximately the same for each agent. The gene group sizes solely responsive to changes in intracellular O22-, O2•- concentrations or to GSH/GSSG redox imbalance were estimated at 7.7, 32.6 and 13.0 %, respectively. Gene groups responsive to diamide, H2O2 and menadione treatments and gene groups influenced by GSH/GSSG, O22- and O2•- were only partly overlapping with distinct enrichment profiles within functional categories. Changes in the GSH/GSSG redox state influenced expression of genes coding for PBS2 like MAPK kinase homologue, PSK2 kinase homologue, AtfA transcription factor, and many elements of ubiquitin tagging, cell division cycle regulators, translation machinery proteins, defense and stress proteins, transport proteins as well as many enzymes of the primary and secondary metabolisms. Meanwhile, a separate set of genes encoding transport proteins, CpcA and JlbA amino acid starvation-responsive transcription factors, and some elements of sexual development

  7. Temperature and metal exposure affect membrane fatty acid composition and transcription of desaturases and elongases in fathead minnow muscle and brain.

    Science.gov (United States)

    Fadhlaoui, Mariem; Pierron, Fabien; Couture, Patrice

    2018-02-01

    In this study, we tested the hypothesis that metal exposure affected the normal thermal response of cell membrane FA composition and of elongase and desaturase gene transcription levels. To this end, muscle and brain membrane FA composition and FA desaturase (fads2, degs2 and scd2) and elongase (elovl2, elovl5 and elovl6) gene transcription levels were analyzed in fathead minnows (Pimephales promelas) acclimated for eight weeks to 15, 25 or 30°C exposed or not to cadmium (Cd, 6μg/l) or nickel (Ni, 450 6μg/l). The response of membrane FA composition to temperature variations or metal exposure differed between muscle and brain. In muscle, an increase of temperature induced a decrease of polyunsaturated FA (PUFA) and an increase of saturated FA (SFA) in agreement with the current paradigm. Although a similar response was observed in brain between 15 and 25°C, at 30°C, brain membrane unsaturation was higher than predicted. In both tissues, metal exposure affected the normal thermal response of membrane FA composition. The transcription of desaturases and elongases was higher in the brain and varied with acclimation temperature and metal exposure but these variations did not generally reflect changes in membrane FA composition. The mismatch between gene transcription and membrane composition highlights that several levels of control other than gene transcription are involved in adjusting membrane FA composition, including post-transcriptional regulation of elongases and desaturases and de novo phospholipid biosynthesis. Our study also reveals that metal exposure affects the mechanisms involved in adjusting cell membrane FA composition in ectotherms. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

    Directory of Open Access Journals (Sweden)

    Juan Ling

    2018-01-01

    Full Text Available Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA and bacteria (AOB, yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR assays, targeting the ammonia monooxygenase-subunit (amoA genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root at the DNA level (P < 0.05. Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle

  9. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Punita Sharma

    2015-12-01

    Full Text Available In prokaryotes, horizontal gene transfer (HGT has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.

  10. Transcriptional, translational, and physiological signatures of undernourished honey bees (Apis mellifera) suggest a role for hormonal factors in hypopharyngeal gland degradation.

    Science.gov (United States)

    Corby-Harris, Vanessa; Meador, Charlotte A D; Snyder, Lucy A; Schwan, Melissa R; Maes, Patrick; Jones, Beryl M; Walton, Alexander; Anderson, Kirk E

    2016-02-01

    Honey bee colonies function as a superorganism, where facultatively sterile female workers perform various tasks that support the hive. Nurse workers undergo numerous anatomical and physiological changes in preparation for brood rearing, including the growth of hypopharyngeal glands (HGs). These glands produce the major protein fraction of a protein- and lipid-rich jelly used to sustain developing larvae. Pollen intake is positively correlated with HG growth, but growth in the first three days is similar regardless of diet, suggesting that initial growth is a pre-determined process while later HG development depends on nutrient availability during a critical window in early adulthood (>3 d). It is unclear whether the resultant size differences in nurse HG are simply due to growth arrest or active degradation of the tissue. To determine what processes cause such differences in HG size, we catalogued the differential expression of both gene transcripts and proteins in the HGs of 8 d old bees that were fed diets containing pollen or no pollen. 3438 genes and 367 proteins were differentially regulated due to nutrition. Of the genes and proteins differentially expressed, undernourished bees exhibited more gene and protein up-regulation compared to well-nourished bees, with the affected processes including salivary gland apoptosis, oogenesis, and hormone signaling. Protein secretion was virtually the only process up-regulated in well-nourished bees. Further assays demonstrated that inhibition of ultraspiracle, one component of the ecdysteroid receptor, in the fat body caused larger HGs. Undernourished bees also had higher acid phosphatase activity, a physiological marker of cell death, compared to well-nourished bees. These results support a connection between poor nutrition, hormonal signaling, and HG degradation. Published by Elsevier Ltd.

  11. Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2010-05-01

    Full Text Available Abstract Background The neonatal bovine mammary fat pad (MFP surrounding the mammary parenchyma (PAR is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. We used bioinformatics to characterize transcriptomics differences between PAR and MFP from ~65 d old Holstein heifers. Data were mined to uncover potential crosstalk through the analyses of signaling molecules preferentially expressed in one tissue relative to the other. Results Over 9,000 differentially expressed genes (DEG; False discovery rate ≤ 0.05 were found of which 1,478 had a ≥1.5-fold difference between PAR and MFP. Within the DEG highly-expressed in PAR vs. MFP (n = 736 we noted significant enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Only actin cytoskeletal signaling was significant among canonical pathways. DEG more highly-expressed in MFP vs. PAR (n = 742 belong to lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism and signaling, particularly immune- and metabolism-related were significantly-enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis suggested a central role for PPARG, KLF2, EGR2, and EPAS1 in regulating expression of more highly-expressed DEG in MFP vs. PAR. Gene network analyses revealed putative inter-tissue crosstalk between cytokines and growth factors preferentially expressed in one tissue (e.g., ANGPTL1, SPP1, IL1B in PAR vs. MFP; ADIPOQ, IL13, FGF2, LEP in MFP vs. PAR with DEG preferentially expressed in the other tissue, particularly transcription factors or pathways (e.g., MYC, TP53, and actin cytoskeletal signaling in PAR vs. MFP; PPARG and LXR/RXR Signaling in MFP vs. PAR. Conclusions Functional analyses underscored a reciprocal influence in

  12. The role of soil biogeochemistry in wine taste: Soil factors influencing grape elemental composition, photosynthetic biomarkers and Cu/Zn isotopic signature of Vitis vinifera

    Science.gov (United States)

    Blotevogel, Simon; Oliva, Priscia; Darrozes, José; Viers, Jérôme; Audry, Stéphane; Courjault-Radé, Pierre; Orgogozo, Laurent; Le Guedard, Marina; Schreck, Eva

    2015-04-01

    Understanding the influence of soil composition in wine taste is of great economic and environmental interest in France and around the world. Nevertheless the impact of soil composition on wine taste is still controversially discussed. Since inorganic soil components do not have a proper taste and do not enter the plant anyway, their influence needs to be induced by nutrient absorption and its impact on plant functioning and grape composition. Indeed recent development of geological tracers of origin proof the existence of soil chemical and isotopic signatures in wine. However, type and scale of the impact of soil composition on wine taste are not well understood yet, and little experimental evidence exists due to the complexity of mechanisms involved. Thus, to provide evidence for the impact of soil composition on grape composition and potentially wine taste, we studied soil and plant material from two relevant vineyards (Soave, Italia). On those two directly adjacent vineyards, two different wines are produced with the same plant material and cultivation techniques. The vineyards only differ by their underlying bedrock - limestone versus basaltic rock - and thus present suitable conditions for investigating the impact of soil composition on grapes and wine. Pedological and mineralogical parameters were analyzed for the two vineyards whereas chemical extractions (citrate, CaCl2) were performed to determine nutrient bioavailability in both soils. Elemental compositions were determined by ICP-MS analyses in different compartments (soils, vine leaves and grapes). Isotopic fractionation of Cu and Zn was investigated in various samples as source tracers and in order to better understand fractionation mechanisms involved. Finally, plant health was studied using the Omega-3 biomarker which determines the fatty acid composition in vine leaves, directly involved in photosynthetic processes. Results show that the vineyards are characterized by two different soil types due

  13. Radiation signatures

    International Nuclear Information System (INIS)

    McGlynn, S.P.; Varma, M.N.

    1992-01-01

    A new concept for modelling radiation risk is proposed. This concept is based on the proposal that the spectrum of molecular lesions, which we dub ''the radiation signature'', can be used to identify the quality of the causal radiation. If the proposal concerning radiation signatures can be established then, in principle, both prospective and retrospective risk determination can be assessed on an individual basis. A major goal of biophysical modelling is to relate physical events such as ionization, excitation, etc. to the production of radiation carcinogenesis. A description of the physical events is provided by track structure. The track structure is determined by radiation quality, and it can be considered to be the ''physical signature'' of the radiation. Unfortunately, the uniqueness characteristics of this signature are dissipated in biological systems in ∼10 -9 s. Nonetheless, it is our contention that this physical disturbance of the biological system eventuates later, at ∼10 0 s, in molecular lesion spectra which also characterize the causal radiation. (author)

  14. Detrital fission-track-compositional signature of an orogenic chain-hinterland basin system: The case of the late Neogene Quaternary Valdelsa basin (Northern Apennines, Italy)

    Science.gov (United States)

    Balestrieri, M. L.; Benvenuti, M.; Tangocci, F.

    2013-05-01

    Detrital thermochronological data collected in syn-tectonic basin deposits are a promising tool for deciphering time and processes of the evolution of orogenic belts. Our study deals with the Valdelsa basin, one of the wider basins of central Tuscany, Italy. The Valdelsa basin is located at the rear of the Northern Apennines, a collisional orogen whose late Neogene Quaternary development is alternatively attributed to extensional and compressional regimes. These contrasting interpretations mostly rely on different reconstructions of the tectono-sedimentary evolution of several basins formed at the rear of the chain since the late Tortonian. Here, we explore the detrital thermochronological-compositional signature of tectonic and surface processes during the Valdelsa basin development. For this aim, detrital apatite fission-track analysis of 21 sand samples from the latest Messinian Gelasian fluvial to shallow marine basin deposits, has been accompanied by a clast composition analysis of 7 representative outcrops of the conglomerate facies. The grain-age distributions of the sediment samples are generally characterized by two distinct components, one younger peak (P1) varying between 5.5 ± 2.8 and 9.5 ± 1.0 Ma and one older peak (P2) varying from 15.0 ± 8.0 to 41.0 ± 10 Ma. By comparison with some bedrock ages obtained from the E-NE basin shoulder, we attributed the P2 peak to the Ligurian Units and the P1 peak to the Macigno Formation (Tuscan Units). These units are arranged one upon the other in the complex nappe pile forming the Northern Apennines orogen. While the gravel composition indicates a predominant feeding from the Ligurian units all along the sedimentary succession with a subordinate occurrence of Macigno pebbles slightly increasing upsection, the P1 peak is present even in the oldest collected sandy sediments. The early P1 occurrence reveals that the Macigno was exposed in the E-NE basin shoulder since at least the latest Messinian-early Zanclean

  15. Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo

    International Nuclear Information System (INIS)

    Anastassiou, Dimitris; Rumjantseva, Viktoria; Cheng, Weiyi; Huang, Jianzhong; Canoll, Peter D; Yamashiro, Darrell J; Kandel, Jessica J

    2011-01-01

    The biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT). We used xenograft models of human cancer cells in immunocompromised mice, profiling the harvested tumors separately with species-specific probes and computationally analyzing the results. Here we show that human cancer cells express in vivo a precise multi-cancer invasion-associated gene expression signature that prominently includes many EMT markers, among them the transcription factor Slug, fibronectin, and α-SMA. We found that human, but not mouse, cells express the signature and Slug is the only upregulated EMT-inducing transcription factor. The signature is also present in samples from many publicly available cancer gene expression datasets, suggesting that it is produced by the cancer cells themselves in multiple cancer types, including nonepithelial cancers such as neuroblastoma. Furthermore, we found that the presence of the signature in human xenografted cells was associated with a downregulation of adipocyte markers in the mouse tissue adjacent to the invasive tumor, suggesting that the signature is triggered by contextual microenvironmental interactions when the cancer cells encounter adipocytes, as previously reported. The known, precise and consistent gene composition of this cancer mesenchymal transition signature, particularly when combined with simultaneous analysis of the adjacent microenvironment, provides unique opportunities for shedding light on the underlying mechanisms of cancer invasiveness as well as identifying potential diagnostic markers and targets for metastasis-inhibiting therapeutics

  16. Cell-specific type I IFN signatures in autoimmunity and viral infection: what makes the difference?

    Directory of Open Access Journals (Sweden)

    Chieko Kyogoku

    Full Text Available Gene expression profiling of peripheral blood mononuclear cells (PBMCs has revealed a crucial role for type I interferon (IFN in the pathogenesis of systemic lupus erythematosus (SLE. However, it is unclear how particular leucocyte subsets contribute to the overall type I IFN signature of PBMCs and whole blood samples.Furthermore, a detailed analysis describing the differences in the IFN signature in autoimmune diseases from that observed after viral infection has not been performed to date. Therefore, in this study, the transcriptional responses in peripheral T helper cells (CD4(+ and monocyte subsets (CD16(- inflammatory and CD16(+ resident monocytes isolated from patients with SLE, healthy donors (ND immunised with the yellow fever vaccine YFV-17Dand untreated controls were compared by global gene expression profiling.It was striking that all of the transcripts that were regulated in response to viral exposure were also found to be differentially regulated in SLE, albeit with markedly lower fold-change values. In addition to this common IFN signature, a pathogenic IFN-associated gene signature was detected in the CD4(+ T cells and monocytes from the lupus patients. IL-10, IL-9 and IL-15-mediated JAK/STAT signalling was shown to be involved in the pathological amplification of IFN responses observed in SLE. Type I IFN signatures identified were successfully applied for the monitoring of interferon responses in PBMCs of an independent cohort of SLE patients and virus-infected individuals. Moreover, these cell-type specific gene signatures allowed a correct classification of PBMCs independent from their heterogenic cellular composition. In conclusion, our data show for the first time that monocytes and CD4 cells are sensitive biosensors to monitor type I interferon response signatures in autoimmunity and viral infection and how these transriptional responses are modulated in a cell- and disease-specific manner.

  17. Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

    Directory of Open Access Journals (Sweden)

    Jung Hans-Joachim G

    2010-05-01

    suggested co-expression of some neighbouring genes on Medicago chromosomes. Conclusions The problems associated with transcript profiling in alfalfa stems using the Medicago GeneChip as a CSH platform were mitigated by masking probes targeting ISV regions and SFPs. Using this masking protocol resulted in the identification of numerous candidate genes that may contribute to differences in cell wall concentration and composition of stems of two alfalfa genotypes.

  18. An individual and a sex odor signature in kittiwakes? Study of the semiochemical composition of preen secretion and preen down feathers

    Science.gov (United States)

    Leclaire, Sarah; Merkling, Thomas; Raynaud, Christine; Giacinti, Géraldine; Bessière, Jean-Marie; Hatch, Scott A.; Danchin, Étienne

    2011-07-01

    The importance of olfaction in birds' social behavior has long been denied. Avian chemical signaling has thus been relatively unexplored. The black-legged kittiwake provides a particularly appropriate model for investigating this topic. Kittiwakes preferentially mate with genetically dissimilar individuals, but the cues used to assess genetic characteristics remain unknown. As in other vertebrates, their body odors may carry individual and sexual signatures thus potentially reliably signaling individual genetic makeup. Here, we test whether body odors in preen gland secretion and preen down feathers in kittiwakes may provide a sex and an individual signature. Using gas chromatography and mass spectrometry, we found that male and female odors differ quantitatively, suggesting that scent may be one of the multiple cues used by birds to discriminate between sexes. We further detected an individual signature in the volatile and nonvolatile fractions of preen secretion and preen down feathers. These results suggest that kittiwake body odor may function as a signal associated with mate recognition. It further suggests that preen odor might broadcast the genetic makeup of individuals, and could be used in mate choice to assess the genetic compatibility of potential mates.

  19. Signature-based User Authentication

    OpenAIRE

    Hámorník, Juraj

    2015-01-01

    This work aims on missing handwritten signature authentication in Windows. Result of this work is standalone software that allow users to log into Windows by writing signature. We focus on security of signature authentification and best overall user experience. We implemented signature authentification service that accept signature and return user access token if signature is genuine. Signature authentification is done by comparing given signature to signature patterns by their similarity. Si...

  20. Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq.

    Science.gov (United States)

    Hu, Peng; Fabyanic, Emily; Kwon, Deborah Y; Tang, Sheng; Zhou, Zhaolan; Wu, Hao

    2017-12-07

    Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Electronic Signature Policy

    Science.gov (United States)

    Establishes the United States Environmental Protection Agency's approach to adopting electronic signature technology and best practices to ensure electronic signatures applied to official Agency documents are legally valid and enforceable

  2. Lesson 6: Signature Validation

    Science.gov (United States)

    Checklist items 13 through 17 are grouped under the Signature Validation Process, and represent CROMERR requirements that the system must satisfy as part of ensuring that electronic signatures it receives are valid.

  3. Exotic signatures from supersymmetry

    International Nuclear Information System (INIS)

    Hall, L.J.

    1989-08-01

    Minor changes to the standard supersymmetric model, such as soft flavor violation and R parity violation, cause large changes in the signatures. The origin of these changes and the resulting signatures are discussed. 15 refs., 7 figs., 2 tabs

  4. Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Hiraku Takada

    Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

  5. Blinding for unanticipated signatures

    NARCIS (Netherlands)

    D. Chaum (David)

    1987-01-01

    textabstractPreviously known blind signature systems require an amount of computation at least proportional to the number of signature types, and also that the number of such types be fixed in advance. These requirements are not practical in some applications. Here, a new blind signature technique

  6. Fair quantum blind signatures

    International Nuclear Information System (INIS)

    Tian-Yin, Wang; Qiao-Yan, Wen

    2010-01-01

    We present a new fair blind signature scheme based on the fundamental properties of quantum mechanics. In addition, we analyse the security of this scheme, and show that it is not possible to forge valid blind signatures. Moreover, comparisons between this scheme and public key blind signature schemes are also discussed. (general)

  7. Real Traceable Signatures

    Science.gov (United States)

    Chow, Sherman S. M.

    Traceable signature scheme extends a group signature scheme with an enhanced anonymity management mechanism. The group manager can compute a tracing trapdoor which enables anyone to test if a signature is signed by a given misbehaving user, while the only way to do so for group signatures requires revealing the signer of all signatures. Nevertheless, it is not tracing in a strict sense. For all existing schemes, T tracing agents need to recollect all N' signatures ever produced and perform RN' “checks” for R revoked users. This involves a high volume of transfer and computations. Increasing T increases the degree of parallelism for tracing but also the probability of “missing” some signatures in case some of the agents are dishonest.

  8. Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies Peroxisome Proliferator-Activated Receptor Gamma as an intrinsic negative regulator of viral replication

    Science.gov (United States)

    2013-01-01

    Background We previously demonstrated that primary Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Molecular mechanisms underlying these differences remain unknown. Results Exposure to replication competent and single-round VSV-G pseudotyped HIV strains provide evidence that superior HIV replication in Th1Th17 vs. Th1 cells was regulated by mechanisms located at entry and post-entry levels. Genome-wide transcriptional profiling identified transcripts upregulated (n = 264) and downregulated (n = 235) in Th1Th17 vs. Th1 cells (p-value Th17 (nuclear receptors, trafficking, p38/MAPK, NF-κB, p53/Ras, IL-23) vs. Th1 cells (proteasome, interferon α/β). Differentially expressed genes were classified into biological categories using Gene Ontology. Th1Th17 cells expressed typical Th17 markers (IL-17A/F, IL-22, CCL20, RORC, IL-26, IL-23R, CCR6) and transcripts functionally linked to regulating cell trafficking (CEACAM1, MCAM), activation (CD28, CD40LG, TNFSF13B, TNFSF25, PTPN13, MAP3K4, LTB, CTSH), transcription (PPARγ, RUNX1, ATF5, ARNTL), apoptosis (FASLG), and HIV infection (CXCR6, FURIN). Differential expression of CXCR6, PPARγ, ARNTL, PTPN13, MAP3K4, CTSH, SERPINB6, PTK2, and ISG20 was validated by RT-PCR, flow cytometry and/or confocal microscopy. The nuclear receptor PPARγ was preferentially expressed by Th1Th17 cells. PPARγ RNA interference significantly increased HIV replication at levels post-entry and prior HIV-DNA integration. Finally, the activation of PPARγ pathway via the agonist Rosiglitazone induced the nuclear translocation of PPARγ and a robust inhibition of viral replication. Conclusions Thus, transcriptional profiling in Th1Th17 vs. Th1 cells demonstrated that HIV permissiveness is associated with a superior state of cellular activation and limited antiviral properties and identified PPARγ as an intrinsic negative regulator of viral replication. Therefore, triggering PPARγ pathway via non

  9. Unconditionally Secure Quantum Signatures

    Directory of Open Access Journals (Sweden)

    Ryan Amiri

    2015-08-01

    Full Text Available Signature schemes, proposed in 1976 by Diffie and Hellman, have become ubiquitous across modern communications. They allow for the exchange of messages from one sender to multiple recipients, with the guarantees that messages cannot be forged or tampered with and that messages also can be forwarded from one recipient to another without compromising their validity. Signatures are different from, but no less important than encryption, which ensures the privacy of a message. Commonly used signature protocols—signatures based on the Rivest–Adleman–Shamir (RSA algorithm, the digital signature algorithm (DSA, and the elliptic curve digital signature algorithm (ECDSA—are only computationally secure, similar to public key encryption methods. In fact, since these rely on the difficulty of finding discrete logarithms or factoring large primes, it is known that they will become completely insecure with the emergence of quantum computers. We may therefore see a shift towards signature protocols that will remain secure even in a post-quantum world. Ideally, such schemes would provide unconditional or information-theoretic security. In this paper, we aim to provide an accessible and comprehensive review of existing unconditionally securesecure signature schemes for signing classical messages, with a focus on unconditionally secure quantum signature schemes.

  10. Radar Signature Calculation Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: The calculation, analysis, and visualization of the spatially extended radar signatures of complex objects such as ships in a sea multipath environment and...

  11. Molecular Signature in HCV-Positive Lymphomas

    Directory of Open Access Journals (Sweden)

    Valli De Re

    2012-01-01

    Full Text Available Hepatitis C virus (HCV is a positive, single-stranded RNA virus, which has been associated to different subtypes of B-cell non-Hodgkin lymphoma (B-NHL. Cumulative evidence suggests an HCV-related antigen driven process in the B-NHL development. The underlying molecular signature associated to HCV-related B-NHL has to date remained obscure. In this review, we discuss the recent developments in this field with a special mention to different sets of genes whose expression is associated with BCR coupled to Blys signaling which in turn was found to be linked to B-cell maturation stages and NF-κb transcription factor. Even if recent progress on HCV-B-NHL signature has been made, the precise relationship between HCV and lymphoma development and phenotype signature remain to be clarified.

  12. Composites

    International Nuclear Information System (INIS)

    Kasen, M.B.

    1983-01-01

    This chapter discusses the roles of composite laminates and aggregates in cryogenic technology. Filamentary-reinforced composites are emphasized because they are the most widely used composite materials. Topics considered include composite systems and terminology, design and fabrication, composite failure, high-pressure reinforced plastic laminates, low-pressure reinforced plastics, reinforced metals, selectively reinforced structures, the effect of cryogenic temperatures, woven-fabric and random-mat composites, uniaxial fiber-reinforced composites, composite joints in cryogenic structures, joining techniques at room temperature, radiation effects, testing laminates at cryogenic temperatures, static and cyclic tensile testing, static and cyclic compression testing, interlaminar shear testing, secondary property tests, and concrete aggregates. It is suggested that cryogenic composite technology would benefit from the development of a fracture mechanics model for predicting the fitness-for-purpose of polymer-matrix composite structures

  13. Investigation of the isotopic composition of lead and of trace elements concentrations in natural uranium materials as a signature in nuclear forensics

    Energy Technology Data Exchange (ETDEWEB)

    Svedkauskaite-LeGore, J. [European Commission, Joint Research Centre, Karlsruhe (Germany). Inst. for Transuranium Elements; Institute of Physics, Vilnius (Lithuania); Mayer, K.; Millet, S.; Nicholl, A.; Rasmussen, G. [European Commission, Joint Research Centre, Karlsruhe (Germany). Inst. for Transuranium Elements; Baltrunas, D. [Institute of Physics, Vilnius (Lithuania)

    2007-07-01

    Lead is contained as trace element in uranium ores and propagates throughout the production process to intermediate products like yellow cake or uranium oxide. The lead isotopes in such material originate from two sources: natural lead and radiogenic lead. The variability of the isotopic composition of lead in ores and yellow cakes was studied and the applicability of this parameter for nuclear forensic investigations was investigated. Furthermore, the chemical impurities contained in these materials were measured in order to identify characteristic differences between materials from different mines. For the samples investigated, it could be shown, that the lead isotopic composition varies largely from mine to mine and it may be used as one of the parameters to distinguish between materials of different origins. Some of the chemical impurities show a similar pattern and support the conclusions drawn from the lead isotope data. (orig.)

  14. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

    Science.gov (United States)

    2011-01-01

    Background Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Results Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Conclusions Our results demonstrate that RNA-Seq can be

  15. Effects of transcription ability and transcription mode on translation: Evidence from written compositions, language bursts and pauses when students in grades 4 to 9, with and without persisting dyslexia or dysgraphia, compose by pen or by keyboard

    Directory of Open Access Journals (Sweden)

    Scott F. Beers

    2017-06-01

    Full Text Available This study explored the effects of transcription on translation products and processes of adolescent students in grades 4 to 9 with and without persisting specific language disabilities in written language (SLDs—WL. To operationalize transcription ability (handwriting and spelling and transcription mode (by pen on digital tablet or by standard US keyboard, diagnostic groups contrasting in patterns of transcription ability were compared while composing autobiographical (personal narratives by handwriting or by keyboarding: Typically developing students (n=15, students with dyslexia (impaired word reading and spelling, n=20, and students with dysgraphia (impaired handwriting, n=19. They were compared on seven outcomes: total words composed, total composing time, words per minute, percent of spelling errors, average length of pauses, average number of pauses per minute, and average length of language bursts. They were also compared on automaticity of transcription modes—writing the alphabet from memory by handwriting or keyboarding (they could look at keys. Mixed ANOVAs yielded main effects for diagnostic group on percent of spelling errors, words per minute, and length of language burst. Main effects for transcription modes were found for automaticity of writing modes, total words composed, words per minute, and length of language bursts; there were no significant interactions. Regardless of mode, the dyslexia group had more spelling errors, showed a slower rate of composing, and produced shorter language bursts than the typical group. The total number of words, total time composing, words composed per minute, and pauses per minute were greater for keyboarding than handwriting, but length of language bursts was greater for handwriting. Implications of these results for conceptual models of composing and educational assessment practices are discussed.

  16. Circulating neutrophil transcriptome may reveal intracranial aneurysm signature.

    Directory of Open Access Journals (Sweden)

    Vincent M Tutino

    Full Text Available Unruptured intracranial aneurysms (IAs are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs.Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls. Samples from the two groups were paired based on demographics and comorbidities. RNA was extracted from isolated neutrophils and subjected to next-generation RNA sequencing to obtain differential expressions for identification of an IA-associated signature. Bioinformatics analyses, including gene set enrichment analysis and Ingenuity Pathway Analysis, were used to investigate the biological function of all differentially expressed transcripts.Transcriptome profiling identified 258 differentially expressed transcripts in patients with and without IAs. Expression differences were consistent with peripheral neutrophil activation. An IA-associated RNA expression signature was identified in 82 transcripts (p<0.05, fold-change ≥2. This signature was able to separate patients with and without IAs on hierarchical clustering. Furthermore, in an independent, unpaired, replication cohort of patients with IAs (n = 5 and controls (n = 5, the 82 transcripts separated 9 of 10 patients into their respective groups.Preliminary findings show that RNA expression from circulating neutrophils carries an IA-associated signature. These findings highlight a potential to use predictive biomarkers from peripheral blood samples to identify patients with IAs.

  17. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2011-01-01

    Strategies are open compositions to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them in full...

  18. Composition

    DEFF Research Database (Denmark)

    2014-01-01

    Memory Pieces are open compositions to be realised solo by an improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound files will in some cases only provide a few minutes' sample. Please DOWNLOAD them to hear them...

  19. Threshold Signature Schemes Application

    Directory of Open Access Journals (Sweden)

    Anastasiya Victorovna Beresneva

    2015-10-01

    Full Text Available This work is devoted to an investigation of threshold signature schemes. The systematization of the threshold signature schemes was done, cryptographic constructions based on interpolation Lagrange polynomial, elliptic curves and bilinear pairings were examined. Different methods of generation and verification of threshold signatures were explored, the availability of practical usage of threshold schemes in mobile agents, Internet banking and e-currency was shown. The topics of further investigation were given and it could reduce a level of counterfeit electronic documents signed by a group of users.

  20. Transcriptomic signatures in cartilage ageing

    Science.gov (United States)

    2013-01-01

    Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome. PMID:23971731

  1. Advanced Missile Signature Center

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Missile Signature Center (AMSC) is a national facility supporting the Missile Defense Agency (MDA) and other DoD programs and customers with analysis,...

  2. THE ELECTRONIC SIGNATURE

    Directory of Open Access Journals (Sweden)

    Voiculescu Madalina Irena

    2009-05-01

    Full Text Available Article refers to significance and the digital signature in electronic commerce. Internet and electronic commerce open up many new opportunities for the consumer, yet, the security (or perceived lack of security of exchanging personal and financial data

  3. Digital signature feasibility study

    Science.gov (United States)

    2008-06-01

    The purpose of this study was to assess the advantages and disadvantages of using digital signatures to assist the Arizona Department of Transportation in conducting business. The Department is evaluating the potential of performing more electronic t...

  4. Physics Signatures at CLIC

    CERN Document Server

    Battaglia, Marco

    2001-01-01

    A set of signatures for physics processes of potential interests for the CLIC programme at = 1 - 5 TeV are discussed. These signatures, that may correspond to the manifestation of different scenarios of new physics as well as to Standard Model precision tests, are proposed as benchmarks for the optimisation of the CLIC accelerator parameters and for a first definition of the required detector response.

  5. Chemical composition of air masses transported from Asia to the U.S. West Coast during ITCT 2K2: Fossil fuel combustion versus biomass-burning signatures

    Science.gov (United States)

    de Gouw, J. A.; Cooper, O. R.; Warneke, C.; Hudson, P. K.; Fehsenfeld, F. C.; Holloway, J. S.; Hübler, G.; Nicks, D. K., Jr.; Nowak, J. B.; Parrish, D. D.; Ryerson, T. B.; Atlas, E. L.; Donnelly, S. G.; Schauffler, S. M.; Stroud, V.; Johnson, K.; Carmichael, G. R.; Streets, D. G.

    2004-12-01

    As part of the Intercontinental Transport and Chemical Transformation experiment in 2002 (ITCT 2K2), a National Oceanic and Atmospheric Administration (NOAA) WP-3D research aircraft was used to study the long-range transport of Asian air masses toward the west coast of North America. During research flights on 5 and 17 May, strong enhancements of carbon monoxide (CO) and other species were observed in air masses that had been transported from Asia. The hydrocarbon composition of the air masses indicated that the highest CO levels were related to fossil fuel use. During the flights on 5 and 17 May and other days, the levels of several biomass-burning indicators increased with altitude. This was true for acetonitrile (CH3CN), methyl chloride (CH3Cl), the ratio of acetylene (C2H2) to propane (C3H8), and, on May 5, the percentage of particles measured by the particle analysis by laser mass spectrometry (PALMS) instrument that were attributed to biomass burning based on their carbon and potassium content. An ensemble of back-trajectories, calculated from the U.S. west coast over a range of latitudes and altitudes for the entire ITCT 2K2 period, showed that air masses from Southeast Asia and China were generally observed at higher altitudes than air from Japan and Korea. Emission inventories estimate the contribution of biomass burning to the total emissions to be low for Japan and Korea, higher for China, and the highest for Southeast Asia. Combined with the origin of the air masses versus altitude, this qualitatively explains the increase with altitude, averaged over the whole ITCT 2K2 period, of the different biomass-burning indicators.

  6. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2014-01-01

    Cue Rondo is an open composition to be realised by improvising musicians. See more about my composition practise in the entry "Composition - General Introduction". Caution: streaming the sound/video files will in some cases only provide a few minutes' sample, or the visuals will not appear at all....... Please DOWNLOAD them to see/hear them in full length! This work is licensed under a Creative Commons "by-nc" License. You may for non-commercial purposes use and distribute it, performance instructions as well as specially designated recordings, as long as the author is mentioned. Please see http...

  7. Circulating neutrophil transcriptome may reveal intracranial aneurysm signature

    Science.gov (United States)

    Tutino, Vincent M.; Poppenberg, Kerry E.; Jiang, Kaiyu; Jarvis, James N.; Sun, Yijun; Sonig, Ashish; Siddiqui, Adnan H.; Snyder, Kenneth V.; Levy, Elad I.; Kolega, John

    2018-01-01

    Background Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. Methods Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls. Samples from the two groups were paired based on demographics and comorbidities. RNA was extracted from isolated neutrophils and subjected to next-generation RNA sequencing to obtain differential expressions for identification of an IA-associated signature. Bioinformatics analyses, including gene set enrichment analysis and Ingenuity Pathway Analysis, were used to investigate the biological function of all differentially expressed transcripts. Results Transcriptome profiling identified 258 differentially expressed transcripts in patients with and without IAs. Expression differences were consistent with peripheral neutrophil activation. An IA-associated RNA expression signature was identified in 82 transcripts (pIAs on hierarchical clustering. Furthermore, in an independent, unpaired, replication cohort of patients with IAs (n = 5) and controls (n = 5), the 82 transcripts separated 9 of 10 patients into their respective groups. Conclusion Preliminary findings show that RNA expression from circulating neutrophils carries an IA-associated signature. These findings highlight a potential to use predictive biomarkers from peripheral blood samples to identify patients with IAs. PMID:29342213

  8. Detection of chemical explosives using multiple photon signatures

    International Nuclear Information System (INIS)

    Loschke, K.W.; Dunn, W.L.

    2008-01-01

    Full text: A template-matching procedure to aid in rapid detection of improvised explosive devices (IEDs) is being investigated. Multiple photon-scattered and photon-induced positron annihilation radiation responses are being used as part of a photon-neutron signature-based radiation scanning (SBRS) approach (see companion reference for description of the neutron component), in an attempt to detect chemical explosives at safe standoff distances. Many past and present photon interrogation methods are based on imaging. Imaging techniques seek to determine at high special resolution the internal structure of a target of interest. Our technique simply seeks to determine if an unknown target contains a detectable amount of chemical explosives by comparing multiple responses (signatures) that depend on both density and composition of portions of a target. In the photon component, beams of photons are used to create back-streaming signatures, which are dependent on the density and composition of part of the target being interrogated. These signatures are compared to templates, which are collections of the same signatures if the interrogated volume contained a significant amount of explosives. The signature analysis produces a figure-of-merit and a standard deviation of the figure-of-merit. These two metrics are used to filter safe from dangerous targets. Experiments have been conducted that show that explosive surrogates (fertilizers) can be distinguished from several inert materials using these photon signatures, demonstrating that these signatures can be used effectively to help IEDs

  9. Uncertainty in hydrological signatures

    Science.gov (United States)

    McMillan, Hilary; Westerberg, Ida

    2015-04-01

    Information that summarises the hydrological behaviour or flow regime of a catchment is essential for comparing responses of different catchments to understand catchment organisation and similarity, and for many other modelling and water-management applications. Such information types derived as an index value from observed data are known as hydrological signatures, and can include descriptors of high flows (e.g. mean annual flood), low flows (e.g. mean annual low flow, recession shape), the flow variability, flow duration curve, and runoff ratio. Because the hydrological signatures are calculated from observed data such as rainfall and flow records, they are affected by uncertainty in those data. Subjective choices in the method used to calculate the signatures create a further source of uncertainty. Uncertainties in the signatures may affect our ability to compare different locations, to detect changes, or to compare future water resource management scenarios. The aim of this study was to contribute to the hydrological community's awareness and knowledge of data uncertainty in hydrological signatures, including typical sources, magnitude and methods for its assessment. We proposed a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrated it for a variety of commonly used signatures. The study was made for two data rich catchments, the 50 km2 Mahurangi catchment in New Zealand and the 135 km2 Brue catchment in the UK. For rainfall data the uncertainty sources included point measurement uncertainty, the number of gauges used in calculation of the catchment spatial average, and uncertainties relating to lack of quality control. For flow data the uncertainty sources included uncertainties in stage/discharge measurement and in the approximation of the true stage-discharge relation by a rating curve. The resulting uncertainties were compared across the different signatures and catchments, to quantify uncertainty

  10. Practical quantum digital signature

    Science.gov (United States)

    Yin, Hua-Lei; Fu, Yao; Chen, Zeng-Bing

    2016-03-01

    Guaranteeing nonrepudiation, unforgeability as well as transferability of a signature is one of the most vital safeguards in today's e-commerce era. Based on fundamental laws of quantum physics, quantum digital signature (QDS) aims to provide information-theoretic security for this cryptographic task. However, up to date, the previously proposed QDS protocols are impractical due to various challenging problems and most importantly, the requirement of authenticated (secure) quantum channels between participants. Here, we present the first quantum digital signature protocol that removes the assumption of authenticated quantum channels while remaining secure against the collective attacks. Besides, our QDS protocol can be practically implemented over more than 100 km under current mature technology as used in quantum key distribution.

  11. Signatures of the Invisible

    CERN Multimedia

    Strom, D

    2003-01-01

    On the Net it is possible to take a look at art from afar via Virtual Museums. One such exhibition was recently in the New York Museum of Modern Art's branch, PS1. Entitled 'Signatures of the Invisible' it was a collaborative effort between artists and physicists (1/2 page).

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

    Science.gov (United States)

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

    2017-12-01

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

  13. A Directed Signature Scheme and its Applications

    OpenAIRE

    Lal, Sunder; Kumar, Manoj

    2004-01-01

    This paper presents a directed signature scheme with the property that the signature can be verified only with the help of signer or signature receiver. We also propose its applications to share verification of signatures and to threshold cryptosystems.

  14. Thermal signature measurements for ammonium nitrate/fuel mixtures by laser heating

    International Nuclear Information System (INIS)

    Nazarian, Ashot; Presser, Cary

    2016-01-01

    Highlights: • LDTR is a useful diagnostic for characterizing AN/fuel mixture thermochemical behavior. • Each AN/fuel mixture thermal signature was different. • AN/fuel mixture signature features were defined by the individual constituents. • Baseline signatures changed after an experiment. - Abstract: Measurements were carried out to obtain thermal signatures of several ammonium nitrate/fuel (ANF) mixtures, using a laser-heating technique referred to as the laser-driven thermal reactor (LDTR). The mixtures were ammonium nitrate (AN)/kerosene, AN/ethylene glycol, AN/paraffin wax, AN/petroleum jelly, AN/confectioner's sugar, AN/cellulose (tissue paper), nitromethane/cellulose, nitrobenzene/cellulose, AN/cellulose/nitromethane, AN/cellulose/nitrobenzene. These mixtures were also compared with AN/nitromethane and AN/diesel fuel oil, obtained from an earlier investigation. Thermograms for the mixtures, as well as individual constituents, were compared to better understand how sample thermal signature changes with mixture composition. This is the first step in development of a thermal-signature database, to be used along with other signature databases, to improve identification of energetic substances of unknown composition. The results indicated that each individual thermal signature was associated unambiguously with a particular mixture composition. The signature features of a particular mixture were shaped by the individual constituent signatures. It was also uncovered that the baseline signature was modified after an experiment due to coating of unreacted residue on the substrate surface and a change in the reactor sphere oxide layer. Thus, care was required to pre-oxidize the sphere prior to an experiment. A minimum sample mass (which was dependent on composition) was required to detect the signature characteristics. Increased laser power served to magnify signal strength while preserving the signature features. For the mixtures examined, the thermal

  15. Improved gene expression signature of testicular carcinoma in situ

    DEFF Research Database (Denmark)

    Almstrup, Kristian; Leffers, Henrik; Lothe, Ragnhild A

    2007-01-01

    on global gene expression in testicular CIS have been previously published. We have merged the two data sets on CIS samples (n = 6) and identified the shared gene expression signature in relation to expression in normal testis. Among the top-20 highest expressed genes, one-third was transcription factors...... development' were significantly altered and could collectively affect cellular pathways like the WNT signalling cascade, which thus may be disrupted in testicular CIS. The merged CIS data from two different microarray platforms, to our knowledge, provide the most precise CIS gene expression signature to date....

  16. Signatures of topological superconductivity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Yang

    2017-07-19

    The prediction and experimental discovery of topological insulators brought the importance of topology in condensed matter physics into the limelight. Topology hence acts as a new dimension along which more and more new states of matter start to emerge. One of these topological states of matter, namely topological superconductors, comes into the focus because of their gapless excitations. These gapless excitations, especially in one dimensional topological superconductors, are Majorana zero modes localized at the ends of the superconductor and exhibit exotic nonabelian statistics, which can be potentially applied to fault-tolerant quantum computation. Given their highly interesting physical properties and potential applications to quantum computation, both theorists and experimentalists spend great efforts to realize topological supercondoctors and to detect Majoranas. In two projects within this thesis, we investigate the properties of Majorana zero modes in realistic materials which are absent in simple theoretical models. We find that the superconducting proximity effect, an essential ingredient in all existing platforms for topological superconductors, plays a significant role in determining the localization property of the Majoranas. Strong proximity coupling between the normal system and the superconducting substrate can lead to strongly localized Majoranas, which can explain the observation in a recent experiment. Motivated by experiments in Molenkamp's group, we also look at realistic quantum spin Hall Josephson junctions, in which charge puddles acting as magnetic impurities are coupled to the helical edge states. We find that with this setup, the junction generically realizes an exotic 8π periodic Josephson effect, which is absent in a pristine Josephson junction. In another two projects, we propose more pronounced signatures of Majoranas that are accessible with current experimental techniques. The first one is a transport measurement, which uses

  17. Modem Signature Analysis.

    Science.gov (United States)

    1982-10-01

    AD-A127 993 MODEM SIGNATURE ANALISIS (U) PAR TECHNOLOGY CORP NEW / HARTFORD NY V EDWARDS ET AL. OCT 82 RADC-TR-82-269 F30602-80-C-0264 NCLASSIFIED F/G...as an indication of the class clustering and separation between different classes in the modem data base. It is apparent from the projection that the...that as the clusters disperse, the likelihood of a sample crossing the boundary into an adjacent region and causing a symbol decision error increases. As

  18. Electronic Signature (eSig)

    Data.gov (United States)

    Department of Veterans Affairs — Beginning with the Government Paperwork Elimination Act of 1998 (GPEA), the Federal government has encouraged the use of electronic / digital signatures to enable...

  19. Expressiveness considerations of XML signatures

    DEFF Research Database (Denmark)

    Jensen, Meiko; Meyer, Christopher

    2011-01-01

    XML Signatures are used to protect XML-based Web Service communication against a broad range of attacks related to man-in-the-middle scenarios. However, due to the complexity of the Web Services specification landscape, the task of applying XML Signatures in a robust and reliable manner becomes...... more and more challenging. In this paper, we investigate this issue, describing how an attacker can still interfere with Web Services communication even in the presence of XML Signatures. Additionally, we discuss the interrelation of XML Signatures and XML Encryption, focussing on their security...

  20. Electronic Warfare Signature Measurement Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Electronic Warfare Signature Measurement Facility contains specialized mobile spectral, radiometric, and imaging measurement systems to characterize ultraviolet,...

  1. Full control and manipulation of heat signatures: cloaking, camouflage and thermal metamaterials.

    Science.gov (United States)

    Han, Tiancheng; Bai, Xue; Thong, John T L; Li, Baowen; Qiu, Cheng-Wei

    2014-03-19

    Thermal camouflage and cloaking can transform an actual heat signature into a pre-controlled one. A viable recipe for controlling and manipulating heat signatures using thermal metamaterials to empower cloaking and camouflage in heat conduction is demonstrated. The thermal signature of the object is thus metamorphosed and perceived as multiple targets with different geometries and compositions, with the original object cloaked. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Signatures of Mechanosensitive Gating.

    Science.gov (United States)

    Morris, Richard G

    2017-01-10

    The question of how mechanically gated membrane channels open and close is notoriously difficult to address, especially if the protein structure is not available. This perspective highlights the relevance of micropipette-aspirated single-particle tracking-used to obtain a channel's diffusion coefficient, D, as a function of applied membrane tension, σ-as an indirect assay for determining functional behavior in mechanosensitive channels. While ensuring that the protein remains integral to the membrane, such methods can be used to identify not only the gating mechanism of a protein, but also associated physical moduli, such as torsional and dilational rigidity, which correspond to the protein's effective shape change. As an example, three distinct D-versus-σ "signatures" are calculated, corresponding to gating by dilation, gating by tilt, and gating by a combination of both dilation and tilt. Both advantages and disadvantages of the approach are discussed. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. A basal stem cell signature identifies aggressive prostate cancer phenotypes

    Science.gov (United States)

    Smith, Bryan A.; Sokolov, Artem; Uzunangelov, Vladislav; Baertsch, Robert; Newton, Yulia; Graim, Kiley; Mathis, Colleen; Cheng, Donghui; Stuart, Joshua M.; Witte, Owen N.

    2015-01-01

    Evidence from numerous cancers suggests that increased aggressiveness is accompanied by up-regulation of signaling pathways and acquisition of properties common to stem cells. It is unclear if different subtypes of late-stage cancer vary in stemness properties and whether or not these subtypes are transcriptionally similar to normal tissue stem cells. We report a gene signature specific for human prostate basal cells that is differentially enriched in various phenotypes of late-stage metastatic prostate cancer. We FACS-purified and transcriptionally profiled basal and luminal epithelial populations from the benign and cancerous regions of primary human prostates. High-throughput RNA sequencing showed the basal population to be defined by genes associated with stem cell signaling programs and invasiveness. Application of a 91-gene basal signature to gene expression datasets from patients with organ-confined or hormone-refractory metastatic prostate cancer revealed that metastatic small cell neuroendocrine carcinoma was molecularly more stem-like than either metastatic adenocarcinoma or organ-confined adenocarcinoma. Bioinformatic analysis of the basal cell and two human small cell gene signatures identified a set of E2F target genes common between prostate small cell neuroendocrine carcinoma and primary prostate basal cells. Taken together, our data suggest that aggressive prostate cancer shares a conserved transcriptional program with normal adult prostate basal stem cells. PMID:26460041

  4. Deciphering the interplay among genotype, maturity stage and low-temperature storage on phytochemical composition and transcript levels of enzymatic antioxidants in Prunus persica fruit.

    Science.gov (United States)

    Manganaris, George A; Drogoudi, Pavlina; Goulas, Vlasios; Tanou, Georgia; Georgiadou, Egli C; Pantelidis, George E; Paschalidis, Konstantinos A; Fotopoulos, Vasileios; Manganaris, Athanasios

    2017-10-01

    The aim of this study was to understand the antioxidant metabolic changes of peach (cvs. 'Royal Glory', 'Red Haven' and 'Sun Cloud') and nectarine fruits (cv. 'Big Top') exposed to different combinations of low-temperature storage (0, 2, 4 weeks storage at 0 °C, 90% R.H.) and additional ripening at room temperature (1, 3 and 5 d, shelf life, 20 °C) with an array of analytical, biochemical and molecular approaches. Initially, harvested fruit of the examined cultivars were segregated non-destructively at advanced and less pronounced maturity stages and qualitative traits, physiological parameters, phytochemical composition and antioxidant capacity were determined. 'Big Top' and 'Royal Glory' fruits were characterized by slower softening rate and less pronounced ripening-related alterations. The coupling of HPLC fingerprints, consisted of 7 phenolic compounds (chlorogenic, neochlorogenic acid, catechin, epicatechin, rutin, quecetin-3-O-glucoside, procyanidin B1) and spectrophotometric methods disclosed a great impact of genotype on peach bioactive composition, with 'Sun Cloud' generally displaying the highest contents. Maturity stage at harvest did not seem to affect fruit phenolic composition and no general guidelines for the impact of cold storage and shelf-life on individual phenolic compounds can be extrapolated. Subsequently, fruit of less pronounced maturity at harvest were used for further molecular analysis. 'Sun Cloud' was proven efficient in protecting plasmid pBR322 DNA against ROO attack throughout the experimental period and against HO attack after 2 and 4 weeks of cold storage. Interestingly, a general down-regulation of key genes implicated in the antioxidant apparatus with the prolongation of storage period was recorded; this was more evident for CAT, cAPX, Cu/ZnSOD2, perAPX3 and GPX8 genes. Higher antioxidant capacity of 'Sun Cloud' fruit could potentially be linked with compounds other than enzymatic antioxidants that further regulate peach

  5. Signatures de l'invisible

    CERN Multimedia

    CERN Press Office. Geneva

    2000-01-01

    "Signatures of the Invisible" is an unique collaboration between contemporary artists and contemporary physicists which has the potential to help redefine the relationship between science and art. "Signatures of the Invisible" is jointly organised by the London Institute - the world's largest college of art and design and CERN*, the world's leading particle physics laboratory. 12 leading visual artists:

  6. An interpretation of signature inversion

    International Nuclear Information System (INIS)

    Onishi, Naoki; Tajima, Naoki

    1988-01-01

    An interpretation in terms of the cranking model is presented to explain why signature inversion occurs for positive γ of the axially asymmetric deformation parameter and emerges into specific orbitals. By introducing a continuous variable, the eigenvalue equation can be reduced to a one dimensional Schroedinger equation by means of which one can easily understand the cause of signature inversion. (author)

  7. Cell short circuit, preshort signature

    Science.gov (United States)

    Lurie, C.

    1980-01-01

    Short-circuit events observed in ground test simulations of DSCS-3 battery in-orbit operations are analyzed. Voltage signatures appearing in the data preceding the short-circuit event are evaluated. The ground test simulation is briefly described along with performance during reconditioning discharges. Results suggest that a characteristic signature develops prior to a shorting event.

  8. Ship Signature Management System : Functionality

    NARCIS (Netherlands)

    Arciszewski, H.F.R.; Lier, L. van; Meijer, Y.G.S.; Noordkamp, H.W.; Wassenaar, A.S.

    2010-01-01

    A signature of a platform is the manner in which the platform manifests itself to a certain type of sensor and how observable it is when such a sensor is used to detect the platform. Because many military platforms use sensors in different media, it is the total of its different signatures that

  9. An algorithm to discover gene signatures with predictive potential

    Directory of Open Access Journals (Sweden)

    Hallett Robin M

    2010-09-01

    Full Text Available Abstract Background The advent of global gene expression profiling has generated unprecedented insight into our molecular understanding of cancer, including breast cancer. For example, human breast cancer patients display significant diversity in terms of their survival, recurrence, metastasis as well as response to treatment. These patient outcomes can be predicted by the transcriptional programs of their individual breast tumors. Predictive gene signatures allow us to correctly classify human breast tumors into various risk groups as well as to more accurately target therapy to ensure more durable cancer treatment. Results Here we present a novel algorithm to generate gene signatures with predictive potential. The method first classifies the expression intensity for each gene as determined by global gene expression profiling as low, average or high. The matrix containing the classified data for each gene is then used to score the expression of each gene based its individual ability to predict the patient characteristic of interest. Finally, all examined genes are ranked based on their predictive ability and the most highly ranked genes are included in the master gene signature, which is then ready for use as a predictor. This method was used to accurately predict the survival outcomes in a cohort of human breast cancer patients. Conclusions We confirmed the capacity of our algorithm to generate gene signatures with bona fide predictive ability. The simplicity of our algorithm will enable biological researchers to quickly generate valuable gene signatures without specialized software or extensive bioinformatics training.

  10. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  11. Dietary Lipid Sources Influence Fatty Acid Composition in Tissue of Large Yellow Croaker (Larmichthys crocea by Regulating Triacylglycerol Synthesis and Catabolism at the Transcriptional Level.

    Directory of Open Access Journals (Sweden)

    Hong Qiu

    Full Text Available An 8-week feeding trial was conducted to evaluate the effects of dietary lipid sources on growth performance, fatty acid composition, rate-limiting enzyme activities and gene expression related to lipid metabolism in large yellow croaker (Larmichthys crocea. Five iso-nitrogenous and iso-lipidic experimental diets were formulated to contain different lipid sources, such as fish oil (FO, soybean oil (SO, linseed oil (LO, rapeseed oil (RO and peanut oil (PO, respectively. Triplicate groups of 50 fish (initial weight 13.77±0.07g were stocked in 15 floating net cages (1.5m×1.5m×2.0m. Fish fed the diets containing RO and LO had lower weight gain and specific growth rates than those fed the FO, SO and PO diets. Survival, feed efficiency, protein efficiency ratio, hepatosomatic index, viscerasomatic index and condition factor were not significantly affected by different dietary lipid sources. Fish fed the diet containing FO had higher lipid content in whole body compared with the other groups, whereas fish fed the SO diet had the lowest muscle lipid content. Fatty acid profiles of muscle and liver reflected the fatty acid composition of the diets. Plasma glucose, triglyceride, and the enzymatic activity of aspartate aminotransferase and alanine aminotransferase were significantly influenced by different dietary lipid sources, while total protein, cholesterol, superoxide dismutase or malondialdehyde in plasma were not affected by the different dietary lipid sources. Fish fed the LO diet had lower adipose triglyceride lipase and fatty acid synthase activities in liver than those fed the diets containing FO and RO, while the LO diet resulted in the highest hepatic carnitine palmitoultransferase-1 activity. Hepatic gene relative expression of adipose triglyceride lipase and carnitine palmitoyltransferase-1 in fish fed PO diet was significantly higher than all other groups, whereas fish fed the SO and LO diets had lower relative expression levels of

  12. Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

    Directory of Open Access Journals (Sweden)

    Xiao-Xiao Li

    2017-06-01

    Full Text Available Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01. In addition, the sulfate-reducing microorganisms (SRMs were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.

  13. Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

    Science.gov (United States)

    Li, Xiao-Xiao; Liu, Jin-Feng; Zhou, Lei; Mbadinga, Serge M.; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2017-01-01

    Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs. PMID:28638372

  14. Thermal Signature Measurements for Ammonium Nitrate/Fuel Mixtures by Laser Heating.

    Science.gov (United States)

    Nazarian, Ashot; Presser, Cary

    2016-01-10

    Measurements were carried out to obtain thermal signatures of several ammonium nitrate/fuel (ANF) mixtures, using a laser-heating technique referred to as the laser-driven thermal reactor (LDTR). The mixtures were ammonium nitrate (AN)/kerosene, AN/ethylene glycol, AN/paraffin wax, AN/petroleum jelly, AN/confectioner's sugar, AN/cellulose (tissue paper), nitromethane/cellulose, nitrobenzene/cellulose, AN/cellulose/nitromethane, AN/cellulose/nitrobenzene. These mixtures were also compared with AN/nitromethane and AN/diesel fuel oil, obtained from an earlier investigation. Thermograms for the mixtures, as well as individual constituents, were compared to better understand how the sample thermal signature changes with mixture composition. This is the first step in development of a thermal-signature database, to be used along with other signature databases, to improve identification of energetic substances of unknown composition. The results indicated that each individual thermal signature was associated unambiguously with a particular mixture composition. The signature features of a particular mixture were shaped by the individual constituent signatures. It was also uncovered that the baseline signature was modified after an experiment due to coating of unreacted residue on the substrate surface and a change in the reactor sphere oxide layer. Thus, care was required to pre-oxidize the sphere prior to an experiment. A minimum sample mass (which was dependent on composition) was required to detect the signature characteristics. Increased laser power served to magnify signal strength while preserving the signature features. For the mixtures examined, the thermal response of each ANF mixture was found to be different, which was based on the mixture composition and the thermal behavior of each mixture constituent.

  15. Initial Semantics for Strengthened Signatures

    Directory of Open Access Journals (Sweden)

    André Hirschowitz

    2012-02-01

    Full Text Available We give a new general definition of arity, yielding the companion notions of signature and associated syntax. This setting is modular in the sense requested by Ghani and Uustalu: merging two extensions of syntax corresponds to building an amalgamated sum. These signatures are too general in the sense that we are not able to prove the existence of an associated syntax in this general context. So we have to select arities and signatures for which there exists the desired initial monad. For this, we follow a track opened by Matthes and Uustalu: we introduce a notion of strengthened arity and prove that the corresponding signatures have initial semantics (i.e. associated syntax. Our strengthened arities admit colimits, which allows the treatment of the λ-calculus with explicit substitution.

  16. Retail applications of signature verification

    Science.gov (United States)

    Zimmerman, Thomas G.; Russell, Gregory F.; Heilper, Andre; Smith, Barton A.; Hu, Jianying; Markman, Dmitry; Graham, Jon E.; Drews, Clemens

    2004-08-01

    The dramatic rise in identity theft, the ever pressing need to provide convenience in checkout services to attract and retain loyal customers, and the growing use of multi-function signature captures devices in the retail sector provides favorable conditions for the deployment of dynamic signature verification (DSV) in retail settings. We report on the development of a DSV system to meet the needs of the retail sector. We currently have a database of approximately 10,000 signatures collected from 600 subjects and forgers. Previous work at IBM on DSV has been merged and extended to achieve robust performance on pen position data available from commercial point of sale hardware, achieving equal error rates on skilled forgeries and authentic signatures of 1.5% to 4%.

  17. Magnetic Signature Analysis & Validation System

    National Research Council Canada - National Science Library

    Vliet, Scott

    2001-01-01

    The Magnetic Signature Analysis and Validation (MAGSAV) System is a mobile platform that is used to measure, record, and analyze the perturbations to the earth's ambient magnetic field caused by object such as armored vehicles...

  18. Reconfiguring waveguide-gratings-based M-signature codecs to enhance OCDMA network confidentiality

    Science.gov (United States)

    Huang, Jen-Fa; Chen, Kai-Sheng; Lin, Ying-Chen; Li, Chung-Yu

    2014-02-01

    A reconfiguration scheme based on composite signature codes over waveguide-gratings-based optical code-division multiple-access (OCDMA) network coder/decoders (codecs) is proposed in the paper. By using central control node to monitor network traffic condition and reconfigure the composite signature codes made up of maximal-length sequence (M-sequence) component codes and random changing the signature codes assigned for each user to improve the confidentiality performance in an OCDMA system. The proposed scheme is analyzed with some practical eavesdroppers' attacks.

  19. 21 CFR 11.50 - Signature manifestations.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Signature manifestations. 11.50 Section 11.50 Food... RECORDS; ELECTRONIC SIGNATURES Electronic Records § 11.50 Signature manifestations. (a) Signed electronic...: (1) The printed name of the signer; (2) The date and time when the signature was executed; and (3...

  20. 76 FR 30542 - Adult Signature Services

    Science.gov (United States)

    2011-05-26

    ... POSTAL SERVICE 39 CFR Part 111 Adult Signature Services AGENCY: Postal Service\\TM\\. ACTION: Final..., Domestic Mail Manual (DMM[supreg]) 503.8, to add a new extra service called Adult Signature. This new service has two available options: Adult Signature Required and Adult Signature Restricted Delivery. DATES...

  1. 1 CFR 18.7 - Signature.

    Science.gov (United States)

    2010-01-01

    ... 1 General Provisions 1 2010-01-01 2010-01-01 false Signature. 18.7 Section 18.7 General Provisions... PREPARATION AND TRANSMITTAL OF DOCUMENTS GENERALLY § 18.7 Signature. The original and each duplicate original... stamped beneath the signature. Initialed or impressed signatures will not be accepted. Documents submitted...

  2. Attribute-Based Digital Signature System

    NARCIS (Netherlands)

    Ibraimi, L.; Asim, Muhammad; Petkovic, M.

    2011-01-01

    An attribute-based digital signature system comprises a signature generation unit (1) for signing a message (m) by generating a signature (s) based on a user secret key (SK) associated with a set of user attributes, wherein the signature generation unit (1) is arranged for combining the user secret

  3. Quantum messages with signatures forgeable in arbitrated quantum signature schemes

    International Nuclear Information System (INIS)

    Kim, Taewan; Choi, Jeong Woon; Jho, Nam-Su; Lee, Soojoon

    2015-01-01

    Even though a method to perfectly sign quantum messages has not been known, the arbitrated quantum signature scheme has been considered as one of the good candidates. However, its forgery problem has been an obstacle to the scheme becoming a successful method. In this paper, we consider one situation, which is slightly different from the forgery problem, that we use to check whether at least one quantum message with signature can be forged in a given scheme, although all the messages cannot be forged. If there are only a finite number of forgeable quantum messages in the scheme, then the scheme can be secured against the forgery attack by not sending forgeable quantum messages, and so our situation does not directly imply that we check whether the scheme is secure against the attack. However, if users run a given scheme without any consideration of forgeable quantum messages, then a sender might transmit such forgeable messages to a receiver and in such a case an attacker can forge the messages if the attacker knows them. Thus it is important and necessary to look into forgeable quantum messages. We show here that there always exists such a forgeable quantum message-signature pair for every known scheme with quantum encryption and rotation, and numerically show that there are no forgeable quantum message-signature pairs that exist in an arbitrated quantum signature scheme. (paper)

  4. SIGNATURE: A workbench for gene expression signature analysis

    Directory of Open Access Journals (Sweden)

    Chang Jeffrey T

    2011-11-01

    Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

  5. Signature molecular descriptor : advanced applications.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (Tennessee Technological University, Cookeville, TN)

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  6. Predicting cellular growth from gene expression signatures.

    Directory of Open Access Journals (Sweden)

    Edoardo M Airoldi

    2009-01-01

    Full Text Available Maintaining balanced growth in a changing environment is a fundamental systems-level challenge for cellular physiology, particularly in microorganisms. While the complete set of regulatory and functional pathways supporting growth and cellular proliferation are not yet known, portions of them are well understood. In particular, cellular proliferation is governed by mechanisms that are highly conserved from unicellular to multicellular organisms, and the disruption of these processes in metazoans is a major factor in the development of cancer. In this paper, we develop statistical methodology to identify quantitative aspects of the regulatory mechanisms underlying cellular proliferation in Saccharomyces cerevisiae. We find that the expression levels of a small set of genes can be exploited to predict the instantaneous growth rate of any cellular culture with high accuracy. The predictions obtained in this fashion are robust to changing biological conditions, experimental methods, and technological platforms. The proposed model is also effective in predicting growth rates for the related yeast Saccharomyces bayanus and the highly diverged yeast Schizosaccharomyces pombe, suggesting that the underlying regulatory signature is conserved across a wide range of unicellular evolution. We investigate the biological significance of the gene expression signature that the predictions are based upon from multiple perspectives: by perturbing the regulatory network through the Ras/PKA pathway, observing strong upregulation of growth rate even in the absence of appropriate nutrients, and discovering putative transcription factor binding sites, observing enrichment in growth-correlated genes. More broadly, the proposed methodology enables biological insights about growth at an instantaneous time scale, inaccessible by direct experimental methods. Data and tools enabling others to apply our methods are available at http://function.princeton.edu/growthrate.

  7. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers

    NARCIS (Netherlands)

    Muñoz, Javier; Stange, Daniel E.; Schepers, Arnout G.; van de Wetering, Marc; Koo, Bon-Kyoung; Itzkovitz, Shalev; Volckmann, Richard; Kung, Kevin S.; Koster, Jan; Radulescu, Sorina; Myant, Kevin; Versteeg, Rogier; Sansom, Owen J.; van Es, Johan H.; Barker, Nick; van Oudenaarden, Alexander; Mohammed, Shabaz; Heck, Albert J. R.; Clevers, Hans

    2012-01-01

    Two types of stem cells are currently defined in small intestinal crypts: cycling crypt base columnar (CBC) cells and quiescent '+4' cells. Here, we combine transcriptomics with proteomics to define a definitive molecular signature for Lgr5(+) CBC cells. Transcriptional profiling of FACS-sorted

  8. Five Guidelines for Selecting Hydrological Signatures

    Science.gov (United States)

    McMillan, H. K.; Westerberg, I.; Branger, F.

    2017-12-01

    Hydrological signatures are index values derived from observed or modeled series of hydrological data such as rainfall, flow or soil moisture. They are designed to extract relevant information about hydrological behavior, such as to identify dominant processes, and to determine the strength, speed and spatiotemporal variability of the rainfall-runoff response. Hydrological signatures play an important role in model evaluation. They allow us to test whether particular model structures or parameter sets accurately reproduce the runoff generation processes within the watershed of interest. Most modeling studies use a selection of different signatures to capture different aspects of the catchment response, for example evaluating overall flow distribution as well as high and low flow extremes and flow timing. Such studies often choose their own set of signatures, or may borrow subsets of signatures used in multiple other works. The link between signature values and hydrological processes is not always straightforward, leading to uncertainty and variability in hydrologists' signature choices. In this presentation, we aim to encourage a more rigorous approach to hydrological signature selection, which considers the ability of signatures to represent hydrological behavior and underlying processes for the catchment and application in question. To this end, we propose a set of guidelines for selecting hydrological signatures. We describe five criteria that any hydrological signature should conform to: Identifiability, Robustness, Consistency, Representativeness, and Discriminatory Power. We describe an example of the design process for a signature, assessing possible signature designs against the guidelines above. Due to their ubiquity, we chose a signature related to the Flow Duration Curve, selecting the FDC mid-section slope as a proposed signature to quantify catchment overall behavior and flashiness. We demonstrate how assessment against each guideline could be used to

  9. Digital Signature Schemes with Complementary Functionality and Applications

    OpenAIRE

    S. N. Kyazhin

    2012-01-01

    Digital signature schemes with additional functionality (an undeniable signature, a signature of the designated confirmee, a signature blind, a group signature, a signature of the additional protection) and examples of their application are considered. These schemes are more practical, effective and useful than schemes of ordinary digital signature.

  10. Signature Pedagogy in Theatre Arts

    Science.gov (United States)

    Kornetsky, Lisa

    2017-01-01

    Critique in undergraduate theatre programs is at the heart of training actors at all levels. It is accepted as the signature pedagogy and is practiced in multiple ways. This essay defines critique and presents the case for why it is used as the single most important way that performers come to understand the language, values, and discourse of the…

  11. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  12. Quark-Gluon Plasma Signatures

    CERN Document Server

    Vogt, Ramona

    1998-01-01

    Aspects of quark-gluon plasma signatures that can be measured by CMS are discussed. First the initial conditions of the system from minijet production are introduced, including shadowing effects. Color screening of the Upsilon family is then presented, followed by energy loss effects on charm and bottom hadrons, high Pt jets and global observables.

  13. Galaxy interactions : The HI signature

    NARCIS (Netherlands)

    Sancisi, R; Barnes, JE; Sanders, DB

    1999-01-01

    HI observations are an excellent tool for investigating tidal interactions. Ongoing major and minor interactions which can lead to traumatic mergers or to accretion and the triggering of star formation, show distinct HI signatures. Interactions and mergers in the recent past can also be recognized

  14. Transcriptional regulation by competing transcription factor modules.

    Directory of Open Access Journals (Sweden)

    Rutger Hermsen

    2006-12-01

    Full Text Available Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of transcription units by binding to cis-regulatory regions on the DNA. The designs of both eukaryotic and prokaryotic cis-regulatory regions are usually highly complex. They frequently consist of both repetitive and overlapping transcription factor binding sites. To unravel the design principles of these promoter architectures, we have designed in silico prokaryotic transcriptional logic gates with predefined input-output relations using an evolutionary algorithm. The resulting cis-regulatory designs are often composed of modules that consist of tandem arrays of binding sites to which the transcription factors bind cooperatively. Moreover, these modules often overlap with each other, leading to competition between them. Our analysis thus identifies a new signal integration motif that is based upon the interplay between intramodular cooperativity and intermodular competition. We show that this signal integration mechanism drastically enhances the capacity of cis-regulatory domains to integrate signals. Our results provide a possible explanation for the complexity of promoter architectures and could be used for the rational design of synthetic gene circuits.

  15. Assessing the robustness of quantitative fatty acid signature analysis to assumption violations

    Science.gov (United States)

    Bromaghin, Jeffrey F.; Budge, Suzanne M.; Thiemann, Gregory W.; Rode, Karyn D.

    2016-01-01

      Knowledge of animal diets can provide important insights into life history and ecology, relationships among species in a community and potential response to ecosystem change or perturbation. Quantitative fatty acid signature analysis (QFASA) is a method of estimating diets from data on the composition, or signature, of fatty acids stored in adipose tissue. Given data on signatures of potential prey, a predator diet is estimated by minimizing the distance between its signature and a mixture of prey signatures. Calibration coefficients, constants derived from feeding trials, are used to account for differential metabolism of individual fatty acids. QFASA has been widely applied since its introduction and several variants of the original estimator have appeared in the literature. However, work to compare the statistical properties of QFASA estimators has been limited.

  16. Genomic signatures characterize leukocyte infiltration in myositis muscles

    Science.gov (United States)

    2012-01-01

    Background Leukocyte infiltration plays an important role in the pathogenesis and progression of myositis, and is highly associated with disease severity. Currently, there is a lack of: efficacious therapies for myositis; understanding of the molecular features important for disease pathogenesis; and potential molecular biomarkers for characterizing inflammatory myopathies to aid in clinical development. Methods In this study, we developed a simple model and predicted that 1) leukocyte-specific transcripts (including both protein-coding transcripts and microRNAs) should be coherently overexpressed in myositis muscle and 2) the level of over-expression of these transcripts should be correlated with leukocyte infiltration. We applied this model to assess immune cell infiltration in myositis by examining mRNA and microRNA (miRNA) expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls. Results Several gene signatures, including a leukocyte index, type 1 interferon (IFN), MHC class I, and immunoglobulin signature, were developed to characterize myositis patients at the molecular level. The leukocyte index, consisting of genes predominantly associated with immune function, displayed strong concordance with pathological assessment of immune cell infiltration. This leukocyte index was subsequently utilized to differentiate transcriptional changes due to leukocyte infiltration from other alterations in myositis muscle. Results from this differentiation revealed biologically relevant differences in the relationship between the type 1 IFN pathway, miR-146a, and leukocyte infiltration within various myositis subtypes. Conclusions Results indicate that a likely interaction between miR-146a expression and the type 1 IFN pathway is confounded by the level of leukocyte infiltration into muscle tissue. Although the role of miR-146a in myositis remains uncertain, our results highlight the potential benefit of deconvoluting the source of

  17. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

    WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469

  18. Online Signature Verification on MOBISIG Finger-Drawn Signature Corpus

    Directory of Open Access Journals (Sweden)

    Margit Antal

    2018-01-01

    Full Text Available We present MOBISIG, a pseudosignature dataset containing finger-drawn signatures from 83 users captured with a capacitive touchscreen-based mobile device. The database was captured in three sessions resulting in 45 genuine signatures and 20 skilled forgeries for each user. The database was evaluated by two state-of-the-art methods: a function-based system using local features and a feature-based system using global features. Two types of equal error rate computations are performed: one using a global threshold and the other using user-specific thresholds. The lowest equal error rate was 0.01% against random forgeries and 5.81% against skilled forgeries using user-specific thresholds that were computed a posteriori. However, these equal error rates were significantly raised to 1.68% (random forgeries case and 14.31% (skilled forgeries case using global thresholds. The same evaluation protocol was performed on the DooDB publicly available dataset. Besides verification performance evaluations conducted on the two finger-drawn datasets, we evaluated the quality of the samples and the users of the two datasets using basic quality measures. The results show that finger-drawn signatures can be used by biometric systems with reasonable accuracy.

  19. Unsupervised signature extraction from forensic logs

    NARCIS (Netherlands)

    Thaler, S.M.; Menkovski, V.; Petkovic, M.; Altun, Y.; Das, K.; Mielikäinen, T.; Malerba, D.; Stefanowski, J.; Read, J.; Žitnik, M.; Ceci, M.

    2017-01-01

    Signature extraction is a key part of forensic log analysis. It involves recognizing patterns in log lines such that log lines that originated from the same line of code are grouped together. A log signature consists of immutable parts and mutable parts. The immutable parts define the signature, and

  20. 7 CFR 718.9 - Signature requirements.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Signature requirements. 718.9 Section 718.9... MULTIPLE PROGRAMS General Provisions § 718.9 Signature requirements. (a) When a program authorized by this chapter or Chapter XIV of this title requires the signature of a producer; landowner; landlord; or tenant...

  1. 42 CFR 424.36 - Signature requirements.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Signature requirements. 424.36 Section 424.36... (CONTINUED) MEDICARE PROGRAM CONDITIONS FOR MEDICARE PAYMENT Claims for Payment § 424.36 Signature requirements. (a) General rule. The beneficiary's own signature is required on the claim unless the beneficiary...

  2. 17 CFR 12.12 - Signature.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 1 2010-04-01 2010-04-01 false Signature. 12.12 Section 12.12... General Information and Preliminary Consideration of Pleadings § 12.12 Signature. (a) By whom. All... document on behalf of another person. (b) Effect. The signature on any document of any person acting either...

  3. 25 CFR 213.10 - Lessor's signature.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Lessor's signature. 213.10 Section 213.10 Indians BUREAU... MEMBERS OF FIVE CIVILIZED TRIBES, OKLAHOMA, FOR MINING How to Acquire Leases § 213.10 Lessor's signature... thumbprint which shall be designated as “right” or “left” thumbmark. Such signatures must be witnessed by two...

  4. Signature effects in 2-qp rotational bands

    International Nuclear Information System (INIS)

    Jain, A.K.; Goel, A.

    1992-01-01

    The authors briefly review the progress in understanding the 2-qp rotational bands in odd-odd nuclei. Signature effects and the phenomenon of signature inversion are discussed. The Coriolis coupling appears to have all the ingredients to explain the inversion. Some recent work on signature dependence in 2-qp bands of even-even nuclei is also discussed; interesting features are pointed out

  5. 27 CFR 17.6 - Signature authority.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Signature authority. 17.6... PRODUCTS General Provisions § 17.6 Signature authority. No claim, bond, tax return, or other required... other proper notification of signature authority has been filed with the TTB office where the required...

  6. High-speed high-security signatures

    NARCIS (Netherlands)

    Bernstein, D.J.; Duif, N.; Lange, T.; Schwabe, P.; Yang, B.Y.

    2011-01-01

    This paper shows that a $390 mass-market quad-core 2.4GHz Intel Westmere (Xeon E5620) CPU can create 108000 signatures per second and verify 71000 signatures per second on an elliptic curve at a 2128 security level. Public keys are 32 bytes, and signatures are 64 bytes. These performance figures

  7. Some Proxy Signature and Designated verifier Signature Schemes over Braid Groups

    OpenAIRE

    Lal, Sunder; Verma, Vandani

    2009-01-01

    Braids groups provide an alternative to number theoretic public cryptography and can be implemented quite efficiently. The paper proposes five signature schemes: Proxy Signature, Designated Verifier, Bi-Designated Verifier, Designated Verifier Proxy Signature And Bi-Designated Verifier Proxy Signature scheme based on braid groups. We also discuss the security aspects of each of the proposed schemes.

  8. Gene Expression Signature in Adipose Tissue of Acromegaly Patients

    Science.gov (United States)

    Hochberg, Irit; Tran, Quynh T.; Barkan, Ariel L.; Saltiel, Alan R.; Chandler, William F.; Bridges, Dave

    2015-01-01

    To study the effect of chronic excess growth hormone on adipose tissue, we performed RNA sequencing in adipose tissue biopsies from patients with acromegaly (n = 7) or non-functioning pituitary adenomas (n = 11). The patients underwent clinical and metabolic profiling including assessment of HOMA-IR. Explants of adipose tissue were assayed ex vivo for lipolysis and ceramide levels. Patients with acromegaly had higher glucose, higher insulin levels and higher HOMA-IR score. We observed several previously reported transcriptional changes (IGF1, IGFBP3, CISH, SOCS2) that are known to be induced by GH/IGF-1 in liver but are also induced in adipose tissue. We also identified several novel transcriptional changes, some of which may be important for GH/IGF responses (PTPN3 and PTPN4) and the effects of acromegaly on growth and proliferation. Several differentially expressed transcripts may be important in GH/IGF-1-induced metabolic changes. Specifically, induction of LPL, ABHD5, and NRIP1 can contribute to enhanced lipolysis and may explain the elevated adipose tissue lipolysis in acromegalic patients. Higher expression of TCF7L2 and the fatty acid desaturases FADS1, FADS2 and SCD could contribute to insulin resistance. Ceramides were not different between the two groups. In summary, we have identified the acromegaly gene expression signature in human adipose tissue. The significance of altered expression of specific transcripts will enhance our understanding of the metabolic and proliferative changes associated with acromegaly. PMID:26087292

  9. Whole Blood Transcriptional Profiling of Interferon-Inducible Genes Identifies Highly Upregulated IFI27 in Primary Myelofibrosis

    DEFF Research Database (Denmark)

    Skov, Vibe; Larsen, Thomas Stauffer; Thomassen, Mads

    2011-01-01

    focused upon the transcriptional profiling of interferon-associated genes in patients with essential thrombocythemia (ET) (n = 19), polycythemia vera (PV) (n = 41), and primary myelofibrosis (PMF) (n = 9). Using whole-blood transcriptional profiling and accordingly obtaining an integrated signature...

  10. Whole-blood transcriptional profiling of interferon-inducible genes identifies highly upregulated IFI27 in primary myelofibrosis

    DEFF Research Database (Denmark)

    Skov, Vibe; Larsen, Thomas Stauffer; Thomassen, Mads

    2011-01-01

    focused upon the transcriptional profiling of interferon-associated genes in patients with essential thrombocythemia (ET) (n = 19), polycythemia vera (PV) (n = 41), and primary myelofibrosis (PMF) (n = 9). Using whole-blood transcriptional profiling and accordingly obtaining an integrated signature...

  11. Nonlinear control of magnetic signatures

    Science.gov (United States)

    Niemoczynski, Bogdan

    Magnetic properties of ferrite structures are known to cause fluctuations in Earth's magnetic field around the object. These fluctuations are known as the object's magnetic signature and are unique based on the object's geometry and material. It is a common practice to neutralize magnetic signatures periodically after certain time intervals, however there is a growing interest to develop real time degaussing systems for various applications. Development of real time degaussing system is a challenging problem because of magnetic hysteresis and difficulties in measurement or estimation of near-field flux data. The goal of this research is to develop a real time feedback control system that can be used to minimize magnetic signatures for ferrite structures. Experimental work on controlling the magnetic signature of a cylindrical steel shell structure with a magnetic disturbance provided evidence that the control process substantially increased the interior magnetic flux. This means near field estimation using interior sensor data is likely to be inaccurate. Follow up numerical work for rectangular and cylindrical cross sections investigated variations in shell wall flux density under a variety of ambient excitation and applied disturbances. Results showed magnetic disturbances could corrupt interior sensor data and magnetic shielding due to the shell walls makes the interior very sensitive to noise. The magnetic flux inside the shell wall showed little variation due to inner disturbances and its high base value makes it less susceptible to noise. This research proceeds to describe a nonlinear controller to use the shell wall data as an input. A nonlinear plant model of magnetics is developed using a constant tau to represent domain rotation lag and a gain function k to describe the magnetic hysteresis curve for the shell wall. The model is justified by producing hysteresis curves for multiple materials, matching experimental data using a particle swarm algorithm, and

  12. High pressure membrane foulants of seawater, brackish water and river water: Origin assessed by sugar and bacteriohopanepolyol signatures

    KAUST Repository

    Mondamert, Leslie; Labanowski, Jé rô me; N'Goye, F.; Talbot, Helen M.; Croue, Jean-Philippe

    2011-01-01

    The present work aimed to study the origin of foulant material recovered on membranes used in water treatment. Firstly, sugar signatures were assessed from the monosaccharide composition. As results were not conclusive, a statistical approach using

  13. Radiation Gene-expression Signatures in Primary Breast Cancer Cells.

    Science.gov (United States)

    Minafra, Luigi; Bravatà, Valentina; Cammarata, Francesco P; Russo, Giorgio; Gilardi, Maria C; Forte, Giusi I

    2018-05-01

    In breast cancer (BC) care, radiation therapy (RT) is an efficient treatment to control localized tumor. Radiobiological research is needed to understand molecular differences that affect radiosensitivity of different tumor subtypes and the response variability. The aim of this study was to analyze gene expression profiling (GEP) in primary BC cells following irradiation with doses of 9 Gy and 23 Gy delivered by intraoperative electron radiation therapy (IOERT) in order to define gene signatures of response to high doses of ionizing radiation. We performed GEP by cDNA microarrays and evaluated cell survival after IOERT treatment in primary BC cell cultures. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate candidate genes. We showed, for the first time, a 4-gene and a 6-gene signature, as new molecular biomarkers, in two primary BC cell cultures after exposure at 9 Gy and 23 Gy respectively, for which we observed a significantly high survival rate. Gene signatures activated by different doses of ionizing radiation may predict response to RT and contribute to defining a personalized biological-driven treatment plan. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  14. Nonlinear analysis of dynamic signature

    Science.gov (United States)

    Rashidi, S.; Fallah, A.; Towhidkhah, F.

    2013-12-01

    Signature is a long trained motor skill resulting in well combination of segments like strokes and loops. It is a physical manifestation of complex motor processes. The problem, generally stated, is that how relative simplicity in behavior emerges from considerable complexity of perception-action system that produces behavior within an infinitely variable biomechanical and environmental context. To solve this problem, we present evidences which indicate that motor control dynamic in signing process is a chaotic process. This chaotic dynamic may explain a richer array of time series behavior in motor skill of signature. Nonlinear analysis is a powerful approach and suitable tool which seeks for characterizing dynamical systems through concepts such as fractal dimension and Lyapunov exponent. As a result, they can be analyzed in both horizontal and vertical for time series of position and velocity. We observed from the results that noninteger values for the correlation dimension indicates low dimensional deterministic dynamics. This result could be confirmed by using surrogate data tests. We have also used time series to calculate the largest Lyapunov exponent and obtain a positive value. These results constitute significant evidence that signature data are outcome of chaos in a nonlinear dynamical system of motor control.

  15. Mechanisms of transcriptional repression by histone lysine methylation

    DEFF Research Database (Denmark)

    Hublitz, Philip; Albert, Mareike; Peters, Antoine H F M

    2009-01-01

    . In this report, we review the recent literature to deduce mechanisms underlying Polycomb and H3K9 methylation mediated repression, and describe the functional interplay with activating H3K4 methylation. We summarize recent data that indicate a close relationship between GC density of promoter sequences......, transcription factor binding and the antagonizing activities of distinct epigenetic regulators such as histone methyltransferases (HMTs) and histone demethylases (HDMs). Subsequently, we compare chromatin signatures associated with different types of transcriptional outcomes from stable repression to highly...

  16. Nuclear stability and transcriptional directionality separate functionally distinct RNA species

    DEFF Research Database (Denmark)

    Andersson, Robin; Refsing Andersen, Peter; Valen, Eivind

    2014-01-01

    Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. Although recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protei...

  17. Spectral signature selection for mapping unvegetated soils

    Science.gov (United States)

    May, G. A.; Petersen, G. W.

    1975-01-01

    Airborne multispectral scanner data covering the wavelength interval from 0.40-2.60 microns were collected at an altitude of 1000 m above the terrain in southeastern Pennsylvania. Uniform training areas were selected within three sites from this flightline. Soil samples were collected from each site and a procedure developed to allow assignment of scan line and element number from the multispectral scanner data to each sampling location. These soil samples were analyzed on a spectrophotometer and laboratory spectral signatures were derived. After correcting for solar radiation and atmospheric attenuation, the laboratory signatures were compared to the spectral signatures derived from these same soils using multispectral scanner data. Both signatures were used in supervised and unsupervised classification routines. Computer-generated maps using the laboratory and multispectral scanner derived signatures resulted in maps that were similar to maps resulting from field surveys. Approximately 90% agreement was obtained between classification maps produced using multispectral scanner derived signatures and laboratory derived signatures.

  18. Time Series Based for Online Signature Verification

    Directory of Open Access Journals (Sweden)

    I Ketut Gede Darma Putra

    2013-11-01

    Full Text Available Signature verification system is to match the tested signature with a claimed signature. This paper proposes time series based for feature extraction method and dynamic time warping for match method. The system made by process of testing 900 signatures belong to 50 participants, 3 signatures for reference and 5 signatures from original user, simple imposters and trained imposters for signatures test. The final result system was tested with 50 participants with 3 references. This test obtained that system accuracy without imposters is 90,44897959% at threshold 44 with rejection errors (FNMR is 5,2% and acceptance errors (FMR is 4,35102%, when with imposters system accuracy is 80,1361% at threshold 27 with error rejection (FNMR is 15,6% and acceptance errors (average FMR is 4,263946%, with details as follows: acceptance errors is 0,391837%, acceptance errors simple imposters is 3,2% and acceptance errors trained imposters is 9,2%.

  19. Littoral Assessment of Mine Burial Signatures (LAMBS) buried land mine/background spectral signature analyses

    Science.gov (United States)

    Kenton, A.C.; Geci, D.M.; Ray, K.J.; Thomas, C.M.; Salisbury, J.W.; Mars, J.C.; Crowley, J.K.; Witherspoon, N.H.; Holloway, J.H.; Harmon R.S.Broach J.T.Holloway, Jr. J.H.

    2004-01-01

    The objective of the Office of Naval Research (ONR) Rapid Overt Reconnaissance (ROR) program and the Airborne Littoral Reconnaissance Technologies (ALRT) project's LAMBS effort is to determine if electro-optical spectral discriminants exist that are useful for the detection of land mines in littoral regions. Statistically significant buried mine overburden and background signature data were collected over a wide spectral range (0.35 to 14 ??m) to identify robust spectral features that might serve as discriminants for new airborne sensor concepts. LAMBS has expanded previously collected databases to littoral areas - primarily dry and wet sandy soils - where tidal, surf, and wind conditions can severely modify spectral signatures. At AeroSense 2003, we reported completion of three buried mine collections at an inland bay, Atlantic and Gulf of Mexico beach sites.1 We now report LAMBS spectral database analyses results using metrics which characterize the detection performance of general types of spectral detection algorithms. These metrics include mean contrast, spectral signal-to-clutter, covariance, information content, and spectral matched filter analyses. Detection performance of the buried land mines was analyzed with regard to burial age, background type, and environmental conditions. These analyses considered features observed due to particle size differences, surface roughness, surface moisture, and compositional differences.

  20. Infrared signatures for remote sensing

    International Nuclear Information System (INIS)

    McDowell, R.S.; Sharpe, S.W.; Kelly, J.F.

    1994-04-01

    PNL's capabilities for infrared and near-infrared spectroscopy include tunable-diode-laser (TDL) systems covering 300--3,000 cm -1 at 2 laser. PNL also has a beam expansion source with a 12-cm slit, which provides a 3-m effective path for gases at ∼10 K, giving a Doppler width of typically 10 MHz; and long-path static gas cells (to 100 m). In applying this equipment to signatures work, the authors emphasize the importance of high spectral resolution for detecting and identifying atmospheric interferences; for identifying the optimum analytical frequencies; for deriving, by spectroscopic analysis, the molecular parameters needed for modeling; and for obtaining data on species and/or bands that are not in existing databases. As an example of such spectroscopy, the authors have assigned and analyzed the C-Cl stretching region of CCl 4 at 770--800 cm -1 . This is an important potential signature species whose IR absorption has remained puzzling because of the natural isotopic mix, extensive hot-band structure, and a Fermi resonance involving a nearby combination band. Instrument development projects include the IR sniffer, a small high-sensitivity, high-discrimination (Doppler-limited) device for fence-line or downwind monitoring that is effective even in regions of atmospheric absorption; preliminary work has achieved sensitivities at the low-ppb level. Other work covers trace species detection with TDLs, and FM-modulated CO 2 laser LIDAR. The authors are planning a field experiment to interrogate the Hanford tank farm for signature species from Rattlesnake Mountain, a standoff of ca. 15 km, to be accompanied by simultaneous ground-truthing at the tanks

  1. Signature of Microbial Dysbiosis in Periodontitis.

    Science.gov (United States)

    Meuric, Vincent; Le Gall-David, Sandrine; Boyer, Emile; Acuña-Amador, Luis; Martin, Bénédicte; Fong, Shao Bing; Barloy-Hubler, Frederique; Bonnaure-Mallet, Martine

    2017-07-15

    Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera ( Veillonella , Neisseria , Rothia , Corynebacterium , and Actinomyces ) were highly prevalent (>95%) in health, while other genera ( Eubacterium , Campylobacter , Treponema , and Tannerella ) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When

  2. Signature Curves Statistics of DNA Supercoils

    OpenAIRE

    Shakiban, Cheri; Lloyd, Peter

    2004-01-01

    In this paper we describe the Euclidean signature curves for two dimensional closed curves in the plane and their generalization to closed space curves. The focus will be on discrete numerical methods for approximating such curves. Further we will apply these numerical methods to plot the signature curves related to three-dimensional simulated DNA supercoils. Our primary focus will be on statistical analysis of the data generated for the signature curves of the supercoils. We will try to esta...

  3. Institute of Geophysics, Planetary Physics, and Signatures

    Data.gov (United States)

    Federal Laboratory Consortium — The Institute of Geophysics, Planetary Physics, and Signatures at Los Alamos National Laboratory is committed to promoting and supporting high quality, cutting-edge...

  4. On reliable discovery of molecular signatures

    Directory of Open Access Journals (Sweden)

    Björkegren Johan

    2009-01-01

    Full Text Available Abstract Background Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control error rates such as the false discovery rate (FDR in signature discovery. Moreover, signatures for cancer gene expression have been shown to be unstable, that is, difficult to replicate in independent studies, casting doubts on their reliability. Results We demonstrate that with modern prediction methods, signatures that yield accurate predictions may still have a high FDR. Further, we show that even signatures with low FDR may fail to replicate in independent studies due to limited statistical power. Thus, neither stability nor predictive accuracy are relevant when FDR control is the primary goal. We therefore develop a general statistical hypothesis testing framework that for the first time provides FDR control for signature discovery. Our method is demonstrated to be correct in simulation studies. When applied to five cancer data sets, the method was able to discover molecular signatures with 5% FDR in three cases, while two data sets yielded no significant findings. Conclusion Our approach enables reliable discovery of molecular signatures from genome-wide data with current sample sizes. The statistical framework developed herein is potentially applicable to a wide range of prediction problems in bioinformatics.

  5. Modeling the Thermal Signature of Natural Backgrounds

    National Research Council Canada - National Science Library

    Gamborg, Marius

    2002-01-01

    Two measuring stations have been established the purpose being to collect comprehensive databases of thermal signatures of background elements in addition to the prevailing meteorological conditions...

  6. An Arbitrated Quantum Signature Scheme without Entanglement*

    International Nuclear Information System (INIS)

    Li Hui-Ran; Luo Ming-Xing; Peng Dai-Yuan; Wang Xiao-Jun

    2017-01-01

    Several quantum signature schemes are recently proposed to realize secure signatures of quantum or classical messages. Arbitrated quantum signature as one nontrivial scheme has attracted great interests because of its usefulness and efficiency. Unfortunately, previous schemes cannot against Trojan horse attack and DoS attack and lack of the unforgeability and the non-repudiation. In this paper, we propose an improved arbitrated quantum signature to address these secure issues with the honesty arbitrator. Our scheme takes use of qubit states not entanglements. More importantly, the qubit scheme can achieve the unforgeability and the non-repudiation. Our scheme is also secure for other known quantum attacks . (paper)

  7. Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival

    NARCIS (Netherlands)

    Chang, Howard Y.; Nuyten, Dimitry S. A.; Sneddon, Julie B.; Hastie, Trevor; Tibshirani, Robert; Sørlie, Therese; Dai, Hongyue; He, Yudong D.; van't Veer, Laura J.; Bartelink, Harry; van de Rijn, Matt; Brown, Patrick O.; van de Vijver, Marc J.

    2005-01-01

    Based on the hypothesis that features of the molecular program of normal wound healing might play an important role in cancer metastasis, we previously identified consistent features in the transcriptional response of normal fibroblasts to serum, and used this "wound-response signature" to reveal

  8. Uranium isotopic signatures measured in samples of dirt collected at two former uranium facilities

    International Nuclear Information System (INIS)

    Meyers, L.A.; Stalcup, A.M.; LaMont, S.P.; Spitz, H.B.

    2014-01-01

    Nuclear forensics is a multidisciplinary science that uses a variety of analytical methods and tools to explore the physical, chemical, and isotopic characteristics of nuclear and radiological materials. These characteristics, when evaluated alone or in combination, become signatures that may reveal how and when the material was fabricated. The signatures contained in samples of dirt collected at two different uranium metal processing facilities in the United States were evaluated to determine uranium isotopic composition and compare results with processes that were conducted at these sites. One site refined uranium and fabricated uranium metal ingots for fuel and targets and the other site rolled hot forged uranium and other metals into dimensional rods. Unique signatures were found that are consistent with the activities and processes conducted at each facility and establish confidence in using these characteristics to reveal the provenance of other materials that exhibit similar signatures. (author)

  9. Geochemical signature of radioactive waste: oil NORM

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Gilberto T. de Paula; Costa-de-Moura, Jorge; Gomes, Carlos de Almeida; Sampaio, Emidio A. Lopes, E-mail: gilberto.costa@cnen.gov.br, E-mail: jcmoura@cnen.gov.br, E-mail: cgomes@cnen.gov.br [Comissao Nacional de Energia Nuclear (CNEN), Rio de Janeiro, RJ (Brazil). Div. de Controle de Rejeitos e Transporte de Materiais Radioativos

    2017-07-01

    The Brazilian Nuclear Agency (CNEN) rules all nuclear activity in Brazil as demanded by the Federal Constitution, articles 21, XXIII, and 177, V, and by the Federal Acts 4.118/62 and 10.308/2001. Therefore, the CNEN is responsible for any radioactive waste disposal in the country. Oil Naturally Occurring Radioactive Materials (Oil NORM) in this paper refers to waste coming from oil exploration. Oil NORM has called much attention during the last decades, mostly because it is not possible to determine its primary source due to the actual absence of regulatory control mechanism. There is no efficient regulatory tool which allows determining the origin of such NORM wastes even among those facilities under regulatory control. This fact may encourage non-authorized radioactive material transportation, smuggling and terrorism. The aim of this project is to provide a geochemical signature for each oil NORM waste using its naturally occurring isotopic composition to identify its origin. The here proposed method is a specific geochemical modeling of oil sludge NORM samples which are analyzed for radioisotopes normally present in oil pipes, such as {sup 228}Ac, {sup 214}Bi and {sup 214}Pb. The activity ratios are plotted in scatter diagrams. This method was successfully tested with data of different sources obtained from analysis reports from the Campos Basin/Brazil and from literature. (author)

  10. Geochemical signature of radioactive waste: oil NORM

    International Nuclear Information System (INIS)

    Costa, Gilberto T. de Paula; Costa-de-Moura, Jorge; Gomes, Carlos de Almeida; Sampaio, Emidio A. Lopes

    2017-01-01

    The Brazilian Nuclear Agency (CNEN) rules all nuclear activity in Brazil as demanded by the Federal Constitution, articles 21, XXIII, and 177, V, and by the Federal Acts 4.118/62 and 10.308/2001. Therefore, the CNEN is responsible for any radioactive waste disposal in the country. Oil Naturally Occurring Radioactive Materials (Oil NORM) in this paper refers to waste coming from oil exploration. Oil NORM has called much attention during the last decades, mostly because it is not possible to determine its primary source due to the actual absence of regulatory control mechanism. There is no efficient regulatory tool which allows determining the origin of such NORM wastes even among those facilities under regulatory control. This fact may encourage non-authorized radioactive material transportation, smuggling and terrorism. The aim of this project is to provide a geochemical signature for each oil NORM waste using its naturally occurring isotopic composition to identify its origin. The here proposed method is a specific geochemical modeling of oil sludge NORM samples which are analyzed for radioisotopes normally present in oil pipes, such as 228 Ac, 214 Bi and 214 Pb. The activity ratios are plotted in scatter diagrams. This method was successfully tested with data of different sources obtained from analysis reports from the Campos Basin/Brazil and from literature. (author)

  11. Microbial Signatures of Cadaver Gravesoil During Decomposition.

    Science.gov (United States)

    Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

    2016-04-01

    Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

  12. Interferon and biologic signatures in dermatomyositis skin: specificity and heterogeneity across diseases.

    Directory of Open Access Journals (Sweden)

    David Wong

    Full Text Available BACKGROUND: Dermatomyositis (DM is an autoimmune disease that mainly affects the skin, muscle, and lung. The pathogenesis of skin inflammation in DM is not well understood. METHODOLOGY AND FINDINGS: We analyzed genome-wide expression data in DM skin and compared them to those from healthy controls. We observed a robust upregulation of interferon (IFN-inducible genes in DM skin, as well as several other gene modules pertaining to inflammation, complement activation, and epidermal activation and differentiation. The interferon (IFN-inducible genes within the DM signature were present not only in DM and lupus, but also cutaneous herpes simplex-2 infection and to a lesser degree, psoriasis. This IFN signature was absent or weakly present in atopic dermatitis, allergic contact dermatitis, acne vulgaris, systemic sclerosis, and localized scleroderma/morphea. We observed that the IFN signature in DM skin appears to be more closely related to type I than type II IFN based on in vitro IFN stimulation expression signatures. However, quantitation of IFN mRNAs in DM skin shows that the majority of known type I IFNs, as well as IFN g, are overexpressed in DM skin. In addition, both IFN-beta and IFN-gamma (but not other type I IFN transcript levels were highly correlated with the degree of the in vivo IFN transcriptional response in DM skin. CONCLUSIONS AND SIGNIFICANCE: As in the blood and muscle, DM skin is characterized by an overwhelming presence of an IFN signature, although it is difficult to conclusively define this response as type I or type II. Understanding the significance of the IFN signature in this wide array of inflammatory diseases will be furthered by identification of the nature of the cells that both produce and respond to IFN, as well as which IFN subtype is biologically active in each diseased tissue.

  13. 21 CFR 11.70 - Signature/record linking.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Signature/record linking. 11.70 Section 11.70 Food... RECORDS; ELECTRONIC SIGNATURES Electronic Records § 11.70 Signature/record linking. Electronic signatures and handwritten signatures executed to electronic records shall be linked to their respective...

  14. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I

    2012-01-01

    mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written......ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  15. 15 CFR 908.16 - Signature.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Signature. 908.16 Section 908.16 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC... SUBMITTING REPORTS ON WEATHER MODIFICATION ACTIVITIES § 908.16 Signature. All reports filed with the National...

  16. 12 CFR 269b.731 - Signature.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Signature. 269b.731 Section 269b.731 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM CHARGES OF UNFAIR LABOR PRACTICES General Rules § 269b.731 Signature. The original of each document filed shall be...

  17. The Pedagogic Signature of the Teaching Profession

    Science.gov (United States)

    Kiel, Ewald; Lerche, Thomas; Kollmannsberger, Markus; Oubaid, Viktor; Weiss, Sabine

    2016-01-01

    Lee S. Shulman deplores that the field of education as a profession does not have a pedagogic signature, which he characterizes as a synthesis of cognitive, practical and moral apprenticeship. In this context, the following study has three goals: 1) In the first theoretical part, the basic problems of constructing a pedagogic signature are…

  18. Infrared ship signature analysis and optimisation

    NARCIS (Netherlands)

    Neele, F.P.

    2005-01-01

    The last decade has seen an increase in the awareness of the infrared signature of naval ships. New ship designs show that infrared signature reduction measures are being incorporated, such as exhaust gas cooling systems, relocation of the exhausts and surface cooling systems. Hull and

  19. Does Social Work Have a Signature Pedagogy?

    Science.gov (United States)

    Earls Larrison, Tara; Korr, Wynne S.

    2013-01-01

    This article contributes to discourse on signature pedagogy by reconceptualizing how our pedagogies are understood and defined for social work education. We critique the view that field education is social work's signature pedagogy and consider what pedagogies are distinct about the teaching and learning of social work. Using Shulman's…

  20. Quantum signature scheme for known quantum messages

    International Nuclear Information System (INIS)

    Kim, Taewan; Lee, Hyang-Sook

    2015-01-01

    When we want to sign a quantum message that we create, we can use arbitrated quantum signature schemes which are possible to sign for not only known quantum messages but also unknown quantum messages. However, since the arbitrated quantum signature schemes need the help of a trusted arbitrator in each verification of the signature, it is known that the schemes are not convenient in practical use. If we consider only known quantum messages such as the above situation, there can exist a quantum signature scheme with more efficient structure. In this paper, we present a new quantum signature scheme for known quantum messages without the help of an arbitrator. Differing from arbitrated quantum signature schemes based on the quantum one-time pad with the symmetric key, since our scheme is based on quantum public-key cryptosystems, the validity of the signature can be verified by a receiver without the help of an arbitrator. Moreover, we show that our scheme provides the functions of quantum message integrity, user authentication and non-repudiation of the origin as in digital signature schemes. (paper)

  1. Analysis of signature wrapping attacks and countermeasures

    DEFF Research Database (Denmark)

    Gajek, Sebastian; Jensen, Meiko; Liao, Lijun

    2009-01-01

    In recent research it turned out that Boolean verification, of digital signatures in the context of WSSecurity, is likely to fail: If parts of a SOAP message, are signed and the signature verification applied to, the whole document returns true, then nevertheless the, document may have been...

  2. 48 CFR 4.102 - Contractor's signature.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Contractor's signature. 4.102 Section 4.102 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION GENERAL ADMINISTRATIVE MATTERS Contract Execution 4.102 Contractor's signature. (a) Individuals. A contract with an...

  3. Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus.

    Directory of Open Access Journals (Sweden)

    Sara Garamszegi

    Full Text Available Ebola virus (EBOV infection in humans and non-human primates (NHPs is highly lethal, and there is limited understanding of the mechanisms associated with pathogenesis and survival. Here, we describe a transcriptomic analysis of NHPs that survived lethal EBOV infection, compared to NHPs that did not survive. It has been previously demonstrated that anticoagulant therapeutics increase the survival rate in EBOV-infected NHPs, and that the characteristic transcriptional profile of immune response changes in anticoagulant-treated NHPs. In order to identify transcriptional signatures that correlate with survival following EBOV infection, we compared the mRNA expression profile in peripheral blood mononuclear cells from EBOV-infected NHPs that received anticoagulant treatment, to those that did not receive treatment. We identified a small set of 20 genes that are highly confident predictors and can accurately distinguish between surviving and non-surviving animals. In addition, we identified a larger predictive signature of 238 genes that correlated with disease outcome and treatment; this latter signature was associated with a variety of host responses, such as the inflammatory response, T cell death, and inhibition of viral replication. Notably, among survival-associated genes were subsets of genes that are transcriptionally regulated by (1 CCAAT/enhancer-binding protein alpha, (2 tumor protein 53, and (3 megakaryoblastic leukemia 1 and myocardin-like protein 2. These pathways merit further investigation as potential transcriptional signatures of host immune response to EBOV infection.

  4. CAR and PXR-dependent transcriptional changes in the mouse liver after exposure to propiconazole

    Science.gov (United States)

    Exposure to the conazoles propiconazole and triadimefon but not myclobutanilled to tumors in mice after 2 years. Transcript profiling studies in the livers ofwild-type mice after short-term exposure to the conazoles revealed signatures indicating the involvement ofthe nuclear rec...

  5. DNA context represents transcription regulation of the gene in mouse embryonic stem cells

    Science.gov (United States)

    Ha, Misook; Hong, Soondo

    2016-04-01

    Understanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.

  6. Real time gamma-ray signature identifier

    Science.gov (United States)

    Rowland, Mark [Alamo, CA; Gosnell, Tom B [Moraga, CA; Ham, Cheryl [Livermore, CA; Perkins, Dwight [Livermore, CA; Wong, James [Dublin, CA

    2012-05-15

    A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

  7. DIGITAL SIGNATURE IN THE WAY OF LAW

    Directory of Open Access Journals (Sweden)

    Ruya Samlı

    2013-01-01

    Full Text Available Signature can be defined as a person’s name or special signs that he/she writes when he/she wants to indicate he/she wrote or confirm that writing. A person signs many times in his/her life. A person’s signature that is used for thousands of times for many things from formal documents to exams has importance for that person. Especially, signing in legal operations is an operation that can build important results. If a person’s signature is imitated by another person, he/she can become beholden, donate his/her whole wealth, commits offences or do some judicial operations. Today, because many operations can be done with digital environments and internet, signature operation that provides identity validation must also be carried to digital environment. In this paper digital signature concept that is approved for this reason and its situation in international areas and Turkish laws are investigated.

  8. Basal transcription machinery

    Indian Academy of Sciences (India)

    2007-03-29

    Mar 29, 2007 ... The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two , , ' and subunits, which lacks promoter selectivity and a sigma () subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor s, in prokaryotes ...

  9. Machine Dictation and Transcription.

    Science.gov (United States)

    Harvey, Evelyn; And Others

    This instructional package contains both an instructor's manual and a student's manual for a course in machine dictation and transcription. The instructor's manual contains an overview with tips on teaching the course, letters for dictation, and a key to the letters. The student's manual contains an overview of the course and of the skills needed…

  10. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    with the capacity to both self-renew and differentiate. This thesis is built upon two studies, which investigate two different aspects of the haematopoietic system; heterogeneity within the HSC compartment (presented in manuscript I), and the interplay between transcription factors controlling granulocyte/ monocyte...

  11. Coupling Between Doppler Radar Signatures and Tornado Damage Tracks

    Science.gov (United States)

    Jedlovec, Gary J.; Molthan, Andrew L.; Carey, Lawrence; Carcione, Brian; Smith, Matthew; Schultz, Elise V.; Schultz, Christopher; Lafontaine, Frank

    2011-01-01

    On April 27, 2011, the southeastern United States was raked with several episodes of severe weather. Numerous tornadoes caused extensive damage, and tragically, the deaths of over 300 people. In Alabama alone, there were 61 confirmed tornados, 4 of them produced EF5 damage, and several were on the ground an hour or more with continuous damage tracks exceeding 80km. The use of Doppler radars covering the region provided reflectivity and velocity signatures that allowed forecasters to monitors the severe storms from beginning to end issuing hundreds of severe weather warnings throughout the day. Meteorologists from the the NWS performed extensive surveys to assess the intensity, duration, and ground track of tornadoes reported during the event. Survey activities included site visits to the affected locations, analysis of radar and satellite data, aerial surveys, and interviews with eyewitnesses. Satellite data from NASA's MODIS and ASTER instruments played a helpful role in determining the location of tornado damage paths and in the assessment. High resolution multispectral and temporal composites helped forecasters corroborate their damage assessments, determine starting and ending points for tornado touchdowns, and helped to provide forecasters with a better big-picture view of the damage region. The imagery also helped to separate damage from the April 27th tornados from severe weather that occurred earlier that month. In a post analysis of the outbreak, tornado damage path signatures observed in the NASA satellite data have been correlated to "debris ball" signatures in the NWS Doppler radars and a special ARMOR dual-polarization radar operated by the University of Alabama Huntsville during the event. The Doppler radar data indicates a circular enhanced reflectivity signal and rotational couplet in the radial velocity likely associated with the tornado that is spatially correlated with the damage tracks in the observed satellite data. An algorithm to detect and

  12. 48 CFR 804.101 - Contracting officer's signature.

    Science.gov (United States)

    2010-10-01

    ... signature. 804.101 Section 804.101 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS GENERAL ADMINISTRATIVE MATTERS Contract Execution 804.101 Contracting officer's signature. (a) If a... signature. ...

  13. Maximizing biomarker discovery by minimizing gene signatures

    Directory of Open Access Journals (Sweden)

    Chang Chang

    2011-12-01

    Full Text Available Abstract Background The use of gene signatures can potentially be of considerable value in the field of clinical diagnosis. However, gene signatures defined with different methods can be quite various even when applied the same disease and the same endpoint. Previous studies have shown that the correct selection of subsets of genes from microarray data is key for the accurate classification of disease phenotypes, and a number of methods have been proposed for the purpose. However, these methods refine the subsets by only considering each single feature, and they do not confirm the association between the genes identified in each gene signature and the phenotype of the disease. We proposed an innovative new method termed Minimize Feature's Size (MFS based on multiple level similarity analyses and association between the genes and disease for breast cancer endpoints by comparing classifier models generated from the second phase of MicroArray Quality Control (MAQC-II, trying to develop effective meta-analysis strategies to transform the MAQC-II signatures into a robust and reliable set of biomarker for clinical applications. Results We analyzed the similarity of the multiple gene signatures in an endpoint and between the two endpoints of breast cancer at probe and gene levels, the results indicate that disease-related genes can be preferably selected as the components of gene signature, and that the gene signatures for the two endpoints could be interchangeable. The minimized signatures were built at probe level by using MFS for each endpoint. By applying the approach, we generated a much smaller set of gene signature with the similar predictive power compared with those gene signatures from MAQC-II. Conclusions Our results indicate that gene signatures of both large and small sizes could perform equally well in clinical applications. Besides, consistency and biological significances can be detected among different gene signatures, reflecting the

  14. Infrared signature modelling of a rocket jet plume - comparison with flight measurements

    International Nuclear Information System (INIS)

    Rialland, V; Perez, P; Roblin, A; Guy, A; Gueyffier, D; Smithson, T

    2016-01-01

    The infrared signature modelling of rocket plumes is a challenging problem involving rocket geometry, propellant composition, combustion modelling, trajectory calculations, fluid mechanics, atmosphere modelling, calculation of gas and particles radiative properties and of radiative transfer through the atmosphere. This paper presents ONERA simulation tools chained together to achieve infrared signature prediction, and the comparison of the estimated and measured signatures of an in-flight rocket plume. We consider the case of a solid rocket motor with aluminized propellant, the Black Brant sounding rocket. The calculation case reproduces the conditions of an experimental rocket launch, performed at White Sands in 1997, for which we obtained high quality infrared signature data sets from DRDC Valcartier. The jet plume is calculated using an in-house CFD software called CEDRE. The plume infrared signature is then computed on the spectral interval 1900-5000 cm -1 with a step of 5 cm -1 . The models and their hypotheses are presented and discussed. Then the resulting plume properties, radiance and spectra are detailed. Finally, the estimated infrared signature is compared with the spectral imaging measurements. The discrepancies are analyzed and discussed. (paper)

  15. Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib.

    Science.gov (United States)

    Klammer, Martin; Dybowski, J Nikolaj; Hoffmann, Daniel; Schaab, Christoph

    2015-01-01

    Multivariate biomarkers that can predict the effectiveness of targeted therapy in individual patients are highly desired. Previous biomarker discovery studies have largely focused on the identification of single biomarker signatures, aimed at maximizing prediction accuracy. Here, we present a different approach that identifies multiple biomarkers by simultaneously optimizing their predictive power, number of features, and proximity to the drug target in a protein-protein interaction network. To this end, we incorporated NSGA-II, a fast and elitist multi-objective optimization algorithm that is based on the principle of Pareto optimality, into the biomarker discovery workflow. The method was applied to quantitative phosphoproteome data of 19 non-small cell lung cancer (NSCLC) cell lines from a previous biomarker study. The algorithm successfully identified a total of 77 candidate biomarker signatures predicting response to treatment with dasatinib. Through filtering and similarity clustering, this set was trimmed to four final biomarker signatures, which then were validated on an independent set of breast cancer cell lines. All four candidates reached the same good prediction accuracy (83%) as the originally published biomarker. Although the newly discovered signatures were diverse in their composition and in their size, the central protein of the originally published signature - integrin β4 (ITGB4) - was also present in all four Pareto signatures, confirming its pivotal role in predicting dasatinib response in NSCLC cell lines. In summary, the method presented here allows for a robust and simultaneous identification of multiple multivariate biomarkers that are optimized for prediction performance, size, and relevance.

  16. Should fatty acid signature proportions sum to 1 for diet estimation?

    Science.gov (United States)

    Bromaghin, Jeffrey F.; Budge, Suzanne M.; Thiemann, Gregory W.

    2016-01-01

    Knowledge of predator diets, including how diets might change through time or differ among predators, provides essential insights into their ecology. Diet estimation therefore remains an active area of research within quantitative ecology. Quantitative fatty acid signature analysis (QFASA) is an increasingly common method of diet estimation. QFASA is based on a data library of prey signatures, which are vectors of proportions summarizing the fatty acid composition of lipids, and diet is estimated as the mixture of prey signatures that most closely approximates a predator’s signature. Diets are typically estimated using proportions from a subset of all fatty acids that are known to be solely or largely influenced by diet. Given the subset of fatty acids selected, the current practice is to scale their proportions to sum to 1.0. However, scaling signature proportions has the potential to distort the structural relationships within a prey library and between predators and prey. To investigate that possibility, we compared the practice of scaling proportions with two alternatives and found that the traditional scaling can meaningfully bias diet estimators under some conditions. Two aspects of the prey types that contributed to a predator’s diet influenced the magnitude of the bias: the degree to which the sums of unscaled proportions differed among prey types and the identifiability of prey types within the prey library. We caution investigators against the routine scaling of signature proportions in QFASA.

  17. Genomic Signatures of Sexual Conflict.

    Science.gov (United States)

    Kasimatis, Katja R; Nelson, Thomas C; Phillips, Patrick C

    2017-10-30

    Sexual conflict is a specific class of intergenomic conflict that describes the reciprocal sex-specific fitness costs generated by antagonistic reproductive interactions. The potential for sexual conflict is an inherent property of having a shared genome between the sexes and, therefore, is an extreme form of an environment-dependent fitness effect. In this way, many of the predictions from environment-dependent selection can be used to formulate expected patterns of genome evolution under sexual conflict. However, the pleiotropic and transmission constraints inherent to having alleles move across sex-specific backgrounds from generation to generation further modulate the anticipated signatures of selection. We outline methods for detecting candidate sexual conflict loci both across and within populations. Additionally, we consider the ability of genome scans to identify sexually antagonistic loci by modeling allele frequency changes within males and females due to a single generation of selection. In particular, we highlight the need to integrate genotype, phenotype, and functional information to truly distinguish sexual conflict from other forms of sexual differentiation. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Reduction of a Ship's Magnetic Field Signatures

    CERN Document Server

    Holmes, John

    2008-01-01

    Decreasing the magnetic field signature of a naval vessel will reduce its susceptibility to detonating naval influence mines and the probability of a submarine being detected by underwater barriers and maritime patrol aircraft. Both passive and active techniques for reducing the magnetic signatures produced by a vessel's ferromagnetism, roll-induced eddy currents, corrosion-related sources, and stray fields are presented. Mathematical models of simple hull shapes are used to predict the levels of signature reduction that might be achieved through the use of alternate construction materials. Al

  19. Molecular signatures of thyroid follicular neoplasia

    DEFF Research Database (Denmark)

    Borup, R.; Rossing, M.; Henao, Ricardo

    2010-01-01

    The molecular pathways leading to thyroid follicular neoplasia are incompletely understood, and the diagnosis of follicular tumors is a clinical challenge. To provide leads to the pathogenesis and diagnosis of the tumors, we examined the global transcriptome signatures of follicular thyroid...... a mechanism for cancer progression, which is why we exploited the results in order to generate a molecular classifier that could identify 95% of all carcinomas. Validation employing public domain and cross-platform data demonstrated that the signature was robust and could diagnose follicular nodules...... and robust genetic signature for the diagnosis of FA and FC. Endocrine-Related Cancer (2010) 17 691-708...

  20. DIGITAL SIGNATURE IN THE WAY OF LAW

    OpenAIRE

    Ruya Samlı

    2013-01-01

    Signature can be defined as a person’s name or special signs that he/she writes when he/she wants to indicate he/she wrote or confirm that writing. A person signs many times in his/her life. A person’s signature that is used for thousands of times for many things from formal documents to exams has importance for that person. Especially, signing in legal operations is an operation that can build important results. If a person’s signature is imitated by another person, he/she can be...

  1. Mapping the space of genomic signatures.

    Directory of Open Access Journals (Sweden)

    Lila Kari

    Full Text Available We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR, is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM, implicitly compares the occurrences of oligomers of length up to k (herein k = 9 in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (superkingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal

  2. Strong signatures of selection in the domestic pig genome

    DEFF Research Database (Denmark)

    Rubin, Carl-Johan; Megens, Hendrik-Jan; Barrio, Alvaro Martinez

    2012-01-01

    Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that un...... to strong directional selection.......Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci...... that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig—the elongation of the back...

  3. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  4. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    The myriad of cells in the human body are all made from the same blueprint: the human genome. At the heart of this diversity lies the concept of gene regulation, the process in which it is decided which genes are used where and when. Genes do not function as on/off buttons, but more like a volume...... mostly near the start of the gene known as the promoter. This region contains patterns scattered in the DNA that the TFs can recognize and bind to. Such binding can prompt the assembly of the pre-initiation complex which ultimately leads to transcription of the gene. In order to achieve the regulation...... on what characterizes a hippocampus promoter. Pairing CAGE with TF binding site prediction we identi¿ed a likely key regulator of hippocampus. Finally, we developed a method for CAGE exploration. While the DeepCAGE library characterized a full 1.4 million transcription initiation events it did not capture...

  5. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

    Directory of Open Access Journals (Sweden)

    Gary Hon

    2008-10-01

    Full Text Available Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory elements. But the vast majority of regulatory elements have yet to be discovered, and it has become increasingly apparent that their discovery will not come from using genetic information alone. Recently, high-throughput technologies have enabled the creation of information-rich epigenetic maps, most notably for histone modifications. However, tools that search for functional elements using this epigenetic information have been lacking. Here, we describe an unsupervised learning method called ChromaSig to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known patterns associated with transcriptional promoters and enhancers. Interestingly, we observe that the distinct chromatin signatures found at enhancers mark distinct functional classes of enhancers in terms of transcription factor and coactivator binding. In addition, we identify three clusters of novel chromatin signatures that contain evolutionarily conserved sequences and potential cis-regulatory elements. Applying ChromaSig to a panel of 21 chromatin marks mapped genomewide by ChIP-Seq reveals 16 classes of genomic elements marked by distinct chromatin signatures. Interestingly, four classes containing enrichment for repressive histone modifications appear to be locally heterochromatic sites and are enriched in quickly evolving regions of the genome. The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications.

  6. Rickettsia conorii transcriptional response within inoculation eschar.

    Directory of Open Access Journals (Sweden)

    Patricia Renesto

    Full Text Available BACKGROUND: Rickettsia conorii, the causative agent of the Mediterranean spotted fever, is transmitted to humans by the bite of infected ticks Rhipicephalus sanguineus. The skin thus constitutes an important barrier for the entry and propagation of R. conorii. Given this, analysis of the survival strategies used by the bacterium within infected skin is critical for our understanding of rickettsiosis. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first genome-wide analysis of R. conorii gene expression from infected human skin biopsies. Our data showed that R. conorii exhibited a striking transcript signature that is remarkably conserved across patients, regardless of genotype. The expression profiles obtained using custom Agilent microarrays were validated by quantitative RT-PCR. Within eschars, the amount of detected R. conorii transcripts was of 55%, this value being of 74% for bacteria grown in Vero cells. In such infected host tissues, approximately 15% (n = 211 of the total predicted R. conorii ORFs appeared differentially expressed compared to bacteria grown in standard laboratory conditions. These genes are mostly down-regulated and encode proteins essential for bacterial replication. Some of the strategies displayed by rickettsiae to overcome the host defense barriers, thus avoiding killing, were also pointed out. The observed up-regulation of rickettsial genes associated with DNA repair is likely to correspond to a DNA-damaging agent enriched environment generated by the host cells to eradicate the pathogens. Survival of R. conorii within eschars also involves adaptation to osmotic stress, changes in cell surface proteins and up-regulation of some virulence factors. Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae. CONCLUSION/SIGNIFICANCE: Because eschar is a site for rickettsial

  7. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    " of the transcription factor networks operating at specific time points during adipogenesis. Using such global "snapshots," we have demonstrated that dramatic remodeling of the chromatin template occurs within the first few hours following adipogenic stimulation and that many of the early transcription factors bind...... in a cooperative fashion to transcription factor hotspots. Such hotspots are likely to represent key chromatin nodes, where many adipogenic signaling pathways converge to drive the adipogenic transcriptional reprogramming....

  8. Magnetic Signature of Brushless Electric Motors

    National Research Council Canada - National Science Library

    Clarke, David

    2006-01-01

    Brushless electric motors are used in a number of underwater vehicles. When these underwater vehicles are used for mine clearance operations the magnetic signature of the brushless motors is important...

  9. Magnetic signature surveillance of nuclear fuel

    International Nuclear Information System (INIS)

    Bernatowicz, H.; Schoenig, F.C.

    1981-01-01

    Typical nuclear fuel material contains tramp ferromagnetic particles of random size and distribution. Also, selected amounts of paramagnetic or ferromagnetic material can be added at random or at known positions in the fuel material. The fuel material in its non-magnetic container is scanned along its length by magnetic susceptibility detecting apparatus whereby susceptibility changes along its length are obtained and provide a unique signal waveform of the container of fuel material as a signature thereof. The output signature is stored. At subsequent times in its life the container is again scanned and respective signatures obtained which are compared with the initially obtained signature, any differences indicating alteration or tampering with the fuel material. If the fuel material includes a paramagnetic additive by taking two measurements along the container the effects thereof can be cancelled out. (author)

  10. Blind Quantum Signature with Blind Quantum Computation

    Science.gov (United States)

    Li, Wei; Shi, Ronghua; Guo, Ying

    2017-04-01

    Blind quantum computation allows a client without quantum abilities to interact with a quantum server to perform a unconditional secure computing protocol, while protecting client's privacy. Motivated by confidentiality of blind quantum computation, a blind quantum signature scheme is designed with laconic structure. Different from the traditional signature schemes, the signing and verifying operations are performed through measurement-based quantum computation. Inputs of blind quantum computation are securely controlled with multi-qubit entangled states. The unique signature of the transmitted message is generated by the signer without leaking information in imperfect channels. Whereas, the receiver can verify the validity of the signature using the quantum matching algorithm. The security is guaranteed by entanglement of quantum system for blind quantum computation. It provides a potential practical application for e-commerce in the cloud computing and first-generation quantum computation.

  11. Signature scheme based on bilinear pairs

    Science.gov (United States)

    Tong, Rui Y.; Geng, Yong J.

    2013-03-01

    An identity-based signature scheme is proposed by using bilinear pairs technology. The scheme uses user's identity information as public key such as email address, IP address, telephone number so that it erases the cost of forming and managing public key infrastructure and avoids the problem of user private generating center generating forgery signature by using CL-PKC framework to generate user's private key.

  12. Signature for the shape of the universe

    International Nuclear Information System (INIS)

    Gomero, G.I.; Reboucas, M.J.; Teixeira, A.F.F.

    2001-03-01

    If the universe has a nontrival shape (topology) the sky may show multiple correlated images of cosmic objects. These correlations can be counched in terms of distance correlations. We propose a statistical quantity which can be used to reveal the topological signature of any Roberston-Walker (RW) spacetime with nontrivial topology. We also show through computer-aided simulations how one can extract the topological signatures of flat elliptic and hyperbolic RW universes with nontrivial topology. (author)

  13. Signature-based store checking buffer

    Science.gov (United States)

    Sridharan, Vilas; Gurumurthi, Sudhanva

    2015-06-02

    A system and method for optimizing redundant output verification, are provided. A hardware-based store fingerprint buffer receives multiple instances of output from multiple instances of computation. The store fingerprint buffer generates a signature from the content included in the multiple instances of output. When a barrier is reached, the store fingerprint buffer uses the signature to verify the content is error-free.

  14. Neutral signature Walker-VSI metrics

    International Nuclear Information System (INIS)

    Coley, A; McNutt, D; Musoke, N; Brooks, D; Hervik, S

    2014-01-01

    We will construct explicit examples of four-dimensional neutral signature Walker (but not necessarily degenerate Kundt) spaces for which all of the polynomial scalar curvature invariants vanish. We then investigate the properties of some particular subclasses of Ricci flat spaces. We also briefly describe some four-dimensional neutral signature Einstein spaces for which all of the polynomial scalar curvature invariants are constant. (paper)

  15. Tightly Secure Signatures From Lossy Identification Schemes

    OpenAIRE

    Abdalla , Michel; Fouque , Pierre-Alain; Lyubashevsky , Vadim; Tibouchi , Mehdi

    2015-01-01

    International audience; In this paper, we present three digital signature schemes with tight security reductions in the random oracle model. Our first signature scheme is a particularly efficient version of the short exponent discrete log-based scheme of Girault et al. (J Cryptol 19(4):463–487, 2006). Our scheme has a tight reduction to the decisional short discrete logarithm problem, while still maintaining the non-tight reduction to the computational version of the problem upon which the or...

  16. Comparative expression profiling in grape (Vitis vinifera berries derived from frequency analysis of ESTs and MPSS signatures

    Directory of Open Access Journals (Sweden)

    Cook Douglas R

    2008-05-01

    Full Text Available Abstract Background Vitis vinifera (V. vinifera is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS and combined it with available Expressed Sequence Tag (EST data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. Results The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS. A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million. Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. Conclusion The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed

  17. RNA-Seq for enrichment and analysis of IRF5 transcript expression in SLE.

    Directory of Open Access Journals (Sweden)

    Rivka C Stone

    Full Text Available Polymorphisms in the interferon regulatory factor 5 (IRF5 gene have been consistently replicated and shown to confer risk for or protection from the development of systemic lupus erythematosus (SLE. IRF5 expression is significantly upregulated in SLE patients and upregulation associates with IRF5-SLE risk haplotypes. IRF5 alternative splicing has also been shown to be elevated in SLE patients. Given that human IRF5 exists as multiple alternatively spliced transcripts with distinct function(s, it is important to determine whether the IRF5 transcript profile expressed in healthy donor immune cells is different from that expressed in SLE patients. Moreover, it is not currently known whether an IRF5-SLE risk haplotype defines the profile of IRF5 transcripts expressed. Using standard molecular cloning techniques, we identified and isolated 14 new differentially spliced IRF5 transcript variants from purified monocytes of healthy donors and SLE patients to generate an IRF5 variant transcriptome. Next-generation sequencing was then used to perform in-depth and quantitative analysis of full-length IRF5 transcript expression in primary immune cells of SLE patients and healthy donors by next-generation sequencing. Evidence for additional alternatively spliced transcripts was obtained from de novo junction discovery. Data from these studies support the overall complexity of IRF5 alternative splicing in SLE. Results from next-generation sequencing correlated with cloning and gave similar abundance rankings in SLE patients thus supporting the use of this new technology for in-depth single gene transcript profiling. Results from this study provide the first proof that 1 SLE patients express an IRF5 transcript signature that is distinct from healthy donors, 2 an IRF5-SLE risk haplotype defines the top four most abundant IRF5 transcripts expressed in SLE patients, and 3 an IRF5 transcript signature enables clustering of SLE patients with the H2 risk haplotype.

  18. A distinct epigenetic signature at targets of a leukemia protein

    Directory of Open Access Journals (Sweden)

    van der Spek Peter

    2007-02-01

    Full Text Available Abstract Background Human myelogenous leukemia characterized by either the non random t(8; 21(q22; q22 or t(16; 21(q24; q22 chromosome translocations differ for both their biological and clinical features. Some of these features could be consequent to differential epigenetic transcriptional deregulation at AML1 targets imposed by AML1-MTG8 and AML1-MTG16, the fusion proteins deriving from the two translocations. Preliminary findings showing that these fusion proteins lead to transcriptional downregulation of AML1 targets, marked by repressive chromatin changes, would support this hypothesis. Here we show that combining conventional global gene expression arrays with the power of bioinformatic genomic survey of AML1-consensus sequences is an effective strategy to identify AML1 targets whose transcription is epigenetically downregulated by the leukemia-associated AML1-MTG16 protein. Results We interrogated mouse gene expression microarrays with probes generated either from 32D cells infected with a retroviral vector carrying AML1-MTG16 and unable of granulocyte differentiation and proliferation in response to the granulocyte colony stimulating factor (G-CSF, or from 32D cells infected with the cognate empty vector. From the analysis of differential gene expression alone (using as criteria a p value 3, we were unable to conclude which of the 37 genes downregulated by AML1-MTG16 were, or not, direct AML1 targets. However, when we applied a bioinformatic approach to search for AML1-consensus sequences in the 10 Kb around the gene transcription start sites, we closed on 17 potential direct AML1 targets. By focusing on the most significantly downregulated genes, we found that both the AML1-consensus and the transcription start site chromatin regions were significantly marked by aberrant repressive histone tail changes. Further, the promoter of one of these genes, containing a CpG island, was aberrantly methylated. Conclusion This study shows that a

  19. Modelling reveals kinetic advantages of co-transcriptional splicing.

    Directory of Open Access Journals (Sweden)

    Stuart Aitken

    2011-10-01

    Full Text Available Messenger RNA splicing is an essential and complex process for the removal of intron sequences. Whereas the composition of the splicing machinery is mostly known, the kinetics of splicing, the catalytic activity of splicing factors and the interdependency of transcription, splicing and mRNA 3' end formation are less well understood. We propose a stochastic model of splicing kinetics that explains data obtained from high-resolution kinetic analyses of transcription, splicing and 3' end formation during induction of an intron-containing reporter gene in budding yeast. Modelling reveals co-transcriptional splicing to be the most probable and most efficient splicing pathway for the reporter transcripts, due in part to a positive feedback mechanism for co-transcriptional second step splicing. Model comparison is used to assess the alternative representations of reactions. Modelling also indicates the functional coupling of transcription and splicing, because both the rate of initiation of transcription and the probability that step one of splicing occurs co-transcriptionally are reduced, when the second step of splicing is abolished in a mutant reporter.

  20. Modelling reveals kinetic advantages of co-transcriptional splicing.

    Science.gov (United States)

    Aitken, Stuart; Alexander, Ross D; Beggs, Jean D

    2011-10-01

    Messenger RNA splicing is an essential and complex process for the removal of intron sequences. Whereas the composition of the splicing machinery is mostly known, the kinetics of splicing, the catalytic activity of splicing factors and the interdependency of transcription, splicing and mRNA 3' end formation are less well understood. We propose a stochastic model of splicing kinetics that explains data obtained from high-resolution kinetic analyses of transcription, splicing and 3' end formation during induction of an intron-containing reporter gene in budding yeast. Modelling reveals co-transcriptional splicing to be the most probable and most efficient splicing pathway for the reporter transcripts, due in part to a positive feedback mechanism for co-transcriptional second step splicing. Model comparison is used to assess the alternative representations of reactions. Modelling also indicates the functional coupling of transcription and splicing, because both the rate of initiation of transcription and the probability that step one of splicing occurs co-transcriptionally are reduced, when the second step of splicing is abolished in a mutant reporter.

  1. Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity

    Science.gov (United States)

    Smith, Milo R.; Burman, Poromendro

    2016-01-01

    Throughout childhood and adolescence, periods of heightened neuroplasticity are critical for the development of healthy brain function and behavior. Given the high prevalence of neurodevelopmental disorders, such as autism, identifying disruptors of developmental plasticity represents an essential step for developing strategies for prevention and intervention. Applying a novel computational approach that systematically assessed connections between 436 transcriptional signatures of disease and multiple signatures of neuroplasticity, we identified inflammation as a common pathological process central to a diverse set of diseases predicted to dysregulate plasticity signatures. We tested the hypothesis that inflammation disrupts developmental cortical plasticity in vivo using the mouse ocular dominance model of experience-dependent plasticity in primary visual cortex. We found that the administration of systemic lipopolysaccharide suppressed plasticity during juvenile critical period with accompanying transcriptional changes in a particular set of molecular regulators within primary visual cortex. These findings suggest that inflammation may have unrecognized adverse consequences on the postnatal developmental trajectory and indicate that treating inflammation may reduce the burden of neurodevelopmental disorders. PMID:28101530

  2. Rank-Based miRNA Signatures for Early Cancer Detection

    Directory of Open Access Journals (Sweden)

    Mario Lauria

    2014-01-01

    Full Text Available We describe a new signature definition and analysis method to be used as biomarker for early cancer detection. Our new approach is based on the construction of a reference map of transcriptional signatures of both healthy and cancer affected individuals using circulating miRNA from a large number of subjects. Once such a map is available, the diagnosis for a new patient can be performed by observing the relative position on the map of his/her transcriptional signature. To demonstrate its efficacy for this specific application we report the results of the application of our method to published datasets of circulating miRNA, and we quantify its performance compared to current state-of-the-art methods. A number of additional features make this method an ideal candidate for large-scale use, for example, as a mass screening tool for early cancer detection or for at-home diagnostics. Specifically, our method is minimally invasive (because it works well with circulating miRNA, it is robust with respect to lab-to-lab protocol variability and batch effects (it requires that only the relative ranking of expression value of miRNA in a profile be accurate not their absolute values, and it is scalable to a large number of subjects. Finally we discuss the need for HPC capability in a widespread application of our or similar methods.

  3. A Black Hole Spectral Signature

    Science.gov (United States)

    Titarchuk, Lev; Laurent, Philippe

    2000-03-01

    An accreting black hole is, by definition, characterized by the drain. Namely, the matter falls into a black hole much the same way as water disappears down a drain matter goes in and nothing comes out. As this can only happen in a black hole, it provides a way to see ``a black hole'', an unique observational signature. The accretion proceeds almost in a free-fall manner close to the black hole horizon, where the strong gravitational field dominates the pressure forces. In this paper we present analytical calculations and Monte-Carlo simulations of the specific features of X-ray spectra formed as a result of upscattering of the soft (disk) photons in the converging inflow (CI) into the black hole. The full relativistic treatment has been implemented to reproduce these spectra. We show that spectra in the soft state of black hole systems (BHS) can be described as the sum of a thermal (disk) component and the convolution of some fraction of this component with the CI upscattering spread (Greens) function. The latter boosted photon component is seen as an extended power-law at energies much higher than the characteristic energy of the soft photons. We demonstrate the stability of the power spectral index over a wide range of the plasma temperature 0 - 10 keV and mass accretion rates (higher than 2 in Eddington units). We also demonstrate that the sharp high energy cutoff occurs at energies of 200-400 keV which are related to the average energy of electrons mec2 impinging upon the event horizon. The spectrum is practically identical to the standard thermal Comptonization spectrum when the CI plasma temperature is getting of order of 50 keV (the typical ones for the hard state of BHS). In this case one can see the effect of the bulk motion only at high energies where there is an excess in the CI spectrum with respect to the pure thermal one. Furthermore we demonstrate that the change of spectral shapes from the soft X-ray state to the hard X-ray state is clearly to be

  4. Does Twitter trigger bursts in signature collections?

    Directory of Open Access Journals (Sweden)

    Rui Yamaguchi

    Full Text Available INTRODUCTION: The quantification of social media impacts on societal and political events is a difficult undertaking. The Japanese Society of Oriental Medicine started a signature-collecting campaign to oppose a medical policy of the Government Revitalization Unit to exclude a traditional Japanese medicine, "Kampo," from the public insurance system. The signature count showed a series of aberrant bursts from November 26 to 29, 2009. In the same interval, the number of messages on Twitter including the keywords "Signature" and "Kampo," increased abruptly. Moreover, the number of messages on an Internet forum that discussed the policy and called for signatures showed a train of spikes. METHODS AND FINDINGS: In order to estimate the contributions of social media, we developed a statistical model with state-space modeling framework that distinguishes the contributions of multiple social media in time-series of collected public opinions. We applied the model to the time-series of signature counts of the campaign and quantified contributions of two social media, i.e., Twitter and an Internet forum, by the estimation. We found that a considerable portion (78% of the signatures was affected from either of the social media throughout the campaign and the Twitter effect (26% was smaller than the Forum effect (52% in total, although Twitter probably triggered the initial two bursts of signatures. Comparisons of the estimated profiles of the both effects suggested distinctions between the social media in terms of sustainable impact of messages or tweets. Twitter shows messages on various topics on a time-line; newer messages push out older ones. Twitter may diminish the impact of messages that are tweeted intermittently. CONCLUSIONS: The quantification of social media impacts is beneficial to better understand people's tendency and may promote developing strategies to engage public opinions effectively. Our proposed method is a promising tool to explore

  5. Does Twitter trigger bursts in signature collections?

    Science.gov (United States)

    Yamaguchi, Rui; Imoto, Seiya; Kami, Masahiro; Watanabe, Kenji; Miyano, Satoru; Yuji, Koichiro

    2013-01-01

    The quantification of social media impacts on societal and political events is a difficult undertaking. The Japanese Society of Oriental Medicine started a signature-collecting campaign to oppose a medical policy of the Government Revitalization Unit to exclude a traditional Japanese medicine, "Kampo," from the public insurance system. The signature count showed a series of aberrant bursts from November 26 to 29, 2009. In the same interval, the number of messages on Twitter including the keywords "Signature" and "Kampo," increased abruptly. Moreover, the number of messages on an Internet forum that discussed the policy and called for signatures showed a train of spikes. In order to estimate the contributions of social media, we developed a statistical model with state-space modeling framework that distinguishes the contributions of multiple social media in time-series of collected public opinions. We applied the model to the time-series of signature counts of the campaign and quantified contributions of two social media, i.e., Twitter and an Internet forum, by the estimation. We found that a considerable portion (78%) of the signatures was affected from either of the social media throughout the campaign and the Twitter effect (26%) was smaller than the Forum effect (52%) in total, although Twitter probably triggered the initial two bursts of signatures. Comparisons of the estimated profiles of the both effects suggested distinctions between the social media in terms of sustainable impact of messages or tweets. Twitter shows messages on various topics on a time-line; newer messages push out older ones. Twitter may diminish the impact of messages that are tweeted intermittently. The quantification of social media impacts is beneficial to better understand people's tendency and may promote developing strategies to engage public opinions effectively. Our proposed method is a promising tool to explore information hidden in social phenomena.

  6. EWS/FLI mediates transcriptional repression via NKX2.2 during oncogenic transformation in Ewing's sarcoma.

    Directory of Open Access Journals (Sweden)

    Leah A Owen

    2008-04-01

    Full Text Available EWS/FLI is a master regulator of Ewing's sarcoma formation. Gene expression studies in A673 Ewing's sarcoma cells have demonstrated that EWS/FLI downregulates more genes than it upregulates, suggesting that EWS/FLI, and/or its targets, function as transcriptional repressors. One critical EWS/FLI target, NKX2.2, is a transcription factor that contains both transcriptional activation and transcriptional repression domains, raising the possibility that it mediates portions of the EWS/FLI transcriptional signature. We now report that microarray analysis demonstrated that the transcriptional profile of NKX2.2 consists solely of downregulated genes, and overlaps with the EWS/FLI downregulated signature, suggesting that NKX2.2 mediates oncogenic transformation via transcriptional repression. Structure-function analysis revealed that the DNA binding and repressor domains in NKX2.2 are required for oncogenesis in Ewing's sarcoma cells, while the transcriptional activation domain is completely dispensable. Furthermore, blockade of TLE or HDAC function, two protein families thought to mediate the repressive function of NKX2.2, inhibited the transformed phenotype and reversed the NKX2.2 transcriptional profile in Ewing's sarcoma cells. Whole genome localization studies (ChIP-chip revealed that a significant portion of the NKX2.2-repressed gene expression signature was directly mediated by NKX2.2 binding. These data demonstrate that the transcriptional repressive function of NKX2.2 is necessary, and sufficient, for the oncogenic phenotype of Ewing's sarcoma, and suggest a therapeutic approach to this disease.

  7. Transcriptional ontogeny of the developing liver

    Directory of Open Access Journals (Sweden)

    Lee Janice S

    2012-01-01

    Full Text Available Abstract Background During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and pancreas. Early in organogenesis the fetal liver is populated by hematopoietic stem cells, the source for a number of blood cells including nucleated erythrocytes. A comprehensive analysis of the transcriptional changes that occur during the early stages of development to adulthood in the liver was carried out. Results We characterized gene expression changes in the developing mouse liver at gestational days (GD 11.5, 12.5, 13.5, 14.5, 16.5, and 19 and in the neonate (postnatal day (PND 7 and 32 compared to that in the adult liver (PND67 using full-genome microarrays. The fetal liver, and to a lesser extent the neonatal liver, exhibited dramatic differences in gene expression compared to adults. Canonical pathway analysis of the fetal liver signature demonstrated increases in functions important in cell replication and DNA fidelity whereas most metabolic pathways of intermediary metabolism were under expressed. Comparison of the dataset to a number of previously published microarray datasets revealed 1 a striking similarity between the fetal liver and that of the pancreas in both mice and humans, 2 a nucleated erythrocyte signature in the fetus and 3 under expression of most xenobiotic metabolism genes throughout development, with the exception of a number of transporters associated with either hematopoietic cells or cell proliferation in hepatocytes. Conclusions Overall, these findings reveal the complexity of gene expression changes during liver development and maturation, and provide a foundation to predict responses to chemical and drug exposure as a function of early life-stages.

  8. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

    DEFF Research Database (Denmark)

    Forslund, Kristoffer; Hildebrand, Falk ; Nielsen, Trine N.

    2015-01-01

    In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported1,2. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs...... on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified......, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa3,4. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures...

  9. Transcript structure and domain display: a customizable transcript visualization tool.

    Science.gov (United States)

    Watanabe, Kenneth A; Ma, Kaiwang; Homayouni, Arielle; Rushton, Paul J; Shen, Qingxi J

    2016-07-01

    Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html : jeffery.shen@unlv.nevada.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. A Meta-Assembly of Selection Signatures in Cattle

    Science.gov (United States)

    Randhawa, Imtiaz A. S.; Khatkar, Mehar S.; Thomson, Peter C.; Raadsma, Herman W.

    2016-01-01

    Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species. PMID:27045296

  11. Research on a New Signature Scheme on Blockchain

    Directory of Open Access Journals (Sweden)

    Chao Yuan

    2017-01-01

    Full Text Available With the rise of Bitcoin, blockchain which is the core technology of Bitcoin has received increasing attention. Privacy preserving and performance on blockchain are two research points in academia and business, but there are still some unresolved issues in both respects. An aggregate signature scheme is a digital signature that supports making signatures on many different messages generated by many different users. Using aggregate signature, the size of the signature could be shortened by compressing multiple signatures into a single signature. In this paper, a new signature scheme for transactions on blockchain based on the aggregate signature was proposed. It was worth noting that elliptic curve discrete logarithm problem and bilinear maps played major roles in our signature scheme. And the security properties of our signature scheme were proved. In our signature scheme, the amount will be hidden especially in the transactions which contain multiple inputs and outputs. Additionally, the size of the signature on transaction is constant regardless of the number of inputs and outputs that the transaction contains, which can improve the performance of signature. Finally, we gave an application scenario for our signature scheme which aims to achieve the transactions of big data on blockchain.

  12. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome.

    Directory of Open Access Journals (Sweden)

    Katherine James

    Full Text Available Fatigue is a debilitating condition with a significant impact on patients' quality of life. Fatigue is frequently reported by patients suffering from primary Sjögren's Syndrome (pSS, a chronic autoimmune condition characterised by dryness of the eyes and the mouth. However, although fatigue is common in pSS, it does not manifest in all sufferers, providing an excellent model with which to explore the potential underpinning biological mechanisms.Whole blood samples from 133 fully-phenotyped pSS patients stratified for the presence of fatigue, collected by the UK primary Sjögren's Syndrome Registry, were used for whole genome microarray. The resulting data were analysed both on a gene by gene basis and using pre-defined groups of genes. Finally, gene set enrichment analysis (GSEA was used as a feature selection technique for input into a support vector machine (SVM classifier. Classification was assessed using area under curve (AUC of receiver operator characteristic and standard error of Wilcoxon statistic, SE(W.Although no genes were individually found to be associated with fatigue, 19 metabolic pathways were enriched in the high fatigue patient group using GSEA. Analysis revealed that these enrichments arose from the presence of a subset of 55 genes. A radial kernel SVM classifier with this subset of genes as input displayed significantly improved performance over classifiers using all pathway genes as input. The classifiers had AUCs of 0.866 (SE(W 0.002 and 0.525 (SE(W 0.006, respectively.Systematic analysis of gene expression data from pSS patients discordant for fatigue identified 55 genes which are predictive of fatigue level using SVM classification. This list represents the first step in understanding the underlying pathophysiological mechanisms of fatigue in patients with pSS.

  13. An orthologous transcriptional signature differentiates responses towards closely related chemicals in Arabidopsis thaliana and brassica napus

    Science.gov (United States)

    Herbicides are structurally diverse chemicals that inhibit plant-specific targets, however their off-target and potentially differentiating side-effects are less well defined. In this study, genome-wide expression profiling based on Affymetrix AtH1 arrays was used to identify dis...

  14. Transcriptional Signatures in Response to Wheat Germ Agglutinin and Starvation in Drosophila melanogaster Larval Midgut

    Science.gov (United States)

    One function of plant lectins such as wheat germ agglutinin (WGA) is to serve as defenses against herbivorous insects. The midgut is one critical site affected by dietary lectins. We observed marked cellular, structural, and gene expression changes in the midguts of Drosophila melanogaster third-i...

  15. Use of DNA Microarrays to Identify Diagnostic Signature Transcriptional Profiles for Host Responses to Infectious Agents

    National Research Council Canada - National Science Library

    Ellner, J. J; Connell, N. D; Gallagher, G; Raveche, E

    2005-01-01

    Infections by agents of bioterrorism, especially bacterial agents such as Bacillus anthracis and Yersinia pestis present their initial symptoms in a way that does not reveal their identity or permit rapid diagnosis...

  16. Lattice-Based Revocable Certificateless Signature

    Directory of Open Access Journals (Sweden)

    Ying-Hao Hung

    2017-10-01

    Full Text Available Certificateless signatures (CLS are noticeable because they may resolve the key escrow problem in ID-based signatures and break away the management problem regarding certificate in conventional signatures. However, the security of the mostly previous CLS schemes relies on the difficulty of solving discrete logarithm or large integer factorization problems. These two problems would be solved by quantum computers in the future so that the signature schemes based on them will also become insecure. For post-quantum cryptography, lattice-based cryptography is significant due to its efficiency and security. However, no study on addressing the revocation problem in the existing lattice-based CLS schemes is presented. In this paper, we focus on the revocation issue and present the first revocable CLS (RCLS scheme over lattices. Based on the short integer solution (SIS assumption over lattices, the proposed lattice-based RCLS scheme is shown to be existential unforgeability against adaptive chosen message attacks. By performance analysis and comparisons, the proposed lattice-based RCLS scheme is better than the previously proposed lattice-based CLS scheme, in terms of private key size, signature length and the revocation mechanism.

  17. Calculated NWIS signatures for enriched uranium metal

    International Nuclear Information System (INIS)

    Valentine, T.E.; Mihalczo, J.T.; Koehler, P.E.

    1995-01-01

    Nuclear Weapons Identification System (NWIS) signatures have been calculated using a Monte Carlo transport code for measurement configurations of a 252 Cf source, detectors, and a uranium metal casting. NWIS signatures consist of a wide variety of time-and frequency-analysis signatures such as the time distribution of neutrons after californium fission, the time distribution of counts in a detector after a previous count, the number of times n pulses occur in a time interval, and various frequency-analysis signatures, such as auto-power and cross-power spectral densities, coherences, and a ratio of spectral densities. This ratio is independent of detection efficiency. The analysis presented here, using the MCNP-DSP code, evaluates the applicability of this method for measurement of the 235 U content of 19-kg castings of depleted uranium and uranium with enrichments of 20, 40, 60, 80, 90, and 93.2 wt % 235 U. The dependence of the wide variety of NWIS signatures on 235 U content and possible configurations of a measurement system are presented. These preliminary calculations indicate short measurement times. Additional calculations are being performed to optimize the source-detector-moderator-casting configuration for the shortest measurement time. Although the NWIS method was developed for nuclear weapons identification, the development of a small processor now allows it to be also applied in a practical way to subcriticality measurements, nuclear fuel process monitoring and qualitative nondestructive assay of special nuclear material

  18. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

    Science.gov (United States)

    Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

    2016-01-19

    Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... of the transcriptional response is essential for cells to progress through the cell cycle in a normal manner. The involvement of cytoplasmic and nuclear accessory molecules, and the general nuclear membrane transport components, are essential for this process. Although nuclear import and export for different...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...

  20. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    . Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral...... transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the t......RNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal...

  1. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  2. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...... regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables....... It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms...

  3. Trace element ink spiking for signature authentication

    International Nuclear Information System (INIS)

    Hatzistavros, V.S.; Kallithrakas-Kontos, N.G.

    2008-01-01

    Signature authentication is a critical question in forensic document examination. Last years the evolution of personal computers made signature copying a quite easy task, so the development of new ways for signature authentication is crucial. In the present work a commercial ink was spiked with many trace elements in various concentrations. Inorganic and organometallic ink soluble compounds were used as spiking agents, whilst ink retained its initial properties. The spiked inks were used for paper writing and the documents were analyzed by a non destructive method, the energy dispersive X-ray fluorescence. The thin target model was proved right for quantitative analysis and a very good linear relationship of the intensity (X-ray signal) against concentration was estimated for all used elements. Intensity ratios between different elements in the same ink gave very stable results, independent on the writing alterations. The impact of time both to written document and prepared inks was also investigated. (author)

  4. A Methodology for Calculating Radiation Signatures

    Energy Technology Data Exchange (ETDEWEB)

    Klasky, Marc Louis [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wilcox, Trevor [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bathke, Charles G. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); James, Michael R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-05-01

    A rigorous formalism is presented for calculating radiation signatures from both Special Nuclear Material (SNM) as well as radiological sources. The use of MCNP6 in conjunction with CINDER/ORIGEN is described to allow for the determination of both neutron and photon leakages from objects of interest. In addition, a description of the use of MCNP6 to properly model the background neutron and photon sources is also presented. Examinations of the physics issues encountered in the modeling are investigated so as to allow for guidance in the user discerning the relevant physics to incorporate into general radiation signature calculations. Furthermore, examples are provided to assist in delineating the pertinent physics that must be accounted for. Finally, examples of detector modeling utilizing MCNP are provided along with a discussion on the generation of Receiver Operating Curves, which are the suggested means by which to determine detectability radiation signatures emanating from objects.

  5. Cryptanalysis of the arbitrated quantum signature protocols

    International Nuclear Information System (INIS)

    Gao Fei; Qin Sujuan; Guo Fenzhuo; Wen Qiaoyan

    2011-01-01

    As a new model for signing quantum messages, arbitrated quantum signature (AQS) has recently received a lot of attention. In this paper we study the cryptanalysis of previous AQS protocols from the aspects of forgery and disavowal. We show that in these protocols the receiver, Bob, can realize existential forgery of the sender's signature under known message attack. Bob can even achieve universal forgery when the protocols are used to sign a classical message. Furthermore, the sender, Alice, can successfully disavow any of her signatures by simple attack. The attack strategies are described in detail and some discussions about the potential improvements of the protocols are given. Finally we also present several interesting topics on AQS protocols that can be studied in future.

  6. Selection signatures in worldwide sheep populations.

    Science.gov (United States)

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

    2014-01-01

    The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

  7. Biomarker Gene Signature Discovery Integrating Network Knowledge

    Directory of Open Access Journals (Sweden)

    Holger Fröhlich

    2012-02-01

    Full Text Available Discovery of prognostic and diagnostic biomarker gene signatures for diseases, such as cancer, is seen as a major step towards a better personalized medicine. During the last decade various methods, mainly coming from the machine learning or statistical domain, have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinical diagnosis is the typical low reproducibility of these signatures combined with the difficulty to achieve a clear biological interpretation. For that purpose in the last years there has been a growing interest in approaches that try to integrate information from molecular interaction networks. Here we review the current state of research in this field by giving an overview about so-far proposed approaches.

  8. Estimating physiological skin parameters from hyperspectral signatures

    Science.gov (United States)

    Vyas, Saurabh; Banerjee, Amit; Burlina, Philippe

    2013-05-01

    We describe an approach for estimating human skin parameters, such as melanosome concentration, collagen concentration, oxygen saturation, and blood volume, using hyperspectral radiometric measurements (signatures) obtained from in vivo skin. We use a computational model based on Kubelka-Munk theory and the Fresnel equations. This model forward maps the skin parameters to a corresponding multiband reflectance spectra. Machine-learning-based regression is used to generate the inverse map, and hence estimate skin parameters from hyperspectral signatures. We test our methods using synthetic and in vivo skin signatures obtained in the visible through the short wave infrared domains from 24 patients of both genders and Caucasian, Asian, and African American ethnicities. Performance validation shows promising results: good agreement with the ground truth and well-established physiological precepts. These methods have potential use in the characterization of skin abnormalities and in minimally-invasive prescreening of malignant skin cancers.

  9. Transcription factor interplay in T helper cell differentiation

    Science.gov (United States)

    Evans, Catherine M.

    2013-01-01

    The differentiation of CD4 helper T cells into specialized effector lineages has provided a powerful model for understanding immune cell differentiation. Distinct lineages have been defined by differential expression of signature cytokines and the lineage-specifying transcription factors necessary and sufficient for their production. The traditional paradigm of differentiation towards Th1 and Th2 subtypes driven by T-bet and GATA3, respectively, has been extended to incorporate additional T cell lineages and transcriptional regulators. Technological advances have expanded our view of these lineage-specifying transcription factors to the whole genome and revealed unexpected interplay between them. From these data, it is becoming clear that lineage specification is more complex and plastic than previous models might have suggested. Here, we present an overview of the different forms of transcription factor interplay that have been identified and how T cell phenotypes arise as a product of this interplay within complex regulatory networks. We also suggest experimental strategies that will provide further insight into the mechanisms that underlie T cell lineage specification and plasticity. PMID:23878131

  10. Transcription factor interplay in T helper cell differentiation.

    Science.gov (United States)

    Evans, Catherine M; Jenner, Richard G

    2013-11-01

    The differentiation of CD4 helper T cells into specialized effector lineages has provided a powerful model for understanding immune cell differentiation. Distinct lineages have been defined by differential expression of signature cytokines and the lineage-specifying transcription factors necessary and sufficient for their production. The traditional paradigm of differentiation towards Th1 and Th2 subtypes driven by T-bet and GATA3, respectively, has been extended to incorporate additional T cell lineages and transcriptional regulators. Technological advances have expanded our view of these lineage-specifying transcription factors to the whole genome and revealed unexpected interplay between them. From these data, it is becoming clear that lineage specification is more complex and plastic than previous models might have suggested. Here, we present an overview of the different forms of transcription factor interplay that have been identified and how T cell phenotypes arise as a product of this interplay within complex regulatory networks. We also suggest experimental strategies that will provide further insight into the mechanisms that underlie T cell lineage specification and plasticity.

  11. High pressure membrane foulants of seawater, brackish water and river water: Origin assessed by sugar and bacteriohopanepolyol signatures

    KAUST Repository

    Mondamert, Leslie

    2011-01-01

    The present work aimed to study the origin of foulant material recovered on membranes used in water treatment. Firstly, sugar signatures were assessed from the monosaccharide composition. As results were not conclusive, a statistical approach using discriminant analysis was applied to the sugar data set in order to predict the origin of the foulant material. Three groups of various origins (algal, microbial, continental dissolved organic matter) were used as sugar references for the prediction. The results of the computation showed that the origin of reverse osmosis (RO) seawater foulant material is influenced by both the location of the water sources and the season. RO brackish water and nanofiltration river water foulant materials had a terrestrial origin. Secondly, bacteriohopanepolyol signatures indicated that RO seawater foulant material had a marine signature, RO brackish water foulant material had both a marine and a terrestrial origin and the nanofiltration river water foulant material contained only a terrestrial signature. © 2011 Taylor & Francis.

  12. Peripheral blood signatures of lead exposure.

    Directory of Open Access Journals (Sweden)

    Heather G LaBreche

    Full Text Available BACKGROUND: Current evidence indicates that even low-level lead (Pb exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways. METHODOLOGY/PRINCIPAL FINDING: Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern. CONCLUSIONS/SIGNIFICANCE: The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway.

  13. Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation.

    Directory of Open Access Journals (Sweden)

    Hongkai Ji

    Full Text Available The functions of key oncogenic transcription factors independent of context have not been fully delineated despite our richer understanding of the genetic alterations in human cancers. The MYC oncogene, which produces the Myc transcription factor, is frequently altered in human cancer and is a major regulatory hub for many cancers. In this regard, we sought to unravel the primordial signature of Myc function by using high-throughput genomic approaches to identify the cell-type independent core Myc target gene signature. Using a model of human B lymphoma cells bearing inducible MYC, we identified a stringent set of direct Myc target genes via chromatin immunoprecipitation (ChIP, global nuclear run-on assay, and changes in mRNA levels. We also identified direct Myc targets in human embryonic stem cells (ESCs. We further document that a Myc core signature (MCS set of target genes is shared in mouse and human ESCs as well as in four other human cancer cell types. Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types. Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes. Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression. Annotation of this gene signature reveals Myc's primordial function in RNA processing, ribosome biogenesis and biomass accumulation as its key roles in cancer and stem cells.

  14. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor

    2006-01-01

    . We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional......Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species...

  15. Doppler Velocity Signatures of Idealized Elliptical Vortices

    Directory of Open Access Journals (Sweden)

    Wen-Chau Lee

    2006-01-01

    Full Text Available Doppler radar observations have revealed a class of atmospheric vortices (tropical cyclones, tornadoes, dust devils that possess elliptical radar reflectivity signatures. One famous example is Typhoon Herb (1996 that maintained its elliptical reflectivity structure over a 40-hour period. Theoretical work and dual-Doppler analyses of observed tropical cyclones have suggested two physical mechanisms that can explain the formation of two types of elliptical vortices observed in nature, namely, the combination of a circular vortex with either a wavenumber two vortex Rossby wave or a deformation field. The characteristics of these two types of elliptical vortices and their corresponding Doppler velocity signatures have not been previously examined.

  16. KEA-71 Smart Current Signature Sensor (SCSS)

    Science.gov (United States)

    Perotti, Jose M.

    2010-01-01

    This slide presentation reviews the development and uses of the Smart Current Signature Sensor (SCSS), also known as the Valve Health Monitor (VHM) system. SCSS provides a way to not only monitor real-time the valve's operation in a non invasive manner, but also to monitor its health (Fault Detection and Isolation) and identify potential faults and/or degradation in the near future (Prediction/Prognosis). This technology approach is not only applicable for solenoid valves, and it could be extrapolated to other electrical components with repeatable electrical current signatures such as motors.

  17. Security problem on arbitrated quantum signature schemes

    International Nuclear Information System (INIS)

    Choi, Jeong Woon; Chang, Ku-Young; Hong, Dowon

    2011-01-01

    Many arbitrated quantum signature schemes implemented with the help of a trusted third party have been developed up to now. In order to guarantee unconditional security, most of them take advantage of the optimal quantum one-time encryption based on Pauli operators. However, in this paper we point out that the previous schemes provide security only against a total break attack and show in fact that there exists an existential forgery attack that can validly modify the transmitted pair of message and signature. In addition, we also provide a simple method to recover security against the proposed attack.

  18. Plasma Signatures of Radial Field Power Dropouts

    International Nuclear Information System (INIS)

    Lucek, E.A.; Horbury, T.S.; Balogh, A.; McComas, D.J.

    1998-01-01

    A class of small scale structures, with a near-radial magnetic field and a drop in magnetic field fluctuation power, have recently been identified in the polar solar wind. An earlier study of 24 events, each lasting for 6 hours or more, identified no clear plasma signature. In an extension of that work, radial intervals lasting for 4 hours or more (89 in total), have been used to search for a statistically significant plasma signature. It was found that, despite considerable variations between intervals, there was a small but significant drop, on average, in plasma temperature, density and β during these events

  19. Transient thermal camouflage and heat signature control

    Science.gov (United States)

    Yang, Tian-Zhi; Su, Yishu; Xu, Weikai; Yang, Xiao-Dong

    2016-09-01

    Thermal metamaterials have been proposed to manipulate heat flux as a new way to cloak or camouflage objects in the infrared world. To date, however, thermal metamaterials only operate in the steady-state and exhibit detectable, transient heat signatures. In this letter, the theoretical basis for a thermal camouflaging technique with controlled transient diffusion is presented. This technique renders an object invisible in real time. More importantly, the thermal camouflaging device instantaneously generates a pre-designed heat signature and behaves as a perfect thermal illusion device. A metamaterial coating with homogeneous and isotropic thermal conductivity, density, and volumetric heat capacity was fabricated and very good camouflaging performance was achieved.

  20. Security problem on arbitrated quantum signature schemes

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jeong Woon [Emerging Technology R and D Center, SK Telecom, Kyunggi 463-784 (Korea, Republic of); Chang, Ku-Young; Hong, Dowon [Cryptography Research Team, Electronics and Telecommunications Research Institute, Daejeon 305-700 (Korea, Republic of)

    2011-12-15

    Many arbitrated quantum signature schemes implemented with the help of a trusted third party have been developed up to now. In order to guarantee unconditional security, most of them take advantage of the optimal quantum one-time encryption based on Pauli operators. However, in this paper we point out that the previous schemes provide security only against a total break attack and show in fact that there exists an existential forgery attack that can validly modify the transmitted pair of message and signature. In addition, we also provide a simple method to recover security against the proposed attack.

  1. MicroRNA signature of the human developing pancreas

    Directory of Open Access Journals (Sweden)

    Correa-Medina Mayrin

    2010-09-01

    Full Text Available Abstract Background MicroRNAs are non-coding RNAs that regulate gene expression including differentiation and development by either inhibiting translation or inducing target degradation. The aim of this study is to determine the microRNA expression signature during human pancreatic development and to identify potential microRNA gene targets calculating correlations between the signature microRNAs and their corresponding mRNA targets, predicted by bioinformatics, in genome-wide RNA microarray study. Results The microRNA signature of human fetal pancreatic samples 10-22 weeks of gestational age (wga, was obtained by PCR-based high throughput screening with Taqman Low Density Arrays. This method led to identification of 212 microRNAs. The microRNAs were classified in 3 groups: Group number I contains 4 microRNAs with the increasing profile; II, 35 microRNAs with decreasing profile and III with 173 microRNAs, which remain unchanged. We calculated Pearson correlations between the expression profile of microRNAs and target mRNAs, predicted by TargetScan 5.1 and miRBase altgorithms, using genome-wide mRNA expression data. Group I correlated with the decreasing expression of 142 target mRNAs and Group II with the increasing expression of 876 target mRNAs. Most microRNAs correlate with multiple targets, just as mRNAs are targeted by multiple microRNAs. Among the identified targets are the genes and transcription factors known to play an essential role in pancreatic development. Conclusions We have determined specific groups of microRNAs in human fetal pancreas that change the degree of their expression throughout the development. A negative correlative analysis suggests an intertwined network of microRNAs and mRNAs collaborating with each other. This study provides information leading to potential two-way level of combinatorial control regulating gene expression through microRNAs targeting multiple mRNAs and, conversely, target mRNAs regulated in

  2. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

    Directory of Open Access Journals (Sweden)

    Amanda M. Ackermann

    2016-03-01

    Conclusions: We have determined the genetic landscape of human α- and β-cells based on chromatin accessibility and transcript levels, which allowed for detection of novel α- and β-cell signature genes not previously known to be expressed in islets. Using fine-mapping of open chromatin, we have identified thousands of potential cis-regulatory elements that operate in an endocrine cell type-specific fashion.

  3. Hippocampal CA3 transcriptome signature correlates with initial precipitating injury in refractory mesial temporal lobe epilepsy.

    Directory of Open Access Journals (Sweden)

    Silvia Y Bando

    Full Text Available BACKGROUND: Prolonged febrile seizures constitute an initial precipitating injury (IPI commonly associated with refractory mesial temporal lobe epilepsy (RMTLE. In order to investigate IPI influence on the transcriptional phenotype underlying RMTLE we comparatively analyzed the transcriptomic signatures of CA3 explants surgically obtained from RMTLE patients with (FS or without (NFS febrile seizure history. Texture analyses on MRI images of dentate gyrus were conducted in a subset of surgically removed sclerotic hippocampi for identifying IPI-associated histo-radiological alterations. METHODOLOGY/PRINCIPAL FINDINGS: DNA microarray analysis revealed that CA3 global gene expression differed significantly between FS and NFS subgroups. An integrative functional genomics methodology was used for characterizing the relations between GO biological processes themes and constructing transcriptional interaction networks defining the FS and NFS transcriptomic signatures and its major gene-gene links (hubs. Co-expression network analysis showed that: i CA3 transcriptomic profiles differ according to the IPI; ii FS distinctive hubs are mostly linked to glutamatergic signalization while NFS hubs predominantly involve GABAergic pathways and neurotransmission modulation. Both networks have relevant hubs related to nervous system development, what is consistent with cell genesis activity in the hippocampus of RMTLE patients. Moreover, two candidate genes for therapeutic targeting came out from this analysis: SSTR1, a relevant common hub in febrile and afebrile transcriptomes, and CHRM3, due to its putative role in epilepsy susceptibility development. MRI texture analysis allowed an overall accuracy of 90% for pixels correctly classified as belonging to FS or NFS groups. Histological examination revealed that granule cell loss was significantly higher in FS hippocampi. CONCLUSIONS/SIGNIFICANCE: CA3 transcriptional signatures and dentate gyrus morphology fairly

  4. The Mediator complex and transcription regulation

    Science.gov (United States)

    Poss, Zachary C.; Ebmeier, Christopher C.

    2013-01-01

    The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module. PMID:24088064

  5. In-situ acoustic signature monitoring in additive manufacturing processes

    Science.gov (United States)

    Koester, Lucas W.; Taheri, Hossein; Bigelow, Timothy A.; Bond, Leonard J.; Faierson, Eric J.

    2018-04-01

    Additive manufacturing is a rapidly maturing process for the production of complex metallic, ceramic, polymeric, and composite components. The processes used are numerous, and with the complex geometries involved this can make quality control and standardization of the process and inspection difficult. Acoustic emission measurements have been used previously to monitor a number of processes including machining and welding. The authors have identified acoustic signature measurement as a potential means of monitoring metal additive manufacturing processes using process noise characteristics and those discrete acoustic emission events characteristic of defect growth, including cracks and delamination. Results of acoustic monitoring for a metal additive manufacturing process (directed energy deposition) are reported. The work investigated correlations between acoustic emissions and process noise with variations in machine state and deposition parameters, and provided proof of concept data that such correlations do exist.

  6. COMPUTER-IMPLEMENTED METHOD OF PERFORMING A SEARCH USING SIGNATURES

    DEFF Research Database (Denmark)

    2017-01-01

    A computer-implemented method of processing a query vector and a data vector), comprising: generating a set of masks and a first set of multiple signatures and a second set of multiple signatures by applying the set of masks to the query vector and the data vector, respectively, and generating...... candidate pairs, of a first signature and a second signature, by identifying matches of a first signature and a second signature. The set of masks comprises a configuration of the elements that is a Hadamard code; a permutation of a Hadamard code; or a code that deviates from a Hadamard code...

  7. Quantum multi-signature protocol based on teleportation

    International Nuclear Information System (INIS)

    Wen Xiao-jun; Liu Yun; Sun Yu

    2007-01-01

    In this paper, a protocol which can be used in multi-user quantum signature is proposed. The scheme of signature and verification is based on the correlation of Greenberger-Horne-Zeilinger (GHZ) states and the controlled quantum teleportation. Different from the digital signatures, which are based on computational complexity, the proposed protocol has perfect security in the noiseless quantum channels. Compared to previous quantum signature schemes, this protocol can verify the signature independent of an arbitrator as well as realize multi-user signature together. (orig.)

  8. A group signature scheme based on quantum teleportation

    International Nuclear Information System (INIS)

    Wen Xiaojun; Tian Yuan; Ji Liping; Niu Xiamu

    2010-01-01

    In this paper, we present a group signature scheme using quantum teleportation. Different from classical group signature and current quantum signature schemes, which could only deliver either group signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum teleportation. Security analysis proved that our scheme has the characteristics of group signature, non-counterfeit, non-disavowal, blindness and traceability. Our quantum group signature scheme has a foreseeable application in the e-payment system, e-government, e-business, etc.

  9. A group signature scheme based on quantum teleportation

    Energy Technology Data Exchange (ETDEWEB)

    Wen Xiaojun; Tian Yuan; Ji Liping; Niu Xiamu, E-mail: wxjun36@gmail.co [Information Countermeasure Technique Research Institute, Harbin Institute of Technology, Harbin 150001 (China)

    2010-05-01

    In this paper, we present a group signature scheme using quantum teleportation. Different from classical group signature and current quantum signature schemes, which could only deliver either group signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum teleportation. Security analysis proved that our scheme has the characteristics of group signature, non-counterfeit, non-disavowal, blindness and traceability. Our quantum group signature scheme has a foreseeable application in the e-payment system, e-government, e-business, etc.

  10. Tethered Nanoparticle–Polymer Composites: Phase Stability and Curvature

    KAUST Repository

    Srivastava, Samanvaya; Agarwal, Praveen; Archer, Lynden A.

    2012-01-01

    different small-angle X-ray scattering signatures in comparison to phase-separated composites comprised of bare or sparsely grafted nanoparticles. A general diagram for the dispersion state and phase stability of polymer tethered nanoparticle-polymer

  11. Characterization of a Genomic Signature of Pregnancy in the Breast

    Science.gov (United States)

    Belitskaya-Lévy, Ilana; Zeleniuch-Jacquotte, Anne; Russo, Jose; Russo, Irma H.; Bordás, Pal; Åhman, Janet; Afanasyeva, Yelena; Johansson, Robert; Lenner, Per; Li, Xiaochun; de Cicco, Ricardo López; Peri, Suraj; Ross, Eric; Russo, Patricia A.; Santucci-Pereira, Julia; Sheriff, Fathima S.; Slifker, Michael; Hallmans, Göran; Toniolo, Paolo; Arslan, Alan A.

    2012-01-01

    The objective of the current study was to comprehensively compare the genomic profiles in the breast of parous and nulliparous postmenopausal women to identify genes that permanently change their expression following pregnancy. The study was designed as a two-phase approach. In the discovery phase, we compared breast genomic profiles of 37 parous with 18 nulliparous postmenopausal women. In the validation phase, confirmation of the genomic patterns observed in the discovery phase was sought in an independent set of 30 parous and 22 nulliparous postmenopausal women. RNA was hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to 54,675 transcripts; scanned and the images analyzed using Affymetrix GCOS software. Surrogate variable analysis, logistic regression and significance analysis for microarrays were used to identify statistically significant differences in expression of genes. The False Discovery Rate (FDR) approach was used to control for multiple comparisons. We found that 208 genes (305 probe sets) were differentially expressed between parous and nulliparous women in both discovery and validation phases of the study at a FDR of 10% and with at least a 1.25-fold change. These genes are involved in regulation of transcription, centrosome organization, RNA splicing, cell cycle control, adhesion and differentiation. The results provide persuasive evidence that full-term pregnancy induces long-term genomic changes in the breast. The genomic signature of pregnancy could be used as an intermediate marker to assess potential chemopreventive interventions with hormones mimicking the effects of pregnancy for prevention of breast cancer. PMID:21622728

  12. Predictive gene signatures: molecular markers distinguishing colon adenomatous polyp and carcinoma.

    Directory of Open Access Journals (Sweden)

    Janice E Drew

    Full Text Available Cancers exhibit abnormal molecular signatures associated with disease initiation and progression. Molecular signatures could improve cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patients for analysis and biopsy samples exhibit broad heterogeneity that cannot be captured using a single marker. This report details application of an in-house custom designed GenomeLab System multiplex gene expression assay, the hCellMarkerPlex, to assess predictive gene signatures of normal, adenomatous polyp and carcinoma colon tissue using archived tissue bank material. The hCellMarkerPlex incorporates twenty-one gene markers: epithelial (EZR, KRT18, NOX1, SLC9A2, proliferation (PCNA, CCND1, MS4A12, differentiation (B4GANLT2, CDX1, CDX2, apoptotic (CASP3, NOX1, NTN1, fibroblast (FSP1, COL1A1, structural (ACTG2, CNN1, DES, gene transcription (HDAC1, stem cell (LGR5, endothelial (VWF and mucin production (MUC2. Gene signatures distinguished normal, adenomatous polyp and carcinoma. Individual gene targets significantly contributing to molecular tissue types, classifier genes, were further characterised using real-time PCR, in-situ hybridisation and immunohistochemistry revealing aberrant epithelial expression of MS4A12, LGR5 CDX2, NOX1 and SLC9A2 prior to development of carcinoma. Identified gene signatures identify aberrant epithelial expression of genes prior to cancer development using in-house custom designed gene expression multiplex assays. This approach may be used to assist in objective classification of disease initiation, staging, progression and therapeutic responses using biopsy material.

  13. Lorentz violations and Euclidean signature metrics

    International Nuclear Information System (INIS)

    Barbero G, J. Fernando; Villasenor, Eduardo J.S.

    2003-01-01

    We show that the families of effective actions considered by Jacobson et al. to study Lorentz invariance violations contain a class of models that represent pure general relativity with a Euclidean signature. We also point out that some members of this family of actions preserve Lorentz invariance in a generalized sense

  14. Mechanical System Simulations for Seismic Signature Modeling

    National Research Council Canada - National Science Library

    Lacombe, J

    2001-01-01

    .... Results for an M1A1 and T72 are discussed. By analyzing the simulated seismic signature data in conjunction with the spectral features associated with the vibrations of specific vehicle sprung and un-sprung components we are able to make...

  15. Exploring Signature Pedagogies in Undergraduate Leadership Education

    Science.gov (United States)

    Jenkins, Daniel M.

    2012-01-01

    This research explores the instructional strategies most frequently used by leadership educators who teach academic credit-bearing undergraduate leadership studies courses through a national survey and identifies signature pedagogies within the leadership discipline. Findings from this study suggest that class discussion--whether in the form of…

  16. The Pedagogic Signature of Special Needs Education

    Science.gov (United States)

    Weiß, Sabine; Kollmannsberger, Markus; Lerche, Thomas; Oubaid, Viktor; Kiel, Ewald

    2014-01-01

    The goal of the following study is to identify a pedagogic signature, according to LS Shulman, for working with students who have special educational needs. Special educational needs are defined as significant limitations in personal development and learning which require particular educational measures beyond regular education. The development of…

  17. Arbitrated quantum signature scheme with message recovery

    International Nuclear Information System (INIS)

    Lee, Hwayean; Hong, Changho; Kim, Hyunsang; Lim, Jongin; Yang, Hyung Jin

    2004-01-01

    Two quantum signature schemes with message recovery relying on the availability of an arbitrator are proposed. One scheme uses a public board and the other does not. However both schemes provide confidentiality of the message and a higher efficiency in transmission

  18. Hyperspectral signature analysis of skin parameters

    Science.gov (United States)

    Vyas, Saurabh; Banerjee, Amit; Garza, Luis; Kang, Sewon; Burlina, Philippe

    2013-02-01

    The temporal analysis of changes in biological skin parameters, including melanosome concentration, collagen concentration and blood oxygenation, may serve as a valuable tool in diagnosing the progression of malignant skin cancers and in understanding the pathophysiology of cancerous tumors. Quantitative knowledge of these parameters can also be useful in applications such as wound assessment, and point-of-care diagnostics, amongst others. We propose an approach to estimate in vivo skin parameters using a forward computational model based on Kubelka-Munk theory and the Fresnel Equations. We use this model to map the skin parameters to their corresponding hyperspectral signature. We then use machine learning based regression to develop an inverse map from hyperspectral signatures to skin parameters. In particular, we employ support vector machine based regression to estimate the in vivo skin parameters given their corresponding hyperspectral signature. We build on our work from SPIE 2012, and validate our methodology on an in vivo dataset. This dataset consists of 241 signatures collected from in vivo hyperspectral imaging of patients of both genders and Caucasian, Asian and African American ethnicities. In addition, we also extend our methodology past the visible region and through the short-wave infrared region of the electromagnetic spectrum. We find promising results when comparing the estimated skin parameters to the ground truth, demonstrating good agreement with well-established physiological precepts. This methodology can have potential use in non-invasive skin anomaly detection and for developing minimally invasive pre-screening tools.

  19. Dictionary of Large Hadron Collider signatures

    Indian Academy of Sciences (India)

    We report on a plan to establish a `Dictionary of LHC Signatures', an initiative that started at the WHEPP-X workshop in Chennai, January 2008. This study aims at the strategy of distinguishing 3 classes of dark matter motivated scenarios such as -parity conserved supersymmetry, little Higgs models with -parity ...

  20. Signatures of mutational processes in human cancer

    NARCIS (Netherlands)

    Alexandrov, L.B.; Nik-Zainal, S.; Wedge, D.C.; Aparicio, S.A.; Behjati, S.; Biankin, A.V.; Bignell, G.R.; Bolli, N.; Borg, A.; Borresen-Dale, A.L.; Boyault, S.; Burkhardt, B.; Butler, A.P.; Caldas, C.; Davies, H.R.; Desmedt, C.; Eils, R.; Eyfjord, J.E.; Foekens, J.A.; Greaves, M.; Hosoda, F.; Hutter, B.; Ilicic, T.; Imbeaud, S.; Imielinsk, M.; Jager, N.; Jones, D.T.; Knappskog, S.; Kool, M.; Lakhani, S.R.; Lopez-Otin, C.; Martin, S.; Munshi, N.C.; Nakamura, H.; Northcott, P.A.; Pajic, M.; Papaemmanuil, E.; Paradiso, A.; Pearson, J.V.; Puente, X.S.; Raine, K.; Ramakrishna, M.; Richardson, A.L.; Richter, J.; Rosenstiel, P.; Schlesner, M.; Schumacher, T.N.; Span, P.N.; Teague, J.W.; Totoki, Y.; Tutt, A.N.; Valdes-Mas, R.; Buuren, M.M. van; Veer, L. van 't; Vincent-Salomon, A.; Waddell, N.; Yates, L.R.; Zucman-Rossi, J.; Futreal, P.A.; McDermott, U.; Lichter, P.; Meyerson, M.; Grimmond, S.M.; Siebert, R.; Campo, E.; Shibata, T.; Pfister, S.M.; Campbell, P.J.; Stratton, M.R.; Schlooz-Vries, M.S.; Tol, J.J. van; Laarhoven, H.W. van; Sweep, F.C.; Bult, P.; et al.,

    2013-01-01

    All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362

  1. Ankle and Other Signatures in Uhecr

    Science.gov (United States)

    Berezinsky, Veniamin

    2015-03-01

    The interaction signatures of UHE protons propagating through CMB are discussed. Much attention is given to ankle, which starting from 1963 is usually interpreted as a feature of transition from galactic to extragalactic cosmic rays. We argue here that this interpretation is now excluded. It gives more credit to alternative explanation of the ankle as an intrinsic part of the pair-production dip.

  2. Detection of proteolytic signatures for Parkinson's disease

    DEFF Research Database (Denmark)

    Jordal, Peter Lüttge; Dyrlund, Thomas F.; Winge, Kristian

    2016-01-01

    Aim: To investigate if idiopathic Parkinson's disease (IPD) is associated with distinct proteolytic signatures relative to non-neurodegenerative controls (NND) and patients with multiple system atrophy (MSA). Materials & methods: A subtiligase-based N-terminomics screening method was exploited...

  3. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription.

    Science.gov (United States)

    Jeronimo, Célia; Robert, François

    2017-10-01

    Mediator is an essential, large, multisubunit, transcriptional co-activator highly conserved across eukaryotes. Mediator interacts with gene-specific transcription factors at enhancers as well as with the RNA polymerase II (RNAPII) transcription machinery bound at promoters. It also interacts with several other factors involved in various aspects of transcription, chromatin regulation, and mRNA processing. Hence, Mediator is at the nexus of RNAPII transcription, regulating its many steps and connecting transcription with co-transcriptional events. To achieve this flexible role, Mediator, which is divided into several functional modules, reorganizes its conformation and composition while making transient contacts with other components. Here, we review the mechanisms of action of Mediator and propose a unifying model for its function. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients.

    Directory of Open Access Journals (Sweden)

    Chris Cheadle

    Full Text Available Gene expression profiling of peripheral blood mononuclear cells (PBMCs is a powerful tool for the identification of surrogate markers involved in disease processes. The hypothesis tested in this study was that chronic exposure of PBMCs to a hypertensive environment in remodeled pulmonary vessels would be reflected by specific transcriptional changes in these cells.The transcript profiles of PBMCs from 30 idiopathic pulmonary arterial hypertension patients (IPAH, 19 patients with systemic sclerosis without pulmonary hypertension (SSc, 42 scleroderma-associated pulmonary arterial hypertensio patients (SSc-PAH, and 8 patients with SSc complicated by interstitial lung disease and pulmonary hypertension (SSc-PH-ILD were compared to the gene expression profiles of PBMCs from 41 healthy individuals. Multiple gene expression signatures were identified which could distinguish various disease groups from controls. One of these signatures, specific for erythrocyte maturation, is enriched specifically in patients with PH. This association was validated in multiple published datasets. The erythropoiesis signature was strongly correlated with hemodynamic measures of increasing disease severity in IPAH patients. No significant correlation of the same type was noted for SSc-PAH patients, this despite a clear signature enrichment within this group overall. These findings suggest an association of the erythropoiesis signature in PBMCs from patients with PH with a variable presentation among different subtypes of disease.In PH, the expansion of immature red blood cell precursors may constitute a response to the increasingly hypoxic conditions prevalent in this syndrome. A correlation of this erythrocyte signature with more severe hypertension cases may provide an important biomarker of disease progression.

  5. Perancangan Aplikasi Undeniable Digital Signature Dengan Algoritma Chaum’s Blind Signature

    OpenAIRE

    Simanjuntak, Martin Dennain

    2012-01-01

    Desperaty need a securiry system in the exchange of information via computer media, so that information can not be accessed by unauthorized parties. One of the security system is to use a system of digital signatures as a means of authenticating the authenticity of digital document that are exchanged. By using a digital a digital signature system is undeniable, the security system can be generated digital document exchange, where the system is free from the from of rejection...

  6. The effects of extrinsic motivation on signature authorship opinions in forensic signature blind trials.

    Science.gov (United States)

    Dewhurst, Tahnee N; Found, Bryan; Ballantyne, Kaye N; Rogers, Doug

    2014-03-01

    Expertise studies in forensic handwriting examination involve comparisons of Forensic Handwriting Examiners' (FHEs) opinions with lay-persons on blind tests. All published studies of this type have reported real and demonstrable skill differences between the specialist and lay groups. However, critics have proposed that any difference shown may be indicative of a lack of motivation on the part of lay participants, rather than a real difference in skill. It has been suggested that qualified FHEs would be inherently more motivated to succeed in blinded validation trials, as their professional reputations could be at risk, should they perform poorly on the task provided. Furthermore, critics suggest that lay-persons would be unlikely to be highly motivated to succeed, as they would have no fear of negative consequences should they perform badly. In an effort to investigate this concern, a blind signature trial was designed and administered to forty lay-persons. Participants were required to compare known (exemplar) signatures of an individual to questioned signatures and asked to express an opinion regarding whether the writer of the known signatures wrote each of the questioned signatures. The questioned signatures comprised a mixture of genuine, disguised and simulated signatures. The forty participants were divided into two separate groupings. Group 'A' were requested to complete the trial as directed and were advised that for each correct answer they would be financially rewarded, for each incorrect answer they would be financially penalized, and for each inconclusive opinion they would receive neither penalty nor reward. Group 'B' was requested to complete the trial as directed, with no mention of financial recompense or penalty. The results of this study do not support the proposition that motivation rather than skill difference is the source of the statistical difference in opinions between individuals' results in blinded signature proficiency trials. Crown

  7. Optical/Infrared Signatures for Space-Based Remote Sensing

    National Research Council Canada - National Science Library

    Picard, R. H; Dewan, E. M; Winick, J. R; O'Neil, R. R

    2007-01-01

    This report describes work carried out under the Air Force Research Laboratory's basic research task in optical remote-sensing signatures, entitled Optical / Infrared Signatures for Space-Based Remote Sensing...

  8. Methods and apparatus for multi-parameter acoustic signature inspection

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Aaron A [Richland, WA; Samuel, Todd J [Pasco, WA; Valencia, Juan D [Kennewick, WA; Gervais, Kevin L [Richland, WA; Tucker, Brian J [Pasco, WA; Kirihara, Leslie J [Richland, WA; Skorpik, James R [Kennewick, WA; Reid, Larry D [Benton City, WA; Munley, John T [Benton City, WA; Pappas, Richard A [Richland, WA; Wright, Bob W [West Richland, WA; Panetta, Paul D [Richland, WA; Thompson, Jason S [Richland, WA

    2007-07-24

    A multiparameter acoustic signature inspection device and method are described for non-invasive inspection of containers. Dual acoustic signatures discriminate between various fluids and materials for identification of the same.

  9. Passive Infrared Signature Augmentation of Full-Scale Plastic Targets

    National Research Council Canada - National Science Library

    Gebus, Lisa M; Sanders, Jeffrey S

    2002-01-01

    ... (IR), and radar signatures of threat systems. To address this need, a program was initiated by TMO to augment an existing full-scale, vacuum-formed plastic target with sufficient signature fidelity to adequately stress U.S...

  10. A metabolic signature of long life in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Viney Jonathan M

    2010-02-01

    Full Text Available Abstract Background Many Caenorhabditis elegans mutations increase longevity and much evidence suggests that they do so at least partly via changes in metabolism. However, up until now there has been no systematic investigation of how the metabolic networks of long-lived mutants differ from those of normal worms. Metabolomic technologies, that permit the analysis of many untargeted metabolites in parallel, now make this possible. Here we use one of these, 1H nuclear magnetic resonance spectroscopy, to investigate what makes long-lived worms metabolically distinctive. Results We examined three classes of long-lived worms: dauer larvae, adult Insulin/IGF-1 signalling (IIS-defective mutants, and a translation-defective mutant. Surprisingly, these ostensibly different long-lived worms share a common metabolic signature, dominated by shifts in carbohydrate and amino acid metabolism. In addition the dauer larvae, uniquely, had elevated levels of modified amino acids (hydroxyproline and phosphoserine. We interrogated existing gene expression data in order to integrate functional (metabolite-level changes with transcriptional changes at a pathway level. Conclusions The observed metabolic responses could be explained to a large degree by upregulation of gluconeogenesis and the glyoxylate shunt as well as changes in amino acid catabolism. These responses point to new possible mechanisms of longevity assurance in worms. The metabolic changes observed in dauer larvae can be explained by the existence of high levels of autophagy leading to recycling of cellular components. See associated minireview: http://jbiol.com/content/9/1/7

  11. Detection of ROS Induced Proteomic Signatures by Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Brian McDonagh

    2017-07-01

    Full Text Available Reversible and irreversible post-translational modifications (PTMs induced by endogenously generated reactive oxygen species (ROS in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations. How the proteome responds to these stimuli is of critical importance in oxidant physiology, as it can regulate the cell stress response by reversible and irreversible PTMs, affecting protein activity and protein-protein interactions. Due to the highly labile nature of many ROS species, applying redox proteomics can provide a signature footprint of the ROS species generated. Ideally redox proteomic approaches would allow; (1 the identification of the specific PTM, (2 identification of the amino acid residue that is modified and (3 the percentage of the protein containing the PTM. New developments in MS offer the opportunity of a more sensitive targeted proteomic approach and retrospective data analysis. Subsequent bioinformatics analysis can provide an insight into the biochemical and physiological pathways or cell signaling cascades that are affected by ROS generation. This mini-review will detail current redox proteomic approaches to identify and quantify ROS induced PTMs and the subsequent effects on cellular signaling.

  12. Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection.

    Science.gov (United States)

    Barah, Pankaj; Winge, Per; Kusnierczyk, Anna; Tran, Diem Hong; Bones, Atle M

    2013-01-01

    Under the threat of global climatic change and food shortages, it is essential to take the initiative to obtain a comprehensive understanding of common and specific defence mechanisms existing in plant systems for protection against different types of biotic invaders. We have implemented an integrated approach to analyse the overall transcriptomic reprogramming and systems-level defence responses in the model plant species Arabidopsis thaliana (A. thaliana henceforth) during insect Brevicoryne brassicae (B. brassicae henceforth) and bacterial Pseudomonas syringae pv. tomato strain DC3000 (P. syringae henceforth) attacks. The main aim of this study was to identify the attacker-specific and general defence response signatures in A. thaliana when attacked by phloem-feeding aphids or pathogenic bacteria. The obtained annotated networks of differentially expressed transcripts indicated that members of transcription factor families, such as WRKY, MYB, ERF, BHLH and bZIP, could be crucial for stress-specific defence regulation in Arabidopsis during aphid and P. syringae attack. The defence response pathways, signalling pathways and metabolic processes associated with aphid attack and P. syringae infection partially overlapped. Components of several important biosynthesis and signalling pathways, such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and glucosinolates, were differentially affected during the two the treatments. Several stress-regulated transcription factors were known to be associated with stress-inducible microRNAs. The differentially regulated gene sets included many signature transcription factors, and our co-expression analysis showed that they were also strongly co-expressed during 69 other biotic stress experiments. Defence responses and functional networks that were unique and specific to aphid or P. syringae stresses were identified. Furthermore, our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and

  13. Re-examining the security of blind quantum signature protocols

    International Nuclear Information System (INIS)

    Wang Mingming; Chen Xiubo; Niu Xinxin; Yang Yixian

    2012-01-01

    Recently, blind quantum signature (BQS) protocols have been proposed with the help of a third-party verifier. However, our research shows that some of the BQS protocols are unable to complete the blind signature task fairly if the verifier is dishonest. Indeed, these protocols can be viewed as variants of the classical digital signature scheme of symmetric-key cryptography. If nobody is trusted in such protocols, digital signature cannot be implemented since disagreements cannot be solved fairly.

  14. Quantum signature scheme based on a quantum search algorithm

    International Nuclear Information System (INIS)

    Yoon, Chun Seok; Kang, Min Sung; Lim, Jong In; Yang, Hyung Jin

    2015-01-01

    We present a quantum signature scheme based on a two-qubit quantum search algorithm. For secure transmission of signatures, we use a quantum search algorithm that has not been used in previous quantum signature schemes. A two-step protocol secures the quantum channel, and a trusted center guarantees non-repudiation that is similar to other quantum signature schemes. We discuss the security of our protocol. (paper)

  15. A Signature Comparing Android Mobile Application Utilizing Feature Extracting Algorithms

    Directory of Open Access Journals (Sweden)

    Paul Grafilon

    2017-08-01

    Full Text Available The paper presented one of the application that can be done using smartphones camera. Nowadays forgery is one of the most undetected crimes. With the forensic technology used today it is still difficult for authorities to compare and define what a real signature is and what a forged signature is. A signature is a legal representation of a person. All transactions are based on a signature. Forgers may use a signature to sign illegal contracts and withdraw from bank accounts undetected. A signature can also be forged during election periods for repeated voting. Addressing the issues a signature should always be secure. Signature verification is a reduced problem that still poses a real challenge for researchers. The literature on signature verification is quite extensive and shows two main areas of research off-line and on-line systems. Off-line systems deal with a static image of the signature i.e. the result of the action of signing while on-line systems work on the dynamic process of generating the signature i.e. the action of signing itself. The researchers have found a way to resolve the concerns. A mobile application that integrates the camera to take a picture of a signature analyzes it and compares it to other signatures for verification. It will exist to help citizens to be more cautious and aware with issues regarding the signatures. This might also be relevant to help organizations and institutions such as banks and insurance companies in verifying signatures that may avoid unwanted transactions and identity theft. Furthermore this might help the authorities in the never ending battle against crime especially against forgers and thieves. The project aimed to design and develop a mobile application that integrates the smartphone camera for verifying and comparing signatures for security using the best algorithm possible. As the result of the development the said smartphone camera application is functional and reliable.

  16. Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.

    Directory of Open Access Journals (Sweden)

    Colin R Lickwar

    2017-08-01

    Full Text Available The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development

  17. Sensitive detection of viral transcripts in human tumor transcriptomes.

    Directory of Open Access Journals (Sweden)

    Sven-Eric Schelhorn

    Full Text Available In excess of 12% of human cancer incidents have a viral cofactor. Epidemiological studies of idiopathic human cancers indicate that additional tumor viruses remain to be discovered. Recent advances in sequencing technology have enabled systematic screenings of human tumor transcriptomes for viral transcripts. However, technical problems such as low abundances of viral transcripts in large volumes of sequencing data, viral sequence divergence, and homology between viral and human factors significantly confound identification of tumor viruses. We have developed a novel computational approach for detecting viral transcripts in human cancers that takes the aforementioned confounding factors into account and is applicable to a wide variety of viruses and tumors. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped 14 transcriptomes of neuroblastoma as well as positive and negative controls to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. Detailed investigation of putative viral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates

  18. Radar micro-doppler signatures processing and applications

    CERN Document Server

    Chen, Victor C; Miceli, William J

    2014-01-01

    Radar Micro-Doppler Signatures: Processing and applications concentrates on the processing and application of radar micro-Doppler signatures in real world situations, providing readers with a good working knowledge on a variety of applications of radar micro-Doppler signatures.

  19. Acoustic Signature Monitoring and Management of Naval Platforms

    NARCIS (Netherlands)

    Basten, T.G.H.; Jong, C.A.F. de; Graafland, F.; Hof, J. van 't

    2015-01-01

    Acoustic signatures make naval platforms susceptible to detection by threat sensors. The variable operational conditions and lifespan of a platform cause variations in the acoustic signature. To deal with these variations, a real time signature monitoring capability is being developed, with advisory

  20. 22 CFR 92.28 - Signature of affiant on affidavit.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Signature of affiant on affidavit. 92.28 Section 92.28 Foreign Relations DEPARTMENT OF STATE LEGAL AND RELATED SERVICES NOTARIAL AND RELATED SERVICES Specific Notarial Acts § 92.28 Signature of affiant on affidavit. The signature of the affiant is...

  1. 45 CFR 81.32 - Signature of documents.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Signature of documents. 81.32 Section 81.32 Public... UNDER PART 80 OF THIS TITLE Form, Execution, Service and Filing of Documents § 81.32 Signature of documents. The signature of a party, authorized officer, employee or attorney constitutes a certificate that...

  2. 21 CFR 1309.32 - Application forms; contents; signature.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Application forms; contents; signature. 1309.32... Application forms; contents; signature. (a) Any person who is required to be registered pursuant to § 1309.21... this paragraph and shall contain the signature of the individual being authorized to sign the...

  3. 17 CFR 201.65 - Identity and signature.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Identity and signature. 201.65... of 1934 § 201.65 Identity and signature. Applications pursuant to this subpart may omit the identity, mailing address, and signature of the applicant; provided, that such identity, mailing address and...

  4. Signature Pedagogies in Support of Teachers' Professional Learning

    Science.gov (United States)

    Parker, Melissa; Patton, Kevin; O'Sullivan, Mary

    2016-01-01

    Signature pedagogies [Shulman, L. 2005. "Signature pedagogies in the professions." "Daedalus" 134 (3): 52--59.] are a focus of teacher educators seeking to improve teaching and teacher education. The purpose of this paper is to present a preliminary common language of signature pedagogies for teacher professional development…

  5. 34 CFR 101.32 - Signature of documents.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Signature of documents. 101.32 Section 101.32 Education Regulations of the Offices of the Department of Education OFFICE FOR CIVIL RIGHTS, DEPARTMENT OF EDUCATION... Documents § 101.32 Signature of documents. The signature of a party, authorized officer, employee or...

  6. 36 CFR 1150.22 - Signature of documents.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Signature of documents. 1150.22 Section 1150.22 Parks, Forests, and Public Property ARCHITECTURAL AND TRANSPORTATION BARRIERS... Documents for Proceedings on Citations § 1150.22 Signature of documents. The signature of a party...

  7. 29 CFR 102.116 - Signature of orders.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 2 2010-07-01 2010-07-01 false Signature of orders. 102.116 Section 102.116 Labor Regulations Relating to Labor NATIONAL LABOR RELATIONS BOARD RULES AND REGULATIONS, SERIES 8 Certification and Signature of Documents § 102.116 Signature of orders. The executive secretary or the associate executive...

  8. 48 CFR 204.101 - Contracting officer's signature.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Contracting officer's signature. 204.101 Section 204.101 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... officer's signature. Follow the procedures at PGI 204.101 for signature of contract documents. [71 FR 9268...

  9. 32 CFR 842.6 - Signature on the claim form.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Signature on the claim form. 842.6 Section 842.6... ADMINISTRATIVE CLAIMS General Information § 842.6 Signature on the claim form. The claimant or authorized agent... authorized agent signing for a claimant shows, after the signature, the title or capacity and attaches...

  10. 38 CFR 18b.21 - Signature of documents.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Signature of documents. 18b.21 Section 18b.21 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Documents § 18b.21 Signature of documents. The signature of a party, authorized officer, employee, or...

  11. 37 CFR 2.74 - Form and signature of amendment.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Form and signature of... signature of amendment. (a) Form of Amendment. Amendments should be set forth clearly and completely... record. (b) Signature. A request for amendment of an application must be signed by the applicant, someone...

  12. 21 CFR 11.200 - Electronic signature components and controls.

    Science.gov (United States)

    2010-04-01

    ... signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1) Employ at least two distinct identification components such as an identification code and password. (i... signatures based upon biometrics shall be designed to ensure that they cannot be used by anyone other than...

  13. Signature of Europa's Ocean Density on Gravity Data

    Science.gov (United States)

    Castillo, J. C.; Rambaux, N.

    2015-12-01

    Observations by the Galileo mission at Europa and Cassini-Huygens mission at Europa, Ganymede, Callisto, Enceladus, and Titan have found deep oceans at these objects with evidence for the presence of salts. Salt compounds are the products of aqueous alteration of the rock phase under hydrothermal conditions and have been predicted theoretically for these objects per analogy with carbonaceous chondrite parent bodies. Evidence for salt enrichment comes from magnetometer measurements (Galilean satellites), direct detection in the case of Enceladus, and inversion of the gravity data obtained at Titan. While there is direct detection for the presence of chlorides in icy grains ejected from Enceladus, the chemistry of the oceans detected so far, or even their densities, remain mostly unconstrained. However the increased ocean density impacts the interpretation of the tidal Love number k2and this may introduce confusion in the inference of the icy shell thickness from that parameter. We will present estimates of k2for a range of assumptions on Europa's hydrospheric structure that build on geophysical observations obtained by the Galileo mission combined with new models of Europa's interior. These models keep track of the compositions of the hydrated core and oceanic composition in a self-consistent manner. We will also estimate the electrical conductivity corresponding to the modeled oceanic composition. Finally we will explore how combining electromagnetic, topographic, and gravity data can decouple the signatures of the shell thickness and ocean composition on these geophysical observations. Acknowledgement: This work is being carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to NASA. Government sponsorship acknowledged.

  14. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian

    2016-10-17

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  15. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian; Alam, Tanvir; Essack, Magbubah; Bajic, Vladimir B.

    2016-01-01

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  16. Dilatonic imprints on exact gravitational wave signatures

    Science.gov (United States)

    McCarthy, Fiona; KubizÅák, David; Mann, Robert B.

    2018-05-01

    By employing the moduli space approximation, we analytically calculate the gravitational wave signatures emitted upon the merger of two extremally charged dilatonic black holes. We probe several values of the dilatonic coupling constant a , and find significant departures from the Einstein-Maxwell (a =0 ) counterpart studied in [Phys. Rev. D 96, 061501 (2017), 10.1103/PhysRevD.96.061501]. For (low-energy) string theory black holes (a =1 ) there are no coalescence orbits and only a memory effect is observed, whereas for an intermediate value of the coupling (a =1 /√{3 } ) the late-time merger signature becomes exponentially suppressed, compared to the polynomial decay in the a =0 case without a dilaton. Such an imprint shows a clear difference between the case with and without a scalar field (as, for example, predicted by string theory) in black hole mergers.

  17. Chameleon dark energy models with characteristic signatures

    International Nuclear Information System (INIS)

    Gannouji, Radouane; Moraes, Bruno; Polarski, David; Mota, David F.; Winther, Hans A.; Tsujikawa, Shinji

    2010-01-01

    In chameleon dark energy models, local gravity constraints tend to rule out parameters in which observable cosmological signatures can be found. We study viable chameleon potentials consistent with a number of recent observational and experimental bounds. A novel chameleon field potential, motivated by f(R) gravity, is constructed where observable cosmological signatures are present both at the background evolution and in the growth rate of the perturbations. We study the evolution of matter density perturbations on low redshifts for this potential and show that the growth index today γ 0 can have significant dispersion on scales relevant for large scale structures. The values of γ 0 can be even smaller than 0.2 with large variations of γ on very low redshifts for the model parameters constrained by local gravity tests. This gives a possibility to clearly distinguish these chameleon models from the Λ-cold-dark-matter (ΛCDM) model in future high-precision observations.

  18. Entanglement as a signature of quantum chaos.

    Science.gov (United States)

    Wang, Xiaoguang; Ghose, Shohini; Sanders, Barry C; Hu, Bambi

    2004-01-01

    We explore the dynamics of entanglement in classically chaotic systems by considering a multiqubit system that behaves collectively as a spin system obeying the dynamics of the quantum kicked top. In the classical limit, the kicked top exhibits both regular and chaotic dynamics depending on the strength of the chaoticity parameter kappa in the Hamiltonian. We show that the entanglement of the multiqubit system, considered for both the bipartite and the pairwise entanglement, yields a signature of quantum chaos. Whereas bipartite entanglement is enhanced in the chaotic region, pairwise entanglement is suppressed. Furthermore, we define a time-averaged entangling power and show that this entangling power changes markedly as kappa moves the system from being predominantly regular to being predominantly chaotic, thus sharply identifying the edge of chaos. When this entangling power is averaged over all states, it yields a signature of global chaos. The qualitative behavior of this global entangling power is similar to that of the classical Lyapunov exponent.

  19. Quark-gluon plasma: experimental signatures

    International Nuclear Information System (INIS)

    Drapier, O.

    1995-01-01

    The existence of a deconfining phase transition of nuclear matter is a clear prediction of lattice quantum chromodynamics calculations. The signatures of this quark-gluon plasma (QGP) have been searched for, since the first high energy ion beams became available at BNL and CERN in 1986, and gold and lead beams are now accelerated at 11 and 160 GeV per nucleon by the AGS and SPS. An overview of the main signatures expected in case of QGP formation is presented here. Although some recent results have been found in agreement with the predictions of the QGP scenario, no clear evidence for its formation has been observed at present. Nevertheless, new high statistics results are expected from CERN lead beams. In addition, future experiments are being prepared at RHIC and LHCC, providing an increase by two orders of magnitude of the c.m.s. energy within a few years. (author). 66 refs., 28 figs

  20. Supernova signatures of neutrino mass ordering

    Science.gov (United States)

    Scholberg, Kate

    2018-01-01

    A suite of detectors around the world is poised to measure the flavor-energy-time evolution of the ten-second burst of neutrinos from a core-collapse supernova occurring in the Milky Way or nearby. Next-generation detectors to be built in the next decade will have enhanced flavor sensitivity and statistics. Not only will the observation of this burst allow us to peer inside the dense matter of the extreme event and learn about the collapse processes and the birth of the remnant, but the neutrinos will bring information about neutrino properties themselves. This review surveys some of the physical signatures that the currently-unknown neutrino mass pattern will imprint on the observed neutrino events at Earth, emphasizing the most robust and least model-dependent signatures of mass ordering.

  1. RNA-guided transcriptional regulation

    Science.gov (United States)

    Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

    2016-02-23

    Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

  2. Transcriptional control of megakaryocyte development.

    Science.gov (United States)

    Goldfarb, A N

    2007-10-15

    Megakaryocytes are highly specialized cells that arise from a bipotent megakaryocytic-erythroid progenitor (MEP). This developmental leap requires coordinated activation of megakaryocyte-specific genes, radical changes in cell cycle properties, and active prevention of erythroid differentiation. These programs result from upregulation of megakaryocyte-selective transcription factors, downregulation of erythroid-selective transcription factors and ongoing mediation of common erythro-megakaryocytic transcription factors. Unlike most developmental programs, no single lineage-unique family of master regulators exerts executive control over the megakaryocytic plan. Rather, an assemblage of non-unique factors and signals converge to determine lineage and differentiation. In human megakaryopoiesis, hereditary disorders of platelet production have confirmed contributions from three distinct transcription factor families. Murine models have extended this repertoire to include multiple additional factors. At a mechanistic level, the means by which these non-unique factors collaborate in the establishment of a perfectly unique cell type remains a central question.

  3. On the origin of cratonic `high-mu' isotopic signatures

    Science.gov (United States)

    Reimink, J. R.; Carlson, R.; Shirey, S. B.; Pearson, D. G.; Kamber, B. S.

    2017-12-01

    Some Archean cratons (i.e. Slave, Wyoming) contain Neoarchean granitoids with initial Pb isotopic compositions indicative of derivation from sources characterized by high time-integrated U/Pb ratios (high-mu [1]). Single-stage high-m precursor source reservoir separation from the depleted mantle occurred no later than 3.9 Ga [2]. However, multi-stage separation could have occurred in the Hadean, suggesting that recycling or reworking of Eoarchean/Hadean crust played a significant role in the generation of Neoarchean granitic crust in many cratons. The Sm-Nd system is similar to the U-Pb system in that it has a short-lived parent-daughter pair (146Sm-142Nd) that is sensitive to very early differentiation events, as well as a long-lived parent-daughter pair (147Sm-143Nd) that is sensitive to differentiation throughout all of Earth history. The 103 Ma half-life of 146Sm makes it sensitive only to Sm/Nd fractionation that occurred in the Hadean, providing a useful tracker for very early differentiation events. Indeed, evidence for Neoarchean remelting of ancient crust in another craton has come from analyses of the paired Sm-Nd isotope systems from the Hudson Bay terrane of the northeastern Superior Province. These results indicate that the source of 2.7 Ga Hudson Bay terrane granitoids was Hadean mafic crust, and not Eoarchean felsic crust [3]. Here, we present new data from Neoarchean granites located in the Slave and Wyoming cratons, along with modeling of the dual paired-isotope systems of U-Pb and Sm-Nd to achieve a tighter constraint on the composition of the precursors and the timing of their melting. Combining our newly collected 142Nd data with the high-m signature of these Neoarchean rocks, we evaluate precursor source separation ages along with the source Sm/Nd and U/Pb compositions. In the simplest end-member scenarios, use of the 142Nd system allows us to test whether the cratonic high-mu signature was created by melting of Hadean mafic crust or Eoarchean

  4. Cryptographic key generation using handwritten signature

    OpenAIRE

    Freire, Manuel R.; Fiérrez, Julián; Ortega-García, Javier

    2006-01-01

    M. Freire-Santos ; J. Fierrez-Aguilar ; J. Ortega-Garcia; "Cryptographic key generation using handwritten signature", Biometric Technology for Human Identification III, Proc. SPIE 6202 (April 17, 2006); doi:10.1117/12.665875. Copyright 2006 Society of Photo‑Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of...

  5. Limits and signatures of relativistic spaceflight

    Science.gov (United States)

    Yurtsever, Ulvi; Wilkinson, Steven

    2018-01-01

    While special relativity imposes an absolute speed limit at the speed of light, our Universe is not empty Minkowski spacetime. The constituents that fill the interstellar/intergalactic vacuum, including the cosmic microwave background photons, impose a lower speed limit on any object travelling at relativistic velocities. Scattering of cosmic microwave photons from an ultra-relativistic object may create radiation with a characteristic signature allowing the detection of such objects at large distances.

  6. Signatures of quark-gluon plasma production

    International Nuclear Information System (INIS)

    Gyulassy, M.

    1985-01-01

    A critical analysis of a variety of proposed signatures for quark-gluon formation in ultrarelativistic nuclear collisions is given. The authors emphasize that longitudinal growth rather than the nuclear radius controls the time scales for expansion. The author pointed out the qualitative difference of the evolution of the plasma produced in the stopping regime E approx. 10 GeV/nucleon and the scaling regime E > 1 TeV/nucleon. This difference reflects itself in the the rmal profile function

  7. Selection signatures in worldwide sheep populations.

    OpenAIRE

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

    2014-01-01

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

  8. Selection Signatures in Worldwide Sheep Populations

    OpenAIRE

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

    2014-01-01

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

  9. ALPs effective field theory and collider signatures

    DEFF Research Database (Denmark)

    Brivio, I.; Gavela, M. B.; Merlo, L.

    2017-01-01

    We study the leading effective interactions between the Standard Model fields and a generic singlet CP-odd (pseudo-) Goldstone boson. Two possible frameworks for electroweak symmetry breaking are considered: linear and non-linear. For the latter case, the basis of leading effective operators is d...... final states are most promising signals expected in both frameworks. In addition, non-standard Higgs decays and mono-Higgs signatures are especially prominent and expected to be dominant in non-linear realisations....

  10. A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

    Science.gov (United States)

    Litichevskiy, Lev; Peckner, Ryan; Abelin, Jennifer G; Asiedu, Jacob K; Creech, Amanda L; Davis, John F; Davison, Desiree; Dunning, Caitlin M; Egertson, Jarrett D; Egri, Shawn; Gould, Joshua; Ko, Tak; Johnson, Sarah A; Lahr, David L; Lam, Daniel; Liu, Zihan; Lyons, Nicholas J; Lu, Xiaodong; MacLean, Brendan X; Mungenast, Alison E; Officer, Adam; Natoli, Ted E; Papanastasiou, Malvina; Patel, Jinal; Sharma, Vagisha; Toder, Courtney; Tubelli, Andrew A; Young, Jennie Z; Carr, Steven A; Golub, Todd R; Subramanian, Aravind; MacCoss, Michael J; Tsai, Li-Huei; Jaffe, Jacob D

    2018-04-25

    Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP). A majority of these drugs elicited reproducible signatures, but notable cell line- and assay-specific differences were observed. Using the "connectivity" framework, we compared signatures across cell types and integrated data across assays, including a transcriptional assay (L1000). Consistent connectivity among cell types revealed cellular responses that transcended lineage, and consistent connectivity among assays revealed unexpected associations between drugs. We further leveraged the resource against public data to formulate hypotheses for treatment of multiple myeloma and acute lymphocytic leukemia. This resource is publicly available at https://clue.io/proteomics. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  11. Staggering in signature partners of A∼190 mass region of superdeformed rotational bands

    International Nuclear Information System (INIS)

    Uma, V.S.; Goel, Alpana; Yadav, Archana

    2014-01-01

    This paper discuss about ΔI=1 signature splitting in signature partner pairs of A∼190 mass region. Around twenty signature partner pairs (usually called as two bands, each with a fixed signature) have been reported in this mass region. For these signature pairs, band head moment of inertia (J 0 ) and intrinsic structure of each pair of signature partners have been found as almost identical. Also, these signature partner pairs showed large amplitude signature splitting. As each of the two signature partner forms a regular spin sequence and signature bands are not equivalent in terms of energies. This difference in energies results in signature splitting

  12. CoverageAnalyzer (CAn: A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

    Directory of Open Access Journals (Sweden)

    Ralf Hauenschild

    2016-11-01

    Full Text Available Combination of reverse transcription (RT and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures of modified ribonucleotides relying on both sequence-dependent mismatch patterns and reverse transcription arrests. Common alignment viewers lack specialized functionality, such as filtering, tailored visualization, image export and differential analysis. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer (CAn was developed in response to the demand for a powerful inspection tool. It is freely available for all three main operating systems. With SAM file format as standard input, CAn is an intuitive and user-friendly tool that is generally applicable to the large community of biomedical users, starting from simple visualization of RNA sequencing (RNA-Seq data, up to sophisticated modification analysis with significance-based modification candidate calling.

  13. On signature change in p-adic space-times

    International Nuclear Information System (INIS)

    Dragovic, B.G.

    1991-01-01

    Change of signature by linear coordinate transformations in p-adic space-times is considered. In this paper it is shown that there exists arbitrary change of trivial signature in Q p n for all n ≥ 1 if p ≡ 1 (mod 4). In other cases it is possible to change only even number of the signs of the signature. The authors suggest new concept of signature with respect to distinct quadratic extensions, of Q p . If space-time dimension is restricted to four there is no signature change

  14. A Digital Signature Scheme Based on MST3 Cryptosystems

    Directory of Open Access Journals (Sweden)

    Haibo Hong

    2014-01-01

    Full Text Available As special types of factorization of finite groups, logarithmic signature and cover have been used as the main components of cryptographic keys for secret key cryptosystems such as PGM and public key cryptosystems like MST1, MST2, and MST3. Recently, Svaba et. al proposed a revised MST3 encryption scheme with greater security. Meanwhile, they put forward an idea of constructing signature schemes on the basis of logarithmic signatures and random covers. In this paper, we firstly design a secure digital signature scheme based on logarithmic signatures and random covers. In order to complete the task, we devise a new encryption scheme based on MST3 cryptosystems.

  15. New particles and their experimental signatures

    International Nuclear Information System (INIS)

    Ellis, J.; Gelmini, G.; Kowalski, H.

    1984-08-01

    This report summarizes work done by our theoretical working group on exotic particles before, during and since the Lausanne meeting. We discuss the motivations, rates and experimental signatures for new physics and new particles in the 1 TeV mass range. Section 2 reviews some of the motivations for expecting new physics in this range. Of particular interest is the physics of gauge symmetry breaking. In section 3 we discuss the rates and experimental signatures of new particles predicted by theoretical models of gauge symmetry breaking, notably the Higgs boson supersymmetry and technicolour. Among the signatures we discuss are multiple Wsup(+-) and/or Z 0 events (for the Higgs), missing transverse energy (for supersymmetry) and multiple anti tt events (for the Higgs and technicolour). We provide many examples of final state differential distributions in rapidity and Psub(T), particularly for Higgses and for supersymmetry. We also analyse some physics backgrounds to the new particle production processes which interest us. Examples include W + W - , Z 0 Z 0 , W(anti tt) and (anti tt) production as backgrounds to Higgs production. However, we do not consider in detail non-physics backgrounds such as the jet fluctuation background to missing energy signals for supersymmetry production. Section 4 summarizes our preliminary conclusions on the observability at a high energy hadron collider of the new particles studied in this report. (orig./HSI)

  16. Mirage: a visible signature evaluation tool

    Science.gov (United States)

    Culpepper, Joanne B.; Meehan, Alaster J.; Shao, Q. T.; Richards, Noel

    2017-10-01

    This paper presents the Mirage visible signature evaluation tool, designed to provide a visible signature evaluation capability that will appropriately reflect the effect of scene content on the detectability of targets, providing a capability to assess visible signatures in the context of the environment. Mirage is based on a parametric evaluation of input images, assessing the value of a range of image metrics and combining them using the boosted decision tree machine learning method to produce target detectability estimates. It has been developed using experimental data from photosimulation experiments, where human observers search for vehicle targets in a variety of digital images. The images used for tool development are synthetic (computer generated) images, showing vehicles in many different scenes and exhibiting a wide variation in scene content. A preliminary validation has been performed using k-fold cross validation, where 90% of the image data set was used for training and 10% of the image data set was used for testing. The results of the k-fold validation from 200 independent tests show a prediction accuracy between Mirage predictions of detection probability and observed probability of detection of r(262) = 0:63, p Pearson correlation) and a MAE = 0:21 (mean absolute error).

  17. SIGNATURES OF LONG-LIVED SPIRAL PATTERNS

    International Nuclear Information System (INIS)

    Martínez-García, Eric E.; González-Lópezlira, Rosa A.

    2013-01-01

    Azimuthal age/color gradients across spiral arms are a signature of long-lived spirals. From a sample of 19 normal (or weakly barred) spirals where we have previously found azimuthal age/color gradient candidates, 13 objects were further selected if a two-armed grand-design pattern survived in a surface density stellar mass map. Mass maps were obtained from optical and near-infrared imaging, by comparison with a Monte Carlo library of stellar population synthesis models that allowed us to obtain the mass-to-light ratio in the J band, (M/L) J , as a function of (g – i) versus (i – J) color. The selected spirals were analyzed with Fourier methods in search of other signatures of long-lived modes related to the gradients, such as the gradient divergence toward corotation, and the behavior of the phase angle of the two-armed spiral in different wavebands, as expected from theory. The results show additional signatures of long-lived spirals in at least 50% of the objects.

  18. On psychoanalytic supervision as signature pedagogy.

    Science.gov (United States)

    Watkins, C Edward

    2014-04-01

    What is signature pedagogy in psychoanalytic education? This paper examines that question, considering why psychoanalytic supervision best deserves that designation. In focusing on supervision as signature pedagogy, I accentuate its role in building psychoanalytic habits of mind, habits of hand, and habits of heart, and transforming theory and self-knowledge into practical product. Other facets of supervision as signature pedagogy addressed in this paper include its features of engagement, uncertainty, formation, and pervasiveness, as well as levels of surface, deep, and implicit structure. Epistemological, ontological, and axiological in nature, psychoanalytic supervision engages trainees in learning to do, think, and value what psychoanalytic practitioners in the field do, think, and value: It is, most fundamentally, professional preparation for competent, "good work." In this paper, effort is made to shine a light on and celebrate the pivotal role of supervision in "making" or developing budding psychoanalysts and psychoanalytic psychotherapists. Now over a century old, psychoanalytic supervision remains unparalleled in (1) connecting and integrating conceptualization and practice, (2) transforming psychoanalytic theory and self-knowledge into an informed analyzing instrument, and (3) teaching, transmitting, and perpetuating the traditions, practice, and culture of psychoanalytic treatment.

  19. Enhanced vibration diagnostics using vibration signature analysis

    International Nuclear Information System (INIS)

    Ahmed, S.; Shehzad, K.; Zahoor, Y.; Mahmood, A.; Bibi, A.

    2001-01-01

    Symptoms will appear in equipment, as well as in human beings. when 'suffering from sickness. Symptoms of abnormality in equipment are vibration, noise, deformation, temperature, pressure, electric current, crack, wearing, leakage etc. these are called modes of failure. If the mode of failure is vibration then the vibration signature analysis can be effectively used in order to diagnose the machinery problems. Much valuable information is contained within these vibration 'Spectra' or 'Signatures' but is only of use if the analyst can unlock its 'Secrets'. This paper documents a vibration problem in the motor of a centrifugal pump (Type ETA). It focuses mainly on the roll of modern vibration monitoring system in problem analysis. The problem experienced was the motor unstability and noise due to high vibration. Using enhanced vibration signature data, the problem was analyzed. which suggested that the rotor eccentricity was the cause of excessive noise and vibration in the motor. In conclusion, advanced electronic monitoring and diagnostic systems provide powerful information for machine's condition assessment and problem analysis. Appropriate interpretation and use of this information is important for accurate and effective vibration analysis. (author)

  20. Measurement-device-independent quantum digital signatures

    Science.gov (United States)

    Puthoor, Ittoop Vergheese; Amiri, Ryan; Wallden, Petros; Curty, Marcos; Andersson, Erika

    2016-08-01

    Digital signatures play an important role in software distribution, modern communication, and financial transactions, where it is important to detect forgery and tampering. Signatures are a cryptographic technique for validating the authenticity and integrity of messages, software, or digital documents. The security of currently used classical schemes relies on computational assumptions. Quantum digital signatures (QDS), on the other hand, provide information-theoretic security based on the laws of quantum physics. Recent work on QDS Amiri et al., Phys. Rev. A 93, 032325 (2016);, 10.1103/PhysRevA.93.032325 Yin, Fu, and Zeng-Bing, Phys. Rev. A 93, 032316 (2016), 10.1103/PhysRevA.93.032316 shows that such schemes do not require trusted quantum channels and are unconditionally secure against general coherent attacks. However, in practical QDS, just as in quantum key distribution (QKD), the detectors can be subjected to side-channel attacks, which can make the actual implementations insecure. Motivated by the idea of measurement-device-independent quantum key distribution (MDI-QKD), we present a measurement-device-independent QDS (MDI-QDS) scheme, which is secure against all detector side-channel attacks. Based on the rapid development of practical MDI-QKD, our MDI-QDS protocol could also be experimentally implemented, since it requires a similar experimental setup.

  1. High order statistical signatures from source-driven measurements of subcritical fissile systems

    International Nuclear Information System (INIS)

    Mattingly, J.K.

    1998-01-01

    This research focuses on the development and application of high order statistical analyses applied to measurements performed with subcritical fissile systems driven by an introduced neutron source. The signatures presented are derived from counting statistics of the introduced source and radiation detectors that observe the response of the fissile system. It is demonstrated that successively higher order counting statistics possess progressively higher sensitivity to reactivity. Consequently, these signatures are more sensitive to changes in the composition, fissile mass, and configuration of the fissile assembly. Furthermore, it is shown that these techniques are capable of distinguishing the response of the fissile system to the introduced source from its response to any internal or inherent sources. This ability combined with the enhanced sensitivity of higher order signatures indicates that these techniques will be of significant utility in a variety of applications. Potential applications include enhanced radiation signature identification of weapons components for nuclear disarmament and safeguards applications and augmented nondestructive analysis of spent nuclear fuel. In general, these techniques expand present capabilities in the analysis of subcritical measurements

  2. FATTY ACID SIGNATURES DIFFERENTIATE MARINE MACROPHYTES AT ORDINAL AND FAMILY RANKS(1).

    Science.gov (United States)

    Galloway, Aaron W E; Britton-Simmons, Kevin H; Duggins, David O; Gabrielson, Paul W; Brett, Michael T

    2012-08-01

    Primary productivity by plants and algae is the fundamental source of energy in virtually all food webs. Furthermore, photosynthetic organisms are the sole source for ω-3 and ω-6 essential fatty acids (EFA) to upper trophic levels. Because animals cannot synthesize EFA, these molecules may be useful as trophic markers for tracking sources of primary production through food webs if different primary producer groups have different EFA signatures. We tested the hypothesis that different marine macrophyte groups have distinct fatty acid (FA) signatures by conducting a phylogenetic survey of 40 marine macrophytes (seaweeds and seagrasses) representing 36 families, 21 orders, and four phyla in the San Juan Archipelago, WA, USA. We used multivariate statistics to show that FA composition differed significantly (P macrophytes confirmed that this pattern was robust on a global scale (P macrophyte taxa shows a clear relationship between macrophyte phylogeny and FA content and strongly suggests that FA signature analyses can offer a viable approach to clarifying fundamental questions about the contribution of different basal resources to food webs. Moreover, these results imply that taxa with commercially valuable EFA signatures will likely share such characteristics with other closely related taxa that have not yet been evaluated for FA content. © 2012 Phycological Society of America.

  3. Newborn Urinary Metabolic Signatures of Prematurity and Other Disorders: A Case Control Study.

    Science.gov (United States)

    Diaz, Sílvia O; Pinto, Joana; Barros, António S; Morais, Elisabete; Duarte, Daniela; Negrão, Fátima; Pita, Cristina; Almeida, Maria do Céu; Carreira, Isabel M; Spraul, Manfred; Gil, Ana M

    2016-01-04

    This work assesses the urinary metabolite signature of prematurity in newborns by nuclear magnetic resonance (NMR) spectroscopy, while establishing the role of possible confounders and signature specificity, through comparison to other disorders. Gender and delivery mode are shown to impact importantly on newborn urine composition, their analysis pointing out at specific metabolite variations requiring consideration in unmatched subject groups. Premature newborns are, however, characterized by a stronger signature of varying metabolites, suggestive of disturbances in nucleotide metabolism, lung surfactants biosynthesis and renal function, along with enhancement of tricarboxylic acid (TCA) cycle activity, fatty acids oxidation, and oxidative stress. Comparison with other abnormal conditions (respiratory depression episode, large for gestational age, malformations, jaundice and premature rupture of membranes) reveals that such signature seems to be largely specific of preterm newborns, showing that NMR metabolomics can retrieve particular disorder effects, as well as general stress effects. These results provide valuable novel information on the metabolic impact of prematurity, contributing to the better understanding of its effects on the newborn's state of health.

  4. National Capital Planning Commission Meeting Transcripts

    Data.gov (United States)

    National Capital Planning Commission — Transcripts of the monthly (with the exception of August) National Capital Planning Commission meeting transcripts are provided for research to confirm actions taken...

  5. Salt-Marsh Landscapes and the Signatures of Biogeomorphic Feedbacks

    Science.gov (United States)

    D'Alpaos, A.; Marani, M.

    2014-12-01

    Salt marshes are coastal ecosystems which play a large role in the bio-geomorphological evolution of intertidal areas. The dense stands of halophytic plants which populate salt-marsh systems largely contribute to govern their dynamics, influencing marsh hydrodynamics and sediment transport through enhanced flow resistance and settling, and direct particle capture by plant stems. In addition, plants are known to increase vertical accretion through direct organic accretion. Looking across the salt-marsh landscape can one see the signatures of feedbacks between landscape and biota? Field evidence and the results of biomorphodynamic models indeed show that the interplay between physical and biological processes generates some striking biological and morphological patterns at different scales. One such pattern, vegetation zonation, consists in a mosaic of vegetation patches, of approximately uniform composition, displaying sharp transitions in the presence of extremely small topographic gradients. Here we extend the model proposed by Marani et al. (2013) to a two-dimensional framework, furthermore including the effect of direct capture of sediment particles by plant stems. This allows us to account for the effect of the drainage density of tidal networks on the observed biogeomorphic patterns and to model the coupled evolution of marsh platforms and channel networks cutting through them. A number of different scenarios have been modelled to analyze the changes induced in bio-geomorphic patterns by plants with different characteristics, within marshes characterized by different drainage densities, or subjected to changing environmental forcing such as rates of relative sea level rise and sediment supply. Model results emphasize that zonation patterns are a signature of bio-geomorphic feedbacks with vegetation acting as a landscape constructor which feeds back on, directly alters, and contributes to shape tidal environments. In addition, model results show that

  6. The electronic identification, signature and security of information systems

    Directory of Open Access Journals (Sweden)

    Horovèák Pavel

    2002-12-01

    Full Text Available The contribution deals with the actual methods and technologies of information and communication systems security. It introduces the overview of electronic identification elements such as static password, dynamic password and single sign-on. Into this category belong also biometric and dynamic characteristics of verified person. Widespread is authentication based on identification elements ownership, such as various cards and authentication calculators. In the next part is specified a definition and characterization of electronic signature, its basic functions and certificate categories. Practical utilization of electronic signature consists of electronic signature acquirement, signature of outgoing email message, receiving of electronic signature and verification of electronic signature. The use of electronic signature is continuously growing and in connection with legislation development it exercises in all resorts.

  7. An evolutionarily conserved sexual signature in the primate brain.

    Directory of Open Access Journals (Sweden)

    Björn Reinius

    2008-06-01

    Full Text Available The question of a potential biological sexual signature in the human brain is a heavily disputed subject. In order to provide further insight into this issue, we used an evolutionary approach to identify genes with sex differences in brain expression level among primates. We reasoned that expression patterns important to uphold key male and female characteristics may be conserved during evolution. We selected cortex for our studies because this specific brain region is responsible for many higher behavioral functions. We compared gene expression profiles in the occipital cortex of male and female humans (Homo sapiens, a great ape and cynomolgus macaques (Macaca fascicularis, an old world monkey, two catarrhine species that show abundant morphological sexual dimorphism, as well as in common marmosets (Callithrix Jacchus, a new world monkey which are relatively sexually monomorphic. We identified hundreds of genes with sex-biased expression patterns in humans and macaques, while fewer than ten were differentially expressed between the sexes in marmosets. In primates, a general rule is that many of the morphological and behavioral sexual dimorphisms seen in polygamous species, such as macaques, are typically less pronounced in monogamous species such as the marmosets. Our observations suggest that this correlation may also be reflected in the extent of sex-biased gene expression in the brain. We identified 85 genes with common sex-biased expression, in both human and macaque and 2 genes, X inactivation-specific transcript (XIST and Heat shock factor binding protein 1 (HSBP1, that were consistently sex-biased in the female direction in human, macaque, and marmoset. These observations imply a conserved signature of sexual gene expression dimorphism in cortex of primates. Further, we found that the coding region of female-biased genes is more evolutionarily constrained compared to the coding region of both male-biased and non sex-biased brain

  8. Testing an aflatoxin B1 gene signature in rat archival tissues.

    Science.gov (United States)

    Merrick, B Alex; Auerbach, Scott S; Stockton, Patricia S; Foley, Julie F; Malarkey, David E; Sills, Robert C; Irwin, Richard D; Tice, Raymond R

    2012-05-21

    Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 μg of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ≤ 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and β-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced

  9. Genome-wide strategies identify downstream target genes of chick connective tissue-associated transcription factors.

    Science.gov (United States)

    Orgeur, Mickael; Martens, Marvin; Leonte, Georgeta; Nassari, Sonya; Bonnin, Marie-Ange; Börno, Stefan T; Timmermann, Bernd; Hecht, Jochen; Duprez, Delphine; Stricker, Sigmar

    2018-03-29

    Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc-finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling of chick limb micromass cultures revealed a set of common genes regulated by all five transcription factors, which we describe as a connective tissue core expression set. This common core was enriched with genes associated with axon guidance and myofibroblast signature, including fibrosis-related genes. In addition, each transcription factor regulated a specific set of signalling molecules and extracellular matrix components. This suggests a concept whereby local molecular niches can be created by the expression of specific transcription factors impinging on the specification of local microenvironments. The regulatory network established here identifies common and distinct molecular signatures of limb connective tissue subtypes, provides novel insight into the signalling pathways governing connective tissue specification, and serves as a resource for connective tissue development. © 2018. Published by The Company of Biologists Ltd.

  10. Signatures of natural selection at the FTO (fat mass and obesity associated locus in human populations.

    Directory of Open Access Journals (Sweden)

    Xuanshi Liu

    Full Text Available Polymorphisms in the first intron of FTO have been robustly replicated for associations with obesity. In the Sorbs, a Slavic population resident in Germany, the strongest effect on body mass index (BMI was found for a variant in the third intron of FTO (rs17818902. Since this may indicate population specific effects of FTO variants, we initiated studies testing FTO for signatures of selection in vertebrate species and human populations.First, we analyzed the coding region of 35 vertebrate FTO orthologs with Phylogenetic Analysis by Maximum Likelihood (PAML, ω = dN/dS to screen for signatures of selection among species. Second, we investigated human population (Europeans/CEU, Yoruba/YRI, Chinese/CHB, Japanese/JPT, Sorbs SNP data for footprints of selection using DnaSP version 4.5 and the Haplotter/PhaseII. Finally, using ConSite we compared transcription factor (TF binding sites at sequences harbouring FTO SNPs in intron three.PAML analyses revealed strong conservation in coding region of FTO (ω<1. Sliding-window results from population genetic analyses provided highly significant (p<0.001 signatures for balancing selection specifically in the third intron (e.g. Tajima's D in Sorbs = 2.77. We observed several alterations in TF binding sites, e.g. TCF3 binding site introduced by the rs17818902 minor allele.Population genetic analysis revealed signatures of balancing selection at the FTO locus with a prominent signal in intron three, a genomic region with strong association with BMI in the Sorbs. Our data support the hypothesis that genes associated with obesity may have been under evolutionary selective pressure.

  11. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Science.gov (United States)

    Amambua-Ngwa, Alfred; Tetteh, Kevin K A; Manske, Magnus; Gomez-Escobar, Natalia; Stewart, Lindsay B; Deerhake, M Elizabeth; Cheeseman, Ian H; Newbold, Christopher I; Holder, Anthony A; Knuepfer, Ellen; Janha, Omar; Jallow, Muminatou; Campino, Susana; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Conway, David J

    2012-01-01

    Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now

  12. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Directory of Open Access Journals (Sweden)

    Alfred Amambua-Ngwa

    Full Text Available Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3, and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%, indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing

  13. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype.

    Directory of Open Access Journals (Sweden)

    Roman Kosoy

    Full Text Available Egg allergy is one of the most common food allergies of childhood. There is a lack of information on the immunologic basis of egg allergy beyond the role of IgE.To use transcriptional profiling as a novel approach to uncover immunologic processes associated with different phenotypes of egg allergy.Peripheral blood mononuclear cells (PBMCs were obtained from egg-allergic children who were defined as reactive (BER or tolerant (BET to baked egg, and from food allergic controls (AC who were egg non-allergic. PBMCs were stimulated with egg white protein. Gene transcription was measured by microarray after 24 h, and cytokine secretion by multiplex assay after 5 days.The transcriptional response of PBMCs to egg protein differed between BER and BET versus AC subjects. Compared to the AC group, the BER group displayed increased expression of genes associated with allergic inflammation as well as corresponding increased secretion of IL-5, IL-9 and TNF-α. A similar pattern was observed for the BET group. Further similarities in gene expression patterns between BER and BET groups, as well as some important differences, were revealed using a novel Immune Annotation resource developed for this project. This approach identified several novel processes not previously associated with egg allergy, including positive associations with TLR4-stimulated myeloid cells and activated NK cells, and negative associations with an induced Treg signature. Further pathway analysis of differentially expressed genes comparing BER to BET subjects showed significant enrichment of IFN-α and IFN-γ response genes, as well as genes associated with virally-infected DCs.Transcriptional profiling identified several novel pathways and processes that differed when comparing the response to egg allergen in BET, BER, and AC groups. We conclude that this approach is a useful hypothesis-generating mechanism to identify novel immune processes associated with allergy and tolerance to forms

  14. The Solar-flux Third Granulation Signature

    Science.gov (United States)

    Gray, David F.; Oostra, Benjamin

    2018-01-01

    The velocity shifts of spectral lines as a function of line strength, so-called the third signature of granulation, are investigated using three published solar-flux atlases. We use flux atlases because we wish to treat the Sun as a star, against which stellar observations can be compared and judged. The atlases are critiqued and compared to the lower-resolution observations taken with the Elginfield stellar spectrograph. Third-signature plots are constructed for the 6020–6340 Å region. No dependence on excitation potential or wavelength is found over this wavelength span. The shape of the plots from the three solar atlases is essentially the same, with rms line-core velocity differences of 30–35 m s‑1. High-resolution atlas data are degraded to the level of the Elginfield spectrograph and compared to direct observations taken with that spectrograph. The line-core velocities show good agreement, with rms differences of 38 m s‑1. A new standard curve is derived and compared with the previously published one. Only small differences in shape are found, but a significant (+97 m s‑1) change in the zero point is indicated. The bisector of the Fe I 6253 line is mapped onto the third-signature plots and flux deficits are derived, which measure the granule/lane flux imbalance. The lower spectral resolution lowers the flux deficit area slightly and moves the peak of the deficit 0.3–0.5 km s‑1 toward higher velocities. These differences, while significant, are not large compared to measurement errors for stellar data.

  15. Identification of host response signatures of infection.

    Energy Technology Data Exchange (ETDEWEB)

    Branda, Steven S.; Sinha, Anupama; Bent, Zachary

    2013-02-01

    Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to the pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for

  16. Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.

    Directory of Open Access Journals (Sweden)

    Matthew R Mason

    Full Text Available Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

  17. Correlations Between Surficial Sulfur and a REE Crustal Assimilation Signature in Martian Shergottites

    Science.gov (United States)

    Jones, J. H.; Franz, H. B.

    2015-01-01

    Compared to terrestrial basalts, the Martian shergottite meteorites have an extraordinary range of Sr and Nd isotopic signatures. In addition, the S isotopic compositions of many shergottites show evidence of interaction with the Martian surface/ atmosphere through mass-independent isotopic fractionations (MIF, positive, non-zero delta(exp 33)S) that must have originated in the Martian atmosphere, yet ultimately were incorporated into igneous sulfides (AVS - acid-volatile sulfur). These positive delta(exp 33)S signatures are thought to be governed by solar UV photochemical processes. And to the extent that S is bound to Mars and not lost to space from the upper atmosphere, a positive delta(exp 33)S reservoir must be mass balanced by a complementary negative reservoir.

  18. Detection of the spectroscopic signatures of explosives and their degradation products

    Science.gov (United States)

    Florian, Vivian; Cabanzo, Andrea; Baez, Bibiana; Correa, Sandra; Irrazabal, Maik; Briano, Julio G.; Castro, Miguel E.; Hernandez-Rivera, Samuel P.

    2005-06-01

    Detection and removal of antipersonnel and antitank landmines is a great challenge and a worldwide enviromental and humanitarian problem. Sensors tuned on the spectroscopic signature of the chemicals released from mines are a potential solution. Enviromental factors (temperature, relative humidity, rainfall precipitation, wind, sun irradiation, pressure, etc.) as well as soil characteristics (water content, compaction, porosity, chemical composition, particle size distribution, topography, vegetation, etc), have a direct impact on the fate and transport of the chemicals released from landmines. Chemicals such as TNT, DNT and their degradation products, are semi-volatile, and somewhat soluble in water. Also, they may adsorb strongly to soil particles, and are susceptible to degradation by microorganisms, light, or chemical agents. Here we show an experimental procedure to quantify the effect of the above variables on the spectroscopic signature. A number of soil tanks under controlled conditions are used to study the effect of temperature, water content, relative humidity and light radiation.

  19. Signatures for quark clustering in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Carlson, C.E. [College of William and Mary, Williamsburg, VA (United States); Lassila, K.E. [Iowa State Univ., Ames, IA (United States)

    1994-04-01

    As a signature for the presence of quark clusters in nuclei, the authors suggest studying backward protons produced by electron scattering off deuterons and suggest a ratio that cancels out much of the detailed properties of deuterons or 6-quark clusters. The test may be viewed as a test that the short range part of the deuteron is still a 2-nucleon system. They make estimates to show how it fails in characteristic and significant ways if the two nucleons at short range coalesce into a kneaded 6-quark cluster.

  20. Study on the signatures for a magazine

    International Nuclear Information System (INIS)

    Chai, Jan Bom; Kim, Tae Hwan; Park, Sung Keun

    2004-01-01

    In this paper, diagnostic algorithms are developed to be utilized to monitor the condition of and to diagnose defects in the magazine of a fuelling machine installed in CANDU plants. The magazine plays a role in storing fuels, plugs and tools. Since the magazine operates in the high radiation area, it is impossible to give direct access to it for measuring the signals. Therefore, inlet and outlet pressures of a hydraulic motor, which can be acquired remotely, were selected as the measuring variables. The measured signals are further processed to extract the diagnostic signatures. They were examined and validated in the various experiments with the magazine mock-up

  1. Signatures for quark clustering in nuclei

    International Nuclear Information System (INIS)

    Carlson, C.E.; Lassila, K.E.

    1994-01-01

    As a signature for the presence of quark clusters in nuclei, the authors suggest studying backward protons produced by electron scattering off deuterons and suggest a ratio that cancels out much of the detailed properties of deuterons or 6-quark clusters. The test may be viewed as a test that the short range part of the deuteron is still a 2-nucleon system. They make estimates to show how it fails in characteristic and significant ways if the two nucleons at short range coalesce into a kneaded 6-quark cluster

  2. Ulysses and the Signature of Things

    OpenAIRE

    Dukes, Hunter

    2017-01-01

    James Joyce’s depiction of autographic signatures resembles the “doctrine of signatures” — a pre-modern system of correspondence between medicinal plants and parts of the body. Certain aspects of this episteme reappear in the late nineteenth century. This recurrence is due, in large part, to developments in the technology of writing that threaten what Friedrich Kittler calls the “surrogate sensuality of handwriting.” Reading the “Nausicaa” episode of Ulysses against fin-de-siècle ideas about ...

  3. Characterizing Resident Space Object Earthshine Signature Variability

    Science.gov (United States)

    Van Cor, Jared D.

    There are three major sources of illumination on objects in the near Earth space environment: Sunshine, Moonshine, and Earthshine. For objects in this environment (satellites, orbital debris, etc.) known as Resident Space Objects (RSOs), the sun and the moon have consistently small illuminating solid angles and can be treated as point sources; this makes their incident illumination easily modeled. The Earth on the other hand has a large illuminating solid angle, is heterogeneous, and is in a constant state of change. The objective of this thesis was to characterize the impact and variability of observed RSO Earthshine on apparent magnitude signatures in the visible optical spectral region. A key component of this research was creating Earth object models incorporating the reflectance properties of the Earth. Two Earth objects were created: a homogeneous diffuse Earth object and a time sensitive heterogeneous Earth object. The homogeneous diffuse Earth object has a reflectance equal to the average global albedo, a standard model used when modeling Earthshine. The time sensitive heterogeneous Earth object was created with two material maps representative of the dynamic reflectance of the surface of the earth, and a shell representative of the atmosphere. NASA's Moderate-resolution Imaging Spectroradiometer (MODIS) Earth observing satellite product libraries, MCD43C1 global surface BRDF map and MOD06 global fractional cloud map, were utilized to create the material maps, and a hybridized version of the Empirical Line Method (ELM) was used to create the atmosphere. This dynamic Earth object was validated by comparing simulated color imagery of the Earth to that taken by: NASAs Earth Polychromatic Imaging Camera (EPIC) located on the Deep Space Climate Observatory (DSCOVR), and by MODIS located on the Terra satellite. The time sensitive heterogeneous Earth object deviated from MODIS imagery by a spectral radiance root mean square error (RMSE) of +/-14.86 [watts/m. 2sr

  4. Unveiling clusters of RNA transcript pairs associated with markers of Alzheimer's disease progression.

    Directory of Open Access Journals (Sweden)

    Ahmed Shamsul Arefin

    Full Text Available BACKGROUND: One primary goal of transcriptomic studies is identifying gene expression patterns correlating with disease progression. This is usually achieved by considering transcripts that independently pass an arbitrary threshold (e.g. p<0.05. In diseases involving severe perturbations of multiple molecular systems, such as Alzheimer's disease (AD, this univariate approach often results in a large list of seemingly unrelated transcripts. We utilised a powerful multivariate clustering approach to identify clusters of RNA biomarkers strongly associated with markers of AD progression. We discuss the value of considering pairs of transcripts which, in contrast to individual transcripts, helps avoid natural human transcriptome variation that can overshadow disease-related changes. METHODOLOGY/PRINCIPAL FINDINGS: We re-analysed a dataset of hippocampal transcript levels in nine controls and 22 patients with varying degrees of AD. A large-scale clustering approach determined groups of transcript probe sets that correlate strongly with measures of AD progression, including both clinical and neuropathological measures and quantifiers of the characteristic transcriptome shift from control to severe AD. This enabled identification of restricted groups of highly correlated probe sets from an initial list of 1,372 previously published by our group. We repeated this analysis on an expanded dataset that included all pair-wise combinations of the 1,372 probe sets. As clustering of this massive dataset is unfeasible using standard computational tools, we adapted and re-implemented a clustering algorithm that uses external memory algorithmic approach. This identified various pairs that strongly correlated with markers of AD progression and highlighted important biological pathways potentially involved in AD pathogenesis. CONCLUSIONS/SIGNIFICANCE: Our analyses demonstrate that, although there exists a relatively large molecular signature of AD progression, only

  5. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: the basis of nerve-dependent limb regeneration in salamanders. Innervated (NR and denervated (DL forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14 days of regeneration. Results Considerable similarity was observed between NR and DL transcriptional programs at 5 and 14 days post amputation (dpa. Genes with extracellular functions that are critical to wound healing were upregulated while muscle-specific genes were downregulated. Thus, many processes that are regulated during early limb regeneration do not depend upon nerve-derived factors. The majority of the transcriptional differences between NR and DL limbs were correlated with blastema formation; cell numbers increased in NR limbs after 5 dpa and this yielded distinct transcriptional signatures of cell proliferation in NR limbs at 14 dpa. These transcriptional signatures were not observed in DL limbs. Instead, gene expression changes within DL limbs suggest more diverse and protracted wound-healing responses. 454 cDNA sequencing complemented the microarray analysis by providing deeper sampling of transcriptional programs and associated biological processes. Assembly of new 454 cDNA sequences with existing expressed sequence tag (EST contigs from the Ambystoma EST database more than doubled (3935 to 9411 the number of non-redundant human-A. mexicanum orthologous sequences. Conclusion Many new candidate gene sequences were discovered for the first time and these will greatly enable future studies of wound healing, epigenetics, genome stability, and nerve-dependent blastema formation and outgrowth using the axolotl model.

  6. Different Blood Cell-Derived Transcriptome Signatures in Cows Exposed to Vaccination Pre- or Postpartum

    Science.gov (United States)

    Weikard, Rosemarie; Demasius, Wiebke; Hadlich, Frieder; Kühn, Christa

    2015-01-01

    Periparturient cows have been found to reveal immunosuppression, frequently associated with increased susceptibility to uterine and mammary infections. To improve understanding of the causes and molecular regulatory mechanisms accounting for this phenomenon around calving, we examined the effect of an antigen challenge on gene expression modulation on cows prior to (BC) or after calving (AC) using whole transcriptome sequencing (RNAseq). The transcriptome analysis of the cows’ blood identified a substantially higher number of loci affected in BC cows (2,235) in response to vaccination compared to AC cows (208) and revealed a divergent transcriptional profile specific for each group. In BC cows, a variety of loci involved in immune defense and cellular signaling processes were transcriptionally activated, whereas protein biosynthesis and posttranslational processes were tremendously impaired in response to vaccination. Furthermore, energy metabolism in the blood cells of BC cows was shifted from oxidative phosphorylation to the glycolytic system. In AC cows, the number and variety of regulated pathways involved in immunomodulation and maintenance of immnunocompetence are considerably lower after vaccination, and upregulation of arginine degradation was suggested as an immunosuppressive mechanism. Elevated transcript levels of erythrocyte-specific genes involved in gas exchange processes were a specific transcriptional signature in AC cows pointing to hematopoiesis activation. The divergent and substantially lower magnitude of transcriptional modulation in response to vaccination in AC cows provides evidence for a suppressed immune capacity of early lactating cows on the molecular level and demonstrates that an efficient immune response of cows is related to their physiological and metabolic status. PMID:26317664

  7. Transcriptional control in the segmentation gene network of Drosophila.

    Directory of Open Access Journals (Sweden)

    Mark D Schroeder

    2004-09-01

    Full Text Available The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross- regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a

  8. Signatures of unstable semiclassical trajectories in tunneling

    International Nuclear Information System (INIS)

    Levkov, D G; Panin, A G; Sibiryakov, S M

    2009-01-01

    It was found recently that processes of multidimensional tunneling are generally described at high energies by unstable semiclassical trajectories. We study two observational signatures related to the instability of trajectories. First, we find an additional power-law dependence of the tunneling probability on the semiclassical parameter as compared to the standard case of potential tunneling. The second signature is a substantial widening of the probability distribution over final-state quantum numbers. These effects are studied using a modified semiclassical technique which incorporates stabilization of the tunneling trajectories. The technique is derived from first principles. We obtain expressions for the inclusive and exclusive tunneling probabilities in the case of unstable semiclassical trajectories. We also investigate the 'phase transition' between the cases of stable and unstable trajectories across certain 'critical' values of energy. Finally, we derive the relation between the semiclassical probabilities of tunneling from the low-lying and highly excited initial states. This puts on firm ground a conjecture made previously in the semiclassical description of collision-induced tunneling in field theory

  9. Theoretical Characterizaiton of Visual Signatures (Muzzle Flash)

    Science.gov (United States)

    Kashinski, D. O.; Scales, A. N.; Vanderley, D. L.; Chase, G. M.; di Nallo, O. E.; Byrd, E. F. C.

    2014-05-01

    We are investigating the accuracy of theoretical models used to predict the visible, ultraviolet and infrared spectra of product materials ejected from the muzzle of currently fielded systems. Recent advances in solid propellants has made the management of muzzle signature (flash) a principle issue in weapons development across the calibers. A priori prediction of the electromagnetic spectra of formulations will allow researchers to tailor blends that yield desired signatures and determine spectrographic detection ranges. We are currently employing quantum chemistry methods at various levels of sophistication to optimize molecular geometries, compute vibrational frequencies, and determine the optical spectra of specific gas-phase molecules and radicals of interest. Electronic excitations are being computed using Time Dependent Density Functional Theory (TD-DFT). A comparison of computational results to experimental values found in the literature is used to assess the affect of basis set and functional choice on calculation accuracy. The current status of this work will be presented at the conference. Work supported by the ARL, and USMA.

  10. Signature inversion in doubly odd 124La

    International Nuclear Information System (INIS)

    Chantler, H.J.; Paul, E.S.; Boston, A.J.; Choy, P.T.W.; Nolan, P.J.; Carpenter, M.P.; Davids, C.N.; Seweryniak, D.; Charity, R.; Devlin, M.; Sarantites, D.G.; Chiara, C.J.; Fossan, D.B.; Koike, T.; LaFosse, D.R.; Starosta, K.; Fletcher, A.M.; Smith, J.F.; Jenkins, D.G.; Kelsall, N.S.

    2002-01-01

    High-spin states have been studied in neutron-deficient 57 124 La 67 , populated through the 64 Zn( 64 Zn,3pn) reaction at 260 MeV. The Gammasphere γ-ray spectrometer has been used in conjunction with the Microball charged-particle detector, the Neutron Shell, and the Argonne Fragment Mass Analyzer, in order to select evaporation residues of interest. The known band structures have been extended and new bands found. Most of the bands are linked together, allowing more consistent spin and parity assignments. Comparison of band properties to cranking calculations has allowed configuration assignments to be made and includes the first identification of the g 9/2 proton-hole in an odd-odd lanthanum isotope. Two bands have been assigned a πh 11/2 xνh 11/2 structure; the yrast one exhibits a signature inversion in its level energies below I=18.5(ℎ/2π), while the excited one exhibits a signature inversion above I=18.5(ℎ/2π)

  11. Persistence of social signatures in human communication.

    Science.gov (United States)

    Saramäki, Jari; Leicht, E A; López, Eduardo; Roberts, Sam G B; Reed-Tsochas, Felix; Dunbar, Robin I M

    2014-01-21

    The social network maintained by a focal individual, or ego, is intrinsically dynamic and typically exhibits some turnover in membership over time as personal circumstances change. However, the consequences of such changes on the distribution of an ego's network ties are not well understood. Here we use a unique 18-mo dataset that combines mobile phone calls and survey data to track changes in the ego networks and communication patterns of students making the transition from school to university or work. Our analysis reveals that individuals display a distinctive and robust social signature, captured by how interactions are distributed across different alters. Notably, for a given ego, these social signatures tend to persist over time, despite considerable turnover in the identity of alters in the ego network. Thus, as new network members are added, some old network members either are replaced or receive fewer calls, preserving the overall distribution of calls across network members. This is likely to reflect the consequences of finite resources such as the time available for communication, the cognitive and emotional effort required to sustain close relationships, and the ability to make emotional investments.

  12. Monotop signature from a fermionic top partner

    Science.gov (United States)

    Gonçalves, Dorival; Kong, Kyoungchul; Sakurai, Kazuki; Takeuchi, Michihisa

    2018-01-01

    We investigate monotop signatures arising from phenomenological models of fermionic top partners, which are degenerate in mass and decay into a bosonic dark matter candidate, either spin 0 or spin 1. Such a model provides a monotop signature as a smoking gun, while conventional searches with t t ¯ + missing transverse momentum are limited. Two such scenarios, (i) a phenomenological third generation extradimensional model with excited top and electroweak sectors, and (ii) a model where only a top partner and a dark matter particle are added to the standard model, are studied in the degenerate mass regime. We find that in the case of extra dimension a number of different processes give rise to effectively the same monotop final state, and a great gain can be obtained in the sensitivity for this channel. We show that the monotop search can explore top-partner masses up to 630 and 300 GeV for the third generation extradimensional model and the minimal fermionic top-partner model, respectively, at the high luminosity LHC.

  13. Automated defect spatial signature analysis for semiconductor manufacturing process

    Science.gov (United States)

    Tobin, Jr., Kenneth W.; Gleason, Shaun S.; Karnowski, Thomas P.; Sari-Sarraf, Hamed

    1999-01-01

    An apparatus and method for performing automated defect spatial signature alysis on a data set representing defect coordinates and wafer processing information includes categorizing data from the data set into a plurality of high level categories, classifying the categorized data contained in each high level category into user-labeled signature events, and correlating the categorized, classified signature events to a present or incipient anomalous process condition.

  14. Provably Secure and Subliminal-Free Variant of Schnorr Signature

    OpenAIRE

    Zhang , Yinghui; Li , Hui; Li , Xiaoqing; Zhu , Hui

    2013-01-01

    Part 2: Asian Conference on Availability, Reliability and Security (AsiaARES); International audience; Subliminal channels present a severe challenge to information security. Currently, subliminal channels still exist in Schnorr signature. In this paper, we propose a subliminal-free variant of Schnorr signature. In the proposed scheme, an honest-but-curious warden is introduced to help the signer to generate a signature on a given message, but it is disallowed to sign messages independently. ...

  15. Invariance Signatures: Characterizing contours by their departures from invariance

    OpenAIRE

    Squire, David; Caelli, Terry M.

    1997-01-01

    In this paper, a new invariant feature of two-dimensional contours is reported: the Invariance Signature. The Invariance Signature is a measure of the degree to which a contour is invariant under a variety of transformations, derived from the theory of Lie transformation groups. It is shown that the Invariance Signature is itself invariant under shift, rotation and scaling of the contour. Since it is derived from local properties of the contour, it is well-suited to a neural network implement...

  16. Analysis of Non-contact Acousto Thermal Signature Data (Postprint)

    Science.gov (United States)

    2016-02-01

    AFRL-RX-WP-JA-2016-0321 ANALYSIS OF NON-CONTACT ACOUSTO-THERMAL SIGNATURE DATA (POSTPRINT) Amanda K. Criner AFRL/RX...October 2014 – 16 September 2015 4. TITLE AND SUBTITLE ANALYSIS OF NON-CONTACT ACOUSTO-THERMAL SIGNATURE DATA (POSTPRINT) 5a. CONTRACT NUMBER...words) The non-contact acousto-thermal signature (NCATS) is a nondestructive evaluation technique with potential to detect fatigue in materials such as

  17. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.

    Science.gov (United States)

    Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, Avi

    2018-05-25

    While gene expression data at the mRNA level can be globally and accurately measured, profiling the activity of cell signaling pathways is currently much more difficult. eXpression2Kinases (X2K) computationally predicts involvement of upstream cell signaling pathways, given a signature of differentially expressed genes. X2K first computes enrichment for transcription factors likely to regulate the expression of the differentially expressed genes. The next step of X2K connects these enriched transcription factors through known protein-protein interactions (PPIs) to construct a subnetwork. The final step performs kinase enrichment analysis on the members of the subnetwork. X2K Web is a new implementation of the original eXpression2Kinases algorithm with important enhancements. X2K Web includes many new transcription factor and kinase libraries, and PPI networks. For demonstration, thousands of gene expression signatures induced by kinase inhibitors, applied to six breast cancer cell lines, are provided for fetching directly into X2K Web. The results are displayed as interactive downloadable vector graphic network images and bar graphs. Benchmarking various settings via random permutations enabled the identification of an optimal set of parameters to be used as the default settings in X2K Web. X2K Web is freely available from http://X2K.cloud.

  18. Chemical signatures of planets: beyond solar-twins

    Science.gov (United States)

    Ramírez, I.; Meléndez, J.; Asplund, M.

    2014-01-01

    Context. Elemental abundance studies of solar twin stars suggest that the solar chemical composition contains signatures of the formation of terrestrial planets in the solar system, namely small but significant depletions of the refractory elements. Aims: To test whether these chemical signatures of planets are real, we study stars which, compared to solar twins, have less massive convective envelopes (therefore increasing the amplitude of the predicted effect) or are, arguably, more likely to host planets (thus increasing the frequency of signature detections). Methods: We measure relative atmospheric parameters and elemental abundances of two groups of stars: a "warm" late-F type dwarf sample (52 stars), and a sample of "metal-rich" solar analogs (59 stars). The strict differential approach that we adopt allows us to determine with high precision (errors ~0.01 dex) the degree of refractory element depletion in our stars independently of Galactic chemical evolution. By examining relative abundance ratio versus condensation temperature plots we are able to identify stars with "pristine" composition in each sample and to determine the degree of refractory-element depletion for the rest of our stars. We calculate what mixture of Earth-like and meteorite-like material corresponds to these depletions. Results: We detect refractory-element depletions with amplitudes up to about 0.15 dex. The distribution of depletion amplitudes for stars known to host gas giant planets is not different from that of the rest of stars. The maximum amplitude of depletion increases with effective temperature from 5650 K to 5950 K, while it appears to be constant for warmer stars (up to 6300 K). The depletions observed in solar twin stars have a maximum amplitude that is very similar to that seen here for both of our samples. Conclusions: Gas giant planet formation alone cannot explain the observed distributions of refractory-element depletions, leaving the formation of rocky material as a

  19. A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus).

    Science.gov (United States)

    Kennerly, Erin; Ballmann, Anne; Martin, Stanton; Wolfinger, Russ; Gregory, Simon; Stoskopf, Michael; Gibson, Greg

    2008-06-01

    The stresses that animals experience as a result of modification of their ecological circumstances induce physiological changes that leave a signature in profiles of gene expression. We illustrate this concept in a comparison of free range and confined North American red wolves (Canis rufus). Transcription profiling of peripheral blood samples from 13 red wolf individuals in the Alligator River region of North Carolina revealed a strong signal of differentiation. Four hundred eighty-two out of 2980 transcripts detected on Illumina HumanRef8 oligonucleotide bead arrays were found to differentiate free range and confined wolves at a false discovery rate of 12.8% and P stress responses in confined animals. Consequently, characterization of differential transcript abundance in an accessible tissue such as peripheral blood identifies biomarkers that could be useful in animal management practices and for evaluating the impact of habitat changes on population health, particularly as attention turns to the impact of climate change on physiology and in turn species distributions.

  20. Transcriptional regulation of hepatic lipogenesis.

    Science.gov (United States)

    Wang, Yuhui; Viscarra, Jose; Kim, Sun-Joong; Sul, Hei Sook

    2015-11-01

    Fatty acid and fat synthesis in the liver is a highly regulated metabolic pathway that is important for very low-density lipoprotein (VLDL) production and thus energy distribution to other tissues. Having common features at their promoter regions, lipogenic genes are coordinately regulated at the transcriptional level. Transcription factors, such as upstream stimulatory factors (USFs), sterol regulatory element-binding protein 1C (SREBP1C), liver X receptors (LXRs) and carbohydrate-responsive element-binding protein (ChREBP) have crucial roles in this process. Recently, insights have been gained into the signalling pathways that regulate these transcription factors. After feeding, high blood glucose and insulin levels activate lipogenic genes through several pathways, including the DNA-dependent protein kinase (DNA-PK), atypical protein kinase C (aPKC) and AKT-mTOR pathways. These pathways control the post-translational modifications of transcription factors and co-regulators, such as phosphorylation, acetylation or ubiquitylation, that affect their function, stability and/or localization. Dysregulation of lipogenesis can contribute to hepatosteatosis, which is associated with obesity and insulin resistance.

  1. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  2. Transcription factor-based biosensor

    Science.gov (United States)

    Dietrich, Jeffrey A; Keasling, Jay D

    2013-10-08

    The present invention provides for a system comprising a BmoR transcription factor, a .sigma..sup.54-RNA polymerase, and a pBMO promoter operatively linked to a reporter gene, wherein the pBMO promoter is capable of expression of the reporter gene with an activated form of the BmoR and the .sigma..sup.54-RNA polymerase.

  3. General Conversion for Obtaining Strongly Existentially Unforgeable Signatures

    Science.gov (United States)

    Teranishi, Isamu; Oyama, Takuro; Ogata, Wakaha

    We say that a signature scheme is strongly existentially unforgeable (SEU) if no adversary, given message/signature pairs adaptively, can generate a signature on a new message or a new signature on a previously signed message. We propose a general and efficient conversion in the standard model that transforms a secure signature scheme to SEU signature scheme. In order to construct that conversion, we use a chameleon commitment scheme. Here a chameleon commitment scheme is a variant of commitment scheme such that one can change the committed value after publishing the commitment if one knows the secret key. We define the chosen message security notion for the chameleon commitment scheme, and show that the signature scheme transformed by our proposed conversion satisfies the SEU property if the chameleon commitment scheme is chosen message secure. By modifying the proposed conversion, we also give a general and efficient conversion in the random oracle model, that transforms a secure signature scheme into a SEU signature scheme. This second conversion also uses a chameleon commitment scheme but only requires the key only attack security for it.

  4. Enhanced arbitrated quantum signature scheme using Bell states

    International Nuclear Information System (INIS)

    Wang Chao; Liu Jian-Wei; Shang Tao

    2014-01-01

    We investigate the existing arbitrated quantum signature schemes as well as their cryptanalysis, including intercept-resend attack and denial-of-service attack. By exploring the loopholes of these schemes, a malicious signatory may successfully disavow signed messages, or the receiver may actively negate the signature from the signatory without being detected. By modifying the existing schemes, we develop counter-measures to these attacks using Bell states. The newly proposed scheme puts forward the security of arbitrated quantum signature. Furthermore, several valuable topics are also presented for further research of the quantum signature scheme

  5. FIR signature verification system characterizing dynamics of handwriting features

    Science.gov (United States)

    Thumwarin, Pitak; Pernwong, Jitawat; Matsuura, Takenobu

    2013-12-01

    This paper proposes an online signature verification method based on the finite impulse response (FIR) system characterizing time-frequency characteristics of dynamic handwriting features. First, the barycenter determined from both the center point of signature and two adjacent pen-point positions in the signing process, instead of one pen-point position, is used to reduce the fluctuation of handwriting motion. In this paper, among the available dynamic handwriting features, motion pressure and area pressure are employed to investigate handwriting behavior. Thus, the stable dynamic handwriting features can be described by the relation of the time-frequency characteristics of the dynamic handwriting features. In this study, the aforesaid relation can be represented by the FIR system with the wavelet coefficients of the dynamic handwriting features as both input and output of the system. The impulse response of the FIR system is used as the individual feature for a particular signature. In short, the signature can be verified by evaluating the difference between the impulse responses of the FIR systems for a reference signature and the signature to be verified. The signature verification experiments in this paper were conducted using the SUBCORPUS MCYT-100 signature database consisting of 5,000 signatures from 100 signers. The proposed method yielded equal error rate (EER) of 3.21% on skilled forgeries.

  6. Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains.

    Science.gov (United States)

    Zanon, Carlo; Tonini, Gian Paolo

    2017-11-01

    Chromosome instability has a pivotal role among the hallmarks of cancer, but its transcriptional counterpart is rarely considered a relevant factor in cell destabilization. To examine transcription instability (TIN), we first devised a metric we named TIN index and used it to evaluate TIN on a dataset containing more than 500 neuroblastoma samples. We found that metastatic tumors from high-risk (HR) patients are characterized by significantly different TIN index values compared to low/intermediate-risk patients. Our results indicate that the TIN index is a good predictor of neuroblastoma patient's outcome, and a related TIN index gene signature (TIN-signature) is also able to predict the neuroblastoma patient's outcome with high confidence. Interestingly, we find that TIN-signature genes have a strong positional association with superenhancers in neuroblastoma tumors. Finally, we show that TIN is linked to chromatin structural domains and interferes with their integrity in HR neuroblastoma patients. This novel approach to gene expression analysis broadens the perspective of genome instability investigations to include functional aspects. © 2017 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

  7. GRAIN SIZE CONSTRAINTS ON HL TAU WITH POLARIZATION SIGNATURE

    Energy Technology Data Exchange (ETDEWEB)

    Kataoka, Akimasa; Dullemond, Cornelis P [Zentrum für Astronomie der Universität Heidelberg, Institut für Theoretische Astrophysik, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Muto, Takayuki [Division of Liberal Arts, Kogakuin University, 1-24-2 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-8677 (Japan); Momose, Munetake; Tsukagoshi, Takashi, E-mail: kataoka@uni-heidelberg.de [College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512 (Japan)

    2016-03-20

    The millimeter-wave polarization of the protoplanetary disk around HL Tau has been interpreted as the emission from elongated dust grains aligned with the magnetic field in the disk. However, the self-scattering of thermal dust emission may also explain the observed millimeter-wave polarization. In this paper, we report a modeling of the millimeter-wave polarization of the HL Tau disk with the self-polarization. Dust grains are assumed to be spherical and to have a power-law size distribution. We change the maximum grain size with a fixed dust composition in a fixed disk model to find the grain size to reproduce the observed signature. We find that the direction of the polarization vectors and the polarization degree can be explained with the self-scattering. Moreover, the polarization degree can be explained only if the maximum grain size is ∼150 μm. The obtained grain size from the polarization is different from that which has been previously expected from the spectral index of the dust opacity coefficient (a millimeter or larger) if the emission is optically thin. We discuss that porous dust aggregates may solve the inconsistency of the maximum grain size between the two constraints.

  8. Monsoon signatures in trace gas records from Cape Rama, India

    International Nuclear Information System (INIS)

    Bhattacharya, S.K.; Jani, R.A.; Borole, D.V.; Francey, R.J.; Allison, C.E.; Masarie, K.A.

    2002-01-01

    Concentrations of trace gases CO 2 , CH 4 , CO, N 2 O and H 2 , and the stable carbon and oxygen isotopic composition of CO 2 have been measured in air samples collected from Cape Rama, a coastal station on the west coast of India, since 1993. The data show clear signatures of continental and oceanic air mass resulting in complex seasonal variation of trace gas characteristics. The regional atmospheric circulation in the Indian Ocean and Arabian Sea undergoes biannual reversal in low-level winds associated with the yearly migration of the inter-tropical convergence zone (ITCZ). From June to September, the wind is from the equatorial Indian Ocean to the Indian subcontinent (southwest monsoon) and brings in pristine marine air. From December to February, dry continental winds blow from the northeast and transport continental emissions to the ocean (northeast monsoon). Detailed transport and chemical modelling will be necessary to interpret these records, however the potential to identify and constrain the regional trace gas emissions appears to be high. (author)

  9. Three plasma metabolite signatures for diagnosing high altitude pulmonary edema

    Science.gov (United States)

    Guo, Li; Tan, Guangguo; Liu, Ping; Li, Huijie; Tang, Lulu; Huang, Lan; Ren, Qian

    2015-10-01

    High-altitude pulmonary edema (HAPE) is a potentially fatal condition, occurring at altitudes greater than 3,000 m and affecting rapidly ascending, non-acclimatized healthy individuals. However, the lack of biomarkers for this disease still constitutes a bottleneck in the clinical diagnosis. Here, ultra-high performance liquid chromatography coupled with Q-TOF mass spectrometry was applied to study plasma metabolite profiling from 57 HAPE and 57 control subjects. 14 differential plasma metabolites responsible for the discrimination between the two groups from discovery set (35 HAPE subjects and 35 healthy controls) were identified. Furthermore, 3 of the 14 metabolites (C8-ceramide, sphingosine and glutamine) were selected as candidate diagnostic biomarkers for HAPE using metabolic pathway impact analysis. The feasibility of using the combination of these three biomarkers for HAPE was evaluated, where the area under the receiver operating characteristic curve (AUC) was 0.981 and 0.942 in the discovery set and the validation set (22 HAPE subjects and 22 healthy controls), respectively. Taken together, these results suggested that this composite plasma metabolite signature may be used in HAPE diagnosis, especially after further investigation and verification with larger samples.

  10. GRAIN SIZE CONSTRAINTS ON HL TAU WITH POLARIZATION SIGNATURE

    International Nuclear Information System (INIS)

    Kataoka, Akimasa; Dullemond, Cornelis P; Muto, Takayuki; Momose, Munetake; Tsukagoshi, Takashi

    2016-01-01

    The millimeter-wave polarization of the protoplanetary disk around HL Tau has been interpreted as the emission from elongated dust grains aligned with the magnetic field in the disk. However, the self-scattering of thermal dust emission may also explain the observed millimeter-wave polarization. In this paper, we report a modeling of the millimeter-wave polarization of the HL Tau disk with the self-polarization. Dust grains are assumed to be spherical and to have a power-law size distribution. We change the maximum grain size with a fixed dust composition in a fixed disk model to find the grain size to reproduce the observed signature. We find that the direction of the polarization vectors and the polarization degree can be explained with the self-scattering. Moreover, the polarization degree can be explained only if the maximum grain size is ∼150 μm. The obtained grain size from the polarization is different from that which has been previously expected from the spectral index of the dust opacity coefficient (a millimeter or larger) if the emission is optically thin. We discuss that porous dust aggregates may solve the inconsistency of the maximum grain size between the two constraints

  11. Twisted Bilayer Graphene. Interlayer configuration and magnetotransport signatures

    Energy Technology Data Exchange (ETDEWEB)

    Rode, Johannes C.; Smirnov, Dmitri; Belke, Christopher; Schmidt, Hennrik; Haug, Rolf J. [Institut fuer Festkoerperphysik, Hannover (Germany)

    2017-11-15

    Twisted Bilayer Graphene may be viewed as very first representative of the now booming class of artificially layered 2D materials. Consisting of two sheets from the same structure and atomic composition, its decisive degree of freedom lies in the rotation between crystallographic axes in the individual graphene monolayers. Geometrical consideration finds angle-dependent Moire patterns as well as commensurate superlattices of opposite sublattice exchange symmetry. Beyond the approach of rigidly interposed lattices, this review takes focus on the evolving topic of lattice corrugation and distortion in response to spatially varying lattice registry. The experimental approach to twisted bilayers requires a basic control over preparation techniques; important methods are summarized and extended on in the case of bilayers folded from monolayer graphene via AFM nanomachining. Central morphological parameters to the twisted bilayer, rotational mismatch and interlayer separation are studied in a broader base of samples. Finally, experimental evidence for a number of theoretically predicted, controversial electronic scenarios are reviewed; magnetotransport signatures are discussed in terms of Fermi velocity, van Hove singularities and Berry phase and assessed with respect to the underlying experimental conditions, thereby referring back to the initially considered variations in relaxed lattice structure. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Chemical Signatures of and Precursors to Fractures Using Fluid Inclusion Stratigraphy

    Energy Technology Data Exchange (ETDEWEB)

    Lorie M. Dilley

    2011-03-30

    Enhanced Geothermal Systems (EGS) are designed to recover heat from the subsurface by mechanically creating fractures in subsurface rocks. Open or recently closed fractures would be more susceptible to enhancing the permeability of the system. Identifying dense fracture areas as well as large open fractures from small fracture systems will assist in fracture stimulation site selection. Geothermal systems are constantly generating fractures (Moore, Morrow et al. 1987), and fluids and gases passing through rocks in these systems leave small fluid and gas samples trapped in healed microfractures. These fluid inclusions are faithful records of pore fluid chemistry. Fluid inclusions trapped in minerals as the fractures heal are characteristic of the fluids that formed them, and this signature can be seen in fluid inclusion gas analysis. This report presents the results of the project to determine fracture locations by the chemical signatures from gas analysis of fluid inclusions. With this project we hope to test our assumptions that gas chemistry can distinguish if the fractures are open and bearing production fluids or represent prior active fractures and whether there are chemical signs of open fracture systems in the wall rock above the fracture. Fluid Inclusion Stratigraphy (FIS) is a method developed for the geothermal industry which applies the mass quantification of fluid inclusion gas data from drill cuttings and applying known gas ratios and compositions to determine depth profiles of fluid barriers in a modern geothermal system (Dilley, 2009; Dilley et al., 2005; Norman et al., 2005). Identifying key gas signatures associated with fractures for isolating geothermal fluid production is the latest advancement in the application of FIS to geothermal systems (Dilley and Norman, 2005; Dilley and Norman, 2007). Our hypothesis is that peaks in FIS data are related to location of fractures. Previous work (DOE Grant DE-FG36-06GO16057) has indicated differences in the

  13. In search of the noble gas 3.52 Ga atmospheric signatures

    Science.gov (United States)

    Pujol, M.; Marty, B.; Philippot, P.

    2008-12-01

    The isotopic signatures of noble gases in the Present-day mantle and in the atmosphere permit exceptional insight into the evolution of these reservoirs through time ([1]). However, related exchange models are under- constrained and would require direct measurements of the atmospheric composition long ago, e.g., in the Archaean. Drilling in the the 3.52 Ga chert-barite ([2]) of the Dresser formation(Pilbara Drilling Project) , North Pole, Pilbara craton (Western Australia), led to recovery of exceptionally fresh samples preserving primary fluid inclusions unaffected by surface weathering. The whole formation is considered to be an already established basin when hydrothermal processes started. The chemical composition of primary fluid inclusions trapped in hydrothermal quartz from vacuolar komatiitic basalt from 110 m depth were determined by synchrotron X-ray microfluorescence (ESRF, Grenoble,France). Data show that fluids are relatively homogenous, consisting of a Ba-rich fluid and a Fe (+Ba)-rich fluid of hydrothermal origin as concluded by Foriel et al.([3]). The isotopic compositions of xenon and argon trapped in these fluids were measured by mass spectrometry following vacuum crushing. The three argon isotopes show a homogeneous signature quite different from present-day Earth atmosphere but we cannot exclude the possibility that secondary nuclear reactions produced these anomalies. Despite this, the Xe isotopic trends indicate a less radiogenic signature than the Present-day atmosphere, and probably represent a remnant of the Archaean atmosphere. If this xenon composition is primitive then it implies that there is no cosmogenic production through time. However, argon ratios could be explained by cosmogenic production which implies significant surface exposure times. Cosmogenic production will produce correlated argon and xenon isotope signatures. Therefore it is necessary to differentiate primary from secondary composition. To investigate the effects of these

  14. The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies.

    Directory of Open Access Journals (Sweden)

    Luis M Valor

    Full Text Available Plasma cells (PC represent the heterogeneous final stage of the B cells (BC differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i tonsil PC, mainly consisting of early PC; ii PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts; and, iii bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others. Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.

  15. Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

    Directory of Open Access Journals (Sweden)

    Pride David T

    2008-09-01

    Full Text Available Abstract Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC, where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of

  16. Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

    Science.gov (United States)

    Pride, David T; Schoenfeld, Thomas

    2008-09-17

    Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs

  17. The transcriptional landscape of hematopoietic stem cell ontogeny

    Science.gov (United States)

    McKinney-Freeman, Shannon; Cahan, Patrick; Li, Hu; Lacadie, Scott A.; Huang, Hsuan-Ting; Curran, Matthew; Loewer, Sabine; Naveiras, Olaia; Kathrein, Katie L.; Konantz, Martina; Langdon, Erin M.; Lengerke, Claudia; Zon, Leonard I.; Collins, James J.; Daley, George Q.

    2012-01-01

    Transcriptome analysis of adult hematopoietic stem cells (HSC) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a similar analysis of HSC development is lacking. Here, we acquired the transcriptomes of developing HSC purified from >2500 murine embryos and adult mice. We found that embryonic hematopoietic elements clustered into three distinct transcriptional states characteristic of the definitive yolk sac, HSCs undergoing specification, and definitive HSCs. We applied a network biology-based analysis to reconstruct the gene regulatory networks of sequential stages of HSC development and functionally validated candidate transcriptional regulators of HSC ontogeny by morpholino-mediated knock-down in zebrafish embryos. Moreover, we found that HSCs from in vitro differentiated embryonic stem cells closely resemble definitive HSC, yet lack a Notch-signaling signature, likely accounting for their defective lymphopoiesis. Our analysis and web resource (http://hsc.hms.harvard.edu) will enhance efforts to identify regulators of HSC ontogeny and facilitate the engineering of hematopoietic specification. PMID:23122293

  18. Quantum liquid signatures in dwarf stars

    Energy Technology Data Exchange (ETDEWEB)

    Gabadadze, Gregory; Pirtskhalava, David, E-mail: gg32@nyu.edu, E-mail: dmp371@nyu.edu [Center for Cosmology and Particle Physics, Department of Physics, New York University, New York, NY 10003 (United States)

    2009-05-15

    We develop further the proposal of arXiv:0806.3692 that a new state of matter - charged condensate of spin-0 nuclei - may exist in helium-core dwarf stars. The charged condensate and its fluctuations are described by an effective field theory Lagrangian. The spectrum of bosonic fluctuations is gapped, while electrons, at temperatures of interest, give rise to gapless excitations near the Fermi surface. These properties determine the evolution of the dwarfs with condensed cores. In particular, we show that such dwarf stars would cool significantly faster than their crystallized counterparts. As a result, the luminosity function for the helium-core dwarfs will have a sharp drop-off after the condensation. It is tempting to interpret the recently discovered abrupt termination of a sequence of 24 helium-core dwarf candidates in NGC 6397 as a signature of the charged condensation.

  19. SSC physics signatures and trigger requirements

    International Nuclear Information System (INIS)

    1985-01-01

    Strategies are considered for triggering on new physics processes on the environment of the SSC, where interaction rates will be very high and most new physics processes quite rare. The quantities available for use in the trigger at various levels are related to the signatures of possible new physics. Two examples were investigated in some detail using the ISAJET Monte Carlo program: Higgs decays to W pairs and a missing energy trigger applied to gluino pair production. In both of the examples studied in detail, it was found that workable strategies for reducing the trigger rate were obtainable which also produced acceptable efficiency for the processes of interest. In future work, it will be necessary to carry out such a program for the full spectrum of suggested new physics

  20. Signatures of massive sgoldstinos at hadron colliders

    International Nuclear Information System (INIS)

    Perazzi, Elena; Ridolfi, Giovanni; Zwirner, Fabio

    2000-01-01

    In supersymmetric extensions of the Standard Model with a very light gravitino, the effective theory at the weak scale should contain not only the goldstino G-tilde, but also its supersymmetric partners, the sgoldstinos. In the simplest case, the goldstino is a gauge-singlet and its superpartners are two neutral spin-0 particles, S and P. We study possible signals of massive sgoldstinos at hadron colliders, focusing on those that are most relevant for the Tevatron. We show that inclusive production of sgoldstinos, followed by their decay into two photons, can lead to observable signals or to stringent combined bounds on the gravitino and sgoldstino masses. Sgoldstino decays into two gluon jets may provide a useful complementary signature

  1. Signatures of chromodynamics in hadron collisions

    International Nuclear Information System (INIS)

    Halzen, F.

    1979-01-01

    The quantum chromodynamics (QCD) describes the interaction of the parton constituents of hadrons (quarks and gluons) via eight colored photons (gluons) interacting with the quarks, and unlike the photons, with each other. The simple picture of Drell-Yan model has made surprising success. The marriage of the old fashion Drell-Yan parton model with QCD has not only made its phenomenological success in the study of lepton pair production, but has allowed to study quantitatively the gluon correction to the model. Information from beam dump and emulsion experiments on charm production is compared with the typical QCD diagram. The results indicate some possible non-perturbative contribution to the photon- and hadron-production of heavy quarks. The definite features of dilepton as well as large transverse momentum data are direct signature of gluons. (Kato, T.)

  2. Collider signatures of flavorful Higgs bosons

    International Nuclear Information System (INIS)

    Altmannshofer, Wolfgang; Eby, Joshua; Gori, Stefania; Lotito, Matteo

    2016-01-01

    Motivated by our limited knowledge of the Higgs couplings to the first two generation fermions, we analyze the collider phenomenology of a class of two Higgs doublet models (2HDMs) with a nonstandard Yukawa sector. One Higgs doublet is mainly responsible for the masses of the weak gauge bosons and the third-generation fermions, while the second Higgs doublet provides mass for the lighter fermion generations. The characteristic collider signatures of this setup differ significantly from well-studied 2HDMs with natural flavor conservation, flavor alignment, or minimal flavor violation. New production mechanisms for the heavy scalar, pseudoscalar, and charged Higgs involving second-generation quarks can become dominant. The most interesting decay modes include H/A → cc,tc,μμ,τμ and H"± → cb,cs,μν. As a result, searches for low-mass dimuon resonances are currently among the best probes of the heavy Higgs bosons in this setup.

  3. ALPs effective field theory and collider signatures

    Energy Technology Data Exchange (ETDEWEB)

    Brivio, I. [Universidad Autonoma de Madrid, Departamento de Fisica Teorica y Instituto de Fisica Teorica, IFT-UAM/CSIC, Madrid (Spain); University of Copenhagen, Niels Bohr International Academy, Copenhagen (Denmark); Gavela, M.B.; Merlo, L.; Rey, R. del [Universidad Autonoma de Madrid, Departamento de Fisica Teorica y Instituto de Fisica Teorica, IFT-UAM/CSIC, Madrid (Spain); Mimasu, K. [University of Sussex, Department of Physics and Astronomy, Brighton (United Kingdom); Universite Catholique de Louvain, Centre for Cosmology, Particle Physics and Phenomenology (CP3), Louvain-la-Neuve (Belgium); No, J.M. [University of Sussex, Department of Physics and Astronomy, Brighton (United Kingdom); King' s College London, Department of Physics, London (United Kingdom); Sanz, V. [University of Sussex, Department of Physics and Astronomy, Brighton (United Kingdom)

    2017-08-15

    We study the leading effective interactions between the Standard Model fields and a generic singlet CP-odd (pseudo-) Goldstone boson. Two possible frameworks for electroweak symmetry breaking are considered: linear and non-linear. For the latter case, the basis of leading effective operators is determined and compared with that for the linear expansion. Associated phenomenological signals at colliders are explored for both scenarios, deriving new bounds and analyzing future prospects, including LHC and High Luminosity LHC sensitivities. Mono-Z, mono-W, W-photon plus missing energy and on-shell top final states are most promising signals expected in both frameworks. In addition, non-standard Higgs decays and mono-Higgs signatures are especially prominent and expected to be dominant in non-linear realisations. (orig.)

  4. Signatures of Beam - and Anisotropy Driven Oscillitons

    Science.gov (United States)

    Sauer, K.; Dubinin, E.; McKenzie, J. F.

    Oscillitons represent a new class of stationary nonlinear waves, first found in bi-ion plasmas (Sauer et al., 1991) where mode splitting of the `individual' wave modes leads to conditions for phase- and group-standing waves near the `crossing points'. The corresponding structures have signatures of the usual solitons, superimposed by spatial oscillations. Oscillitons may also occur in single-ion plasmas, e.g. in the elec- tron whistler branch. The characteristic features of different types of oscillitons under realistic conditions in space plasmas including damping, beams and anisotropies are analyzed. Relevant mechanisms of coherent waves observed in different frequency ranges (Lion Roars at Earth, ion cyclotron waves near Io and Mars) are discussed.

  5. Thermal Signature Identification System (TheSIS)

    Science.gov (United States)

    Merritt, Scott; Bean, Brian

    2015-01-01

    We characterize both nonlinear and high order linear responses of fiber-optic and optoelectronic components using spread spectrum temperature cycling methods. This Thermal Signature Identification System (TheSIS) provides much more detail than conventional narrowband or quasi-static temperature profiling methods. This detail allows us to match components more thoroughly, detect subtle reversible shifts in performance, and investigate the cause of instabilities or irreversible changes. In particular, we create parameterized models of athermal fiber Bragg gratings (FBGs), delay line interferometers (DLIs), and distributed feedback (DFB) lasers, then subject the alternative models to selection via the Akaike Information Criterion (AIC). Detailed pairing of components, e.g. FBGs, is accomplished by means of weighted distance metrics or norms, rather than on the basis of a single parameter, such as center wavelength.

  6. Spin-3/2 Pentaquark Resonance Signature

    International Nuclear Information System (INIS)

    Ben Lasscock; John Hedditch; Derek Leinweber; Anthony Williams; Waseem Kamleh; Wolodymyr Melnitchouk; Anthony Thomas; Ross Young; James Zanotti

    2005-01-01

    We search for the standard lattice resonance signature of attraction between the resonance constituents which leads to a bound state at quark masses near the physical regime. We study a variety of spin-1/2 interpolators and for the first time, interpolators providing access to spin-3/2 pentaquark states. In looking for evidence of binding, a precise determination of the mass splitting between the pentaquark state and its lowest-lying decay channel is performed by constructing the effective mass splitting from the various two-point correlation functions. While the binding of the pentaquark state is not a requirement, the observation of such binding would provide compelling evidence for the existence of the theta+ pentaquark resonance. Evidence of binding is observed in the isoscalar spin-3/2 positive parity channel, making it an interesting state for further research

  7. Experimental signatures of gravitational wave bursters

    International Nuclear Information System (INIS)

    Dubath, Florian; Foffa, Stefano; Gasparini, Maria Alice; Maggiore, Michele; Sturani, Riccardo

    2005-01-01

    Gravitational wave bursters are sources which emit repeatedly bursts of gravitational waves, and have been recently suggested as potentially interesting candidates for gravitational wave (GW) detectors. Mechanisms that could give rise to a GW burster can be found for instance in highly magnetized neutron stars (the 'magnetars' which explain the phenomenon of soft gamma repeaters), in accreting neutron stars and in hybrid stars with a quark core. We point out that these sources have very distinctive experimental signatures. In particular, as already observed in the γ-ray bursts from soft gamma repeaters, the energy spectrum of the events is a power-law, dN∼E -γ dE with γ≅1.6, and they have a distribution of waiting times (the times between one outburst and the next) significantly different from the distribution of uncorrelated events. We discuss possible detection strategies that could be used to search for these events in existing gravitational wave detectors

  8. Continuous-variable quantum homomorphic signature

    Science.gov (United States)

    Li, Ke; Shang, Tao; Liu, Jian-wei

    2017-10-01

    Quantum cryptography is believed to be unconditionally secure because its security is ensured by physical laws rather than computational complexity. According to spectrum characteristic, quantum information can be classified into two categories, namely discrete variables and continuous variables. Continuous-variable quantum protocols have gained much attention for their ability to transmit more information with lower cost. To verify the identities of different data sources in a quantum network, we propose a continuous-variable quantum homomorphic signature scheme. It is based on continuous-variable entanglement swapping and provides additive and subtractive homomorphism. Security analysis shows the proposed scheme is secure against replay, forgery and repudiation. Even under nonideal conditions, it supports effective verification within a certain verification threshold.

  9. Machine monitoring via current signature analysis techniques

    International Nuclear Information System (INIS)

    Smith, S.F.; Castleberry, K.N.; Nowlin, C.H.

    1992-01-01

    A significant need in the effort to provide increased production quality is to provide improved plant equipment monitoring capabilities. Unfortunately, in today's tight economy, even such monitoring instrumentation must be implemented in a recognizably cost effective manner. By analyzing the electric current drawn by motors, actuator, and other line-powered industrial equipment, significant insights into the operations of the movers, driven equipment, and even the power source can be obtained. The generic term 'current signature analysis' (CSA) has been coined to describe several techniques for extracting useful equipment or process monitoring information from the electrical power feed system. A patented method developed at Oak Ridge National Laboratory is described which recognizes the presence of line-current modulation produced by motors and actuators driving varying loads. The in-situ application of applicable linear demodulation techniques to the analysis of numerous motor-driven systems is also discussed. The use of high-quality amplitude and angle-demodulation circuitry has permitted remote status monitoring of several types of medium and high-power gas compressors in (US DOE facilities) driven by 3-phase induction motors rated from 100 to 3,500 hp, both with and without intervening speed increasers. Flow characteristics of the compressors, including various forms of abnormal behavior such as surging and rotating stall, produce at the output of the specialized detectors specific time and frequency signatures which can be easily identified for monitoring, control, and fault-prevention purposes. The resultant data are similar in form to information obtained via standard vibration-sensing techniques and can be analyzed using essentially identical methods. In addition, other machinery such as refrigeration compressors, brine pumps, vacuum pumps, fans, and electric motors have been characterized

  10. Extracellular Signatures as Indicators of Processing Methods

    Energy Technology Data Exchange (ETDEWEB)

    Wahl, Karen L.

    2012-01-09

    As described in other chapters within this volume, many aspects of microbial cells vary with culture conditions and therefore can potentially be analyzed as forensic signatures of growth conditions. In addition to changes or variations in components of the microbes themselves, extracellular materials indicative of production processes may remain associated with the final bacterial product. It is well recognized that even with considerable effort to make pure products such as fine chemicals or pharmaceuticals, trace impurities from components or synthesis steps associated with production processes can be detected in the final product. These impurities can be used as indicators of production source or methods, such as to help connect drugs of abuse to supply chains. Extracellular residue associated with microbial cells could similarly help to characterize production processes. For successful growth of microorganisms on culture media there must be an available source of carbon, nitrogen, inorganic phosphate and sulfur, trace metals, water and vitamins. The pH, temperature, and a supply of oxygen or other gases must also be appropriate for a given organism for successful culture. The sources of these components and the range in temperature, pH and other variables has adapted over the years with currently a wide range of possible combinations of media components, recipes and parameters to choose from for a given organism. Because of this wide variability in components, mixtures of components, and other parameters, there is the potential for differentiation of cultured organisms based on changes in culture conditions. The challenge remains how to narrow the field of potential combinations and be able to attribute variations in the final bacterial product and extracellular signatures associated with the final product to information about the culture conditions or recipe used in the production of that product.

  11. Acoustic signature of thunder from seismic records

    Science.gov (United States)

    Kappus, Mary E.; Vernon, Frank L.

    1991-06-01

    Thunder, the sound wave through the air associated with lightning, transfers sufficient energy to the ground to trigger seismometers set to record regional earthquakes. The acoustic signature recorded on seismometers, in the form of ground velocity as a function of time, contains the same type features as pressure variations recorded with microphones in air. At a seismic station in Kislovodsk, USSR, a nearly direct lightning strike caused electronic failure of borehole instruments while leaving a brief impulsive acoustic signature on the surface instruments. The peak frequency of 25-55 Hz is consistent with previously published values for cloud-to-ground lightning strikes, but spectra from this station are contaminated by very strong wind noise in this band. A thunderstorm near a similar station in Karasu triggered more than a dozen records of individual lightning strikes during a 2-hour period. The spectra for these events are fairly broadband, with peaks at low frequencies, varying from 6 to 13 Hz. The spectra were all computed by multitaper analysis, which deals appropriately with the nonstationary thunder signal. These independent measurements of low-frequency peaks corroborate the occasional occurrences in traditional microphone records, but a theory concerning the physical mechanism to account for them is still in question. Examined separately, the individual claps in each record have similar frequency distributions, discounting a need for multiple mechanisms to explain different phases of the thunder sequence. Particle motion, determined from polarization analysis of the three-component records, is predominantly vertical downward, with smaller horizontal components indicative of the direction to the lightning bolt. In three of the records the azimuth to the lightning bolt changes with time, confirming a significant horizontal component to the lightning channel itself.

  12. Thermal-Signature-Based Sleep Analysis Sensor

    Directory of Open Access Journals (Sweden)

    Ali Seba

    2017-10-01

    Full Text Available This paper addresses the development of a new technique in the sleep analysis domain. Sleep is defined as a periodic physiological state during which vigilance is suspended and reactivity to external stimulations diminished. We sleep on average between six and nine hours per night and our sleep is composed of four to six cycles of about 90 min each. Each of these cycles is composed of a succession of several stages of sleep that vary in depth. Analysis of sleep is usually done via polysomnography. This examination consists of recording, among other things, electrical cerebral activity by electroencephalography (EEG, ocular movements by electrooculography (EOG, and chin muscle tone by electromyography (EMG. Recordings are made mostly in a hospital, more specifically in a service for monitoring the pathologies related to sleep. The readings are then interpreted manually by an expert to generate a hypnogram, a curve showing the succession of sleep stages during the night in 30s epochs. The proposed method is based on the follow-up of the thermal signature that makes it possible to classify the activity into three classes: “awakening,” “calm sleep,” and “restless sleep”. The contribution of this non-invasive method is part of the screening of sleep disorders, to be validated by a more complete analysis of the sleep. The measure provided by this new system, based on temperature monitoring (patient and ambient, aims to be integrated into the tele-medicine platform developed within the framework of the Smart-EEG project by the SYEL–SYstèmes ELectroniques team. Analysis of the data collected during the first surveys carried out with this method showed a correlation between thermal signature and activity during sleep. The advantage of this method lies in its simplicity and the possibility of carrying out measurements of activity during sleep and without direct contact with the patient at home or hospitals.

  13. Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan

    2014-01-01

    Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in iden......-karyotype AML, which allowed for the generation of a highly prognostic survival signature. Collectively, our CvN method holds great potential as a tool for the analysis of gene expression profiles of cancer patients....

  14. Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat.

    Directory of Open Access Journals (Sweden)

    Sara E Pacheco

    Full Text Available Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1 identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD using microarrays; 2 expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3 test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ. Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q<0.05. All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p<0.05. In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p<0.05. The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions. Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat.

  15. Kinetic control on Zn isotope signatures recorded in marine diatoms

    Science.gov (United States)

    Köbberich, Michael; Vance, Derek

    2017-08-01

    Marine diatoms dominate the oceanic cycle of the essential micronutrient zinc (Zn). The stable isotopes of zinc and other metals are increasingly used to understand trace metal micronutrient cycling in the oceans. One clear feature of the early isotope data is the heavy Zn isotope signature of the average oceanic dissolved pool relative to the inputs, potentially driven by uptake of light isotopes into phytoplankton cells and export to sediments. However, despite the fact that diatoms strip Zn from surface waters across the Antarctic polar front in the Southern Ocean, the local upper ocean is not isotopically heavy. Here we use culturing experiments to quantify the extent of Zn isotope fractionation by diatoms and to elucidate the mechanisms driving it. We have cultured two different open-ocean diatom species (T. oceanica and Chaetoceros sp.) in a series of experiments at constant medium Zn concentration but at bioavailable medium Fe ranging from limiting to replete. We find that T. oceanica can maintain high growth rates and Zn uptake rates over the full range of bioavailable iron (Fe) investigated, and that the Zn taken up has a δ66Zn that is unfractionated relative to that of the bioavailable free Zn in the medium. The studied representative of the genus Chaetoceros, on the other hand, shows more significantly reduced Zn uptake rates at low Fe and records more variable biomass δ66Zn signatures, of up to 0.85‰ heavier than the medium. We interpret the preferential uptake of heavy isotopes at extremely low Zn uptake rates as potentially due to either of the following two mechanisms. First, the release of extracellular polymeric substances (EPS), at low Fe levels, may preferentially scavenge heavy Zn isotopes. Second, the Zn uptake rate may be slow enough to establish pseudo-equilibrium conditions at the transporter site, with heavy Zn isotopes forming more stable surface complexes. Thus we find that, in our experiments, Fe-limitation exerts a key control that

  16. Multidimensional Raman spectroscopic signature of sweat and its potential application to forensic body fluid identification.

    Science.gov (United States)

    Sikirzhytski, Vitali; Sikirzhytskaya, Aliaksandra; Lednev, Igor K

    2012-03-09

    This proof-of-concept study demonstrated the potential of Raman microspectroscopy for nondestructive identification of traces of sweat for forensic purposes. Advanced statistical analysis of Raman spectra revealed that dry sweat was intrinsically heterogeneous, and its biochemical composition varies significantly with the donor. As a result, no single Raman spectrum could adequately represent sweat traces. Instead, a multidimensional spectroscopic signature of sweat was built that allowed for the presentation of any single experimental spectrum as a linear combination of two fluorescent backgrounds and three Raman spectral components dominated by the contribution from lactate, lactic acid, urea and single amino acids. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Searches with long-lived or unusual signatures

    CERN Document Server

    Haug, S; The ATLAS collaboration

    2013-01-01

    We present recent ATLAS and CMS results from searches with long-lived and unusual signatures. They are based on analysis of LHC proton-proton collisions at center of mass energies at 7 and 8 TeV. Long-lived and heavy particles may cause peculiar signatures in the detectors, but are in several Standard Model extensions well motivated.

  18. 27 CFR 70.52 - Signature presumed authentic.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false Signature presumed authentic. 70.52 Section 70.52 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... Collection of Excise and Special (Occupational) Tax Collection-General Provisions § 70.52 Signature presumed...

  19. 25 CFR 117.33 - Signature of illiterates.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Signature of illiterates. 117.33 Section 117.33 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FINANCIAL ACTIVITIES DEPOSIT AND EXPENDITURE OF... Signature of illiterates. An Indian who cannot write shall be required to endorse checks payable to his...

  20. 26 CFR 301.6064-1 - Signature presumed authentic.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Signature presumed authentic. 301.6064-1 Section 301.6064-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED....6064-1 Signature presumed authentic. An individual's name signed to a return, statement, or other...

  1. Field Education as the Signature Pedagogy of Social Work Education

    Science.gov (United States)

    Wayne, Julianne; Bogo, Marion; Raskin, Miriam

    2010-01-01

    In its EPAS, CSWE (2008) identifies field education as the signature pedagogy (Shulman, 2005b) of social work education. This article analyzes the field education-signature pedagogy fit. It finds congruence in selected organizational arrangements that are pervasive and routine, and disparities with respect to expectations about public student…

  2. 12 CFR 18.6 - Signature and attestation.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Signature and attestation. 18.6 Section 18.6 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY DISCLOSURE OF FINANCIAL AND OTHER INFORMATION BY NATIONAL BANKS § 18.6 Signature and attestation. A duly authorized officer of the...

  3. 12 CFR 350.6 - Signature and attestation.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Signature and attestation. 350.6 Section 350.6 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL POLICY DISCLOSURE OF FINANCIAL AND OTHER INFORMATION BY FDIC-INSURED STATE NONMEMBER BANKS § 350.6 Signature and...

  4. 13 CFR 134.209 - Requirement of signature.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Requirement of signature. 134.209 Section 134.209 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION RULES OF PROCEDURE GOVERNING... of signature. Every written submission to OHA, other than evidence, must be signed by the party...

  5. 48 CFR 4.101 - Contracting officer's signature.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Contracting officer's signature. 4.101 Section 4.101 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION GENERAL ADMINISTRATIVE MATTERS Contract Execution 4.101 Contracting officer's signature. Only contracting officers shall...

  6. Selective forgery of RSA signatures with fixed-pattern padding

    NARCIS (Netherlands)

    Lenstra, A.K.; Shparlinski, I.E.; Naccache, D.; Paillier, P.

    2002-01-01

    We present a practical selective forgery attack against RSA signatures with fixed-pattern padding shorter than two thirds of the modulus length. Our result extends the practical existential forgery of such RSA signatures that was presented at Crypto 2001. For an n-bit modulus the heuristic

  7. Subsurface signatures and timing of extreme wave events along the ...

    Indian Academy of Sciences (India)

    The diagnostic event signatures include the extent and elevation of the deposits, as well as morphologic similarity ... Historical archives of the origin, timing, and impact of tsunamis, storms, and floods along the mar- gins of ... High-resolution GPR studies (by the IIT Madras group) of erosional signatures from the beach ridge.

  8. Restrictive partially blind signature for resource-constrained information systems

    NARCIS (Netherlands)

    Qiu, Weidong; Gong, Zheng; Liu, Bozhong; Long, Yu; Chen, Kefei

    2010-01-01

    Restrictive partially blind signature, which is designed for privacy oriented information systems, allows a user to obtain a blind signature from a signer whilst the blind message must obey some certain rules. In order to reduce storage and communication costs, several public-key cryptosystems are

  9. Electronic Signatures in Global and National Commerce Act. Public Law.

    Science.gov (United States)

    Congress of the U.S., Washington, DC.

    This document presents the text of Public Law 106-229, the "Electronic Signatures in Global and National Commerce Act." The act states that, with respect to any transaction in or affecting interstate or foreign commerce: a signature, contract, or other record relating to such transaction may not be denied legal effect, validity, or…

  10. Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation

    Science.gov (United States)

    2009-09-01

    Introduction This presentation summarizes recent activity in monitoring spacecraft health status using passive remote optical nonimaging ...Approved for public release; distribution is unlimited. Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation...It is beneficial to the observer/analyst to understand the fundamental optical signature variability associated with these detection and

  11. Alternative staffing services. Contract transcription.

    Science.gov (United States)

    Tessier, C

    1992-03-01

    Contract medical transcription services can be of great assistance in meeting the demands for transcription, without jeopardizing patient, physician, or institutional confidentiality. You simply must require the contract service to provide at least the same degree of protection and preservation of confidentiality that you should require inhouse. To achieve this you must make these requirements explicit, comprehensive, comprehensible, believable, and enforceable. Discuss the requirements with prospective contractors. Review them at least annually with existing contractors and when contracts are due for renewal. Be sure to specify the consequence of breaching confidentiality, and if there are breaches, enforce the terms of the contract. Consult your institution's legal counsel both in developing the contract and in enforcing its provisions. Take into consideration your department's and institution's policies, AHIMA's statement on confidentiality, as well as local, state, and federal laws. Above all, never lose sight of the patient. Ultimately, it is not patient information that you are obligated to protect. It is the patient.

  12. The post-transcriptional operon

    DEFF Research Database (Denmark)

    Tenenbaum, Scott A.; Christiansen, Jan; Nielsen, Henrik

    2011-01-01

    model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...... of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses....

  13. Online Signature Verification using Recurrent Neural Network and Length-normalized Path Signature

    OpenAIRE

    Lai, Songxuan; Jin, Lianwen; Yang, Weixin

    2017-01-01

    Inspired by the great success of recurrent neural networks (RNNs) in sequential modeling, we introduce a novel RNN system to improve the performance of online signature verification. The training objective is to directly minimize intra-class variations and to push the distances between skilled forgeries and genuine samples above a given threshold. By back-propagating the training signals, our RNN network produced discriminative features with desired metrics. Additionally, we propose a novel d...

  14. A semi-classical approach to signature splitting and signature inversion in odd–odd nuclei

    International Nuclear Information System (INIS)

    Kumar, Vinod; Kumar, Suresh; Kumar, Sushil; Hasan, Zafrul; Koranga, B.S.; Kumar, Deepak; Negi, D.; Angus, Lee

    2011-01-01

    The signature inversion observed in rotational bands belonging to high-j configurations of odd–odd deformed nuclei has been analyzed within the framework of an axially symmetric rotor plus two-particle model. The Coriolis and n–p interaction are considered the main cause of energy staggering. However, γ-triaxial deformation and the numbers of valence protons, N p , and neutrons, N n also contribute to the energy staggering between odd- and even-spin states. (author)

  15. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

    Science.gov (United States)

    Forslund, Kristoffer; Hildebrand, Falk; Nielsen, Trine; Falony, Gwen; Le Chatelier, Emmanuelle; Sunagawa, Shinichi; Prifti, Edi; Vieira-Silva, Sara; Gudmundsdottir, Valborg; Pedersen, Helle K; Arumugam, Manimozhiyan; Kristiansen, Karsten; Voigt, Anita Yvonne; Vestergaard, Henrik; Hercog, Rajna; Costea, Paul Igor; Kultima, Jens Roat; Li, Junhua; Jørgensen, Torben; Levenez, Florence; Dore, Joël; Nielsen, H Bjørn; Brunak, Søren; Raes, Jeroen; Hansen, Torben; Wang, Jun; Ehrlich, S Dusko; Bork, Peer; Pedersen, Oluf

    2015-12-10

    In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.

  16. Survey of pickup ion signatures in the vicinity of Titan using CAPS/IMS

    Science.gov (United States)

    Regoli, L. H.; Coates, A. J.; Thomsen, M. F.; Jones, G. H.; Roussos, E.; Waite, J. H.; Krupp, N.; Cox, G.

    2016-09-01

    Pickup ion detection at Titan is challenging because ion cyclotron waves are rarely detected in the vicinity of the moon. In this work, signatures left by freshly produced pickup heavy ions (m/q ˜ 16 to m/q ˜ 28) as detected in the plasma data by the Cassini Plasma Spectrometer/Ion Mass Spectrometer (CAPS/IMS) instrument on board Cassini are analyzed. In order to discern whether these correspond to ions of exospheric origin, one of the flybys during which the reported signatures were observed is investigated in detail. For this purpose, ion composition data from time-of-flight measurements and test particle simulations to constrain the ions' origin are used. After being validated, the detection method is applied to all the flybys for which the CAPS/IMS instrument gathered valid data, constraining the region around the moon where the signatures are observed. The results reveal an escape region located in the anti-Saturn direction as expected from the nominal corotation electric field direction. These findings provide new constraints for the area of freshly produced pickup ion escape, giving an approximate escape rate of 3.3-2+3×1023 ions· s-1.

  17. Time-dependent delayed signatures from energetic photon interrogations

    International Nuclear Information System (INIS)

    Norman, Daren R.; Jones, James L.; Blackburn, Brandon W.; Haskell, Kevin J.; Johnson, James T.; Watson, Scott M.; Hunt, Alan W.; Spaulding, Randy; Harmon, Frank

    2007-01-01

    Pulsed photonuclear interrogation environments generated by 8-24 MeV electron linac are rich with time-dependent, material-specific, radiation signatures. Nitrogen-based explosives and nuclear materials can be detected by exploiting these signatures in different delayed-time regions. Numerical and experimental results presented in this paper show the unique time and energy dependence of these signatures. It is shown that appropriate delayed-time windows are essential to acquire material-specific signatures in pulsed photonuclear assessment environments. These developments demonstrate that pulsed, high-energy, photon-inspection environments can be exploited for time-dependent, material-specific signatures through the proper operation of specialized detectors and detection methods

  18. Signature scheme for the microscopic description of nuclear collective excitations

    International Nuclear Information System (INIS)

    Ogawa, K.

    1980-04-01

    The symmetries between the proton and neutron systems in a nucleus are described in terms of the signatures. Three kinds of signatures (i.e. the pn-, p anti n- and p anti p- (or n anti n-) signatures) are introduced and they are related to the appearance of various collective motions such as rotations or vibrations. It is shown that the pn-signature scheme provides a band-like structure of deformed nuclei, while the features associated with the quadrupole vibration are obtained in the p anti n- and p anti p-signature scheme. From the detail investigation of the p anti n-symmetric wave functions, it is concluded that the reguralities provided by the present shell model are more analogous to those of the γ-unstable surface vibration model (Wilets-Jean model) than to those of harmonic phonon model. (author)

  19. An Efficient Homomorphic Aggregate Signature Scheme Based on Lattice

    Directory of Open Access Journals (Sweden)

    Zhengjun Jing

    2014-01-01

    Full Text Available Homomorphic aggregate signature (HAS is a linearly homomorphic signature (LHS for multiple users, which can be applied for a variety of purposes, such as multi-source network coding and sensor data aggregation. In order to design an efficient postquantum secure HAS scheme, we borrow the idea of the lattice-based LHS scheme over binary field in the single-user case, and develop it into a new lattice-based HAS scheme in this paper. The security of the proposed scheme is proved by showing a reduction to the single-user case and the signature length remains invariant. Compared with the existing lattice-based homomorphic aggregate signature scheme, our new scheme enjoys shorter signature length and high efficiency.

  20. Effects Of Hydrothermal Alteration On Magnetic Properties And Magnetic Signatures - Implications For Predictive Magnetic Exploration Models

    Science.gov (United States)

    Clark, D.

    2012-12-01

    Magnetics is the most widely used geophysical method in hard rock exploration and magnetic surveys are an integral part of exploration programs for many types of mineral deposit, including porphyry Cu, intrusive-related gold, volcanic-hosted epithermal Au, IOCG, VMS, and Ni sulfide deposits. However, the magnetic signatures of ore deposits and their associated mineralized systems are extremely variable and exploration that is based simply on searching for signatures that resemble those of known deposits and systems is rarely successful. Predictive magnetic exploration models are based upon well-established geological models, combined with magnetic property measurements and geological information from well-studied deposits, and guided by magnetic petrological understanding of the processes that create, destroy and modify magnetic minerals in rocks. These models are designed to guide exploration by predicting magnetic signatures that are appropriate to specific geological settings, taking into account factors such as tectonic province; protolith composition; post-formation tilting/faulting/ burial/ exhumation and partial erosion; and metamorphism. Patterns of zoned hydrothermal alteration are important indicators of potentially mineralized systems and, if properly interpreted, can provided vectors to ore. Magnetic signatures associated with these patterns at a range of scales can provide valuable information on prospectivity and can guide drilling, provided they are correctly interpreted in geological terms. This presentation reviews effects of the important types of hydrothermal alteration on magnetic properties within mineralized systems, with particular reference to porphyry copper and IOCG deposits. For example, an unmodified gold-rich porphyry copper system, emplaced into mafic-intermediate volcanic host rocks (such as Bajo de la Alumbrera, Argentina) exhibits an inner potassic zone that is strongly mineralized and magnetite-rich, which is surrounded by an outer

  1. Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection.

    Directory of Open Access Journals (Sweden)

    Pankaj Barah

    Full Text Available BACKGROUND: Under the threat of global climatic change and food shortages, it is essential to take the initiative to obtain a comprehensive understanding of common and specific defence mechanisms existing in plant systems for protection against different types of biotic invaders. We have implemented an integrated approach to analyse the overall transcriptomic reprogramming and systems-level defence responses in the model plant species Arabidopsis thaliana (A. thaliana henceforth during insect Brevicoryne brassicae (B. brassicae henceforth and bacterial Pseudomonas syringae pv. tomato strain DC3000 (P. syringae henceforth attacks. The main aim of this study was to identify the attacker-specific and general defence response signatures in A. thaliana when attacked by phloem-feeding aphids or pathogenic bacteria. RESULTS: The obtained annotated networks of differentially expressed transcripts indicated that members of transcription factor families, such as WRKY, MYB, ERF, BHLH and bZIP, could be crucial for stress-specific defence regulation in Arabidopsis during aphid and P. syringae attack. The defence response pathways, signalling pathways and metabolic processes associated with aphid attack and P. syringae infection partially overlapped. Components of several important biosynthesis and signalling pathways, such as salicylic acid (SA, jasmonic acid (JA, ethylene (ET and glucosinolates, were differentially affected during the two the treatments. Several stress-regulated transcription factors were known to be associated with stress-inducible microRNAs. The differentially regulated gene sets included many signature transcription factors, and our co-expression analysis showed that they were also strongly co-expressed during 69 other biotic stress experiments. CONCLUSIONS: Defence responses and functional networks that were unique and specific to aphid or P. syringae stresses were identified. Furthermore, our analysis revealed a probable link between

  2. Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression.

    Directory of Open Access Journals (Sweden)

    Byungwoo Ryu

    2007-07-01

    Full Text Available Gene expression profiling has revolutionized our ability to molecularly classify primary human tumors and significantly enhanced the development of novel tumor markers and therapies; however, progress in the diagnosis and treatment of melanoma over the past 3 decades has been limited, and there is currently no approved therapy that significantly extends lifespan in patients with advanced disease. Profiling studies of melanoma to date have been inconsistent due to the heterogeneous nature of this malignancy and the limited availability of informative tissue specimens from early stages of disease.In order to gain an improved understanding of the molecular basis of melanoma progression, we have compared gene expression profiles from a series of melanoma cell lines representing discrete stages of malignant progression that recapitulate critical characteristics of the primary lesions from which they were derived. Here we describe the unsupervised hierarchical clustering of profiling data from melanoma cell lines and melanocytes. This clustering identifies two distinctive molecular subclasses of melanoma segregating aggressive metastatic tumor cell lines from less-aggressive primary tumor cell lines. Further analysis of expression signatures associated with melanoma progression using functional annotations categorized these transcripts into three classes of genes: 1 Upregulation of activators of cell cycle progression, DNA replication and repair (CDCA2, NCAPH, NCAPG, NCAPG2, PBK, NUSAP1, BIRC5, ESCO2, HELLS, MELK, GINS1, GINS4, RAD54L, TYMS, and DHFR, 2 Loss of genes associated with cellular adhesion and melanocyte differentiation (CDH3, CDH1, c-KIT, PAX3, CITED1/MSG-1, TYR, MELANA, MC1R, and OCA2, 3 Upregulation of genes associated with resistance to apoptosis (BIRC5/survivin. While these broad classes of transcripts have previously been implicated in the progression of melanoma and other malignancies, the specific genes identified within each class

  3. Pen and platen, piezo-electric (Engineering Materials). [Signature verification for access to restricted areas

    Energy Technology Data Exchange (ETDEWEB)

    The set of five drawings defines a writing instrument system that will reliably verify signatures, thus providing a method useful in screening persons seeking entrance to restricted areas or access to computer programs. Using a conventional ballpoint pen refill, the instrument's input derives from signals generated in its writing tip and from pressure exerted by a person writing his name or a code word on the platen (tablet). The basic principle is that accelerations of the writing tip and pressures exerted by the person writing are recorded in three axes. This combination of signals can be processed by a computer and compared with a record in the computer's memory, or a graphic transcription may be compared visually with an earlier record.

  4. Pen and platen, piezo-electric (21 Aug 1978) (Engineering Materials). [Signature verification

    Energy Technology Data Exchange (ETDEWEB)

    The set of five drawings defines a writing instrument system that will reliably verify signatures, thus providing a method useful in screening persons seeking entrance to restricted areas or access to computer programs. Using a conventional ballpoint pen refill, the instrument's input derives from signals generated in its writing tip and from pressure exerted by a person writing his name or a code word on the platen (tablet). The basic principle is that accelerations of the writing tip and pressures exerted by the person writing are recorded in three axes. This combination of signals can be processed by a computer and compared with a record in the computer's memory, or a graphic transcription may be compared visually with an earlier record.

  5. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  6. Gibberellic acid and cGMP-dependent transcriptional regulation in arabidopsis thaliana

    KAUST Repository

    Bastian, René

    2010-03-01

    An ever increasing amount of transcriptomic data and analysis tools provide novel insight into complex responses of biological systems. Given these resources we have undertaken to review aspects of transcriptional regulation in response to the plant hormone gibberellic acid (GA) and its second messenger guanosine 3\\',5\\'-cyclic monophosphate (cGMP) in Arabidopsis thaliana, both wild type and selected mutants. Evidence suggests enrichment of GA-responsive (GARE) elements in promoters of genes that are transcriptionally upregulated in response to cGMP but downregulated in a GA insensitive mutant (ga1-3). In contrast, in the genes upregulated in the mutant, no enrichment in the GARE is observed suggesting that GARE motifs are diagnostic for GA-induced and cGMP-dependent transcriptional upregulation. Further, we review how expression studies of GA-dependent transcription factors and transcriptional networks based on common promoter signatures derived from ab initio analyses can contribute to our understanding of plant responses at the systems level. © 2010 Landes Bioscience.

  7. Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs.

    Science.gov (United States)

    Kutejova, Eva; Sasai, Noriaki; Shah, Ankita; Gouti, Mina; Briscoe, James

    2016-03-21

    In the vertebrate neural tube, a morphogen-induced transcriptional network produces multiple molecularly distinct progenitor domains, each generating different neuronal subtypes. Using an in vitro differentiation system, we defined gene expression signatures of distinct progenitor populations and identified direct gene-regulatory inputs corresponding to locations of specific transcription factor binding. Combined with targeted perturbations of the network, this revealed a mechanism in which a progenitor identity is installed by active repression of the entire transcriptional programs of other neural progenitor fates. In the ventral neural tube, sonic hedgehog (Shh) signaling, together with broadly expressed transcriptional activators, concurrently activates the gene expression programs of several domains. The specific outcome is selected by repressive input provided by Shh-induced transcription factors that act as the key nodes in the network, enabling progenitors to adopt a single definitive identity from several initially permitted options. Together, the data suggest design principles relevant to many developing tissues. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  9. Interplay between DNA supercoiling and transcription elongation.

    Science.gov (United States)

    Ma, Jie; Wang, Michelle

    2014-01-01

    Transcription-coupled DNA supercoiling has been shown to be an important regulator of transcription that is broadly present in the cell. Here we review experimental work which shows that RNA polymerase is a powerful torsional motor that can alter DNA topology and structure, and DNA supercoiling in turn directly affects transcription elongation.

  10. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei.

    Directory of Open Access Journals (Sweden)

    Ence Yang

    2014-10-01

    Full Text Available Systemic dimorphic fungi cause more than one million new infections each year, ranking them among the significant public health challenges currently encountered. Penicillium marneffei is a systemic dimorphic fungus endemic to Southeast Asia. The temperature-dependent dimorphic phase transition between mycelium and yeast is considered crucial for the pathogenicity and transmission of P. marneffei, but the underlying mechanisms are still poorly understood. Here, we re-sequenced P. marneffei strain PM1 using multiple sequencing platforms and assembled the genome using hybrid genome assembly. We determined gene expression levels using RNA sequencing at the mycelial and yeast phases of P. marneffei, as well as during phase transition. We classified 2,718 genes with variable expression across conditions into 14 distinct groups, each marked by a signature expression pattern implicated at a certain stage in the dimorphic life cycle. Genes with the same expression patterns tend to be clustered together on the genome, suggesting orchestrated regulations of the transcriptional activities of neighboring genes. Using qRT-PCR, we validated expression levels of all genes in one of clusters highly expressed during the yeast-to-mycelium transition. These included madsA, a gene encoding MADS-box transcription factor whose gene family is exclusively expanded in P. marneffei. Over-expression of madsA drove P. marneffei to undergo mycelial growth at 37°C, a condition that restricts the wild-type in the yeast phase. Furthermore, analyses of signature expression patterns suggested diverse roles of secreted proteins at different developmental stages and the potential importance of non-coding RNAs in mycelium-to-yeast transition. We also showed that RNA structural transition in response to temperature changes may be related to the control of thermal dimorphism. Together, our findings have revealed multiple molecular mechanisms that may underlie the dimorphic transition

  11. Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack.

    Science.gov (United States)

    De Vos, Martin; Van Oosten, Vivian R; Van Poecke, Remco M P; Van Pelt, Johan A; Pozo, Maria J; Mueller, Martin J; Buchala, Antony J; Métraux, Jean-Pierre; Van Loon, L C; Dicke, Marcel; Pieterse, Corné M J

    2005-09-01

    Plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) play key roles. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. Arabidopsis plants were exposed to a pathogenic leaf bacterium (Pseudomonas syringae pv. tomato), a pathogenic leaf fungus (Alternaria brassicicola), tissue-chewing caterpillars (Pieris rapae), cell-content-feeding thrips (Frankliniella occidentalis), or phloem-feeding aphids (Myzus persicae). Monitoring the signal signature in each plant-attacker combination showed that the kinetics of SA, JA, and ET production varies greatly in both quantity and timing. Analysis of global gene expression profiles demonstrated that the signal signature characteristic of each Arabidopsis-attacker combination is orchestrated into a surprisingly complex set of transcriptional alterations in which, in all cases, stress-related genes are overrepresented. Comparison of the transcript profiles revealed that consistent changes induced by pathogens and insects with very different modes of attack can show considerable overlap. Of all consistent changes induced by A. brassicicola, Pieris rapae, and E occidentalis, more than 50% also were induced consistently by P. syringae. Notably, although these four attackers all stimulated JA biosynthesis, the majority of the changes in JA-responsive gene expression were attacker specific. All together, our study shows that SA, JA, and ET play a primary role in the orchestration of the plant's defense response, but other regulatory mechanisms, such as pathway cross-talk or additional attacker-induced signals, eventually shape the highly complex attacker-specific defense response.

  12. PARP-1 cleavage fragments: signatures of cell-death proteases in neurodegeneration

    Directory of Open Access Journals (Sweden)

    Alexander Jonathan S

    2010-12-01

    Full Text Available Abstract The normal function of poly (ADP-ribose polymerase-1 (PARP-1 is the routine repair of DNA damage by adding poly (ADP ribose polymers in response to a variety of cellular stresses. Recently, it has become widely appreciated that PARP-1 also participates in diverse physiological and pathological functions from cell survival to several forms of cell death and has been implicated in gene transcription, immune responses, inflammation, learning, memory, synaptic functions, angiogenesis and aging. In the CNS, PARP inhibition attenuates injury in pathologies like cerebral ischemia, trauma and excitotoxicity demonstrating a central role of PARP-1 in these pathologies. PARP-1 is also a preferred substrate for several 'suicidal' proteases and the proteolytic action of suicidal proteases (caspases, calpains, cathepsins, granzymes and matrix metalloproteinases (MMPs on PARP-1 produces several specific proteolytic cleavage fragments with different molecular weights. These PARP-1 signature fragments are recognized biomarkers for specific patterns of protease activity in unique cell death programs. This review focuses on specific suicidal proteases active towards PARP-1 to generate signature PARP-1 fragments that can identify key proteases and particular forms of cell death involved in pathophysiology. The roles played by some of the PARP-1 fragments and their associated binding partners in the control of different forms of cell death are also discussed.

  13. Enhanced anti-counterfeiting measures for additive manufacturing: coupling lanthanide nanomaterial chemical signatures with blockchain technology

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, Zachary C.; Stephenson, David E.; Christ, Josef F.; Pope, Timothy R.; Arey, Bruce W.; Barrett, Christopher A.; Warner, Marvin G.

    2017-08-18

    The significant rise of additive manufacturing (AM) in recent years is in part due to the open sourced nature of the printing processes and reduced cost and capital barriers relative to traditional manufacturing. However, this democratization of manufacturing spurs an increased demand for producers and end-users to verify the authenticity and quality of individual parts. To this end, we introduce an anti-counterfeiting method composed of first embedding engineered nanomaterials into features of a 3D-printed part followed by non-destructive interrogation of these features to quantify a chemical signature profile. The part specific chemical signature data is then linked to a securitized, distributed, and time-stamped blockchain ledger entry. To demonstrate the utility of this approach, lanthanide-aspartic acid nanoscale coordination polymers (Ln3+- Asp NCs) / poly(lactic) acid (PLA) composites were formulated and transformed into a filament feedstock for fused deposition modeling (FDM) 3D printing. In the present case, a quick-response (QR) code containing the doped Ln3+-Asp NCs was printed using a dual-extruder FDM printer into pure PLA parts. The QR code provides a searchable reference to an Ethereum-based blockchain entry. The QR code physical features also serve as defined areas to probe the signatures arising from the embedded Ln3+-Asp NCs. Visible fluorescence emission with UV-excitation was quantified in terms of color using a smartphone camera and incorporated into blockchain entries. Ultimately, linking unique chemical signature data to blockchain databases is anticipated to make the costs of counterfeiting AM materials significantly more prohibitive and transactions between those in the supply chain more trustworthy.

  14. Proteomic and lipidomic signatures of lipid metabolism in NASH-associated hepatocellular carcinoma.

    Science.gov (United States)

    Muir, Kyle; Hazim, Antonious; He, Ying; Peyressatre, Marion; Kim, Do-Young; Song, Xiaoling; Beretta, Laura

    2013-08-01

    Nonalcoholic steatohepatitis (NASH) is a common preneoplastic condition of hepatocellular carcinoma (HCC). Mice with hepatocytic deletion of Pten develop NASH and HCC later in life. This model is highly valuable for studies aimed at identifying the molecular mechanism by which metabolic disorders contribute to tumor development. We applied proteomic and lipidomic profiling approaches to Pten-null NASH liver and tumors. Circulating fatty acid composition was also characterized in these mice. The relevance to human NASH and HCC was further validated. This integrative proteomic and lipidomic study from mouse to human and from liver to blood identified the following disease signatures: (i) an HCC signature: upregulated hepatic scd1/scd2, fads2, and acsl5:acsl1 ratio, elevated vaccenic and erucic acids, and reduced margaric and linoleic acids in both liver and plasma; (ii) a NASH signature that correlates with tumor burden: upregulated hepatic elovl6, elevated oleic, adrenic, and osbond acids, and reduced cervonic acid in liver and plasma; and (iii) a NASH signature: reduced hepatic and circulating lignoceric and eicosapentaenoic acids. Altogether, these results show the role of lipid-modifying enzymes converting saturated fatty acids (SFA) to monounsaturated fatty acids (MUFA) in HCC and the importance of an increased ratio of long chain n6-polyunsaturated fatty acids over n3-polyunsaturated fatty acids in NASH and HCC risk. They also highlight the relevance of the Pten-null model for studies related to NASH and HCC and show that circulating lipid metabolome provides a direct read of lipid changes in the liver. Most importantly, novel candidate targets for HCC diagnosis, therapy, risk assessment, and prevention were identified. ©2013 AACR.

  15. Transcriptional profiling reveals gland-specific differential expression in the three major salivary glands of the adult mouse.

    Science.gov (United States)

    Gao, Xin; Oei, Maria S; Ovitt, Catherine E; Sincan, Murat; Melvin, James E

    2018-04-01

    RNA-Seq was used to better understand the molecular nature of the biological differences among the three major exocrine salivary glands in mammals. Transcriptional profiling found that the adult murine parotid, submandibular, and sublingual salivary glands express greater than 14,300 protein-coding genes, and nearly 2,000 of these genes were differentially expressed. Principle component analysis of the differentially expressed genes revealed three distinct clusters according to gland type. The three salivary gland transcriptomes were dominated by a relatively few number of highly expressed genes (6.3%) that accounted for more than 90% of transcriptional output. Of the 912 transcription factors expressed in the major salivary glands, greater than 90% of them were detected in all three glands, while expression for ~2% of them was enriched in an individual gland. Expression of these unique transcription factors correlated with sublingual and parotid specific subsets of both highly expressed and differentially expressed genes. Gene ontology analyses revealed that the highly expressed genes common to all glands were associated with global functions, while many of the genes expressed in a single gland play a major role in the function of that gland. In summary, transcriptional profiling of the three murine major salivary glands identified a limited number of highly expressed genes, differentially expressed genes, and unique transcription factors that represent the transcriptional signatures underlying gland-specific biological properties.

  16. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.

    Science.gov (United States)

    Hao, Nan; Palmer, Adam C; Dodd, Ian B; Shearwin, Keith E

    2017-03-15

    Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.

  17. Identification of Signatures to Detect Undeclared Nuclear Activities at the Front-end of the Fuel Cycle

    International Nuclear Information System (INIS)

    Varga, Z.; Mayer, K.; Krajko, J.; Ho, D.; Wallenius, M.; )

    2015-01-01

    Several parameters of the nuclear materials can be used to verify their sources and the declared origin for safeguards purposes, such as chemical composition, nuclear material content, impurities or the isotopic compositions of major or trace-level constituents. Combining these parameters (also known as signatures) enables the verification of the safeguarded materials at high confidence, and also allows detecting the use of undeclared nuclear materials. Moreover, several signatures can be used not only as a comparative indicator against another samples or datasets, but also permits to reveal the possible origin of the undeclared feed material without any prior knowledge on the provenance. The measurable signatures, however, have different strength and require diverse analytical techniques, thus the knowledge of their variations throughout the complex production processes is of vital importance to use them for safeguards. The aim of the present study is to investigate the behaviour and relevance of as many signatures for safeguards as possible in a respective uranium ore concentrate production process. Within the framework of the European Commission Support Programme A 1753 the production of uranium ore concentrate from uranium ore was followed and sampled at each stage. By the comprehensive analysis of the samples (major and minor constituents, molecular structure, morphology, rare-earth elemental pattern, trace-level organic residues, age measurement, isotopic study of S, Pb, Sr, Nd and Th), together with the process information, the role and applicability of the various signatures can be assessed. By this means the appropriate and relevant safeguards parameters can be identified, their advantages and limitations can be revealed. (author)

  18. Implementing Signature Neural Networks with Spiking Neurons.

    Science.gov (United States)

    Carrillo-Medina, José Luis; Latorre, Roberto

    2016-01-01

    Spiking Neural Networks constitute the most promising approach to develop realistic Artificial Neural Networks (ANNs). Unlike traditional firing rate-based paradigms, information coding in spiking models is based on the precise timing of individual spikes. It has been demonstrated that spiking ANNs can be successfully and efficiently applied to multiple realistic problems solvable with traditional strategies (e.g., data classification or pattern recognition). In recent years, major breakthroughs in neuroscience research have discovered new relevant computational principles in different living neural systems. Could ANNs benefit from some of these recent findings providing novel elements of inspiration? This is an intriguing question for the research community and the development of spiking ANNs including novel bio-inspired information coding and processing strategies is gaining attention. From this perspective, in this work, we adapt the core concepts of the recently proposed Signature Neural Network paradigm-i.e., neural signatures to identify each unit in the network, local information contextualization during the processing, and multicoding strategies for information propagation regarding the origin and the content of the data-to be employed in a spiking neural network. To the best of our knowledge, none of these mechanisms have been used yet in the context of ANNs of spiking neurons. This paper provides a proof-of-concept for their applicability in such networks. Computer simulations show that a simple network model like the discussed here exhibits complex self-organizing properties. The combination of multiple simultaneous encoding schemes allows the network to generate coexisting spatio-temporal patterns of activity encoding information in different spatio-temporal spaces. As a function of the network and/or intra-unit parameters shaping the corresponding encoding modality, different forms of competition among the evoked patterns can emerge even in the absence

  19. Noble Gas signatures of Enhanced Oil Recovery

    Science.gov (United States)

    Barry, P. H.; Kulongoski, J. T.; Tyne, R. L.; Hillegonds, D.; Byrne, D. J.; Landon, M. K.; Ballentine, C. J.

    2017-12-01

    Noble gases are powerful tracers of fluids from various oil and gas production activities in hydrocarbon reservoirs and nearby groundwater. Non-radiogenic noble gases are introduced into undisturbed oil and natural gas reservoirs through exchange with formation waters [1-3]. Reservoirs with extensive hydraulic fracturing, injection for enhanced oil recovery (EOR), and/or waste disposal also show evidence for a component of noble gases introduced from air [4]. Isotopic and elemental ratios of noble gases can be used to 1) assess the migration history of the injected and formation fluids, and 2) determine the extent of exchange between multiphase fluids in different reservoirs. We present noble gas isotope and abundance data from casing, separator and injectate gases of the Lost Hills and Fruitvale oil fields in the San Joaquin basin, California. Samples were collected as part of the California State Water Resource Control Board's Oil and Gas Regional Groundwater Monitoring Program. Lost Hills (n=7) and Fruitvale (n=2) gases are geochemically distinct and duplicate samples are highly reproducible. Lost Hills casing gas samples were collected from areas where EOR and hydraulic fracturing has occurred in the past several years, and from areas where EOR is absent. The Fruitvale samples were collected from a re-injection port. All samples are radiogenic in their He isotopes, typical of a crustal environment, and show enrichments in heavy noble gases, resulting from preferential adsorption on sediments. Fruitvale samples reflect air-like surface conditions, with higher air-derived noble gas concentrations. Lost Hills gases show a gradation from pristine crustal signatures - indicative of closed-system exchange with formation fluids - to strongly air-contaminated signatures in the EOR region. Pristine samples can be used to determine the extent of hydrocarbon exchange with fluids, whereas samples with excess air can be used to quantify the extent of EOR. Determining noble

  20. Signature change events: a challenge for quantum gravity?

    International Nuclear Information System (INIS)

    White, Angela; Weinfurtner, Silke; Visser, Matt

    2010-01-01

    Within the framework of either Euclidean (functional integral) quantum gravity or canonical general relativity the signature of the manifold is a priori unconstrained. Furthermore, recent developments in the emergent spacetime programme have led to a physically feasible implementation of (analogue) signature change events. This suggests that it is time to revisit the sometimes controversial topic of signature change in general relativity. Specifically, we shall focus on the behaviour of a quantum field defined on a manifold containing regions of different signature. We emphasize that regardless of the underlying classical theory, there are severe problems associated with any quantum field theory residing on a signature-changing background. (Such as the production of what is naively an infinite number of particles, with an infinite energy density.) We show how the problem of quantum fields exposed to finite regions of Euclidean-signature (Riemannian) geometry has similarities with the quantum barrier penetration problem. Finally we raise the question as to whether signature change transitions could be fully understood and dynamically generated within (modified) classical general relativity, or whether they require the knowledge of a theory of quantum gravity.