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Sample records for linking element specific

  1. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

    Directory of Open Access Journals (Sweden)

    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  2. ABO alleles are linked with haplotypes of an erythroid cell-specific regulatory element in intron 1 with a few exceptions attributable to genetic recombination.

    Science.gov (United States)

    Nakajima, T; Sano, R; Takahashi, Y; Watanabe, K; Kubo, R; Kobayashi, M; Takahashi, K; Takeshita, H; Kominato, Y

    2016-01-01

    Recent investigation of transcriptional regulation of the ABO genes has identified a candidate erythroid cell-specific regulatory element, named the +5·8-kb site, in the first intron of ABO. Six haplotypes of the site have been reported previously. The present genetic population study demonstrated that each haplotype was mostly linked with specific ABO alleles with a few exceptions, possibly as a result of hybrid formation between common ABO alleles. Thus, investigation of these haplotypes could provide a clue to further elucidation of ABO alleles. © 2015 International Society of Blood Transfusion.

  3. S-LINK, a data link interface specification for the LHC era

    International Nuclear Information System (INIS)

    Bij, H.C. van der; McLaren, R.A.; Boyle, O.

    1996-01-01

    In the Technical Proposals for ATLAS, CMS and ALICE there is a requirement for several thousand data links. Although there is an obvious need for standardization, this seems difficult to achieve as the links run at different speeds, over different distances and have various constraints of power consumption, size and radiation hardness. An additional complication is that today we cannot decide which will be the most cost effective technology for the implementation of the final links. Furthermore, we must allow designers of boards at each end of the link, for example readout electronics and input buffers, to work in parallel with the development of the links. The S-LINK is a new concept which should provide the benefits of standardization without the limitations. The S-LINK specification defines, at both ends of the link, a simple FIFO-like user interface which remains independent of the technology used to implement the physical link. The physical link provides transfer of event data and control words, error detection, optional flow control and test facilities. This paper describes the S-LINK specification and gives examples of the use of the S-LINK, the physical links being designed, and the test equipment that is being developed

  4. Link-N: The missing link towards intervertebral disc repair is species-specific.

    Directory of Open Access Journals (Sweden)

    Frances C Bach

    Full Text Available Degeneration of the intervertebral disc (IVD is a frequent cause for back pain in humans and dogs. Link-N stabilizes proteoglycan aggregates in cartilaginous tissues and exerts growth factor-like effects. The human variant of Link-N facilitates IVD regeneration in several species in vitro by inducing Smad1 signaling, but it is not clear whether this is species specific. Dogs with IVD disease could possibly benefit from Link-N treatment, but Link-N has not been tested on canine IVD cells. If Link-N appears to be effective in canines, this would facilitate translation of Link-N into the clinic using the dog as an in vivo large animal model for human IVD degeneration.This study's objective was to determine the effect of the human and canine variant of Link-N and short (s Link-N on canine chondrocyte-like cells (CLCs and compare this to those on already studied species, i.e. human and bovine CLCs. Extracellular matrix (ECM production was determined by measuring glycosaminoglycan (GAG content and histological evaluation. Additionally, the micro-aggregates' DNA content was measured. Phosphorylated (p Smad1 and -2 levels were determined using ELISA.Human (sLink-N induced GAG deposition in human and bovine CLCs, as expected. In contrast, canine (sLink-N did not affect ECM production in human CLCs, while it mainly induced collagen type I and II deposition in bovine CLCs. In canine CLCs, both canine and human (sLink-N induced negligible GAG deposition. Surprisingly, human and canine (sLink-N did not induce Smad signaling in human and bovine CLCs. Human and canine (sLink-N only mildly increased pSmad1 and Smad2 levels in canine CLCs.Human and canine (sLink-N exerted species-specific effects on CLCs from early degenerated IVDs. Both variants, however, lacked the potency as canine IVD regeneration agent. While these studies demonstrate the challenges of translational studies in large animal models, (sLink-N still holds a regenerative potential for humans.

  5. Variable Delay Element For Jitter Control In High Speed Data Links

    Science.gov (United States)

    Livolsi, Robert R.

    2002-06-11

    A circuit and method for decreasing the amount of jitter present at the receiver input of high speed data links which uses a driver circuit for input from a high speed data link which comprises a logic circuit having a first section (1) which provides data latches, a second section (2) which provides a circuit generates a pre-destorted output and for compensating for level dependent jitter having an OR function element and a NOR function element each of which is coupled to two inputs and to a variable delay element as an input which provides a bi-modal delay for pulse width pre-distortion, a third section (3) which provides a muxing circuit, and a forth section (4) for clock distribution in the driver circuit. A fifth section is used for logic testing the driver circuit.

  6. Reliable and Persistent Identification of Linked Data Elements

    Science.gov (United States)

    Wood, David

    Linked Data techniques rely upon common terminology in a manner similar to a relational database'vs reliance on a schema. Linked Data terminology anchors metadata descriptions and facilitates navigation of information. Common vocabularies ease the human, social tasks of understanding datasets sufficiently to construct queries and help to relate otherwise disparate datasets. Vocabulary terms must, when using the Resource Description Framework, be grounded in URIs. A current bestpractice on the World Wide Web is to serve vocabulary terms as Uniform Resource Locators (URLs) and present both human-readable and machine-readable representations to the public. Linked Data terminology published to theWorldWideWeb may be used by others without reference or notification to the publishing party. That presents a problem: Vocabulary publishers take on an implicit responsibility to maintain and publish their terms via the URLs originally assigned, regardless of the inconvenience such a responsibility may cause. Over the course of years, people change jobs, publishing organizations change Internet domain names, computers change IP addresses,systems administrators publish old material in new ways. Clearly, a mechanism is required to manageWeb-based vocabularies over a long term. This chapter places Linked Data vocabularies in context with the wider concepts of metadata in general and specifically metadata on the Web. Persistent identifier mechanisms are reviewed, with a particular emphasis on Persistent URLs, or PURLs. PURLs and PURL services are discussed in the context of Linked Data. Finally, historic weaknesses of PURLs are resolved by the introduction of a federation of PURL services to address needs specific to Linked Data.

  7. Cross-modal working memory binding and word recognition skills: how specific is the link?

    Science.gov (United States)

    Wang, Shinmin; Allen, Richard J

    2018-04-01

    Recent research has suggested that the creation of temporary bound representations of information from different sources within working memory uniquely relates to word recognition abilities in school-age children. However, it is unclear to what extent this link is attributable specifically to the binding ability for cross-modal information. This study examined the performance of Grade 3 (8-9 years old) children on binding tasks requiring either temporary association formation of two visual items (i.e., within-modal binding) or pairs of visually presented abstract shapes and auditorily presented nonwords (i.e., cross-modal binding). Children's word recognition skills were related to performance on the cross-modal binding task but not on the within-modal binding task. Further regression models showed that cross-modal binding memory was a significant predictor of word recognition when memory for its constituent elements, general abilities, and crucially, within-modal binding memory were taken into account. These findings may suggest a specific link between the ability to bind information across modalities within working memory and word recognition skills.

  8. Increased Elemental Specificity of Positron Annihilation Spectra

    International Nuclear Information System (INIS)

    Asoka-Kumar, P.; Alatalo, M.; Ghosh, V.J.; Kruseman, A.C.; Nielsen, B.; Lynn, K.G.

    1996-01-01

    Positron annihilation spectroscopy (PAS) is a sensitive probe for studying the electronic structure of defects in solids. We show that the high-momentum part of the Doppler-broadened annihilation spectra can be used to distinguish different elements. This is achieved by using a new two-detector coincidence system to examine the line shape variations originating from high-momentum core electrons. Because the core electrons retain their atomic character even when atoms form a solid, these results can be directly compared to simple theoretical predictions. The new approach adds increased elemental specificity to the PAS technique, and is useful in studying the elemental variations around a defect site. copyright 1996 The American Physical Society

  9. Survey of elemental specificity in positron annihilation peak shapes

    Science.gov (United States)

    Myler, U.; Simpson, P. J.

    1997-12-01

    Recently the detailed interpretation of positron-annihilation γ-ray peak shapes has proven to be of interest with respect to their chemical specificity. In this contribution, we show highly resolved spectra for a number of different elements. To this purpose, annihilation spectra with strongly reduced background intensities were recorded in the two detector geometry, using a variable-energy positron beam. Division of the subsequently normalized spectra by a standard spectrum (in our case the spectrum of pure silicon) yields quotient spectra, which display features characteristic of the sample material. First we ascertain that the specific spectrum of an element is conserved in different chemical compounds, demonstrated here by identical oxygen spectra obtained from both SiO2/Si and MgO/Mg. Second, we show highly resolved spectra for a number of different elements (Fe...Zn, Ag, Ir...Au). We show that the characteristic features in these spectra vary in a systematic fashion with the atomic number of the element and can be tentatively identified with particular orbitals. Finally, for 26 different elements we compare the maximum intensity in the quotient spectra with the relative atomic density in the corresponding element. To our knowledge, this is the most comprehensive survey of such data made to date.

  10. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

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    Nicholas C. Gomez

    2016-11-01

    Full Text Available Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by distinct histone modifications. Differentiation is accompanied by chromatin remodeling at repetitive elements associated with altered expression of genes in relevant developmental pathways. Remarkably, we found that the chromatin environment of Ewing sarcoma, a mesenchymally derived tumor, is shared with primary mesenchymal stem cells (MSCs. Accessibility at repetitive elements in MSCs offers a permissive environment that is exploited by the critical oncogene responsible for this cancer. Our data demonstrate that stem cells harbor a unique chromatin landscape characterized by accessibility at repetitive elements, a feature associated with differentiation and oncogenesis.

  11. Air rudder mechanism dynamics considering two elements:Joint clearance and link flexibility

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yuntao; Quan, Qiquan; Li, He; Tang, Dewei; Li, Zhonghong; Fan, Wenyang; Deng, Zongquan [Harbin Institute of Technology, Harbin (China)

    2017-07-15

    Both the impact phenomenon in the clearance revolute joint and the link deformation will influence the dynamics of the air rudder transmission mechanism, which could reduce the flight quality of an aircraft. Given the effect of the two elements, a feasible simulation method with two improvements of previous methods is proposed to analyze the dynamic characteristics of the mechanism. In previous studies, the parameters of the contact force model in multi-body dynamics software were generally determined by experience, which may cause uncertainty in the calculation precision of the contact force. Furthermore, it is difficult to solve for the elastic link deformation in the practical mechanism using the available analytical methods due to the complicated section of the link. In this paper, a Continuous contact force (CCF) model was proposed and embedded in the ADAMS by developing a routine of the CCF model. Then, the flexible model was obtained by ANSYS to obtain the elastic link deformation. The experimental results indicate that the proposed simulation method can be effectively applied to predict the dynamic behavior of the mechanism.

  12. Development of Multidimensional Gap Conductance model using Virtual Link Gap Element

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyo Chan; Yang, Yong Sik; Kim, Dae Ho; Bang, Je Geon; Kim, Sun Ki; Koo, Yang Hyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-10-15

    The gap conductance that determines temperature gradient between pellet and cladding can be quite sensitive to gap thickness. For instance, once the gap size increases up to several micrometers in certain region, difference of pellet surface temperatures increases up to 100 Kelvin. Therefore, iterative thermo-mechanical coupled analysis is required to solve temperature distribution throughout pellet and cladding. Recently, multidimensional fuel performance codes have been being developed in the advanced countries to evaluate thermal behavior of fuel for off normal conditions and DBA(design based accident) conditions using the Finite Element Method (FEM). FRAPCON-FRAPTRAN code system, which is well known as the verified and reliable code, incorporates 1D thermal module and multidimensional mechanical module. In this code, multidimensional gap conductance model is not applied. ALCYONE developed by CEA introduces equivalent heat convection coefficient that represents multidimensional gap conductance as a function of gap thickness. BISON, which is multidimensional fuel performance code developed by INL, owns multidimensional gap conductance model using projected thermal contact. In general, thermal contact algorithm is nonlinear calculation which is expensive approach numerically. The gap conductance model for multi-dimension is difficult issue in terms of convergence and nonlinearity because gap conductance is function of gap thickness which depends on mechanical analysis at each iteration step. In this paper, virtual link gap (VLG) element has been proposed to resolve convergence issue and nonlinear characteristic of multidimensional gap conductance. In terms of calculation accuracy and convergence efficiency, the proposed VLG model was evaluated. LWR fuel performance codes should incorporate thermo-mechanical loop to solve gap conductance problem, iteratively. However, gap conductance in multidimensional model is difficult issue owing to its nonlinearity and

  13. Specificity determinants for the abscisic acid response element ?

    OpenAIRE

    Sarkar, Aditya Kumar; Lahiri, Ansuman

    2013-01-01

    Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interac...

  14. Mesh-morphing algorithms for specimen-specific finite element modeling.

    Science.gov (United States)

    Sigal, Ian A; Hardisty, Michael R; Whyne, Cari M

    2008-01-01

    Despite recent advances in software for meshing specimen-specific geometries, considerable effort is still often required to produce and analyze specimen-specific models suitable for biomechanical analysis through finite element modeling. We hypothesize that it is possible to obtain accurate models by adapting a pre-existing geometry to represent a target specimen using morphing techniques. Here we present two algorithms for morphing, automated wrapping (AW) and manual landmarks (ML), and demonstrate their use to prepare specimen-specific models of caudal rat vertebrae. We evaluate the algorithms by measuring the distance between target and morphed geometries and by comparing response to axial loading simulated with finite element (FE) methods. First a traditional reconstruction process based on microCT was used to obtain two natural specimen-specific FE models. Next, the two morphing algorithms were used to compute mappings from the surface of one model, the source, to the other, the target, and to use this mapping to morph the source mesh to produce a target mesh. The microCT images were then used to assign element-specific material properties. In AW the mappings were obtained by wrapping the source and target surfaces with an auxiliary triangulated surface. In ML, landmarks were manually placed on corresponding locations on the surfaces of both source and target. Both morphing algorithms were successful in reproducing the shape of the target vertebra with a median distance between natural and morphed models of 18.8 and 32.2 microm, respectively, for AW and ML. Whereas AW-morphing produced a surface more closely resembling that of the target, ML guaranteed correspondence of the landmark locations between source and target. Morphing preserved the quality of the mesh producing models suitable for FE simulation. Moreover, there were only minor differences between natural and morphed models in predictions of deformation, strain and stress. We therefore conclude that

  15. Specificity determinants for the abscisic acid response element.

    Science.gov (United States)

    Sarkar, Aditya Kumar; Lahiri, Ansuman

    2013-01-01

    Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences. We have also examined the variation in the stability of the protein-DNA complex upon mutating ABRE sequences using the protein design algorithm FoldX. The high throughput free energy calculations successfully predicted the ability of ABF1 to bind to alternative core motifs like GCGT or AAGT and also rationalized the role of the flanking sequences in determining the specificity of the protein-DNA interaction.

  16. Finite Element Analysis for Active-force Control on Vibration of a Flexible Single-link Manipulator

    Directory of Open Access Journals (Sweden)

    Abdul Kadir Muhammad

    2015-10-01

    Full Text Available The purposes of this research are to formulate the equations of motion of the system, to develop computational codes by a finite element analysis in order to perform dynamics simulation with vibration control, to propose an effective control scheme using active-force (AF control a flexible single-link manipulator. The system used in this paper consists of an aluminum beam as a flexible link, a clamp-part, a servo motor to rotate the link and a piezoelectric actuator to control vibration. Computational codes on time history responses, FFT (Fast Fourier Transform processing and eigenvalues-eigenvectors analysis were developed to calculate dynamic behavior of the link. Furthermore, the AF control was designed to drive the piezoelectric actuator. Calculated results have revealed that the vibration of the system can be suppressed effectively.

  17. CONSIDERATIONS REGARDING THE SPECIFIC ELEMENTS OF THE REPURCHASE AGREEMENT (REPO

    Directory of Open Access Journals (Sweden)

    Bujorel Florea

    2014-11-01

    Full Text Available The current article focuses on the specific elements of the repurchase agreement, as they are regulated in the new Civil Code (Law no. 287/2009. In the beginning the author makes a general characterization of this type of contract, from the perspective of the specific elements regarding the contracting parties, the object of the contract and the moment of fulfilling certain obligations assumed by the parties. Then, the study defines the notions of “repo” and “reverse repo” and differentiates the repurchase agreement (repo from other similar contracts, configuring thus more clearly the analyzed convention. A specific element of the contract is represented by its legal nature of sui-generis contract, which the author explains by the fact that in the doctrine there is no unanimous opinion concerning this aspect. At the same time, the specificity of the repo is highlighted by presenting its main effects: the double transfer of property, the transmission of the accessory rights, the original buyer’s obligation to exercise his option, and the original seller’s obligations to make available for the original buyer the funds necessary for exercising the right of option and for making the payment. Last but not least, the specificity of this type of contract is revealed through reflecting the differences between the liquidation, prorogation and renewal of the debated convention. The study presents the viewpoints expressed in the literature, as well as the author’s opinions as regards the controversial legal problems in the studied field.

  18. Multiple cis-regulatory elements are involved in the complex regulation of the sieve element-specific MtSEO-F1 promoter from Medicago truncatula.

    Science.gov (United States)

    Bucsenez, M; Rüping, B; Behrens, S; Twyman, R M; Noll, G A; Prüfer, D

    2012-09-01

    The sieve element occlusion (SEO) gene family includes several members that are expressed specifically in immature sieve elements (SEs) in the developing phloem of dicotyledonous plants. To determine how this restricted expression profile is achieved, we analysed the SE-specific Medicago truncatula SEO-F1 promoter (PMtSEO-F1) by constructing deletion, substitution and hybrid constructs and testing them in transgenic tobacco plants using green fluorescent protein as a reporter. This revealed four promoter regions, each containing cis-regulatory elements that activate transcription in SEs. One of these segments also contained sufficient information to suppress PMtSEO-F1 transcription in the phloem companion cells (CCs). Subsequent in silico analysis revealed several candidate cis-regulatory elements that PMtSEO-F1 shares with other SEO promoters. These putative sieve element boxes (PSE boxes) are promising candidates for cis-regulatory elements controlling the SE-specific expression of PMtSEO-F1. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  19. Highly specific detection of genetic modification events using an enzyme-linked probe hybridization chip.

    Science.gov (United States)

    Zhang, M Z; Zhang, X F; Chen, X M; Chen, X; Wu, S; Xu, L L

    2015-08-10

    The enzyme-linked probe hybridization chip utilizes a method based on ligase-hybridizing probe chip technology, with the principle of using thio-primers for protection against enzyme digestion, and using lambda DNA exonuclease to cut multiple PCR products obtained from the sample being tested into single-strand chains for hybridization. The 5'-end amino-labeled probe was fixed onto the aldehyde chip, and hybridized with the single-stranded PCR product, followed by addition of a fluorescent-modified probe that was then enzymatically linked with the adjacent, substrate-bound probe in order to achieve highly specific, parallel, and high-throughput detection. Specificity and sensitivity testing demonstrated that enzyme-linked probe hybridization technology could be applied to the specific detection of eight genetic modification events at the same time, with a sensitivity reaching 0.1% and the achievement of accurate, efficient, and stable results.

  20. Photoshop Elements 5 The Missing Manual

    CERN Document Server

    Brundage, Barbara

    2006-01-01

    Anyone still think that Adobe Photoshop Elements is a toy version of the real thing? As the most popular photo-editing program on the market, Photoshop Elements not only has Photoshop's marvelous powers, but also has capabilities the mothership lacks. Each new version includes more tools designed specifically for today's consumer digital photo enthusiasts. The latest edition, Photoshop Elements 5, solidifies the reputation of this superb and inexpensive product with new scrapbook features, a link to online photo services, and many other improvements. In fact, there's so much to Photoshop Ele

  1. Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

    Science.gov (United States)

    Glinsky, Gennadi V

    2018-03-01

    regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

  2. Element-specific and site-specific ion desorption from adsorbed molecules by deep core-level photoexcitation at the K-edges

    CERN Document Server

    Baba, Y H

    2003-01-01

    This article reviews our recent works on the ion desorption from adsorbed and condensed molecules at low temperature following the core-level photoexcitations using synchrotron soft x-rays. The systems investigated here are adsorbed molecules with relatively heavy molecular weight containing third-row elements such as Si, P, S, and Cl. Compared with molecules composed of second-row elements, the highly element-specific and site-specific fragment-ion desorption were observed when we tune the photon energy at the dipole-allowed 1s -> sigma sup * (3p sup *) resonance. On the basis of the resonance Auger decay spectra around the 1s ionization thresholds, the observed highly specific ion desorption is interpreted by the localization of the excited electrons (here we call as 'spectator electrons') in the antibonding sigma sup * orbital. In order to separate the direct photo-induced process from the indirect processes triggered by the secondary electrons, the photon-stimulated ion desorption was also investigated in...

  3. OTULIN antagonizes LUBAC signaling by specifically hydrolyzing met1-linked polyubiquitin

    DEFF Research Database (Denmark)

    Keusekotten, K.; Elliott, P.R.; Kulathu, Y.

    2013-01-01

    The linear ubiquitin (Ub) chain assembly complex (LUBAC) is an E3 ligase that specifically assembles Met1-linked (also known as linear) Ub chains that regulate nuclear factor κB (NF-κB) signaling. Deubiquitinases (DUBs) are key regulators of Ub signaling, but a dedicated DUB for Met1 linkages has...... not been identified. Here, we reveal a previously unannotated human DUB, OTULIN (also known as FAM105B), which is exquisitely specific for Met1 linkages. Crystal structures of the OTULIN catalytic domain in complex with diubiquitin reveal Met1-specific Ub-binding sites and a mechanism of substrate...

  4. Data-processing strategies for nano-tomography with elemental specification

    Science.gov (United States)

    Liu, Yijin; Cats, Korneel H.; Nelson Weker, Johanna; Andrews, Joy C.; Weckhuysen, Bert M.; Pianetta, Piero

    2013-10-01

    Combining the energy tunability provided by synchrotron X-ray sources with transmission X-ray microscopy, the morphology of materials can be resolved in 3D at spatial resolution down to 30 nm with elemental/chemical specification. In order to study the energy dependence of the absorption coefficient over the investigated volume, the tomographic reconstruction and image registration (before and/or after the tomographic reconstruction) are critical. We show in this paper the comparison of two different data processing strategies and conclude that the signal to noise ratio (S/N) in the final result can be improved via performing tomographic reconstruction prior to the evaluation of energy dependence. Our result echoes the dose fractionation theorem, and is particularly helpful when the element of interest has low concentration.

  5. Finite Element Analysis for Active-force Control on Vibration of a Flexible Single-link Manipulator

    Directory of Open Access Journals (Sweden)

    Abdul Kadir Muhammad

    2017-03-01

    Full Text Available The purposes of this research are to formulate theequations of motion of the system, to develop computationalcodes by a finite element analysis in order to perform dynamicssimulation with vibration control, to propose an effective controlscheme using active-force (AF control a flexible single-linkmanipulator. The system used in this paper consists of analuminum beam as a flexible link, a clamp-part, a servo motor torotate the link and a piezoelectric actuator to control vibration.Computational codes on time history responses, FFT (FastFourier Transform processing and eigenvalues-eigenvectorsanalysis were developed to calculate dynamic behavior of thelink. Furthermore, the AF control was designed to drive thepiezoelectric actuator. Calculated results have revealed that thevibration of the system can be suppressed effectively

  6. A constructionist review of morality and emotions: no evidence for specific links between moral content and discrete emotions.

    Science.gov (United States)

    Cameron, C Daryl; Lindquist, Kristen A; Gray, Kurt

    2015-11-01

    Morality and emotions are linked, but what is the nature of their correspondence? Many "whole number" accounts posit specific correspondences between moral content and discrete emotions, such that harm is linked to anger, and purity is linked to disgust. A review of the literature provides little support for these specific morality-emotion links. Moreover, any apparent specificity may arise from global features shared between morality and emotion, such as affect and conceptual content. These findings are consistent with a constructionist perspective of the mind, which argues against a whole number of discrete and domain-specific mental mechanisms underlying morality and emotion. Instead, constructionism emphasizes the flexible combination of basic and domain-general ingredients such as core affect and conceptualization in creating the experience of moral judgments and discrete emotions. The implications of constructionism in moral psychology are discussed, and we propose an experimental framework for rigorously testing morality-emotion links. © 2015 by the Society for Personality and Social Psychology, Inc.

  7. Element specificity of ortho-positronium annihilation for alkali-metal loaded SiO2 glasses.

    Science.gov (United States)

    Sato, K; Hatta, T

    2015-03-07

    Momentum distributions associated with ortho-positronium (o-Ps) pick-off annihilation photon are often influenced by light elements, as, e.g., carbon, oxygen, and fluorine. This phenomenon, so-called element specificity of o-Ps pick-off annihilation, has been utilized for studying the elemental environment around the open spaces. To gain an insight into the element specificity of o-Ps pick-off annihilation, the chemical shift of oxygen 1s binding energy and the momentum distributions associated with o-Ps pick-off annihilation were systematically investigated for alkali-metal loaded SiO2 glasses by means of X-ray photoelectron spectroscopy and positron-age-momentum correlation spectroscopy, respectively. Alkali metals introduced into the open spaces surrounded by oxygen atoms cause charge transfer from alkali metals to oxygen atoms, leading to the lower chemical shift for the oxygen 1s binding energy. The momentum distribution of o-Ps localized into the open spaces is found to be closely correlated with the oxygen 1s chemical shift. This correlation with the deepest 1s energy level evidences that the element specificity of o-Ps originates from pick-off annihilation with orbital electrons, i.e., dominantly with oxygen 2p valence electrons and s electrons with lower probability.

  8. CRISPR/Cas9 Promotes Functional Study of Testis Specific X-Linked Gene In Vivo.

    Directory of Open Access Journals (Sweden)

    Minyan Li

    Full Text Available Mammalian spermatogenesis is a highly regulated multistage process of sperm generation. It is hard to uncover the real function of a testis specific gene in vitro since the in vitro model is not yet mature. With the development of the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 system, we can now rapidly generate knockout mouse models of testis specific genes to study the process of spermatogenesis in vivo. SYCP3-like X-linked 2 (SLX2 is a germ cell specific component, which contains a Cor1 domain and belongs to the XLR (X-linked, lymphocyte regulated family. Previous studies suggested that SLX2 might play an important role in mouse spermatogenesis based on its subcellular localization and interacting proteins. However, the function of SLX2 in vivo is still elusive. Here, to investigate the functions of SLX2 in spermatogenesis, we disrupted the Slx2 gene by using the CRISPR/Cas9 system. Since Slx2 is a testis specific X-linked gene, we obtained knockout male mice in the first generation and accelerated the study process. Compared with wild-type mice, Slx2 knockout mice have normal testis and epididymis. Histological observation of testes sections showed that Slx2 knockout affected none of the three main stages of spermatogenesis: mitosis, meiosis and spermiogenesis. In addition, we further confirmed that disruption of Slx2 did not affect the number of spermatogonial stem cells, meiosis progression or XY body formation by immunofluorescence analysis. As spermatogenesis was normal in Slx2 knockout mice, these mice were fertile. Taken together, we showed that Slx2 itself is not an essential gene for mouse spermatogenesis and CRISPR/Cas9 technique could speed up the functional study of testis specific X-linked gene in vivo.

  9. Link-Based Similarity Measures Using Reachability Vectors

    Directory of Open Access Journals (Sweden)

    Seok-Ho Yoon

    2014-01-01

    Full Text Available We present a novel approach for computing link-based similarities among objects accurately by utilizing the link information pertaining to the objects involved. We discuss the problems with previous link-based similarity measures and propose a novel approach for computing link based similarities that does not suffer from these problems. In the proposed approach each target object is represented by a vector. Each element of the vector corresponds to all the objects in the given data, and the value of each element denotes the weight for the corresponding object. As for this weight value, we propose to utilize the probability of reaching from the target object to the specific object, computed using the “Random Walk with Restart” strategy. Then, we define the similarity between two objects as the cosine similarity of the two vectors. In this paper, we provide examples to show that our approach does not suffer from the aforementioned problems. We also evaluate the performance of the proposed methods in comparison with existing link-based measures, qualitatively and quantitatively, with respect to two kinds of data sets, scientific papers and Web documents. Our experimental results indicate that the proposed methods significantly outperform the existing measures.

  10. Functional dissection of the promoter of the pollen-specific gene NTP303 reveals a novel pollen-specific, and conserved cis-regulatory element.

    Science.gov (United States)

    Weterings, K; Schrauwen, J; Wullems, G; Twell, D

    1995-07-01

    Regulatory elements within the promoter of the pollen-specific NTP303 gene from tobacco were analysed by transient and stable expression analyses. Analysis of precisely targeted mutations showed that the NTP303 promoter is not regulated by any of the previously described pollen-specific cis-regulatory elements. However, two adjacent regions from -103 to -86 bp and from -86 to -59 bp were shown to contain sequences which positively regulated the NTP303 promoter. Both of these regions were capable of driving pollen-specific expression from a heterologous promoter, independent of orientation and in an additive manner. The boundaries of the minimal, functional NTP303 promoter were determined to lie within the region -86 to -51 bp. The sequence AAATGA localized from -94 to -89 bp was identified as a novel cis-acting element, of which the TGA triplet was shown to comprise an active part. This element was shown to be completely conserved in the similarly regulated promoter of the Bp 10 gene from Brassica napus encoding a homologue of the NTP303 gene.

  11. A prosthesis-specific multi-link segment model of lower-limb amputee sprinting.

    Science.gov (United States)

    Rigney, Stacey M; Simmons, Anne; Kark, Lauren

    2016-10-03

    Lower-limb amputees commonly utilize non-articulating energy storage and return (ESAR) prostheses for high impact activities such as sprinting. Despite these prostheses lacking an articulating ankle joint, amputee gait analysis conventionally features a two-link segment model of the prosthetic foot. This paper investigated the effects of the selected link segment model׳s marker-set and geometry on a unilateral amputee sprinter׳s calculated lower-limb kinematics, kinetics and energetics. A total of five lower-limb models of the Ottobock ® 1E90 Sprinter were developed, including two conventional shank-foot models that each used a different version of the Plug-in-Gait (PiG) marker-set to test the effect of prosthesis ankle marker location. Two Hybrid prosthesis-specific models were then developed, also using the PiG marker-sets, with the anatomical shank and foot replaced by prosthesis-specific geometry separated into two segments. Finally, a Multi-link segment (MLS) model was developed, consisting of six segments for the prosthesis as defined by a custom marker-set. All full-body musculoskeletal models were tested using four trials of experimental marker trajectories within OpenSim 3.2 (Stanford, California, USA) to find the affected and unaffected hip, knee and ankle kinematics, kinetics and energetics. The geometry of the selected lower-limb prosthesis model was found to significantly affect all variables on the affected leg (p prosthesis-specific spatial, inertial and elastic properties from full-body models significantly affects the calculated amputee gait characteristics, and we therefore recommend the implementation of a MLS model. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Toward an evidence-based patient-provider communication in rehabilitation: linking communication elements to better rehabilitation outcomes.

    Science.gov (United States)

    Jesus, Tiago Silva; Silva, Isabel Lopes

    2016-04-01

    There is a growing interest in linking aspects of patient-provider communication to rehabilitation outcomes. However, the field lacks a conceptual understanding on: (a) 'how' rehabilitation outcomes can be improved by communication; and (b) through 'which' elements in particular. This article elaborates on the conceptual developments toward informing further practice and research. Existing models of communication in healthcare were adapted to rehabilitation, and its outcomes through a comprehensive literature review. After depicting mediating mechanisms and variables (e.g. therapeutic engagement, adjustment toward disability), this article presents the '4 Rehab Communication Elements' deemed likely to underpin rehabilitation outcomes. The four elements are: (a) knowing the person and building a supportive relationship; (b) effective information exchange and education; (c) shared goal-setting and action planning; and (d) fostering a more positive, yet realistic, cognitive and self-reframing. This article describes an unprecedented, outcomes-oriented approach toward the design of rehabilitation communication, which has resulted in the development of a new intervention model: the '4 Rehab Communication Elements'. Further trials are needed to evaluate the impact of this whole intervention model on rehabilitation outcomes. © The Author(s) 2015.

  13. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

    Science.gov (United States)

    Davies, Kalina T J; Tsagkogeorga, Georgia; Rossiter, Stephen J

    2014-12-19

    The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise

  14. Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells.

    Science.gov (United States)

    Zhao, Ming-Tao; Shao, Ning-Yi; Hu, Shijun; Ma, Ning; Srinivasan, Rajini; Jahanbani, Fereshteh; Lee, Jaecheol; Zhang, Sophia L; Snyder, Michael P; Wu, Joseph C

    2017-11-10

    Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31 + CD144 + ), cardiac progenitor cells (Sca-1 + ), fibroblasts (DDR2 + ), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was identified with ubiquitous enhancer (H3K4me1) and promoter (H3K4me3) marks in all cell types, whereas class II was enriched with H3K4me1 and H3K4me3 in a cell type-specific manner. Both class I and class II regulatory elements exhibited stimulatory roles in nearby gene expression in a given cell type. However, class I promoters displayed more dominant regulatory effects on transcriptional abundance regardless of distal enhancers. Transcription factor network analysis indicated that human induced pluripotent stem cells and somatic cells from the heart selected their preferential regulatory elements to maintain cell type-specific gene expression. In addition, we validated the function of these enhancer elements in transgenic mouse embryos and human cells and identified a few enhancers that could possibly regulate the cardiac-specific gene expression. Given that a large number of genetic variants associated with human diseases are located in regulatory DNA elements, our study provides valuable resources for deciphering

  15. Development of an Enzyme Linked Immunosorbent Assay to Detect Chicken Parvovirus Specific Antibodies

    Science.gov (United States)

    Here we report the development and application of an enzyme linked immunosorbent assay to detect parvovirus-specific antibodies in chicken sera. We used an approach previously described for other parvoviruses to clone and express viral structural proteins in insect cells from recombinant baculovirus...

  16. Specific accumulation of 20 trace elements in great cormorants (Phalacrocorax carbo) from Japan

    International Nuclear Information System (INIS)

    Nam, Dong-Ha; Anan, Yasumi; Ikemoto, Tokutaka; Okabe, Yuko; Kim, Eun-Young; Subramanian, Annamalai; Saeki, Kazutoshi; Tanabe, Shinsuke

    2005-01-01

    This study is to elucidate the specific accumulation of 20 trace elements in tissues/organs of great cormorants from two different colonies (Lake Biwa and Mie) in Japan. In the body distribution of trace elements, some elements revealed tissue-specific accumulation such as most of the burden of Mo, Ag and Cd in liver, Tl and Cd in kidney, Cu, Rb and Cs in muscle, and V, Sr and Ba in bone. Gender-related variation was not observed in both populations for most of the trace elements, except for higher hepatic Sr in males from Lake Biwa. Hepatic V, muscular Hg and Tl, and Cd in liver, kidney and muscle increased with growth. Comparison of trace element levels in tissues between the two colonies showed that Cr, Rb, Sr, Cd, Cs, Ba and Tl levels were higher in Lake Biwa than in Mie, whereas Zn, Co and Hg in Mie samples were greater than Lake Biwa. Variations of elemental levels in stomach contents also showed similar patterns, thus, showing that dietary sources tended to be the main factor for these regional variations. Toxic Hg and Cd concentrations in the liver of cormorants from the two colonies were lower than those from other areas, implying relatively low exposure to these metals in the present study sites. Concentrations of V, Co, Ag, Cd, Cs, Hg, Tl, Pb and Bi in liver remained more or less at the same level between 1993 and 2003, while hepatic Cr, Mn, Cu, Zn, Se, Rb, Sr and Ba showed apparent decrease, which might be related to the biological factors. - Dietary sources seemed to be the main reason for variable results

  17. Linking chemical elements in forest floor humus (Oh-horizon) in the Czech Republic to contamination sources

    International Nuclear Information System (INIS)

    Sucharova, Julie; Suchara, Ivan; Hola, Marie; Reimann, Clemens; Boyd, Rognvald; Filzmoser, Peter; Englmaier, Peter

    2011-01-01

    While terrestrial moss and other plants are frequently used for environmental mapping and monitoring projects, data on the regional geochemistry of humus are scarce. Humus, however, has a much larger life span than any plant material. It can be seen as the 'environmental memory' of an area for at least the last 60-100 years. Here concentrations of 39 elements determined by ICP-MS and ICP AES, pH and ash content are presented for 259 samples of forest floor humus collected at an average sample density of 1 site/300 km 2 in the Czech Republic. The scale of anomalies linked to known contamination sources (e.g., lignite mining and burning, metallurgical industry, coal fired power plants, metal smelters) is documented and discussed versus natural processes influencing humus quality. Most maps indicate a local impact from individual contamination sources: often more detailed sampling than used here would be needed to differentiate between likely sources. - Highlights: → Concentrations of 39 elements in forest floor humus are provided. → The capabilities of humus sampling for bio-monitoring purposes are demonstrated. → Geochemical anomalies are linked to known contamination sources. → The study shows the importance of scale for geochemical mapping projects. → Humus provides a picture of the long term contamination history of a country. - Forest floor humus, the atmosphere-biosphere-pedosphere interface, archives an environmental contamination signal over long time periods.

  18. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

    Directory of Open Access Journals (Sweden)

    Ryan M. Williams

    2014-01-01

    Full Text Available Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE specific for bromacil. We have identified one MRE with high affinity (Kd=9.6 nM and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.

  19. Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements.

    Science.gov (United States)

    Hayes, James E; Trynka, Gosia; Vijai, Joseph; Offit, Kenneth; Raychaudhuri, Soumya; Klein, Robert J

    2015-01-01

    Though numerous polymorphisms have been associated with risk of developing lymphoma, how these variants function to promote tumorigenesis is poorly understood. Here, we report that lymphoma risk SNPs, especially in the non-Hodgkin's lymphoma subtype chronic lymphocytic leukemia, are significantly enriched for co-localization with epigenetic marks of active gene regulation. These enrichments were seen in a lymphoid-specific manner for numerous ENCODE datasets, including DNase-hypersensitivity as well as multiple segmentation-defined enhancer regions. Furthermore, we identify putatively functional SNPs that are both in regulatory elements in lymphocytes and are associated with gene expression changes in blood. We developed an algorithm, UES, that uses a Monte Carlo simulation approach to calculate the enrichment of previously identified risk SNPs in various functional elements. This multiscale approach integrating multiple datasets helps disentangle the underlying biology of lymphoma, and more broadly, is generally applicable to GWAS results from other diseases as well.

  20. Element-specific density profiles in interacting biomembrane models

    International Nuclear Information System (INIS)

    Schneck, Emanuel; Rodriguez-Loureiro, Ignacio; Bertinetti, Luca; Gochev, Georgi; Marin, Egor; Novikov, Dmitri; Konovalov, Oleg

    2017-01-01

    Surface interactions involving biomembranes, such as cell–cell interactions or membrane contacts inside cells play important roles in numerous biological processes. Structural insight into the interacting surfaces is a prerequisite to understand the interaction characteristics as well as the underlying physical mechanisms. Here, we work with simplified planar experimental models of membrane surfaces, composed of lipids and lipopolymers. Their interaction is quantified in terms of pressure–distance curves using ellipsometry at controlled dehydrating (interaction) pressures. For selected pressures, their internal structure is investigated by standing-wave x-ray fluorescence (SWXF). This technique yields specific density profiles of the chemical elements P and S belonging to lipid headgroups and polymer chains, as well as counter-ion profiles for charged surfaces. (paper)

  1. Cross-Linking Mast Cell Specific Gangliosides Stimulates the Release of Newly Formed Lipid Mediators and Newly Synthesized Cytokines

    Directory of Open Access Journals (Sweden)

    Edismauro Garcia Freitas Filho

    2016-01-01

    Full Text Available Mast cells are immunoregulatory cells that participate in inflammatory processes. Cross-linking mast cell specific GD1b derived gangliosides by mAbAA4 results in partial activation of mast cells without the release of preformed mediators. The present study examines the release of newly formed and newly synthesized mediators following ganglioside cross-linking. Cross-linking the gangliosides with mAbAA4 released the newly formed lipid mediators, prostaglandins D2 and E2, without release of leukotrienes B4 and C4. The effect of cross-linking these gangliosides on the activation of enzymes in the arachidonate cascade was then investigated. Ganglioside cross-linking resulted in phosphorylation of cytosolic phospholipase A2 and increased expression of cyclooxygenase-2. Translocation of 5-lipoxygenase from the cytosol to the nucleus was not induced by ganglioside cross-linking. Cross-linking of GD1b derived gangliosides also resulted in the release of the newly synthesized mediators, interleukin-4, interleukin-6, and TNF-α. The effect of cross-linking the gangliosides on the MAP kinase pathway was then investigated. Cross-linking the gangliosides induced the phosphorylation of ERK1/2, JNK1/2, and p38 as well as activating both NFκB and NFAT in a Syk-dependent manner. Therefore, cross-linking the mast cell specific GD1b derived gangliosides results in the activation of signaling pathways that culminate with the release of newly formed and newly synthesized mediators.

  2. Gender-specific mediational links between parenting styles, parental monitoring, impulsiveness, drinking control, and alcohol-related problems.

    Science.gov (United States)

    Patock-Peckham, Julie A; King, Kevin M; Morgan-Lopez, Antonio A; Ulloa, Emilio C; Moses, Jennifer M Filson

    2011-03-01

    Recently, it has been suggested that traits may dynamically change as conditions change. One possible mechanism that may influence impulsiveness is parental monitoring. Parental monitoring reflects a knowledge regarding one's offspring's whereabouts and social connections. The aim of this investigation was to examine potential gender-specific parental influences to impulsiveness (general behavioral control), control over one's own drinking (specific behavioral control), and alcohol-related problems among individuals in a period of emerging adulthood. Direct and mediational links between parenting styles (permissive, authoritarian, and authoritative), parental monitoring, impulsiveness, drinking control, and alcohol-related problems were investigated. A multiple-group, SEM model with (316 women, 265 men) university students was examined. In general, the overall pattern among male and female respondents was distinct. For daughters, perceptions of a permissive father were indirectly linked to more alcohol-related problems through lower levels of monitoring by fathers and more impulsive symptoms. Perceptions of an authoritative father were also indirectly linked to fewer impulsive symptoms through higher levels of monitoring by fathers among daughters. For men, perceptions of a permissive mother were indirectly linked to more alcohol-related problems through lower levels of monitoring by mothers and more impulsive symptoms. For sons, perceptions of mother authoritativeness were indirectly linked to fewer alcohol-related problems through more monitoring by mothers and fewer impulsive symptoms. Monitoring by an opposite-gender parent mediated the link between parenting styles (i.e., permissive, authoritative) on impulsiveness.

  3. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

    Science.gov (United States)

    Muramoto, Hiroki; Yagi, Shintaro; Hirabayashi, Keiji; Sato, Shinya; Ohgane, Jun; Tanaka, Satoshi; Shiota, Kunio

    2010-08-01

    Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T-DMRs were predominantly present in SINE-rich/LINE-poor genomic loci. The enrichment for SINEs spread over 300 kb in cis and there existed SINE-rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T-DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T-DMRs in ESCs at Dppa3 gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T-DMRs in ESCs, which is a novel aspect of the ESC-specific epigenomic information.

  4. Identification and characterization of cell-specific enhancer elements for the mouse ETF/Tead2 gene.

    Science.gov (United States)

    Tanoue, Y; Yasunami, M; Suzuki, K; Ohkubo, H

    2001-12-21

    We have identified and characterized by transient transfection assays the cell-specific 117-bp enhancer sequence in the first intron of the mouse ETF (Embryonic TEA domain-containing factor)/Tead2 gene required for transcriptional activation in ETF/Tead2 gene-expressing cells, such as P19 cells. The 117-bp enhancer contains one GC-rich sequence (5'-GGGGCGGGG-3'), termed the GC box, and two tandemly repeated GA-rich sequences (5'-GGGGGAGGGG-3'), termed the proximal and distal GA elements. Further analyses, including transfection studies and electrophoretic mobility shift assays using a series of deletion and mutation constructs, indicated that Sp1, a putative activator, may be required to predominate over its competition with another unknown putative repressor, termed the GA element-binding factor, for binding to both the GC box, which overlapped with the proximal GA element, and the distal GA element in the 117-bp sequence in order to achieve a full enhancer activity. We also discuss a possible mechanism underlying the cell-specific enhancer activity of the 117-bp sequence.

  5. Capturing structured, pulmonary disease-specific data elements in electronic health records.

    Science.gov (United States)

    Gronkiewicz, Cynthia; Diamond, Edward J; French, Kim D; Christodouleas, John; Gabriel, Peter E

    2015-04-01

    Electronic health records (EHRs) have the potential to improve health-care quality by allowing providers to make better decisions at the point of care based on electronically aggregated data and by facilitating clinical research. These goals are easier to achieve when key, disease-specific clinical information is documented as structured data elements (SDEs) that computers can understand and process, rather than as free-text/natural-language narrative. This article reviews the benefits of capturing disease-specific SDEs. It highlights several design and implementation considerations, including the impact on efficiency and expressivity of clinical documentation and the importance of adhering to data standards when available. Pulmonary disease-specific examples of collection instruments are provided from two commonly used commercial EHRs. Future developments that can leverage SDEs to improve clinical quality and research are discussed.

  6. Selective pressures to maintain attachment site specificity of integrative and conjugative elements.

    Directory of Open Access Journals (Sweden)

    Kayla L Menard

    Full Text Available Integrative and conjugative elements (ICEs are widespread mobile genetic elements that are usually found integrated in bacterial chromosomes. They are important agents of evolution and contribute to the acquisition of new traits, including antibiotic resistances. ICEs can excise from the chromosome and transfer to recipients by conjugation. Many ICEs are site-specific in that they integrate preferentially into a primary attachment site in the bacterial genome. Site-specific ICEs can also integrate into secondary locations, particularly if the primary site is absent. However, little is known about the consequences of integration of ICEs into alternative attachment sites or what drives the apparent maintenance and prevalence of the many ICEs that use a single attachment site. Using ICEBs1, a site-specific ICE from Bacillus subtilis that integrates into a tRNA gene, we found that integration into secondary sites was detrimental to both ICEBs1 and the host cell. Excision of ICEBs1 from secondary sites was impaired either partially or completely, limiting the spread of ICEBs1. Furthermore, induction of ICEBs1 gene expression caused a substantial drop in proliferation and cell viability within three hours. This drop was dependent on rolling circle replication of ICEBs1 that was unable to excise from the chromosome. Together, these detrimental effects provide selective pressure against the survival and dissemination of ICEs that have integrated into alternative sites and may explain the maintenance of site-specific integration for many ICEs.

  7. Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis.

    Science.gov (United States)

    Shim, Won-Bo; Dunkle, Larry D

    2005-01-01

    Two fungal pathogens, Cercospora zeae-maydis Groups I and II, cause gray leaf spot of maize. During the sequencing of a cosmid library from C. zeae-maydis Group I, we discovered a sequence with high similarity to Maggy, a transposable element from Magnaporthe grisea. The element from C. zeae-maydis, named Malazy, contained 194-base-pair terminal repeats and sequences with high similarity to reverse transcriptase and integrase, components of the POL gene in the gypsy-like retrotransposons in fungi. Sequences with similarity to other POL gene components, protease and ribonuclease, were not detected in Malazy. A single copy of the element was detected by PCR and Southern analyses in all six North American isolates of C. zeae-maydis Group I but was not detected in the four isolates of C. zeae-maydis Group II from three continents or in phylogenetically related species. Fragments of the core domains of reverse transcriptase and integrase contained a high frequency of stop codons that were conserved in all six isolates of Group I. Additional C:G to T:A transitions in occasional isolates usually were silent mutations, while two resulted in isolate-specific stop codons. The absence of Malazy from related species suggests that it was acquired after the divergence of C. zeae-maydis Groups I and II. The high frequency of stop codons and the presence of a single copy of the element suggest that it was inactivated soon after it was acquired. Because the element is inactive and because reading frames for other genes were not found in sequences flanking the element, Malazy does not appear to be the cause of differences leading to speciation or genetic diversity between C. zeae-maydis Groups I and II.

  8. Trace elements at the intersection of marine biological and geochemical evolution

    Science.gov (United States)

    Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

    2016-01-01

    Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

  9. Evaluation of Populus and Salix continuously irrigated with landfill leachate I. Genotype-specific elemental phytoremediation.

    Science.gov (United States)

    Zalesny, Ronald S; Bauer, Edmund O

    2007-01-01

    There is a need for the identification and selection of specific tree genotypes that can sequester elements from contaminated soils, with elevated rates of uptake. We irrigated Populus (DN17, DN182, DN34, NM2, NM6) and Salix (94003, 94012, S287, S566, SX61) genotypes planted in large soil-filled containers with landfill leachate or municipal water and tested for differences in inorganic element concentrations (P, K, Ca, Mg, S, Zn, B, Mn, Fe, Cu, Al, Na, and Cl) in the leaves, stems, and roots. Trees were irrigated with leachate or water during the final 12 wk of the 18-wk study. Genotype-specific uptake existed. For genera, tissue concentrations exhibited four responses. First, Populus had the greatest uptake of P, K, S, Cu, and Cl. Second, Salix exhibited the greatest uptake of Zn, B, Fe, and Al. Third, Salix had greater concentrations of Ca and Mg in leaves, while Populus had greater concentrations in stems and roots. Fourth, Populus had greater concentrations of Mn and Na in leaves and stems, while Salix had greater concentrations in roots. Populus deltoides x P. nigra clones exhibited better overall phytoremediation than the P. nigra x P. maximowiczii genotypes tested. Phytoremediation for S. purpurea clones 94003 and 94012 was generally less than for other Salix genotypes. Overall, concentrations of elements in the leaves, stems, and roots corroborated those in the plant-sciences literature. Uptake was dependent upon the specific genotype for most elements. Our results corroborated the need for further testing and selecting of specific clones for various phytoremediation needs, while providing a baseline for future researchers developing additional studies and resource managers conducting on-site remediation.

  10. Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription.

    Science.gov (United States)

    Jiang, Nan; Emberly, Eldon; Cuvier, Olivier; Hart, Craig M

    2009-07-01

    Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.

  11. Cell type-specific termination of transcription by transposable element sequences.

    Science.gov (United States)

    Conley, Andrew B; Jordan, I King

    2012-09-30

    Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. Rarefaction curve analysis suggests that there may be twice as many TE-derived termination sites (TE-TTS) genome-wide among all human cell types. The local chromatin environment for these TE-TTS is similar to that seen for 3' UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. Alu sequences were found to provide a large number of relatively weak TTS, whereas LTR elements provided a smaller number of much stronger TTS. TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. Thus, TE sequences provide a powerful mechanism for the diversification of transcriptional profiles between cell types and among evolutionary lineages, since most TE-TTS are evolutionarily young. The extent of transcription

  12. Mutations in Cytosine-5 tRNA Methyltransferases Impact Mobile Element Expression and Genome Stability at Specific DNA Repeats

    Directory of Open Access Journals (Sweden)

    Bianca Genenncher

    2018-02-01

    Full Text Available The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5 RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects. In contrast, NSun2 function affected mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicated that tRNA-dependent processes affected mobile element expression and DNA repeat stability. Importantly, further experiments indicated that complex formation with RNA could also contribute to the impact of RCMT function on gene expression control. These results thus uncover a link between tRNA modification enzymes, the expression of repeat DNA, and genomic integrity.

  13. Theoretical basis for a transient thermal elastic-plastic stress analysis of nuclear reactor fuel elements

    International Nuclear Information System (INIS)

    Hsu, T.R.; Bertels, A.W.M.; Banerjee, S.; Harrison, W.C.

    1976-07-01

    This report presents the theoretical basis for a transient thermal elastic-plastic stress analysis of a nuclear reactor fuel element subject to severe transient thermo-mechanical loading. A finite element formulation is used for both the non-linear stress analysis and thermal analysis. These two major components are linked together to form an integrated program capable of predicting fuel element transient behaviour in two dimensions. Specific case studies are presented to illustrate capabilities of the analysis. (author)

  14. Linking chemical elements in forest floor humus (O{sub h}-horizon) in the Czech Republic to contamination sources

    Energy Technology Data Exchange (ETDEWEB)

    Sucharova, Julie; Suchara, Ivan; Hola, Marie [Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Kvetnove namesti 391, 252 43 Pruhonice (Czech Republic); Reimann, Clemens, E-mail: Clemens.Reimann@ngu.no [Geological Survey of Norway, P.O. Box 6315 Sluppen, 7491 Trondheim (Norway); Boyd, Rognvald [Geological Survey of Norway, P.O. Box 6315 Sluppen, 7491 Trondheim (Norway); Filzmoser, Peter [Institute for Statistics and Probability Theory, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Wien (Austria); Englmaier, Peter [Faculty of Life Science, University of Vienna, Althanstr. 14, A-1090 Vienna (Austria)

    2011-05-15

    While terrestrial moss and other plants are frequently used for environmental mapping and monitoring projects, data on the regional geochemistry of humus are scarce. Humus, however, has a much larger life span than any plant material. It can be seen as the 'environmental memory' of an area for at least the last 60-100 years. Here concentrations of 39 elements determined by ICP-MS and ICP AES, pH and ash content are presented for 259 samples of forest floor humus collected at an average sample density of 1 site/300 km{sup 2} in the Czech Republic. The scale of anomalies linked to known contamination sources (e.g., lignite mining and burning, metallurgical industry, coal fired power plants, metal smelters) is documented and discussed versus natural processes influencing humus quality. Most maps indicate a local impact from individual contamination sources: often more detailed sampling than used here would be needed to differentiate between likely sources. - Highlights: > Concentrations of 39 elements in forest floor humus are provided. > The capabilities of humus sampling for bio-monitoring purposes are demonstrated. > Geochemical anomalies are linked to known contamination sources. > The study shows the importance of scale for geochemical mapping projects. > Humus provides a picture of the long term contamination history of a country. - Forest floor humus, the atmosphere-biosphere-pedosphere interface, archives an environmental contamination signal over long time periods.

  15. Cell type-specific termination of transcription by transposable element sequences

    Directory of Open Access Journals (Sweden)

    Conley Andrew B

    2012-09-01

    Full Text Available Abstract Background Transposable elements (TEs encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. Results Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. Rarefaction curve analysis suggests that there may be twice as many TE-derived termination sites (TE-TTS genome-wide among all human cell types. The local chromatin environment for these TE-TTS is similar to that seen for 3′ UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. Alu sequences were found to provide a large number of relatively weak TTS, whereas LTR elements provided a smaller number of much stronger TTS. Conclusions TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. Thus, TE sequences provide a powerful mechanism for the diversification of transcriptional profiles between cell types and among evolutionary lineages, since most TE-TTS are

  16. Review of element-specific data for biosphere assessment BSA-2009

    International Nuclear Information System (INIS)

    Helin, J.; Ikonen, A. T. K.; Hjerpe, T.

    2010-06-01

    A literature review on distribution coefficients (Kd) to soil, sediment and suspended matter and on concentration ratios to forest, aquatic and crop plants and to edibles was performed and is documented in this report. The literature data were combined, in some cases involving also site-specific data, using the methods of Bayesian updating. Their application is also explained in the report. Based on the derived data, aggregated concentration ratios (production-weighted average concentration ratio to edibles specific to an ecosystem type) were calculated. Finally, the quality of the established data basis is evaluated. The work provides the 2009 biosphere assessment of spent nuclear fuel disposal the in Olkiluoto site, BSA-2009, with the abovementioned parameter values and distributions, but most importantly demonstrates the methodology adopted to combine various data sources and derive such assessment data. It is acknowledged that for many parameters and/or elements the data basis needs improvement by the forthcoming 2012 assessment. (orig.)

  17. Covalent cross-linking of insulin-like growth factor-1 to a specific inhibitor from human serum

    International Nuclear Information System (INIS)

    Ooi, G.T.; Herington, A.C.

    1986-01-01

    Previous studies have shown that a specific inhibitor of insulin-like growth factor (IGF) action in vitro can be isolated from normal human serum and subsequently partially purified on an IGF-affinity column. The ability of the inhibitor to bind the IGFs has now been confirmed directly using covalent cross-linking techniques. When 125 I-IGF-1 was cross-linked to inhibitor using disuccinimidyl suberate, five specifically labelled bands were seen on SDS-PAGE and autoradiography. Two bands (MW 21.5 K and 25.5 K) were intensely labelled, while the remaining three (MW 37 K, 34 K and 18 K) appeared as minor bands only. Inhibitor bioactivity, following further analysis by hydrophobic interaction chromatography or Con A-Sepharose affinity chromatography, was always associated with the presence of the 21.5 K and/or 25.5 K bands

  18. Atlas-Based Automatic Generation of Subject-Specific Finite Element Tongue Meshes.

    Science.gov (United States)

    Bijar, Ahmad; Rohan, Pierre-Yves; Perrier, Pascal; Payan, Yohan

    2016-01-01

    Generation of subject-specific 3D finite element (FE) models requires the processing of numerous medical images in order to precisely extract geometrical information about subject-specific anatomy. This processing remains extremely challenging. To overcome this difficulty, we present an automatic atlas-based method that generates subject-specific FE meshes via a 3D registration guided by Magnetic Resonance images. The method extracts a 3D transformation by registering the atlas' volume image to the subject's one, and establishes a one-to-one correspondence between the two volumes. The 3D transformation field deforms the atlas' mesh to generate the subject-specific FE mesh. To preserve the quality of the subject-specific mesh, a diffeomorphic non-rigid registration based on B-spline free-form deformations is used, which guarantees a non-folding and one-to-one transformation. Two evaluations of the method are provided. First, a publicly available CT-database is used to assess the capability to accurately capture the complexity of each subject-specific Lung's geometry. Second, FE tongue meshes are generated for two healthy volunteers and two patients suffering from tongue cancer using MR images. It is shown that the method generates an appropriate representation of the subject-specific geometry while preserving the quality of the FE meshes for subsequent FE analysis. To demonstrate the importance of our method in a clinical context, a subject-specific mesh is used to simulate tongue's biomechanical response to the activation of an important tongue muscle, before and after cancer surgery.

  19. Determination of the element-specific complex permittivity using a soft x-ray phase modulator

    Science.gov (United States)

    Kubota, Y.; Hirata, Y.; Miyawaki, J.; Yamamoto, S.; Akai, H.; Hobara, R.; Yamamoto, Sh.; Yamamoto, K.; Someya, T.; Takubo, K.; Yokoyama, Y.; Araki, M.; Taguchi, M.; Harada, Y.; Wadati, H.; Tsunoda, M.; Kinjo, R.; Kagamihata, A.; Seike, T.; Takeuchi, M.; Tanaka, T.; Shin, S.; Matsuda, I.

    2017-12-01

    We report on directly determining the complex permittivity tensor using a method combining a developed light source from a segmented cross undulator of synchrotron radiation and the magneto-optical Kerr effect. The empirical permittivity, which carries the electronic and magnetic information of a material, has element specificity and has perfect confirmation using the quantum-mechanical calculation for itinerant electrons systems. These results help in understanding the interaction of light and matter, and they provide an interesting approach to seek the best materials as optical elements, for example, in extended-ultraviolet lithographic technologies or in state-of-the-art laser technologies.

  20. Relationships and cardiovascular risk: perceived spousal ambivalence in specific relationship contexts and its links to inflammation

    NARCIS (Netherlands)

    Uchino, B.N.; Bosch, J.A.; Smith, T.W.; Carlisle, M.; Birmingham, W.; Bowen, K.S.; Light, K.C.; O'Hartaigh, B.

    2013-01-01

    Objectives: Although perceiving one’s social ties as sources of ambivalence has been linked to negative health outcomes, the more specific contexts by which such relationships influence health remain less studied. We thus examined if perceived spousal relationship quality in three theoretically

  1. Functional dissection of a napin gene promoter: identification of promoter elements required for embryo and endosperm-specific transcription.

    Science.gov (United States)

    Ellerström, M; Stålberg, K; Ezcurra, I; Rask, L

    1996-12-01

    The promoter region (-309 to +44) of the Brassica napus storage protein gene napA was studied in transgenic tobacco by successive 5' as well as internal deletions fused to the reporter gene GUS (beta-glucuronidase). The expression in the two main tissues of the seed, the endosperm and the embryo, was shown to be differentially regulated. This tissue-specific regulation within the seed was found to affect the developmental expression during seed development. The region between -309 to -152, which has a large effect on quantitative expression, was shown to harbour four elements regulating embryo and one regulating endosperm expression. This region also displayed enhancer activity. Deletion of eight bp from position -152 to position -144 totally abolished the activity of the napA promoter. This deletion disrupted a cis element with similarity to an ABA-responsive element (ABRE) overlapping with an E-box, demonstrating its crucial importance for quantitative expression. An internal deletion of the region -133 to -120, resulted in increased activity in both leaves and endosperm and a decreased activity in the embryo. Within this region, a cis element similar to the (CA)n element, found in other storage protein promoters, was identified. This suggest that the (CA)n element is important for conferring seed specificity by serving both as an activator and a repressor element.

  2. Development of the methodology on priority of element-specific biosphere parameters for geological disposal applicable to any proposed repository site

    International Nuclear Information System (INIS)

    Kato, Tomoko; Ohi, Takao; Suzuki, Yuji

    2009-01-01

    It is difficult to acquire all of biosphere parameters for geological disposal at the repository site because several hundreds of the parameters have to be dealt with in one calculation case of the biosphere assessment. Before site-specific activities, it is important to develop the data acquisition methodology of biosphere parameters applicable to any proposed repository site. The methodology for identification of the priority of the parameters was developed for the effective data acquisition of biosphere parameters at the site. First of all, flow diagram was constructed to evaluate the availability of the existing generic biosphere dataset. It was found to be effective for the data acquisition at the site to focus on the element-specific parameters with the existing dataset. Secondly, the priority of the data acquisition was identified for element-specific parameters at the site, with considering the variation of dose rate by combining the significant element-specific parameters. The availability of the existing generic biosphere dataset and the priority on data acquisition were identified for the element-specific parameters of key radionuclides in the safety assessment of geological disposal that should be acquired at the site. This priority list would be useful for effective data acquisition at the site. (author)

  3. Morphing methods to parameterize specimen-specific finite element model geometries.

    Science.gov (United States)

    Sigal, Ian A; Yang, Hongli; Roberts, Michael D; Downs, J Crawford

    2010-01-19

    Shape plays an important role in determining the biomechanical response of a structure. Specimen-specific finite element (FE) models have been developed to capture the details of the shape of biological structures and predict their biomechanics. Shape, however, can vary considerably across individuals or change due to aging or disease, and analysis of the sensitivity of specimen-specific models to these variations has proven challenging. An alternative to specimen-specific representation has been to develop generic models with simplified geometries whose shape is relatively easy to parameterize, and can therefore be readily used in sensitivity studies. Despite many successful applications, generic models are limited in that they cannot make predictions for individual specimens. We propose that it is possible to harness the detail available in specimen-specific models while leveraging the power of the parameterization techniques common in generic models. In this work we show that this can be accomplished by using morphing techniques to parameterize the geometry of specimen-specific FE models such that the model shape can be varied in a controlled and systematic way suitable for sensitivity analysis. We demonstrate three morphing techniques by using them on a model of the load-bearing tissues of the posterior pole of the eye. We show that using relatively straightforward procedures these morphing techniques can be combined, which allows the study of factor interactions. Finally, we illustrate that the techniques can be used in other systems by applying them to morph a femur. Morphing techniques provide an exciting new possibility for the analysis of the biomechanical role of shape, independently or in interaction with loading and material properties. Copyright 2009 Elsevier Ltd. All rights reserved.

  4. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

    Directory of Open Access Journals (Sweden)

    Kevin B. Reed

    2018-03-01

    Full Text Available Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.

  5. The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes.

    Science.gov (United States)

    Fabry, S; Müller, K; Lindauer, A; Park, P B; Cornelius, T; Schmitt, R

    1995-09-01

    The genome of the green alga Chlamydomonas reinhardtii contains approximately 15 gene clusters of the nucleosomal (or core) histone H2A, H2B, H3 and H4 genes and at least one histone H1 gene. Seven non-allelic histone gene loci were isolated from a genomic library, physically mapped, and the nucleotide sequences of three isotypes of each core histone gene species and one linked H1 gene determined. The core histone genes are organized in clusters of H2A-H2B and H3-H4 pairs, in which each gene pair shows outwardly divergent transcription from a short (< 300 bp) intercistronic region. These intercistronic regions contain typically conserved promoter elements, namely a TATA-box and the three motifs TGGCCAG-G(G/C)-CGAG, CGTTGACC and CGGTTG. Different from the genes of higher plants, but like those of animals and the related alga Volvox, the 3' untranslated regions contain no poly A signal, but a palindromic sequence (3' palindrome) essential for mRNA processing is present. One single H1 gene was found in close linkage to a H2A-H2B pair. The H1 upstream region contains the octameric promoter element GGTTGACC (also found upstream of the core histone genes) and two specific sequence motifs that are shared only with the Volvox H1 promoters. This suggests differential transcription of the H1 and the core histone genes. The H1 gene is interrupted by two introns. Unlike Volvox H3 genes, the three sequenced H3 isoforms are intron-free. Primer-directed PCR of genomic DNA demonstrated, however, that at least 8 of the about 15 H3 genes do contain one intron at a conserved position. In synchronized C. reinhardtii cells, H4 mRNA levels (representative of all core histone mRNAs) peak during cell division, suggesting strict replication-dependent gene control. The derived peptide sequences place C. reinhardtii core histones closer to plants than to animals, except that the H2A histones are more animal-like. The peptide sequence of histone H1 is closely related to the V. carteri VH1-II

  6. Identification of choriogenin cis-regulatory elements and production of estrogen-inducible, liver-specific transgenic Medaka.

    Science.gov (United States)

    Ueno, Tetsuro; Yasumasu, Shigeki; Hayashi, Shinji; Iuchi, Ichiro

    2004-07-01

    Choriogenins (chg-H, chg-L) are precursor proteins of egg envelope of medaka and synthesized in the spawning female liver in response to estrogen. We linked a gene construct chg-L1.5 kb/GFP (a 1.5 kb 5'-upstream region of the chg-L gene fused with a green fluorescence protein (GFP) gene) to another construct emgb/RFP (a cis-regulatory region of embryonic globin gene fused with an RFP gene), injected the double fusion gene construct into 1- or 2-cell-stage embryos, and selected embryos expressing the RFP in erythroid cells. From the embryos, we established two lines of chg-L1.5 kb/GFP-emgb/RFP-transgenic medaka. The 3-month-old spawning females and estradiol-17beta (E2)-exposed males displayed the liver-specific GFP expression. The E2-dependent GFP expression was detected in the differentiating liver of the stage 37-38 embryos. In addition, RT-PCR and whole-mount in situ hybridization showed that the E2-dependent chg expression was found in the liver of the stage 34 embryos of wild medaka, suggesting that such E2-dependency is achieved shortly after differentiation of the liver. Analysis using serial deletion mutants fused with GFP showed that the region -426 to -284 of the chg-L gene or the region -364 to -265 of the chg-H gene had the ability to promote the E2-dependent liver-specific GFP expression of its downstream gene. Further analyses suggested that an estrogen response element (ERE) at -309, an ERE half-site at -330 and a binding site for C/EBP at -363 of the chg-L gene played important roles in its downstream chg-L gene expression. In addition, this transgenic medaka may be useful as one of the test animals for detecting environmental estrogenic steroids.

  7. Berkeley new element program

    International Nuclear Information System (INIS)

    Ghiorso, A.

    1975-09-01

    The work done with element 106 is reviewed, and a new experiment which bears on the properties of the isotope of mass 260 with atomic number 104 is discussed. It is noted that in the case of element 106 a link is demonstrated to the granddaughter as well as the daughter

  8. Soft-x-ray magneto-optical Kerr effect and element-specific hysteresis measurement

    Energy Technology Data Exchange (ETDEWEB)

    Kortright, J.B.; Rice, M. [Lawrence Berkeley National Lab., CA (United States)

    1997-04-01

    Interest in the utilization of x-ray magneto-optical properties to provide element-specific magnetic information, combined with recent development of tunable linear polarizers for spectroscopic polarization measurement, have led the authors to the study of magneto-optical rotation (MOR) near core levels of magnetic atoms in magnetic multilayer and alloy films. Their initial observation of Faraday rotation (in transmission) demonstrated that for Fe MOR is easily measured and is larger at its L{sub 3} resonance than in the near-visible spectral regions. This work also demonstrated that the spectroscopic behavior of the MOR signal in transmission, resulting from the differential reaction of left- and right-circular components of a linearly polarized beam, is related to the magnetic circular dichroism (MCD), or differential absorption, as expected by a Kramers-Kronig transformation. Thus MCD measurements using circular polarization and MOR measurements using linear polarization can provide complementary, and in some cases equivalent, information. On beamline 6.3.2 the authors have begun to investigate soft x-ray MOR in the reflection geometry, the x-ray magneto-optic Kerr effect (XMOKE). Early measurements have demonstrated the ability to measure element-specific hysteresis loops and large rotations compared to analogous near-visible measurements. The authors are investigating the spectral dependence of the XMOKE signal, and have initiated systematic materials studies of sputter-deposited films of Fe, Fe{sub x}Cr{sub 1{minus}x} alloys, and Fe/Cr multilayers.

  9. Linking trace element variations with macronutrients and major cations in marine mussels Mytilus edulis and Perna viridis.

    Science.gov (United States)

    Liu, Fengjie; Wang, Wen-Xiong

    2015-09-01

    Marine mussels have long been used as biomonitors of contamination of trace elements, but little is known about whether variation in tissue trace elements is significantly associated with those of macronutrients and major cations. The authors examined the variability of macronutrients and major cations and their potential relationships with bioaccumulation of trace elements. The authors analyzed the concentrations of macronutrients (C, N, P, S), major cations (Na, Mg, K, Ca), and trace elements (Al, V, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Ba, Pb) in the whole soft tissues of marine mussels Mytilus edulis and Perna viridis collected globally from 21 sites. The results showed that 12% to 84% of the variances in the trace elements was associated with major cations, and the tissue concentration of major cations such as Na and Mg in mussels was a good proxy for ambient seawater concentrations of the major cations. Specifically, bioaccumulation of most of the trace elements was significantly associated with major cations, and the relationships of major cations with trace cations and trace oxyanions were totally opposite. Furthermore, 14% to 69% of the variances in the trace elements were significantly associated with macronutrients. Notably, more than half of the variance in the tissue concentrations of As, Cd, V, Ba, and Pb was explained by the variance in macronutrients in one or both species. Because the tissue macronutrient concentrations were strongly associated with animal growth and reproduction, the observed coupling relationships indicated that these biological processes strongly influenced the bioaccumulation of some trace elements. The present study indicated that simultaneous quantification of macronutrients and major cations with trace elements can improve the interpretation of biomonitoring data. © 2015 SETAC.

  10. Element-specific and constant parameters used for dose calculations in SR-Site

    International Nuclear Information System (INIS)

    Norden, Sara; Avila, Rodolfo; De la Cruz, Idalmis; Stenberg, Kristofer; Grolander, Sara

    2010-12-01

    The report presents Best Estimate (BE) values and Probability Distribution Functions (PDFs) of Concentration Ratios (CR) for different types of terrestrial and aquatic biota and distribution coefficients (K d ) for organic and inorganic deposits, as well as for suspended matter in freshwater and marine ecosystems. The BE values have been used in deterministic simulations for derivation of Landscape Dose Factors (LDF) applied for dose assessments in SR-Site. The PDFs have been used in probabilistic simulations for uncertainty and sensitivity analysis of the LDFs. The derivation of LDFs for SR-Site is described in /Avila et al. 2010/. The CR and K d values have been derived using both site-specific data measured at Laxemar and Forsmark during the site investigation program and literature data. These two data sources have been combined using Bayesian updating methods, which are described in detail in an Appendix, along with the input data used in the statistical analyses and the results obtained. The report also describes a kinetic-allometric model that was applied for deriving values of CR for terrestrial herbivores in cases when site and literature data for an element were missing. In addition, the report presents values for a number of other parameters used in the SR-Site Radionuclide Model for the biosphere: radionuclide decay-ingrowth data, elemental diffusivities, fractions of element content released during decomposition processes, ingestion of food, water and soil by cattle, elements retention fraction on plant surfaces during irrigation. The report also presents parameter values used in calculation of doses to a reference man: dose coefficients for inhalation, ingestion and external exposure, inhalation rates, ingestion rates of food and water

  11. Element-specific and constant parameters used for dose calculations in SR-Site

    Energy Technology Data Exchange (ETDEWEB)

    Norden, Sara (Svensk Kaernbraenslehantering AB (Sweden)); Avila, Rodolfo; De la Cruz, Idalmis; Stenberg, Kristofer; Grolander, Sara (Facilia AB (Sweden))

    2010-12-15

    The report presents Best Estimate (BE) values and Probability Distribution Functions (PDFs) of Concentration Ratios (CR) for different types of terrestrial and aquatic biota and distribution coefficients (K{sub d}) for organic and inorganic deposits, as well as for suspended matter in freshwater and marine ecosystems. The BE values have been used in deterministic simulations for derivation of Landscape Dose Factors (LDF) applied for dose assessments in SR-Site. The PDFs have been used in probabilistic simulations for uncertainty and sensitivity analysis of the LDFs. The derivation of LDFs for SR-Site is described in /Avila et al. 2010/. The CR and K{sub d} values have been derived using both site-specific data measured at Laxemar and Forsmark during the site investigation program and literature data. These two data sources have been combined using Bayesian updating methods, which are described in detail in an Appendix, along with the input data used in the statistical analyses and the results obtained. The report also describes a kinetic-allometric model that was applied for deriving values of CR for terrestrial herbivores in cases when site and literature data for an element were missing. In addition, the report presents values for a number of other parameters used in the SR-Site Radionuclide Model for the biosphere: radionuclide decay-ingrowth data, elemental diffusivities, fractions of element content released during decomposition processes, ingestion of food, water and soil by cattle, elements retention fraction on plant surfaces during irrigation. The report also presents parameter values used in calculation of doses to a reference man: dose coefficients for inhalation, ingestion and external exposure, inhalation rates, ingestion rates of food and water

  12. Finite Element Analysis and Die Design of Non-specific Engineering Structure of Aluminum Alloy during Extrusion

    International Nuclear Information System (INIS)

    Chen, D.-C.; Lu, Y.-Y.

    2010-01-01

    Aluminum extension applies to industrial structure, light load, framework rolls and conveyer system platform. Many factors must be controlled in processing the non-specific engineering structure (hollow shape) of the aluminum alloy during extrusion, to obtain the required plastic strain and desired tolerance values. The major factors include the forming angle of the die and temperature of billet and various materials. This paper employs rigid-plastic finite element (FE) DEFORM 3D software to investigate the plastic deformation behavior of an aluminum alloy (A6061, A5052, A3003) workpiece during extrusion for the engineering structure of the aluminum alloy. This work analyzes effective strain, effective stress, damage and die radius load distribution of the billet under various conditions. The analytical results confirm the suitability of the current finite element software for the non-specific engineering structure of aluminum alloy extrusion.

  13. Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

    Science.gov (United States)

    Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

    2016-01-07

    Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  14. CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, accumulates at the postsynaptic density in an activity-dependent manner

    International Nuclear Information System (INIS)

    Dosemeci, Ayse; Thein, Soe; Yang, Yijung; Reese, Thomas S.; Tao-Cheng, Jung-Hwa

    2013-01-01

    Highlights: ► CYLD is a deubiquitinase specific for lysine63-linked polyubiquitins. ► Presence of CYLD in PSDs is established by biochemistry and immunoEM. ► CYLD accumulates on PSDs upon depolarization of neurons. ► Accumulation of CYLD at PSDs may regulate trafficking/degradation of synaptic proteins. -- Abstract: Polyubiquitin chains on proteins flag them for distinct fates depending on the type of polyubiquitin linkage. While lysine48-linked polyubiquitination directs proteins to proteasomal degradation, lysine63-linked polyubiquitination promotes different protein trafficking and is involved in autophagy. Here we show that postsynaptic density (PSD) fractions from adult rat brain contain deubiquitinase activity that targets both lysine48 and lysine63-linked polyubiquitins. Comparison of PSD fractions with parent subcellular fractions by Western immunoblotting reveals that CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, is highly enriched in the PSD fraction. Electron microscopic examination of hippocampal neurons in culture under basal conditions shows immunogold label for CYLD at the PSD complex in approximately one in four synapses. Following depolarization by exposure to high K+, the proportion of CYLD-labeled PSDs as well as the labeling intensity of CYLD at the PSD increased by more than eighty percent, indicating that neuronal activity promotes accumulation of CYLD at the PSD. An increase in postsynaptic CYLD following activity would promote removal of lysine63-polyubiquitins from PSD proteins and thus could regulate their trafficking and prevent their autophagic degradation.

  15. Radioimmunodetection of rat and rabbit cartilage using a monoclonal antibody specific to link proteins

    Energy Technology Data Exchange (ETDEWEB)

    Cassiede, P.; Amedee, J.; Rouais, F.; Bareille, R.; Bordenave, L.; Basse-Cathalinat, B.; Harmand, M.F. (Institut National de la Sante et de la Recherche Medicale (INSERM), 33 - Bordeaux (France)); Vuillemin, L.; Ducassou, D. (Hopital du Haut-Leveque, 33 - Pessac (France))

    1993-10-01

    Biodistribution analysis using [[sup 125]I]Fab-6F3 specific to link proteins from human articular cartilage performed in rats by autoradiography showed a high concentration of radioactivity in all cartilaginous tissues. Preliminary immunoscinitgraphic assays were performed in rabbits. Front and side view images of whole animals exhibited high uptake in cartilage tissue of the knee articulation, in the invertebral disk and the humeral head. This fixation was still detected 24 h post-injection, although high washout of radioactivity was observed. (Author).

  16. Fluid element in SAP IV

    International Nuclear Information System (INIS)

    Yilmaz, C.; Akkas, N.

    1979-01-01

    In previous studies a fluid element is incorporated in the widely used general purpose finite element program SAPIV. This type of problem is of interest in the design of nuclear components involving geometric complexities and nonlinearities. The elasticity matrix of a general-purpose finite element program is modified in such a way that it becomes possible to idealize fluid as a structural finite element with zero shear modulus and a given bulk modules. Using the modified version of SAPIV, several solid-fluid interactions problems are solved. The numerical solutions are compared with the available analytical solutions. They are shown to be in reasonable aggrement. It is also shown that by solving an exterior-fluid interaction problem, the pressure wave propagation in the acoustic medium can be solved with the same approach. In this study, two of the problem not studied in the previous work will be presented. These problems are namely the effects of the link elements used at solid-fluid interfaces and of the concentrated loads on the response of the fluid medium. Truss elements are used as the link elements. After these investigations, it is decided that general purpose finite element programs with slight modifications can be used in the safety analysis of nuclear reactor plants. By this procedure it is possible to handle two-dimensional plane strain and tridimensional axisymmetric problems of this type. (orig.)

  17. In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking.

    Science.gov (United States)

    Chang, Chungyu; Amer, Brendan R; Osipiuk, Jerzy; McConnell, Scott A; Huang, I-Hsiu; Hsieh, Van; Fu, Janine; Nguyen, Hong H; Muroski, John; Flores, Erika; Ogorzalek Loo, Rachel R; Loo, Joseph A; Putkey, John A; Joachimiak, Andrzej; Das, Asis; Clubb, Robert T; Ton-That, Hung

    2018-06-12

    Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction, first cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate and then joining the terminal Thr to the nucleophilic Lys residue residing within the pilin motif of another pilin protomer. To date, the determinants of class C enzymes that uniquely enable them to construct pili remain unknown. Here, informed by high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and utilizing a structural variant of the enzyme (SrtA 2M ), whose catalytic pocket has been unmasked by activating mutations, we successfully reconstituted in vitro polymerization of the cognate major pilin (SpaA). Mass spectrometry, electron microscopy, and biochemical experiments authenticated that SrtA 2M synthesizes pilus fibers with correct Lys-Thr isopeptide bonds linking individual pilins via a thioacyl intermediate. Structural modeling of the SpaA-SrtA-SpaA polymerization intermediate depicts SrtA 2M sandwiched between the N- and C-terminal domains of SpaA harboring the reactive pilin and LPXTG motifs, respectively. Remarkably, the model uncovered a conserved TP(Y/L)XIN(S/T)H signature sequence following the catalytic Cys, in which the alanine substitutions abrogated cross-linking activity but not cleavage of LPXTG. These insights and our evidence that SrtA 2M can terminate pilus polymerization by joining the terminal pilin SpaB to SpaA and catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile platform for protein engineering and bio-conjugation that has major implications for biotechnology.

  18. Theoretical aspects of the internal element connectivity parameterization approach for topology optimization

    DEFF Research Database (Denmark)

    Yoon, Gil Ho; Kim, Y.Y.; Langelaar, M.

    2008-01-01

    The internal element connectivity parameterization (I-ECP) method is an alternative approach to overcome numerical instabilities associated with low-stiffness element states in non-linear problems. In I-ECP, elements are connected by zero-length links while their link stiffness values are varied....... Therefore, it is important to interpolate link stiffness properly to obtain stably converging results. The main objective of this work is two-fold (1) the investigation of the relationship between the link stiffness and the stiffness of a domain-discretizing patch by using a discrete model and a homogenized...

  19. Finite element speaker-specific face model generation for the study of speech production.

    Science.gov (United States)

    Bucki, Marek; Nazari, Mohammad Ali; Payan, Yohan

    2010-08-01

    In situations where automatic mesh generation is unsuitable, the finite element (FE) mesh registration technique known as mesh-match-and-repair (MMRep) is an interesting option for quickly creating a subject-specific FE model by fitting a predefined template mesh onto the target organ. The irregular or poor quality elements produced by the elastic deformation are corrected by a 'mesh reparation' procedure ensuring that the desired regularity and quality standards are met. Here, we further extend the MMRep capabilities and demonstrate the possibility of taking into account additional relevant anatomical features. We illustrate this approach with an example of biomechanical model generation of a speaker's face comprising face muscle insertions. While taking advantage of the a priori knowledge about tissues conveyed by the template model, this novel, fast and automatic mesh registration technique makes it possible to achieve greater modelling realism by accurately representing the organ surface as well as inner anatomical or functional structures of interest.

  20. CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, accumulates at the postsynaptic density in an activity-dependent manner

    Energy Technology Data Exchange (ETDEWEB)

    Dosemeci, Ayse, E-mail: dosemeca@mail.nih.gov [Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States); Thein, Soe; Yang, Yijung; Reese, Thomas S. [Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States); Tao-Cheng, Jung-Hwa [EM Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 (United States)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer CYLD is a deubiquitinase specific for lysine63-linked polyubiquitins. Black-Right-Pointing-Pointer Presence of CYLD in PSDs is established by biochemistry and immunoEM. Black-Right-Pointing-Pointer CYLD accumulates on PSDs upon depolarization of neurons. Black-Right-Pointing-Pointer Accumulation of CYLD at PSDs may regulate trafficking/degradation of synaptic proteins. -- Abstract: Polyubiquitin chains on proteins flag them for distinct fates depending on the type of polyubiquitin linkage. While lysine48-linked polyubiquitination directs proteins to proteasomal degradation, lysine63-linked polyubiquitination promotes different protein trafficking and is involved in autophagy. Here we show that postsynaptic density (PSD) fractions from adult rat brain contain deubiquitinase activity that targets both lysine48 and lysine63-linked polyubiquitins. Comparison of PSD fractions with parent subcellular fractions by Western immunoblotting reveals that CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, is highly enriched in the PSD fraction. Electron microscopic examination of hippocampal neurons in culture under basal conditions shows immunogold label for CYLD at the PSD complex in approximately one in four synapses. Following depolarization by exposure to high K+, the proportion of CYLD-labeled PSDs as well as the labeling intensity of CYLD at the PSD increased by more than eighty percent, indicating that neuronal activity promotes accumulation of CYLD at the PSD. An increase in postsynaptic CYLD following activity would promote removal of lysine63-polyubiquitins from PSD proteins and thus could regulate their trafficking and prevent their autophagic degradation.

  1. Plasticity during Sleep Is Linked to Specific Regulation of Cortical Circuit Activity

    Directory of Open Access Journals (Sweden)

    Niels Niethard

    2017-09-01

    Full Text Available Sleep is thought to be involved in the regulation of synaptic plasticity in two ways: by enhancing local plastic processes underlying the consolidation of specific memories and by supporting global synaptic homeostasis. Here, we briefly summarize recent structural and functional studies examining sleep-associated changes in synaptic morphology and neural excitability. These studies point to a global down-scaling of synaptic strength across sleep while a subset of synapses increases in strength. Similarly, neuronal excitability on average decreases across sleep, whereas subsets of neurons increase firing rates across sleep. Whether synapse formation and excitability is down or upregulated across sleep appears to partly depend on the cell’s activity level during wakefulness. Processes of memory-specific upregulation of synapse formation and excitability are observed during slow wave sleep (SWS, whereas global downregulation resulting in elimination of synapses and decreased neural firing is linked to rapid eye movement sleep (REM sleep. Studies of the excitation/inhibition balance in cortical circuits suggest that both processes are connected to a specific inhibitory regulation of cortical principal neurons, characterized by an enhanced perisomatic inhibition via parvalbumin positive (PV+ cells, together with a release from dendritic inhibition by somatostatin positive (SOM+ cells. Such shift towards increased perisomatic inhibition of principal cells appears to be a general motif which underlies the plastic synaptic changes observed during sleep, regardless of whether towards up or downregulation.

  2. Total and species-specific quantitative analyses of trace elements in sediment by isotope dilution inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    Inagaki, Kazumi; Takatsu, Akiko; Yarita, Takashi; Okamoto, Kensaku; Chiba, Koichi

    2009-01-01

    Isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) is one of the reliable methods for total and species-specific quantitative analysis of trace elements. However, several technical problems (e.g. spectral interference caused from sample constituents) should be overcome to obtain reliable analytical results when environmental samples are analyzed by ID-ICP-MS. In our laboratory, various methods based on ID-ICP-MS have been investigated for reliable quantitative analyses of trace elements in environmental samples. In this paper, coprecipitate separation/ID-ICP-MS for the determination of trace elements in sediment, cation exchange disk filtration/ID-ICP-MS for the determination of selenium in sediment, species-specific ID-ICP-MS using 118 Sn/labeled organotin compounds for the determination of butyltins and phenyltins, and the application of the ID-ICP-MS methods to the certification of sediment reference materials are described. (author)

  3. Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

    Directory of Open Access Journals (Sweden)

    Amyotte Stefan G

    2012-07-01

    Full Text Available Abstract Background Verticillium dahliae (Vd and Verticillium albo-atrum (Va are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs have contributed to the generation of four lineage-specific (LS regions in VdLs.17. Results We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102. Conclusions Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these

  4. Characterization of a cis-acting element involved in cell-specific expression of the zebrafish brain aromatase gene.

    Science.gov (United States)

    Le Page, Yann; Menuet, Arnaud; Kah, Olivier; Pakdel, Farzad

    2008-10-01

    The cytochrome P450 Aromatase is the key enzyme catalyzing the conversion of androgens into estrogens. In zebrafish, the brain aromatase is encoded by cyp19b. Expression of cyp19b is restricted to radial glial cells bordering forebrain ventricles and is strongly stimulated by estrogens during development. At the promoter level, we have previously shown that an estrogen responsive element (ERE) is required for induction by estrogens. Here, we investigated the role of ERE flanking regions in the control of cell-specific expression. First, we show that a 20 bp length motif, named G x RE (glial x responsive element), acts in synergy with the ERE to mediate the estrogenic induction specifically in glial cells. Second, we demonstrate that, in vitro, this sequence binds factors exclusively present in glial or neuro-glial cells and is able to confer a glial specificity to an artificial estrogen-dependent gene. Taken together, these results contribute to the understanding of the molecular mechanisms allowing cyp19b regulation by estrogens and allowed to identify a promoter sequence involved in the strong estrogen inducibility of cyp19b which is specific for glial cells. The exceptional aromatase activity measured in the brain of teleost fish could rely on such mechanisms.

  5. Predicting risk of trace element pollution from municipal roads using site-specific soil samples and remotely sensed data.

    Science.gov (United States)

    Reeves, Mari Kathryn; Perdue, Margaret; Munk, Lee Ann; Hagedorn, Birgit

    2018-07-15

    Studies of environmental processes exhibit spatial variation within data sets. The ability to derive predictions of risk from field data is a critical path forward in understanding the data and applying the information to land and resource management. Thanks to recent advances in predictive modeling, open source software, and computing, the power to do this is within grasp. This article provides an example of how we predicted relative trace element pollution risk from roads across a region by combining site specific trace element data in soils with regional land cover and planning information in a predictive model framework. In the Kenai Peninsula of Alaska, we sampled 36 sites (191 soil samples) adjacent to roads for trace elements. We then combined this site specific data with freely-available land cover and urban planning data to derive a predictive model of landscape scale environmental risk. We used six different model algorithms to analyze the dataset, comparing these in terms of their predictive abilities and the variables identified as important. Based on comparable predictive abilities (mean R 2 from 30 to 35% and mean root mean square error from 65 to 68%), we averaged all six model outputs to predict relative levels of trace element deposition in soils-given the road surface, traffic volume, sample distance from the road, land cover category, and impervious surface percentage. Mapped predictions of environmental risk from toxic trace element pollution can show land managers and transportation planners where to prioritize road renewal or maintenance by each road segment's relative environmental and human health risk. Published by Elsevier B.V.

  6. THE INFLUENCE OF CERTAIN TESTS FOR EVALUATING THE ANTROPOMETRIC, MOTOR AND SPECIFIC MOTOR DIMENSIONS ON THE ELEMENTS OF THE ATTACK IN SPORT KARATE FIGHTING

    Directory of Open Access Journals (Sweden)

    Žarko Kostovski

    2011-08-01

    Full Text Available The research involved 48 participants - top male karate competitors, juniors from karate clubs from Republic of Macedonia. The subject of this research are the defining elements of karate attack in sports karate fighting, and the basic aim is to establish the influence of anthropometric, motor and specific motor dimensions on the karate elements that use in sport karate fighting. In the research were used 36 variables: 4 antropomotorical variables, 4 variables for estimate on the explosive strength, 4 variables for estimate on the segmentary speed (movement frequency, 12 variables of the specific karate elements used in the sport karate fighting and 12 variables for estimate on the specifically karate abilities in 3 motor space: 4 variables for estimate on the specific karate coordination, 4 variables for estimate on the specific karate precision and 4 variables for estimate on the specific karate balance, which are predictive system of variables. The criterion set of variables of this research are represented by 4 karate elements which define the attack in sports karate fighting. From the received results was determined existing of groups in the different spaces of the treated variables and influence of the predictive system of variables on the criterion set of variables

  7. Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements.

    Directory of Open Access Journals (Sweden)

    Meghana Deepak Shirke

    Full Text Available Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck, finger millet (leaf and neck, foxtail millet (leaf and buffel grass (leaf. Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors.

  8. SPCC- Software Elements for Security Partition Communication Controller

    Science.gov (United States)

    Herpel, H. J.; Willig, G.; Montano, G.; Tverdyshev, S.; Eckstein, K.; Schoen, M.

    2016-08-01

    Future satellite missions like Earth Observation, Telecommunication or any other kind are likely to be exposed to various threats aiming at exploiting vulnerabilities of the involved systems and communications. Moreover, the growing complexity of systems coupled with more ambitious types of operational scenarios imply increased security vulnerabilities in the future. In the paper we will describe an architecture and software elements to ensure high level of security on-board a spacecraft. First the threats to the Security Partition Communication Controller (SPCC) will be addressed including the identification of specific vulnerabilities to the SPCC. Furthermore, appropriate security objectives and security requirements are identified to be counter the identified threats. The security evaluation of the SPCC will be done in accordance to the Common Criteria (CC). The Software Elements for SPCC has been implemented on flight representative hardware which consists of two major elements: the I/O board and the SPCC board. The SPCC board provides the interfaces with ground while the I/O board interfaces with typical spacecraft equipment busses. Both boards are physically interconnected by a high speed spacewire (SpW) link.

  9. Human apolipoprotein CIII gene expression is regulated by positive and negative cis-acting elements and tissue-specific protein factors

    International Nuclear Information System (INIS)

    Reue, K.; Leff, T.; Breslow, J.L.

    1988-01-01

    Apolipoprotein CIII (apoCIII) is a major protein constituent of triglyceride-rich lipoproteins and is synthesized primarily in the liver. Cis-acting DNA elements required for liver-specific apoCIII gene transcription were identified with transient expression assays in the human hepatoma (HepG2) and epithelial carcinoma (HeLa) cell lines. In liver cells, 821 nucleotides of the human apoCIII gene 5'-flanking sequence were required for maximum levels of gene expression, while the proximal 110 nucleotides alone were sufficient. No expression was observed in similar studies with HeLa cells. The level of expression was modulated by a combination of positive and negative cis-acting sequences, which interact with distinct sets of proteins from liver and HeLa cell nuclear extracts. The proximal positive regulatory region shares homology with similarly located sequences of other genes strongly expressed in the liver, including α 1 -antitrypsin and other apolipoprotein genes. The negative regulatory region is striking homologous to the human β-interferon gene regulatory element. The distal positive region shares homology with some viral enhancers and has properties of a tissue-specific enhancer. The regulation of the apoCIII gene is complex but shares features with other genes, suggesting shuffling of regulatory elements as a common mechanism for cell type-specific gene expression

  10. A novel core 1 O-linked glycan-specific binding lectin from the fruiting body of Hericium erinaceus.

    Science.gov (United States)

    Kim, Seonghun

    2018-02-01

    Mucin-type O-glycans are involved in biological functions on the cell surface as well as the glycoproteins and can also be used as specific carbohydrate biomarkers of many diseases. In this study, I purified a novel core 1 O-linked glycan specific lectin, Hericium erinaceus lecin (HeL), from the fruiting body of the mushroom Hericium erinaceus, which is known as the natural source for a sialic acid-binding lectin. Upon optimization of the purification conditions, a sequence of ion exchange, affinity, ion exchange, and size-exclusion chromatography resulted in the highest yield and best quality of lectin without protease activity. The resulting purified HeL is an apparent hexameric protein with a subunit molecular weight of 15kDa, and a pI of 4.3. In hemagglutination inhibition assay, the purified lectin was only inhibited by glycoproteins containing mucin-type O-glycans and reacted weakly with Galβ(1,3)GalNAc. Glycan array analyses showed that HeL specifically interacts with core 1 O-linked glycans as well as extended O-glycan structures containing sialylation or fucosylation. The glycan binding specificity of HeL is comparable to that of peanut agglutinin for detection of a broader range of extended core 1 O-glycan structures. Taken together, these results provide an efficient and optimized procedure for the purification of HeL from the fruiting body of the mushroom Hericium erinaceus. Moreover, HeL represents a powerful tool for analyzing core 1 and extended core 1 O- glycan structures in diagnosis assays. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Characterization of an estrogen-responsive element implicated in regulation of the rainbow trout estrogen receptor gene.

    Science.gov (United States)

    Le Dréan, Y; Lazennec, G; Kern, L; Saligaut, D; Pakdel, F; Valotaire, Y

    1995-08-01

    We previously reported that the expression of the rainbow trout estrogen receptor (rtER) gene is markedly increased by estradiol (E2). In this paper, we have used transient transfection assays with reporter plasmids expressing chloramphenicol acetyl transferase (CAT), linked to 5' flanking regions of the rtER gene promoter, to identify cis-elements responsible for E2 inducibility. Deletion analysis localized an estrogen-responsive element (ERE), at position +242, with one mutation on the first base compared with the consensus sequence. This element confers estrogen responsiveness to CAT reporter linked to both the herpes simplex virus thymidine kinase promoter and the homologous rtER promoter. Moreover, using a 0.2 kb fragment of the rtER promoter encompassing the ERE and the rtER DNA binding domain obtained from a bacterial expression system, DNase I footprinting experiments demonstrated a specific protection covering 20 bp (+240/+260) containing the ERE sequence. Based on these studies, we believe that this ERE sequence, identified in the rtER gene promoter, may be a major cis-acting element involved in the regulation of the gene by estrogen.

  12. Effects of Surface Modification and Bulk Geometry on the Biotribological Behavior of Cross-Linked Polyethylene: Wear Testing and Finite Element Analysis

    Directory of Open Access Journals (Sweden)

    Kenichi Watanabe

    2015-01-01

    phosphorylcholine- (PMPC- grafted CLPE, through wear tests and finite element analysis. The gravimetric and volumetric degrees of wear of disks (3 or 6 mm in thickness of these materials against a cobalt-chromium-molybdenum alloy pin were examined using a multidirectional pin-on-disk tester. Cross-linking and PMPC grafting decreased the gravimetric wear of the PE disks significantly. The volumetric wear at the bearing surface and the volumetric penetration in the backside of the 3-mm thick PE disk were higher than those of the 6-mm thick PE disk, regardless of the bearing material. The geometrical changes induced in the PE disks consisted of creep, because the calculated internal von Mises stress at the bearing side of all disks and that at the backside of the 3-mm thick disks exceeded their actual yield strengths. A highly hydrated bearing surface layer, formed by PMPC grafting, and a cross-linking-strengthened substrate of adequate thickness are essential for increasing the wear and creep deformation resistances.

  13. Linking actions and objects: Context-specific learning of novel weight priors.

    Science.gov (United States)

    Trewartha, Kevin M; Flanagan, J Randall

    2017-06-01

    Distinct explicit and implicit memory processes support weight predictions used when lifting objects and making perceptual judgments about weight, respectively. The first time that an object is encountered weight is predicted on the basis of learned associations, or priors, linking size and material to weight. A fundamental question is whether the brain maintains a single, global representation of priors, or multiple representations that can be updated in a context specific way. A second key question is whether the updating of priors, or the ability to scale lifting forces when repeatedly lifting unusually weighted objects requires focused attention. To investigate these questions we compared the adaptability of weight predictions used when lifting objects and judging their weights in different groups of participants who experienced size-weight inverted objects passively (with the objects placed on the hands) or actively (where participants lift the objects) under full or divided attention. To assess weight judgments we measured the size-weight illusion after every 20 trials of experience with the inverted objects both passively and actively. The attenuation of the illusion that arises when lifting inverted object was found to be context-specific such that the attenuation was larger when the mode of interaction with the inverted objects matched the method of assessment of the illusion. Dividing attention during interaction with the inverted objects had no effect on attenuation of the illusion, but did slow the rate at which lifting forces were scaled to the weight inverted objects. These findings suggest that the brain stores multiple representations of priors that are context specific, and that focused attention is important for scaling lifting forces, but not for updating weight predictions used when judging object weight. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Interactive effects of genotype and food quality on consumer growth rate and elemental content.

    Science.gov (United States)

    Prater, Clay; Wagner, Nicole D; Frost, Paul C

    2017-05-01

    Consumer body stoichiometry is a key trait that links organismal physiology to population and ecosystem-level dynamics. However, as elemental composition has traditionally been considered to be constrained within a species, the ecological and evolutionary factors shaping consumer elemental composition have not been clearly resolved. To this end, we examined the causes and extent of variation in the body phosphorus (P) content and the expression of P-linked traits, mass specific growth rate (MSGR), and P use efficiency (PUE) of the keystone aquatic consumer Daphnia using lake surveys and common garden experiments. While daphnid body %P was relatively constrained in field assemblages sampled across an environmental P gradient, unique genotypes isolated from these lakes showed highly variable phenotypic responses when raised across dietary P gradients in the laboratory. Specifically, we observed substantial inter- and intra-specific variation and differences in daphnid responses within and among our study lakes. While variation in Daphnia body %P was mostly due to plastic phenotypic changes, we documented considerable genetic differences in daphnid MSGR and PUE, and relationships between MSGR and body P content were highly variable among genotypes. Overall, our study found that consumer responses to food quality may differ considerably among genotypes and that relationships between organismal life-history traits and body stoichiometry may be strongly influenced by genetic and environmental variation in natural assemblages. © 2017 by the Ecological Society of America.

  15. Linking chemical elements in forest floor humus (Oh-horizon) in the Czech Republic to contamination sources.

    Science.gov (United States)

    Sucharova, Julie; Suchara, Ivan; Hola, Marie; Reimann, Clemens; Boyd, Rognvald; Filzmoser, Peter; Englmaier, Peter

    2011-05-01

    While terrestrial moss and other plants are frequently used for environmental mapping and monitoring projects, data on the regional geochemistry of humus are scarce. Humus, however, has a much larger life span than any plant material. It can be seen as the "environmental memory" of an area for at least the last 60-100 years. Here concentrations of 39 elements determined by ICP-MS and ICP AES, pH and ash content are presented for 259 samples of forest floor humus collected at an average sample density of 1 site/300 km2 in the Czech Republic. The scale of anomalies linked to known contamination sources (e.g., lignite mining and burning, metallurgical industry, coal fired power plants, metal smelters) is documented and discussed versus natural processes influencing humus quality. Most maps indicate a local impact from individual contamination sources: often more detailed sampling than used here would be needed to differentiate between likely sources. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. New functionalities in abundant element oxides: ubiquitous element strategy

    International Nuclear Information System (INIS)

    Hosono, Hideo; Hayashi, Katsuro; Kamiya, Toshio; Atou, Toshiyuki; Susaki, Tomofumi

    2011-01-01

    While most ceramics are composed of ubiquitous elements (the ten most abundant elements within the Earth's crust), many advanced materials are based on rare elements. A 'rare-element crisis' is approaching owing to the imbalance between the limited supply of rare elements and the increasing demand. Therefore, we propose a 'ubiquitous element strategy' for materials research, which aims to apply abundant elements in a variety of innovative applications. Creation of innovative oxide materials and devices based on conventional ceramics is one specific challenge. This review describes the concept of ubiquitous element strategy and gives some highlights of our recent research on the synthesis of electronic, thermionic and structural materials using ubiquitous elements. (topical review)

  17. Effects of Surface Modification and Bulk Geometry on the Biotribological Behavior of Cross-Linked Polyethylene: Wear Testing and Finite Element Analysis.

    Science.gov (United States)

    Watanabe, Kenichi; Kyomoto, Masayuki; Saiga, Kenichi; Taketomi, Shuji; Inui, Hiroshi; Kadono, Yuho; Takatori, Yoshio; Tanaka, Sakae; Ishihara, Kazuhiko; Moro, Toru

    2015-01-01

    The wear and creep deformation resistances of polymeric orthopedic bearing materials are both important for extending their longevity. In this study, we evaluated the wear and creep deformation resistances, including backside damage, of different polyethylene (PE) materials, namely, conventional PE, cross-linked PE (CLPE), and poly(2-methacryloyloxyethyl phosphorylcholine)- (PMPC-) grafted CLPE, through wear tests and finite element analysis. The gravimetric and volumetric degrees of wear of disks (3 or 6 mm in thickness) of these materials against a cobalt-chromium-molybdenum alloy pin were examined using a multidirectional pin-on-disk tester. Cross-linking and PMPC grafting decreased the gravimetric wear of the PE disks significantly. The volumetric wear at the bearing surface and the volumetric penetration in the backside of the 3-mm thick PE disk were higher than those of the 6-mm thick PE disk, regardless of the bearing material. The geometrical changes induced in the PE disks consisted of creep, because the calculated internal von Mises stress at the bearing side of all disks and that at the backside of the 3-mm thick disks exceeded their actual yield strengths. A highly hydrated bearing surface layer, formed by PMPC grafting, and a cross-linking-strengthened substrate of adequate thickness are essential for increasing the wear and creep deformation resistances.

  18. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

    OpenAIRE

    Lescot, Magali; Déhais, Patrice; Thijs, Gert; Marchal, Kathleen; Moreau, Yves; Van de Peer, Yves; Rouzé, Pierre; Rombauts, Stephane

    2002-01-01

    PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific t...

  19. Site-specific glycoprofiling of N-linked glycopeptides using MALDI-TOF MS: strong correlation between signal strength and glycoform quantities

    DEFF Research Database (Denmark)

    Thaysen-Andersen, Morten; Mysling, Simon; Højrup, Peter

    2009-01-01

    Site-specific glycoprofiling of N-linked glycopeptides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an emerging technique, but its quantitative accuracy lacks documentation. Thus, a systematic study of widely different glycopeptides was perf......Site-specific glycoprofiling of N-linked glycopeptides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an emerging technique, but its quantitative accuracy lacks documentation. Thus, a systematic study of widely different glycopeptides...... was performed to determine the relationship between the relative abundances of the individual glycoforms and the MALDI-TOF MS signal strength. Glycopeptides derived from glycoproteins containing neutral glycans (ribonuclease B, IgG, and ovalbumin) were initially profiled and yielded excellent and reproducible...... quantitation (correlation coefficient r = 0.9958, n = 5) when evaluated against a normal phase HPLC 2-AB glycan profile. Similarly, precise quantitation was observed for various forms of N-glycans (free, permethylated, and fluorescence-labeled) using MS. In addition, three different sialoglycopeptides from...

  20. Finite element analysis of three dimensional crack growth by the use of a boundary element sub model

    DEFF Research Database (Denmark)

    Lucht, Tore

    2009-01-01

    A new automated method to model non-planar three dimensional crack growth is proposed which combines the advantages of both the boundary element method and the finite element method. The proposed method links the two methods by a submodelling strategy in which the solution of a global finite...... element model containing an approximation of the crack is interpolated to a much smaller boundary element model containing a fine discretization of the real crack. The method is validated through several numerical comparisons and by comparison to crack growth measured in a test specimen for an engineering...

  1. Assessing element-specific patterns of bioaccumulation across New England lakes

    Energy Technology Data Exchange (ETDEWEB)

    Ward, Darren M.; Mayes, Brandon; Sturup, Stefan; Folt, Carol L.; Chen, Celia Y., E-mail: celia.chen@dartmouth.edu

    2012-04-01

    Little is known about differences among trace elements in patterns of bioaccumulation in freshwater food webs. Our goal was to identify patterns in bioaccumulation of different elements that are large and consistent enough to discern despite variation across lakes. We measured methylmercury (MeHg) and trace element (As, Cd, Hg, Pb, and Zn) concentrations in food web components of seven New England lakes on 3-5 dates per lake, and contrasted patterns of bioaccumulation across lakes, metals and seasons. In each lake, trace element concentrations were compared across trophic levels, including three size fractions of zooplankton, planktivorous fish, and piscivorous fish. The trophic position of each food web component was estimated from N isotope analysis. Trace element concentrations varied widely among taxa, lakes and sampling dates. Yet, we identified four consistent patterns of bioaccumulation that were consistent across lakes: (1) MeHg concentration increased (i.e., was biomagnified) and Pb concentration decreased (i.e., was biodiminished) with increased trophic position. (2) Zinc concentration (as with MeHg) was higher in fish than in zooplankton, but overall variation in Zn concentration (unlike MeHg) was low. (3) Arsenic and Cd concentrations (as with Pb) were lower in fish than in zooplankton, but (unlike Pb) were not significantly correlated with trophic position within zooplankton or fish groups. (4) Average summer concentrations of As, Pb, Hg, and MeHg in zooplankton significantly predicted their concentrations in either planktivorous or piscivorous fish. Our secondary goal was to review sampling approaches in forty-five published studies to determine the extent to which current sampling programs facilitate cross-lake and cross-study comparisons of bioaccumulation. We found that studies include different components of the food web and sample too infrequently to enable strong cross-lake and cross-study comparisons. We discuss sampling strategies that would

  2. Assessing element-specific patterns of bioaccumulation across New England lakes

    International Nuclear Information System (INIS)

    Ward, Darren M.; Mayes, Brandon; Sturup, Stefan; Folt, Carol L.; Chen, Celia Y.

    2012-01-01

    Little is known about differences among trace elements in patterns of bioaccumulation in freshwater food webs. Our goal was to identify patterns in bioaccumulation of different elements that are large and consistent enough to discern despite variation across lakes. We measured methylmercury (MeHg) and trace element (As, Cd, Hg, Pb, and Zn) concentrations in food web components of seven New England lakes on 3–5 dates per lake, and contrasted patterns of bioaccumulation across lakes, metals and seasons. In each lake, trace element concentrations were compared across trophic levels, including three size fractions of zooplankton, planktivorous fish, and piscivorous fish. The trophic position of each food web component was estimated from N isotope analysis. Trace element concentrations varied widely among taxa, lakes and sampling dates. Yet, we identified four consistent patterns of bioaccumulation that were consistent across lakes: (1) MeHg concentration increased (i.e., was biomagnified) and Pb concentration decreased (i.e., was biodiminished) with increased trophic position. (2) Zinc concentration (as with MeHg) was higher in fish than in zooplankton, but overall variation in Zn concentration (unlike MeHg) was low. (3) Arsenic and Cd concentrations (as with Pb) were lower in fish than in zooplankton, but (unlike Pb) were not significantly correlated with trophic position within zooplankton or fish groups. (4) Average summer concentrations of As, Pb, Hg, and MeHg in zooplankton significantly predicted their concentrations in either planktivorous or piscivorous fish. Our secondary goal was to review sampling approaches in forty-five published studies to determine the extent to which current sampling programs facilitate cross-lake and cross-study comparisons of bioaccumulation. We found that studies include different components of the food web and sample too infrequently to enable strong cross-lake and cross-study comparisons. We discuss sampling strategies that would

  3. LIBS, LA-ICPMS and synchrotron hard x-ray micro-radiography and micro-tomography complementary study of elemental distributions in biominerals

    International Nuclear Information System (INIS)

    Kaiser, J.; Novotny, K.; Hola, M.; Kanicky, V.; Martinec, P.; Hahn, D.W.; Diwakar, P.K.; Mancini, L.; Tromba, G.; Sodini, N.

    2009-01-01

    Full text: Analysis of bio-minerals can provide information about the chronology, diet and palaeoenvironment of past populations. More specifically, e.g. line scans of uroliths cross-sections may be used to detect the accumulation history of the selected elements. This can be linked to the patients' exposure to environmental effects. Together with the main components, biogenous and toxic trace elements can be monitored. We report on utilization of two laser-ablation based analytical techniques for mapping elemental distribution in bio-minerals, coupled to hard x-ray microradiography and micro-CT measurements for visualization of the inner structure of the investigated samples. (author)

  4. Finite element analysis of reticulated ceramics under compression

    International Nuclear Information System (INIS)

    D’Angelo, Claudio; Ortona, Alberto; Colombo, Paolo

    2012-01-01

    Graphical abstract: - Abstract: This paper shows how finite element analysis can be used to study the effect of the morphological features of reticulated ceramics on their mechanical properties under compression. Quantitative morphological data, obtained by X-ray computed tomography (XCT) for a commercially available Si–SiC foam produced by the replica method, have been linked to a set of computer generated cells in which one morphological parameter was varied at a time. The findings indicate how the modification of some morphological features, which depend on the careful selection of appropriate and specific processing parameters, would enable the production of ceramic foams possessing higher strength for a given total porosity value.

  5. Microbial links and element flows in nested detrital food-webs.

    NARCIS (Netherlands)

    Pokarzhevskii, A.D.; van Straalen, N.M.; Zaboev, D.P.; Zaitsev, A.S.

    2003-01-01

    Microbial links are obligate in any food chain in soil, because detritivorous animals derive essential amino acids and other resources from microorganisms. To degrade recalcitrant substrates such as cellulose, soil animals do not produce their own cellulase, but they use cellulases derived from gut

  6. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

    Science.gov (United States)

    Rhie, Suhn Kyong; Guo, Yu; Tak, Yu Gyoung; Yao, Lijing; Shen, Hui; Coetzee, Gerhard A; Laird, Peter W; Farnham, Peggy J

    2016-01-01

    Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. Using DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called Tracing Enhancer Networks using Epigenetic Traits that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors. Our studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms

  7. Study on predicting residual life of elevator links by fracture mechanics approach

    Energy Technology Data Exchange (ETDEWEB)

    Li Helin; Zhang Yi; Deng Zengjie [China National Petroleum Corp., Xi`an, Shaanxi (China). Tubular Goods Research Center; Jin Dazeng [Xi`an Jiaotong Univ., Xi`an, Shaanxi (China)

    1995-12-31

    On the basis of investigation, failure and fracture analysis of elevator links, residual life prediction of links using fracture mechanics approach is studied, and mechanical properties, fracture toughness value K{sub IC} and fatigue crack propagation rage da/dN of the steel for elevator links are determined. Using the relation between stress intensity factor K{sub I} and the strain-energy release rate, the two-dimensional conversion thickness finite element method has been used to calculate the stress intensity factors K{sub I} for dangerous sections in the ring part of links. Furthermore, the reliability of calculations of the finite element stress intensity factors K{sub I} for dangerous sections of elevator links and the residual life computation for links are verified by fatigue tests of actual links. Finally, the experimental verification of computed results by 150T link fractured at site indicates that the computed critical crack lengths and residual life tally well with those measured and meet the needs of oil drilling.

  8. A novel mutation in the nerve-specific 5'UTR of the GJB1 gene causes X-linked Charcot-Marie-Tooth disease.

    LENUS (Irish Health Repository)

    Murphy, Sinéad M

    2011-03-01

    X-linked Charcot-Marie-Tooth disease (CMT1X) is the second most common cause of CMT, and is usually caused by mutations in the gap junction protein beta 1 (GJB1) gene which codes for connexin 32 (CX32). CX32 has three tissue-specific promoters, P1 which is specific for liver and pancreas, P1a specific for liver, oocytes and embryonic stem cells, and P2 which is nerve-specific. Over 300 mutations have been described in GJB1, spread throughout the coding region. We describe two families with X-linked inheritance and a phenotype consistent with CMT1X who did not have mutations in the GJB1 coding region. The non-coding region of GJB1 was sequenced and an upstream exon-splicing variant found at approximately - 373G>A which segregated with the disease in both families and was not present in controls. This substitution is located at the last base of the nerve-specific 5\\'UTR and thus may disrupt splicing of the nerve-specific transcript. Online consensus splice-site programs predict a reduced score for the mutant sequence vs. the normal sequence. It is likely that other mutations within the GJB1 non-coding regions account for the CMT1X families who do not have coding region mutations.

  9. Testing the Technology Acceptance Model: HIV case managers' intention to use a continuity of care record with context-specific links.

    Science.gov (United States)

    Schnall, Rebecca; Bakken, Suzanne

    2011-09-01

    To assess the applicability of the Technology Acceptance Model (TAM) constructs in explaining HIV case managers' behavioural intention to use a continuity of care record (CCR) with context-specific links designed to meet their information needs. Data were collected from 94 case managers who provide care to persons living with HIV (PLWH) using an online survey comprising three components: (1) demographic information: age, gender, ethnicity, race, Internet usage and computer experience; (2) mock-up of CCR with context-specific links; and items related to TAM constructs. Data analysis included: principal components factor analysis (PCA), assessment of internal consistency reliability and univariate and multivariate analysis. PCA extracted three factors (Perceived Ease of Use, Perceived Usefulness and Perceived Barriers to Use), explained variance = 84.9%, Cronbach's ά = 0.69-0.91. In a linear regression model, Perceived Ease of Use, Perceived Usefulness and Perceived Barriers to Use explained 43.6% (p Technology assessed.

  10. Tactical Decision Aids High Bandwidth Links Using Autonomous Vehicles

    Science.gov (United States)

    2004-01-01

    1 Tactical Decision Aids (High Bandwidth Links Using Autonomous Vehicles ) A. J. Healey, D. P. Horner, Center for Autonomous Underwater Vehicle...SUBTITLE Tactical Decision Aids (High Bandwidth Links Using Autonomous Vehicles ) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

  11. Design specification for the European Spallation Source neutron generating target element

    International Nuclear Information System (INIS)

    Aguilar, A.; Sordo, F.; Mora, T.; Mena, L.; Mancisidor, M.; Aguilar, J.; Bakedano, G.; Herranz, I.; Luna, P.; Magan, M.; Vivanco, R.; Jimenez-Villacorta, F.; Sjogreen, K.; Oden, U.; Perlado, J.M.

    2017-01-01

    The paper addresses some of the most relevant issues concerning the thermal hydraulics and radiation damage of the neutron generation target to be built at the European Spallation Source as recently approved after a critical design review. The target unit consists of a set of Tungsten blocks placed inside a wheel of 2.5 m diameter which rotates at some 0.5 Hz in order to distribute the heat generated from incoming protons which reach the target in the radial direction. The spallation material elements are composed of an array of Tungsten pieces which rest on a rotating steel support (the cassette) and are distributed in a cross-flow configuration. The thermal, mechanical and radiation effects resulting from the impact of a 2 GeV proton pulse are analysed in detail as well as an evaluation of the inventory of spallation products. The current design is found to conform to specifications and found to be robust enough to deal with several accident scenarios.

  12. Design specification for the European Spallation Source neutron generating target element

    Energy Technology Data Exchange (ETDEWEB)

    Aguilar, A. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Sordo, F., E-mail: fernando.sordo@essbilbao.org [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Instituto de Fusión Nuclear, José Gutiérrez Abascal, 2, 28006 Madrid (Spain); Mora, T. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Mena, L. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Instituto de Fusión Nuclear, José Gutiérrez Abascal, 2, 28006 Madrid (Spain); Mancisidor, M.; Aguilar, J.; Bakedano, G.; Herranz, I.; Luna, P. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Magan, M.; Vivanco, R. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Instituto de Fusión Nuclear, José Gutiérrez Abascal, 2, 28006 Madrid (Spain); Jimenez-Villacorta, F. [Consorcio ESS-BILBAO. Parque Tecnológico Bizkaia. Poligono Ugaldeguren III, Pol. A, 7B, 48170 Zamudio (Spain); Sjogreen, K.; Oden, U. [European Spallation Source ERIC, P.O Box 176, SE-221 00 Lund (Sweden); Perlado, J.M. [Instituto de Fusión Nuclear, José Gutiérrez Abascal, 2, 28006 Madrid (Spain); and others

    2017-06-01

    The paper addresses some of the most relevant issues concerning the thermal hydraulics and radiation damage of the neutron generation target to be built at the European Spallation Source as recently approved after a critical design review. The target unit consists of a set of Tungsten blocks placed inside a wheel of 2.5 m diameter which rotates at some 0.5 Hz in order to distribute the heat generated from incoming protons which reach the target in the radial direction. The spallation material elements are composed of an array of Tungsten pieces which rest on a rotating steel support (the cassette) and are distributed in a cross-flow configuration. The thermal, mechanical and radiation effects resulting from the impact of a 2 GeV proton pulse are analysed in detail as well as an evaluation of the inventory of spallation products. The current design is found to conform to specifications and found to be robust enough to deal with several accident scenarios.

  13. Trace elements record complex histories in diogenites

    Science.gov (United States)

    Balta, J. B.; Beck, A. W.; McSween, H. Y.

    2012-12-01

    Diogenite meteorites are cumulate rocks composed mostly of orthopyroxene and chemically linked to eucrites (basaltic) and howardites (brecciated mixtures of diogenites and eucrites). Together, they represent the largest single family of achondrite meteorites delivered to Earth, and have been spectrally linked to the asteroid 4 Vesta, the largest remaining basaltic protoplanet. However, this spectral link is non-unique as many basaltic asteroids likely formed and were destroyed in the early solar system. Recent work suggested that Vesta may be an unlikely parent body for the diogenites based on correlations between trace elements and short-lived isotope decay products, which would be unlikely to survive on a body as large as Vesta due to its long cooling history [1]. Recent analyses of terrestrial and martian olivines have demonstrated that trace element spatial distributions can preserve evidence of their crystallization history even when major elements have been homogenized [2]. We have mapped minor elements including Cr, Al, and Ti in seemingly homogeneous diogenite orthopyroxenes and found a variety of previously unobserved textures. The pyroxenes in one sample (GRA 98108) are seemingly large grains of variable shapes and sizes, but the trace elements reveal internal grain boundaries between roughly-equal sized original subgrains, with equilibrated metamorphic triple junctions between them and trace element depletions at the boundaries. These trends suggest extraction of trace elements by a magma along those relict grain boundaries during a reheating event. Two other samples show evidence of fracturing and annealing, with trace element mobility within grains. One sample appears to have remained a closed system during annealing (MET 01084), while the other has interacted with a fluid or magma to move elements along annealed cracks (LEW 88679). These relict features establish that the history of diogenite pyroxenes is more complex than their homogeneous major

  14. The S-LINK in the data sources for trigger demonstrators in the LHC environment

    International Nuclear Information System (INIS)

    Hajduk, Z.; Iwanski, W.; Korcyl, K.; Olszowska, J.; Bij, H.C. van der

    1998-01-01

    The hardware for the data sources to be used in the ATLAS trigger demonstrator program has been designed and built. As a basic element, the SLATE2 module has been used. The S-LINK protocol, as a transferring data standard, has been chosen. A cheap implementation of the S-LINK, the Parallel Electrical S-LINK, has been built. Featuring all the specification laid down in the standard it uses a parallel twisted pair copper cable as a physical layer. A standard SCSI cable has been used. Both the Source and Destination Cards have the same PCB layout. The link may receive 32-bit wide data words at max 40 MHz input rate. Running with 40 MHz link clock, it outputs 32-bit data at a rate of 20 MHz, giving a total a bandwidth of 80 MB/s. The authors report on main characteristics of these implementations. The SLATE2SLINK cad has been built to interface the SLATE motherboard to the S-LINK environment. This daughter card is capable to house and independently control 3 S-LINK sites. Running with the 25 MHz SLATE's clock and 32-bit data, it features a total bandwidth up to 300 MB/s

  15. UV cross-linking of polypeptides associated with 3'-terminal exons

    International Nuclear Information System (INIS)

    Stolow, D.T.; Berget, S.M.

    1990-01-01

    Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro

  16. Linking chemical elements in forest floor humus (O-h-horizon) in the Czech Republic to contamination sources

    Energy Technology Data Exchange (ETDEWEB)

    Sucharova, J.; Suchara, I.; Hola, M.; Reimann, C.; Boyd, R.; Filzmoser, P.; Englmaier, P. [Geological Survey of Norway, Trondheim (Norway)

    2011-05-15

    While terrestrial moss and other plants are frequently used for environmental mapping and monitoring projects, data on the regional geochemistry of humus are scarce. Humus, however, has a much larger life span than any plant material. It can be seen as the 'environmental memory' of an area for at least the last 60-100 years. Here concentrations of 39 elements determined by ICP-MS and ICP AES, pH and ash content are presented for 259 samples of forest floor humus collected at an average sample density of 1 site/300 km{sup 2} in the Czech Republic. The scale of anomalies linked to known contamination sources (e.g., lignite mining and burning, metallurgical industry, coal fired power plants, metal smelters) is documented and discussed versus natural processes influencing humus quality. Most maps indicate a local impact from individual contamination sources: often more detailed sampling than used here would be needed to differentiate between likely sources.

  17. Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.

    Science.gov (United States)

    Li, Yang Eric; Xiao, Mu; Shi, Binbin; Yang, Yu-Cheng T; Wang, Dong; Wang, Fei; Marcia, Marco; Lu, Zhi John

    2017-09-08

    Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. Furthermore, we validate two RBP-RBP interactions in cell lines. Our approach links proteins and RNA motifs known to possess similar biochemical and cellular properties and can, when used in conjunction with additional experimental data, identify high-confidence RBP groups and their associated RNA regulatory elements.

  18. Decoupling Identification for Serial Two-Link Two-Inertia System

    Science.gov (United States)

    Oaki, Junji; Adachi, Shuichi

    The purpose of our study is to develop a precise model by applying the technique of system identification for the model-based control of a nonlinear robot arm, under taking joint-elasticity into consideration. We previously proposed a systematic identification method, called “decoupling identification,” for a “SCARA-type” planar two-link robot arm with elastic joints caused by the Harmonic-drive® reduction gears. The proposed method serves as an extension of the conventional rigid-joint-model-based identification. The robot arm is treated as a serial two-link two-inertia system with nonlinearity. The decoupling identification method using link-accelerometer signals enables the serial two-link two-inertia system to be divided into two linear one-link two-inertia systems. The MATLAB®'s commands for state-space model estimation are utilized in the proposed method. Physical parameters such as motor inertias, link inertias, joint-friction coefficients, and joint-spring coefficients are estimated through the identified one-link two-inertia systems using a gray-box approach. This paper describes accuracy evaluations using the two-link arm for the decoupling identification method under introducing closed-loop-controlled elements and varying amplitude-setup of identification-input. Experimental results show that the identification method also works with closed-loop-controlled elements. Therefore, the identification method is applicable to a “PUMA-type” vertical robot arm under gravity.

  19. The Drosophila Translational Control Element (TCE is required for high-level transcription of many genes that are specifically expressed in testes.

    Directory of Open Access Journals (Sweden)

    Rebeccah J Katzenberger

    Full Text Available To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE. The TCE functions in the 5' untranslated region of Mst(3CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300-400 bp genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and

  20. The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.

    Science.gov (United States)

    Katzenberger, Rebeccah J; Rach, Elizabeth A; Anderson, Ashley K; Ohler, Uwe; Wassarman, David A

    2012-01-01

    To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5' untranslated region of Mst(3)CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300-400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the

  1. Identification of cis-acting regulatory elements in the human oxytocin gene promoter.

    Science.gov (United States)

    Richard, S; Zingg, H H

    1991-12-01

    The expression of hormone-inducible genes is determined by the interaction of trans-acting factors with hormone-inducible elements and elements mediating basal and cell-specific expression. We have shown earlier that the gene encoding the hypothalamic nonapeptide oxytocin (OT) is under the control of an estrogen response element (ERE). The present study was aimed at identifying cis-acting elements mediating basal expression of the OT gene. A construct containing sequences -381 to +36 of the human OT gene was linked to a reporter gene and transiently transfected into a series of neuronal and nonneuronal cell lines. Expression of this construct was cell specific: it was highest in the neuroblastoma-derived cell line, Neuro-2a, and lowest in NIH 3T3 and JEG-3 cells. By 5' deletion analysis, we determined that a segment from -49 to +36 was capable of mediating cells-pecific promoter activity. Within this segment, we identified three proximal promoter elements (PPE-1, PPE-2, and PPE-3) that are each required for promoter activity. Most notably, mutation of a conserved purine-rich element (GAGAGA) contained within PPE-2 leads to a 10-fold decrease in promoter strength. Gel mobility shift analysis with three different double-stranded oligonucleotides demonstrated that each proximal promoter element binds distinct nuclear factors. In each case, only the homologous oligonucleotide, but neither of the oligonucleotides corresponding to adjacent elements, was able to act as a competitor. Thus, a different set of factors appears to bind independently to each element. By reinserting the homologous ERE or a heterologous glucocorticoid response element upstream of intact or altered proximal promoter segments we determined that removal or mutation of proximal promoter elements decreases basal expression, but does not abrogate the hormone responsiveness of the promoter. In conclusion, these results indicate that an important component of the transcriptional activity of the OT

  2. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

    Directory of Open Access Journals (Sweden)

    Garcia Sònia

    2012-06-01

    Full Text Available Abstract Background In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement or, less commonly, linked to 35 S rDNA units (L-type. The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6 but not all species. Two species contained major L-type and minor S-type units (termed Ls-type. The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’ is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.

  3. LinkED: A Novel Methodology for Publishing Linked Enterprise Data

    Directory of Open Access Journals (Sweden)

    Shreyas Suresh Rao

    2017-01-01

    Full Text Available Semantic Web technologies have redefined and strengthened the Enterprise-Web interoperability over the last decade. Linked Open Data (LOD refers to a set of best practices that empower enterprises to publish and interlink their data using existing ontologies on the World Wide Web. Current research in LOD focuses on expert search, the creation of unified information space and augmentation of core data from an enterprise context. However, existing approaches for publication of enterprise data as LOD are domain-specific, ad-hoc and suffer from lack of uniform representation across domains. The paper proposes a novel methodology called LinkED that contributes towards LOD literature in two ways: (a streamlines the publishing process through five stages of cleaning, triplification, interlinking, storage and visualization; (b addresses the latest challenges in LOD publication, namely: inadequate links, inconsistencies in the quality of the dataset and replicability of the LOD publication process. Further, the methodology is demonstrated via the publication of digital repository data as LOD in a university setting, which is evaluated based on two semantic standards: Five-Star model and data quality metrics. Overall, the paper provides a generic LOD publication process that is applicable across various domains such as healthcare, e-governance, banking, and tourism, to name a few.

  4. Sex-specific expression of the X-linked histone demethylase gene Jarid1c in brain.

    Directory of Open Access Journals (Sweden)

    Jun Xu

    Full Text Available Jarid1c, an X-linked gene coding for a histone demethylase, plays an important role in brain development and function. Notably, JARID1C mutations cause mental retardation and increased aggression in humans. These phenotypes are consistent with the expression patterns we have identified in mouse brain where Jarid1c mRNA was detected in hippocampus, hypothalamus, and cerebellum. Jarid1c expression and associated active histone marks at its 5'end are high in P19 neurons, indicating that JARID1C demethylase plays an important role in differentiated neuronal cells. We found that XX mice expressed Jarid1c more highly than XY mice, independent of their gonadal types (testes versus ovaries. This increased expression in XX mice is consistent with Jarid1c escape from X inactivation and is not compensated by expression from the Y-linked paralogue Jarid1d, which is expressed at a very low level compared to the X paralogue in P19 cells. Our observations suggest that sex-specific expression of Jarid1c may contribute to sex differences in brain function.

  5. Linking advanced fracture models to structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chiesa, Matteo

    2001-07-01

    Shell structures with defects occur in many situations. The defects are usually introduced during the welding process necessary for joining different parts of the structure. Higher utilization of structural materials leads to a need for accurate numerical tools for reliable prediction of structural response. The direct discretization of the cracked shell structure with solid finite elements in order to perform an integrity assessment of the structure in question leads to large size problems, and makes such analysis infeasible in structural application. In this study a link between local material models and structural analysis is outlined. An ''ad hoc'' element formulation is used in order to connect complex material models to the finite element framework used for structural analysis. An improved elasto-plastic line spring finite element formulation, used in order to take cracks into account, is linked to shell elements which are further linked to beam elements. In this way one obtain a global model of the shell structure that also accounts for local flexibilities and fractures due to defects. An important advantage with such an approach is a direct fracture mechanics assessment e.g. via computed J-integral or CTOD. A recent development in this approach is the notion of two-parameter fracture assessment. This means that the crack tip stress tri-axiality (constraint) is employed in determining the corresponding fracture toughness, giving a much more realistic capacity of cracked structures. The present thesis is organized in six research articles and an introductory chapter that reviews important background literature related to this work. Paper I and II address the performance of shell and line spring finite elements as a cost effective tool for performing the numerical calculation needed to perform a fracture assessment. In Paper II a failure assessment, based on the testing of a constraint-corrected fracture mechanics specimen under tension, is

  6. Population genetics of Phytophthora infestans in Denmark reveals dominantly clonal populations and specific alleles linked to metalaxyl-M resistance

    DEFF Research Database (Denmark)

    Montes, M. S.; Nielsen, Bent Jørgen; Schmidt, S. G.

    2016-01-01

    population of P. infestans was characterized over the course of the 2013 growing season, as was the population genetic structure, using simple sequence repeat (SSR) genotypes and single nucleotide polymorphism (SNP)-based mitochondrial haplotyping of over 80 isolates. Both mating types A1 and A2 were present...... in most fields, but tests for recombination showed that clonal reproduction dominates in Danish populations. Genotype was not linked to haplotype and no differentiation was observed at the haplotype level, but rather between fields. Resistance phenotypes were linked to specific SSR alleles, demonstrating...

  7. Microwaves photonic links components and circuits

    CERN Document Server

    Rumelhard, Christian; Billabert, Anne-Laure

    2013-01-01

    This book presents the electrical models for the different elements of a photonic microwave link like lasers, external modulators, optical fibers, photodiodes and phototransistors. The future trends of these components are also introduced: lasers to VCSEL, external modulators to electro-absorption modulators, glass optical fibers to plastic optical fibers, photodiodes to UTC photodiodes or phototransistors. It also describes an original methodology to evaluate the performance of a microwave photonic link, based on the developed elcetrical models, that can be easily incorporated in

  8. Source origin of trace elements in PM from regional background, urban and industrial sites of Spain

    Science.gov (United States)

    Querol, X.; Viana, M.; Alastuey, A.; Amato, F.; Moreno, T.; Castillo, S.; Pey, J.; de la Rosa, J.; Sánchez de la Campa, A.; Artíñano, B.; Salvador, P.; García Dos Santos, S.; Fernández-Patier, R.; Moreno-Grau, S.; Negral, L.; Minguillón, M. C.; Monfort, E.; Gil, J. I.; Inza, A.; Ortega, L. A.; Santamaría, J. M.; Zabalza, J.

    Despite their significant role in source apportionment analysis, studies dedicated to the identification of tracer elements of emission sources of atmospheric particulate matter based on air quality data are relatively scarce. The studies describing tracer elements of specific sources currently available in the literature mostly focus on emissions from traffic or large-scale combustion processes (e.g. power plants), but not on specific industrial processes. Furthermore, marker elements are not usually determined at receptor sites, but during emission. In our study, trace element concentrations in PM 10 and PM 2.5 were determined at 33 monitoring stations in Spain throughout the period 1995-2006. Industrial emissions from different forms of metallurgy (steel, stainless steel, copper, zinc), ceramic and petrochemical industries were evaluated. Results obtained at sites with no significant industrial development allowed us to define usual concentration ranges for a number of trace elements in rural and urban background environments. At industrial and traffic hotspots, average trace metal concentrations were highest, exceeding rural background levels by even one order of magnitude in the cases of Cr, Mn, Cu, Zn, As, Sn, W, V, Ni, Cs and Pb. Steel production emissions were linked to high levels of Cr, Mn, Ni, Zn, Mo, Cd, Se and Sn (and probably Pb). Copper metallurgy areas showed high levels of As, Bi, Ga and Cu. Zinc metallurgy was characterised by high levels of Zn and Cd. Glazed ceramic production areas were linked to high levels of Zn, As, Se, Zr, Cs, Tl, Li, Co and Pb. High levels of Ni and V (in association) were tracers of petrochemical plants and/or fuel-oil combustion. At one site under the influence of heavy vessel traffic these elements could be considered tracers (although not exclusively) of shipping emissions. Levels of Zn-Ba and Cu-Sb were relatively high in urban areas when compared with industrialised regions due to tyre and brake abrasion, respectively.

  9. High resolution quantitative element mapping of neuromelanin-containing neurons

    Energy Technology Data Exchange (ETDEWEB)

    Reinert, Tilo [Nukleare Festkoerperphysik, Universitaet Leipzig, Linnestrasse 5, 04103 Leipzig (Germany)]. E-mail: reinert@physik.uni-leipzig.de; Fiedler, Anja [Nukleare Festkoerperphysik, Universitaet Leipzig, Linnestrasse 5, 04103 Leipzig (Germany); Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany); Morawski, Markus [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany); Arendt, Thomas [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany)

    2007-07-15

    Neuromelanin is a dark coloured intracellular pigment that appears in a specific population of neurons (dopaminergic and noradrenergic) predominantly in the substantia nigra and in the locus coeruleus. In recent years, there is increasing interest in the role of neuromelanin because of a hypothesised link between this pigment and the cell death of neuromelanin-containing neurons in Parkinson's disease (PD). Therefore, the role of neuromelanin in the pathology of PD is an actual focus in neuroscience. We have investigated the elemental contents and distributions of sulphur, calcium, iron, nickel and copper of neuromelanin in dopaminergic neurons for a Parkinson case and a control case (in situ, 6 {mu}m brain sections). There was no difference in the iron concentration between the two cases. However, the calcium concentration was 3-fold higher in the Parkinson case, whereas the copper and nickel concentrations decreased. An ultrastructural investigation of the concentrations of calcium and iron within the neuromelanin suggests that these two elements are not necessarily co-localized.

  10. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs.

    Directory of Open Access Journals (Sweden)

    Christopher D Brown

    Full Text Available Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL mapping has paralleled the adoption of genome-wide association studies (GWAS for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human

  11. Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution

    Science.gov (United States)

    Kobayashi, Ichizo

    2001-01-01

    Restriction–modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and

  12. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

    Science.gov (United States)

    Kobayashi, I

    2001-09-15

    Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and

  13. Substrate specificity of low-molecular mass bacterial DD-peptidases.

    Science.gov (United States)

    Nemmara, Venkatesh V; Dzhekieva, Liudmila; Sarkar, Kumar Subarno; Adediran, S A; Duez, Colette; Nicholas, Robert A; Pratt, R F

    2011-11-22

    The bacterial DD-peptidases or penicillin-binding proteins (PBPs) catalyze the formation and regulation of cross-links in peptidoglycan biosynthesis. They are classified into two groups, the high-molecular mass (HMM) and low-molecular mass (LMM) enzymes. The latter group, which is subdivided into classes A-C (LMMA, -B, and -C, respectively), is believed to catalyze DD-carboxypeptidase and endopeptidase reactions in vivo. To date, the specificity of their reactions with particular elements of peptidoglycan structure has not, in general, been defined. This paper describes the steady-state kinetics of hydrolysis of a series of specific peptidoglycan-mimetic peptides, representing various elements of stem peptide structure, catalyzed by a range of LMM PBPs (the LMMA enzymes, Escherichia coli PBP5, Neisseria gonorrhoeae PBP4, and Streptococcus pneumoniae PBP3, and the LMMC enzymes, the Actinomadura R39 dd-peptidase, Bacillus subtilis PBP4a, and N. gonorrhoeae PBP3). The R39 enzyme (LMMC), like the previously studied Streptomyces R61 DD-peptidase (LMMB), specifically and rapidly hydrolyzes stem peptide fragments with a free N-terminus. In accord with this result, the crystal structures of the R61 and R39 enzymes display a binding site specific to the stem peptide N-terminus. These are water-soluble enzymes, however, with no known specific function in vivo. On the other hand, soluble versions of the remaining enzymes of those noted above, all of which are likely to be membrane-bound and/or associated in vivo and have been assigned particular roles in cell wall biosynthesis and maintenance, show little or no specificity for peptides containing elements of peptidoglycan structure. Peptidoglycan-mimetic boronate transition-state analogues do inhibit these enzymes but display notable specificity only for the LMMC enzymes, where, unlike peptide substrates, they may be able to effectively induce a specific active site structure. The manner in which LMMA (and HMM) DD

  14. Simulation of Controller Pilot Data Link Communications over VHF Digital Link Mode 3

    Science.gov (United States)

    Bretmersky, Steven C.; Murawski, Robert; Nguyen, Thanh C.; Raghavan, Rajesh S.

    2004-01-01

    The Federal Aviation Administration (FAA) has established an operational plan for the future Air Traffic Management (ATM) system, in which the Controller Pilot Data Link Communications (CPDLC) is envisioned to evolve into digital messaging that will take on an ever increasing role in controller to pilot communications, significantly changing the way the National Airspace System (NAS) is operating. According to FAA, CPDLC represents the first phase of the transition from the current analog voice system to an International Civil Aviation Organization (ICAO) compliant system in which digital communication becomes the alternate and perhaps primary method of routine communication. The CPDLC application is an Air Traffic Service (ATS) application in which pilots and controllers exchange messages via an addressed data link. CPDLC includes a set of clearance, information, and request message elements that correspond to existing phraseology employed by current Air Traffic Control (ATC) procedures. These message elements encompass altitude assignments, crossing constraints, lateral deviations, route changes and clearances, speed assignments, radio frequency assignments, and various requests for information. The pilot is provided with the capability to respond to messages, to request clearances and information, to report information, and to declare/rescind an emergency. A 'free text' capability is also provided to exchange information not conforming to defined formats. This paper presents simulated results of the aeronautical telecommunication application Controller Pilot Data Link Communications over VHF Digital Link Mode 3 (VDL Mode 3). The objective of this simulation study was to determine the impact of CPDLC traffic loads, in terms of timely message delivery and capacity of the VDL Mode 3 subnetwork. The traffic model is based on and is used for generating air/ground messages with different priorities. Communication is modeled for the en route domain of the Cleveland

  15. The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF-κB p50

    Science.gov (United States)

    Cheng, Christine S.; Feldman, Kristyn E.; Lee, James; Verma, Shilpi; Huang, De-Bin; Huynh, Kim; Chang, Mikyoung; Ponomarenko, Julia V.; Sun, Shao-Cong; Benedict, Chris A.; Ghosh, Gourisankar; Hoffmann, Alexander

    2011-01-01

    The specific binding of transcription factors to cognate sequence elements is thought to be critical for the generation of specific gene expression programs. Members of the nuclear factor κB (NF-κB) and interferon (IFN) regulatory factor (IRF) transcription factor families bind to the κB site and the IFN response element (IRE), respectively, of target genes, and they are activated in macrophages after exposure to pathogens. However, how these factors produce pathogen-specific inflammatory and immune responses remains poorly understood. Combining top-down and bottom-up systems biology approaches, we have identified the NF-κB p50 homodimer as a regulator of IRF responses. Unbiased genome-wide expression and biochemical and structural analyses revealed that the p50 homodimer repressed a subset of IFN-inducible genes through a previously uncharacterized subclass of guanine-rich IRE (G-IRE) sequences. Mathematical modeling predicted that the p50 homodimer might enforce the stimulus specificity of composite promoters. Indeed, the production of the antiviral regulator IFN-β was rendered stimulus-specific by the binding of the p50 homodimer to the G-IRE–containing IFNβ enhancer to suppress cytotoxic IFN signaling. Specifically, a deficiency in p50 resulted in the inappropriate production of IFN-β in response to bacterial DNA sensed by Toll-like receptor 9. This role for the NF-κB p50 homodimer in enforcing the specificity of the cellular response to pathogens by binding to a subset of IRE sequences alters our understanding of how the NF-κB and IRF signaling systems cooperate to regulate antimicrobial immunity. PMID:21343618

  16. Discrete Element Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Morris, J; Johnson, S

    2007-12-03

    The Distinct Element Method (also frequently referred to as the Discrete Element Method) (DEM) is a Lagrangian numerical technique where the computational domain consists of discrete solid elements which interact via compliant contacts. This can be contrasted with Finite Element Methods where the computational domain is assumed to represent a continuum (although many modern implementations of the FEM can accommodate some Distinct Element capabilities). Often the terms Discrete Element Method and Distinct Element Method are used interchangeably in the literature, although Cundall and Hart (1992) suggested that Discrete Element Methods should be a more inclusive term covering Distinct Element Methods, Displacement Discontinuity Analysis and Modal Methods. In this work, DEM specifically refers to the Distinct Element Method, where the discrete elements interact via compliant contacts, in contrast with Displacement Discontinuity Analysis where the contacts are rigid and all compliance is taken up by the adjacent intact material.

  17. On the specification of bus voltages and radial link transfer impedance modes

    Energy Technology Data Exchange (ETDEWEB)

    El-Sadik, F.M. [Khartoum Univ., Aljamaa, Khartoum (Sudan)

    2010-07-01

    No algebraic equation has been derived for the steady-state stability limit (SSSL) of radial power system components in terms of their resistive sectional impedance elements and associated scalar node voltage constraints. While many criterion have been developed in the literature for the steady state angle and voltage stability limits of systems with losses, speculation exists about certain advocated metrics for these systems in terms of stability reserve margins as a measure of the risk of blackout and the representation of reactance modes associated with Putman's model for synchronous machines. This paper presented the results of a generalized algebraic statement for the reactance modes under stability conditions in voltage-specified power system components cited in the single machine-infinite bus (SMIB) and the radial power link (RPL) systems. The direct analytical solution to the problem enabled the identification of 2 different constraint relations for the sending (E) and receiving-end voltage regulator (VR) voltages. The paper discussed the general SSSL function plan, conditions for SMIB system reactances, and index results for the voltage stability of radial lines. The results for the R2 influence and influence on radial compensation levels were also presented. Index results for non-operational reactance zones were provided. It was concluded that the algebraic solution in a full representation of system losses would enable identification of additional function discontinuities that might not reveal in a step-by-step numerical algorithm and that may account for the many unresolved transmission system phenomenon associated with SSSL predictions and capacitance compensation schemes. 11 refs., 1 tab., 5 figs., 3 appendices.

  18. Gauge links for transverse momentum dependent correlators at tree-level

    NARCIS (Netherlands)

    Buffing, M.G.A.; Mulders, P.J.G.

    2011-01-01

    In this paper we discuss the incorporation of gauge links in hadronic matrix elements that describe the soft hadronic physics in high energy scattering processes. In this description the matrix elements appear in soft correlators and they contain non-local combinations of quark and gluon fields. In

  19. Patient-specific non-linear finite element modelling for predicting soft organ deformation in real-time: application to non-rigid neuroimage registration.

    Science.gov (United States)

    Wittek, Adam; Joldes, Grand; Couton, Mathieu; Warfield, Simon K; Miller, Karol

    2010-12-01

    Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) biomechanical models have been regarded as one of the key factors preventing application of such models in predicting organ deformation for image-guided surgery. This contribution presents real-time patient-specific computation of the deformation field within the brain for six cases of brain shift induced by craniotomy (i.e. surgical opening of the skull) using specialised non-linear finite element procedures implemented on a graphics processing unit (GPU). In contrast to commercial finite element codes that rely on an updated Lagrangian formulation and implicit integration in time domain for steady state solutions, our procedures utilise the total Lagrangian formulation with explicit time stepping and dynamic relaxation. We used patient-specific finite element meshes consisting of hexahedral and non-locking tetrahedral elements, together with realistic material properties for the brain tissue and appropriate contact conditions at the boundaries. The loading was defined by prescribing deformations on the brain surface under the craniotomy. Application of the computed deformation fields to register (i.e. align) the preoperative and intraoperative images indicated that the models very accurately predict the intraoperative deformations within the brain. For each case, computing the brain deformation field took less than 4 s using an NVIDIA Tesla C870 GPU, which is two orders of magnitude reduction in computation time in comparison to our previous study in which the brain deformation was predicted using a commercial finite element solver executed on a personal computer. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Human-specific subcellular compartmentalization of P-element induced wimpy testis-like (PIWIL) granules during germ cell development and spermatogenesis

    NARCIS (Netherlands)

    Gomes Fernandes, Maria; He, Nannan; Wang, Fang; Van Iperen, Liesbeth; Eguizabal, Cristina; Matorras, Roberto; Roelen, Bernard A J; Chuva de Sousa Lopes, Susana M

    2018-01-01

    STUDY QUESTION: What is the dynamics of expression of P-element induced wimpy testis-like (PIWIL) proteins in the germline during human fetal development and spermatogenesis? SUMMARY ANSWER: PIWIL1, PIWIL2, PIWIL3 and PIWIL4 were expressed in a sex-specific fashion in human germ cells (GC) during

  1. Integrating Environmentally Responsive Elements in Buildings

    DEFF Research Database (Denmark)

    Heiselberg, Per

    2006-01-01

    Significant improvement have been achieved on efficiency improvements of specific building elements like the building envelope and building equipment and services and whilst most building elements still offer opportunities for efficiency improvements, the greatest future potential lie with techno......Significant improvement have been achieved on efficiency improvements of specific building elements like the building envelope and building equipment and services and whilst most building elements still offer opportunities for efficiency improvements, the greatest future potential lie...

  2. Carbon and nitrogen elemental and isotopic ratios of filter-feeding bivalves along the French coasts: An assessment of specific, geographic, seasonal and multi-decadal variations.

    Science.gov (United States)

    Briant, Nicolas; Savoye, Nicolas; Chouvelon, Tiphaine; David, Valérie; Rodriguez, Samuel; Charlier, Karine; Sonke, Jeroen E; Chiffoleau, Jean François; Brach-Papa, Christophe; Knoery, Joël

    2018-02-01

    Primary consumers play a key role in coastal ecosystems by transferring organic matter from primary producers to predators. Among them, suspension-feeders, like bivalve molluscs are widely used in trophic web studies. The main goal of this study was to investigate variations of C and N elemental and isotopic ratios in common bivalves (M. edulis, M. galloprovincialis, and C. gigas) at large spatial (i.e. among three coastal regions) and different temporal (i.e. from seasonal to multi-decadal) scales in France, in order to identify potential general or specific patterns and speculate on their drivers. The observed spatial variability was related to the trophic status of the coastal regions (oligotrophic Mediterranean Sea versus meso- to eutrophic English Channel and Atlantic ocean), but not to ecosystem typology (estuaries, versus lagoons versus bays versus littoral systems). Furthermore, it highlighted local specificities in terms of the origin of the POM assimilated by bivalves (e.g., mainly continental POM vs. marine phytoplankton vs. microphytobenthic algae). Likewise, seasonal variability was related both to the reproduction cycle for C/N ratios of Mytilus spp. and to changes in trophic resources for δ 13 C of species located close to river mouth. Multi-decadal evolution exhibited shifts and trends for part of the 30-year series with decreases in δ 13 C and δ 15 N. Specifically, shifts appeared in the early 2000's, likely linking bivalve isotopic ratios to a cascade of processes affected by local drivers. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Fluidic Elements based on Coanda Effect

    Directory of Open Access Journals (Sweden)

    Constantin OLIVOTTO

    2010-12-01

    Full Text Available This paper contains first some definitions and classifications regarding the fluidic elements. Thegeneral current status is presented, nominating the main specific elements based on the Coanda effect developedspecially in Romania. In particularly the development of an original bistable element using industrial compressedair at industrial pressure supply is presented. The function of this element is based on the controlled attachmentof the main jet at a curved wall through the Coanda effect. The methods used for particular calculation andexperiments are nominated. The main application of these elements was to develop a specific execution element:a fluidic step–by-step motor based on the Coanda effect.

  4. Radiolabelled cellular blood elements

    International Nuclear Information System (INIS)

    Sinzinger, H.

    1990-01-01

    This book reports on radiolabelled cellular blood elements, covering new advances made during the past several years, in particular the use of Tc-99 as a tracer for blood elements. Coverage extends to several radiolabelled monoclonal antibodies that are specific for blood components and may label blood elements in vivo

  5. Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

    Science.gov (United States)

    Galindo-González, Leonardo; Mhiri, Corinne; Grandbastien, Marie-Angèle; Deyholos, Michael K

    2016-12-07

    Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant

  6. Age- and sex-specific thorax finite element model development and simulation.

    Science.gov (United States)

    Schoell, Samantha L; Weaver, Ashley A; Vavalle, Nicholas A; Stitzel, Joel D

    2015-01-01

    The shape, size, bone density, and cortical thickness of the thoracic skeleton vary significantly with age and sex, which can affect the injury tolerance, especially in at-risk populations such as the elderly. Computational modeling has emerged as a powerful and versatile tool to assess injury risk. However, current computational models only represent certain ages and sexes in the population. The purpose of this study was to morph an existing finite element (FE) model of the thorax to depict thorax morphology for males and females of ages 30 and 70 years old (YO) and to investigate the effect on injury risk. Age- and sex-specific FE models were developed using thin-plate spline interpolation. In order to execute the thin-plate spline interpolation, homologous landmarks on the reference, target, and FE model are required. An image segmentation and registration algorithm was used to collect homologous rib and sternum landmark data from males and females aged 0-100 years. The Generalized Procrustes Analysis was applied to the homologous landmark data to quantify age- and sex-specific isolated shape changes in the thorax. The Global Human Body Models Consortium (GHBMC) 50th percentile male occupant model was morphed to create age- and sex-specific thoracic shape change models (scaled to a 50th percentile male size). To evaluate the thoracic response, 2 loading cases (frontal hub impact and lateral impact) were simulated to assess the importance of geometric and material property changes with age and sex. Due to the geometric and material property changes with age and sex, there were observed differences in the response of the thorax in both the frontal and lateral impacts. Material property changes alone had little to no effect on the maximum thoracic force or the maximum percent compression. With age, the thorax becomes stiffer due to superior rotation of the ribs, which can result in increased bone strain that can increase the risk of fracture. For the 70-YO models

  7. Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope

    DEFF Research Database (Denmark)

    Matthews, Philippa C; Koyanagi, Madoka; Kløverpris, Henrik N

    2012-01-01

    -clade sequences, which critically reduces recognition of the Gag NY10 epitope. These data suggest that in spite of any inherent HLA-linked T-cell receptor repertoire differences that may exist, maximizing the breadth of the Gag-specific CD8(+) T-cell response, by the addition of even a single epitope, may......The strongest genetic influence on immune control in HIV-1 infection is the HLA class I genotype. Rapid disease progression in B-clade infection has been linked to HLA-B*35 expression, in particular to the less common HLA-B*3502 and HLA-B*3503 subtypes but also to the most prevalent subtype, HLA...

  8. Quantification of methanogenic biomass by enzyme-linked immunosorbent assay and by analysis of specific methanogenic cofactors

    Energy Technology Data Exchange (ETDEWEB)

    Gorris, L G.M.; Kemp, H A; Archer, D B

    1987-01-01

    The reliability and accuracy with which enzyme-linked immunosorbent assay (ELISA) and an assay of methanogenic cofactors detect and quantify methanogenic species were investigated. Both assays required standardization with laboratory cultures of methanogenic bacteria and were applied to mixtures of pure cultures and samples from anaerobic digesters. ELISA was shown to be a simple method for detecting and quantifying individual methanogenic species. The range of species which can be assayed is limited by the range of antisera available but, potentially, ELISA can be applied to all methanogens. Although the cofactor assay is not species-specific it can distinguish hydrogenotrophic and acetotrophic methanogens and is quantitative.

  9. Two ABREs, two redundant root-specific and one W-box cis-acting elements are functional in the sunflower HAHB4 promoter.

    Science.gov (United States)

    Manavella, Pablo A; Dezar, Carlos A; Ariel, Federico D; Chan, Raquel L

    2008-10-01

    HAHB4 is a sunflower gene encoding a homeodomain-leucine zipper (HD-Zip) transcription factor. It was previously demonstrated that this gene is regulated at the transcriptional level by several abiotic factors and hormones. A previous analysis in the PLACE database revealed the presence of four putative ABREs. In this work these four elements and also one W-box and two root-specific expression elements were characterized as functional. Site-directed mutagenesis on the promoter, stable transformation of Arabidopis plants as well as transient transformation of sunflower leaves, were performed. The analysis of the transformants was carried out by histochemistry and real time RT-PCR. The results indicate that just one ABRE out of the four is responsible for ABA, NaCl and drought regulation. However, NaCl induction occurs also by an additional ABA-independent way involving another two overlapped ABREs. On the other hand, it was determined that the W-box located 5' upstream is responsive to ethylene and only two root-specific expression elements, among the several detected, are functional but redundant. Conservation of molecular mechanisms between sunflower and Arabidopsis is strongly supported by this experimental work.

  10. Core-Mantle Partitioning of Volatile Elements and the Origin of Volatile Elements in Earth and Moon

    Science.gov (United States)

    Righter, K.; Pando, K.; Danielson, L.; Nickodem, K.

    2014-01-01

    Depletions of siderophile elements in mantles have placed constraints on the conditions on core segregation and differentiation in bodies such as Earth, Earth's Moon, Mars, and asteroid 4 Vesta. Among the siderophile elements there are a sub-set that are also volatile (volatile siderophile elements or VSE; Ga, Ge, In, As, Sb, Sn, Bi, Zn, Cu, Cd), and thus can help to constrain the origin of volatile elements in these bodies, and in particular the Earth and Moon. One of the fundamental observations of the geochemistry of the Moon is the overall depletion of volatile elements relative to the Earth, but a satisfactory explanation has remained elusive. Hypotheses for Earth include addition during accretion and core formation and mobilized into the metallic core, multiple stage origin, or addition after the core formed. Any explanation for volatile elements in the Earth's mantle must also be linked to an explanation of these elements in the lunar mantle. New metal-silicate partitioning data will be applied to the origin of volatile elements in both the Earth and Moon, and will evaluate theories for exogenous versus endogenous origin of volatile elements.

  11. Interaction of a nodule specific, trans-acting factor with distinct DNA elements in the soybean leghaemoglobin Ibc(3) 5' upstream region

    DEFF Research Database (Denmark)

    Jensen, Erik Østergaard; Marcker, Kjeld A; Schell, J

    1988-01-01

    Nuclear extracts from soybean nodules, leaves and roots were used to investigate protein-DNA interactions in the 5' upstream (promoter) region of the soybean leghaemoglobin lbc(3) gene. Two distinct regions were identified which strongly bind a nodule specific factor. A Bal31 deletion analysis......, but with different affinities. Elements 1 and 2 share a common motif, although their AT-rich DNA sequences differ. Element 2 is highly conserved at an analogous position in other soybean lb gene 5' upstream regions. Udgivelsesdato: 1988-May...

  12. Discovery of undefined protein cross-linking chemistry: a comprehensive methodology utilizing 18O-labeling and mass spectrometry.

    Science.gov (United States)

    Liu, Min; Zhang, Zhongqi; Zang, Tianzhu; Spahr, Chris; Cheetham, Janet; Ren, Da; Zhou, Zhaohui Sunny

    2013-06-18

    Characterization of protein cross-linking, particularly without prior knowledge of the chemical nature and site of cross-linking, poses a significant challenge, because of their intrinsic structural complexity and the lack of a comprehensive analytical approach. Toward this end, we have developed a generally applicable workflow-XChem-Finder-that involves four stages: (1) detection of cross-linked peptides via (18)O-labeling at C-termini; (2) determination of the putative partial sequences of each cross-linked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search; (3) extension to full sequences based on protease specificity, the unique combination of mass, and other constraints; and (4) deduction of cross-linking chemistry and site. The mass difference between the sum of two putative full-length peptides and the cross-linked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross-linking. Combined with sequence restraint from MS/MS data, plausible cross-linking chemistry and site were inferred, and ultimately confirmed, by matching with all data. Applying our approach to a stressed IgG2 antibody, 10 cross-linked peptides were discovered and found to be connected via thioethers originating from disulfides at locations that had not been previously recognized. Furthermore, once the cross-link chemistry was revealed, a targeted cross-link search yielded 4 additional cross-linked peptides that all contain the C-terminus of the light chain.

  13. Comparison of trace element contamination levels (Cu, Zn, Fe, Cd ...

    African Journals Online (AJOL)

    Comparison of trace element contamination levels (Cu, Zn, Fe, Cd and Pb) in the soft tissues of the gastropods Tympanotonus fuscatus fuscatus and Tf radula collected in the Ebrié Lagoon (Côte d'Ivoire): Evidence of the risks linked to linked to lead and.

  14. Variable Domain N-Linked Glycans Acquired During Antigen-Specific Immune Responses Can Contribute to Immunoglobulin G Antibody Stability

    Directory of Open Access Journals (Sweden)

    Fleur S. van de Bovenkamp

    2018-04-01

    Full Text Available Immunoglobulin G (IgG can contain N-linked glycans in the variable domains, the so-called Fab glycans, in addition to the Fc glycans in the CH2 domains. These Fab glycans are acquired following introduction of N-glycosylation sites during somatic hypermutation and contribute to antibody diversification. We investigated whether Fab glycans may—in addition to affecting antigen binding—contribute to antibody stability. By analyzing thermal unfolding profiles of antibodies with or without Fab glycans, we demonstrate that introduction of Fab glycans can improve antibody stability. Strikingly, removal of Fab glycans naturally acquired during antigen-specific immune responses can deteriorate antibody stability, suggesting in vivo selection of stable, glycosylated antibodies. Collectively, our data show that variable domain N-linked glycans acquired during somatic hypermutation can contribute to IgG antibody stability. These findings indicate that introducing Fab glycans may represent a mechanism to improve therapeutic/diagnostic antibody stability.

  15. Hierarchical Linked Views

    Energy Technology Data Exchange (ETDEWEB)

    Erbacher, Robert; Frincke, Deb

    2007-07-02

    Coordinated views have proven critical to the development of effective visualization environments. This results from the fact that a single view or representation of the data cannot show all of the intricacies of a given data set. Additionally, users will often need to correlate more data parameters than can effectively be integrated into a single visual display. Typically, development of multiple-linked views results in an adhoc configuration of views and associated interactions. The hierarchical model we are proposing is geared towards more effective organization of such environments and the views they encompass. At the same time, this model can effectively integrate much of the prior work on interactive and visual frameworks. Additionally, we expand the concept of views to incorporate perceptual views. This is related to the fact that visual displays can have information encoded at various levels of focus. Thus, a global view of the display provides overall trends of the data while focusing in on individual elements provides detailed specifics. By integrating interaction and perception into a single model, we show how one impacts the other. Typically, interaction and perception are considered separately, however, when interaction is being considered at a fundamental level and allowed to direct/modify the visualization directly we must consider them simultaneously and how they impact one another.

  16. Highly Siderophile Elements in Pallasites and Diogenites, Including the New Pallasite, CMS 04071

    Science.gov (United States)

    Danielson, L. R.; Humayun, M.; Righter, K.

    2006-01-01

    Pallasites are long thought to represent a metallic core-silicate mantle boundary, where the IIIAB irons are linked to the crystallization history of the metallic fraction, and the HED meteorites may be linked to the silicate fraction. However, measurement of trace elements in individual metallic and silicate phases is necessary in order to fully under-stand the petrogenetic history of pallasites, as well as any magmatic processes which may link pallasites to both IIIAB irons and HED meteorites. In order to achieve this objective, abundances of a suite of elements were measured, including the highly siderophile elements (HSEs), in kamacite, taenite, troilite, schreibersite, chromite and olivine for the pallasites Admire, Imilac, Springwater, CMS 04071. In the diogenites GRO 95555, LAP 91900, and MET 00436, metal, sulfide, spinel, pyroxene, and silica were individually measured.

  17. Linking DC together with TRSL

    DEFF Research Database (Denmark)

    Haxthausen, Anne; Yong, Xia

    1999-01-01

    In this talk we present a method for linking the Duration Calculus together with the Timed RAISE Specification Language. Duration Calculus (DC) [ZHR91] is an interval-based real time logic, which can be used naturally in capturing and eliciting users' real time requirements in the form of constra......In this talk we present a method for linking the Duration Calculus together with the Timed RAISE Specification Language. Duration Calculus (DC) [ZHR91] is an interval-based real time logic, which can be used naturally in capturing and eliciting users' real time requirements in the form.......TRSL is a real-time extension of the RAISE Specification Language (RSL) [Rlg92] which together with its associated method [Rmg95]and tools has shown to be very useful in the industrial development of software systems. Therefore, a promising approach for the development of real-time systemscould be to use DC...... for high-level specifications of real-time requirementsand TRSL for specifying real-time implementations in the form of timed communicating concurrent processes.In order to link DC and TRSL together in a well-founded way, we formally define what it means for a TRSL process to satisfy a DC requirement...

  18. Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides).

    Science.gov (United States)

    Domb, Katherine; Keidar, Danielle; Yaakov, Beery; Khasdan, Vadim; Kashkush, Khalil

    2017-10-27

    Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes

  19. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

    Directory of Open Access Journals (Sweden)

    Yoichiro Shibata

    2012-06-01

    Full Text Available Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species.

  20. FAA airborne data link human factors research plan

    Science.gov (United States)

    1993-07-01

    This report contains a five-year plan to perform research of human factors issues and topics : related to Data Link implementations in general aviation and transport category aircraft. : Elements such as resource allocation and management and coordin...

  1. Essential Specification Elements for Heat Exchanger Replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bower, L.

    2015-07-01

    Performance upgrade and equipment degradation are the primary impetuses for a nuclear power plant to engage in the large capital cost project of heat exchanger replacement. Along with attention to these issues, consideration of heat exchanger Codes and Standards, material improvements, thermal redesign, and configuration are essential for developing User’s Design Specifications for successful replacement projects. The User’s Design Specification is the central document in procuring ASME heat exchangers. Properly stated objectives for the heat exchanger replacement are essential for obtaining the materials, configurations and thermal designs best suited for the nuclear power plant. Additionally, the code of construction required and the applied manufacturing standard (TEMA or HEI) affects how the heat exchanger may be designed or configured to meet the replacement goals. Knowledge of how Codes and Standards affect design and configuration details will aid in writing the User’s Design Specification. Joseph Oat Corporation has designed and fabricated many replacement heat exchangers for the nuclear power industry. These heat exchangers have been constructed per ASME Section III to various Code-Years or ASME Section VIII-1 to the current Code-Year also in accordance with TEMA and HEI. These heat exchangers have been a range of like-for-like replacement to complete thermal, material and configuration redesigns. Several examples of these heat exchangers with their Code, Standard and specification implications are presented. (Author.

  2. Simplified Qualitative Discrete Numerical Model to Determine Cracking Pattern in Brittle Materials by Means of Finite Element Method

    OpenAIRE

    Ochoa-Avendaño, J.; Garzon-Alvarado, D. A.; Linero, Dorian L.; Cerrolaza, M.

    2017-01-01

    This paper presents the formulation, implementation, and validation of a simplified qualitative model to determine the crack path of solids considering static loads, infinitesimal strain, and plane stress condition. This model is based on finite element method with a special meshing technique, where nonlinear link elements are included between the faces of the linear triangular elements. The stiffness loss of some link elements represents the crack opening. Three experimental tests of bending...

  3. Linking salinity stress tolerance with tissue-specific Na+ sequestration in wheat roots

    Directory of Open Access Journals (Sweden)

    Honghong eWu

    2015-02-01

    Full Text Available Salinity stress tolerance is a physiologically complex trait that is conferred by the large array of interacting mechanisms. Among these, vacuolar Na+ sequestration has always been considered as one of the key components differentiating between sensitive and tolerant species and genotypes. However, vacuolar Na+ sequestration has been rarely considered in the context of the tissue-specific expression and regulation of appropriate transporters contributing to Na+ removal from the cytosol. In this work, six bread wheat varieties contrasting in their salinity tolerance (three tolerant and three sensitive were used to understand the essentiality of vacuolar Na+ sequestration between functionally different root tissues, and link it with the overall salinity stress tolerance in this species. Roots of 4-d old wheat seedlings were treated with 100 mM NaCl for 3 days, and then Na+ distribution between cytosol and vacuole was quantified by CoroNa Green fluorescent dye imaging. Our major observations were as follows: 1 salinity stress tolerance correlated positively with vacuolar Na+ sequestration ability in the mature root zone but not in the root apex; 2 Contrary to expectations, cytosolic Na+ levels in root meristem were significantly higher in salt tolerant than sensitive group, while vacuolar Na+ levels showed an opposite trend. These results are interpreted as meristem cells playing a role of the salt sensor; 3 No significant difference in the vacuolar Na+ sequestration ability was found between sensitive and tolerant group in either transition or elongation zones; 4 The overall Na+ accumulation was highest in the elongation zone, suggesting its role in osmotic adjustment and turgor maintenance required to drive root expansion growth. Overall, the reported results suggest high tissue-specificity of Na+ uptake, signalling, and sequestration in wheat root. The implications of these findings for plant breeding for salinity stress tolerance are discussed.

  4. Linking consumer experiences

    DEFF Research Database (Denmark)

    Smed, Karina Madsen

    become part of the individual self, worldview, and behaviour. This paper seeks to explore links between consumer experiences through the exploration of narrative sequences in travel blogs. Findings indicate that non-consumption is a central element to the bloggers and also indicative of a community......Consumers consume products in various ways serving a number of purposes. Much attention has been paid to experiences attached to consumption, sometimes very explicitly, e.g. in tourism, the essence of which is experiences of various sorts, but often also implicitly as internalised experiences...

  5. Knots and links

    CERN Document Server

    Rolfsen, Dale

    2003-01-01

    Rolfsen's beautiful book on knots and links can be read by anyone, from beginner to expert, who wants to learn about knot theory. Beginners with a basic background find an inviting introduction to the elements of topology, emphasizing the tools needed for understanding knots, the fundamental group and van Kampen's theorem, for example, which are then applied to concrete problems, such as computing knot groups. For experts, Rolfsen explains advanced topics, such as the connections between knot theory and surgery and how they are useful to understanding three-manifolds. Besides providing a guide

  6. Virtual gap element approach for the treatment of non-matching interface using three-dimensional solid elements

    Science.gov (United States)

    Song, Yeo-Ul; Youn, Sung-Kie; Park, K. C.

    2017-10-01

    A method for three-dimensional non-matching interface treatment with a virtual gap element is developed. When partitioned structures contain curved interfaces and have different brick meshes, the discretized models have gaps along the interfaces. As these gaps bring unexpected errors, special treatments are required to handle the gaps. In the present work, a virtual gap element is introduced to link the frame and surface domain nodes in the frame work of the mortar method. Since the surface of the hexahedron element is quadrilateral, the gap element is pyramidal. The pyramidal gap element consists of four domain nodes and one frame node. Zero-strain condition in the gap element is utilized for the interpolation of frame nodes in terms of the domain nodes. This approach is taken to satisfy the momentum and energy conservation. The present method is applicable not only to curved interfaces with gaps, but also to flat interfaces in three dimensions. Several numerical examples are given to describe the effectiveness and accuracy of the proposed method.

  7. Sensitivity analysis of a validated subject-specific finite element model of the human craniofacial skeleton.

    Science.gov (United States)

    Szwedowski, T D; Fialkov, J; Whyne, C M

    2011-01-01

    Developing a more complete understanding of the mechanical response of the craniofacial skeleton (CFS) to physiological loads is fundamental to improving treatment for traumatic injuries, reconstruction due to neoplasia, and deformities. Characterization of the biomechanics of the CFS is challenging due to its highly complex structure and heterogeneity, motivating the utilization of experimentally validated computational models. As such, the objective of this study was to develop, experimentally validate, and parametrically analyse a patient-specific finite element (FE) model of the CFS to elucidate a better understanding of the factors that are of intrinsic importance to the skeletal structural behaviour of the human CFS. An FE model of a cadaveric craniofacial skeleton was created from subject-specific computed tomography data. The model was validated based on bone strain measurements taken under simulated physiological-like loading through the masseter and temporalis muscles (which are responsible for the majority of craniofacial physiologic loading due to mastication). The baseline subject-specific model using locally defined cortical bone thicknesses produced the strongest correlation to the experimental data (r2 = 0.73). Large effects on strain patterns arising from small parametric changes in cortical thickness suggest that the very thin bony structures present in the CFS are crucial to characterizing the local load distribution in the CFS accurately.

  8. Application of the X-ray analyses on bioaccumulation and biomineralization for the specific elements

    Energy Technology Data Exchange (ETDEWEB)

    Numako, Chiya [Tokushima Univ., Faculty of Integrated Arts and Sciences, Tokushima (Japan)

    2003-03-01

    Specific accumulation of the elements by biological activity has a large influence on a material recycling on the earth. Some non-distractive characterizations by X-ray spectroscopy, XRF and/or XAFS measurements with synchrotron radiation have been applied to some solid state specimens which accumulate heavy metals at high concentration in order to elucidate its mechanism or purpose of the phenomena for each marine creature. It has been known that a few bivalves including giant clams stock kidney granules that accumulate Mn and Zn specifically. The results of two-dimensional elemental analyses by EPMA indicate zoning structures of the concentration of Mn, Zn and Mg negative correlation between Mg and (Mn + Zn) inside of a granule. Fluorescence XAFS analyses for Mn and Zn in the kidney granules, held at BL-7C, PF, KEK, shows that Mn and Zn exist as divalent cations in amorphous calcium phosphate matrix. It is considered that Mn and Zn have got a detoxication by substitution for Mg into amorphous calcium phosphate with flexible crystal structure. The teeth of chiton, which accumulate magnetite as a major substance of the teeth, have been also studied by SR-XRF and micro XAFS technique with microbeam focused in 6 {mu}m {phi} from undulator at SPring-8, BL-39XU. In the early stage of the teeth formation, abrupt accumulation of Fe into a feeding plane of a tooth, while the concentration of Ca has been remained equally at the back of a tooth. Micro-XAFS measurement for Fe in the teeth indicates that a major material of the feeding plane is magnetite while trivalent iron compounds appears along the junction zone of the tooth and a base membrane. There is a complex scheme in the tooth formation of chiton, which is available to create some kinds of iron species and allocates those into different positions in a tooth. (author)

  9. Application of the X-ray analyses on bioaccumulation and biomineralization for the specific elements

    International Nuclear Information System (INIS)

    Numako, Chiya

    2003-01-01

    Specific accumulation of the elements by biological activity has a large influence on a material recycling on the earth. Some non-distractive characterizations by X-ray spectroscopy, XRF and/or XAFS measurements with synchrotron radiation have been applied to some solid state specimens which accumulate heavy metals at high concentration in order to elucidate its mechanism or purpose of the phenomena for each marine creature. It has been known that a few bivalves including giant clams stock kidney granules that accumulate Mn and Zn specifically. The results of two-dimensional elemental analyses by EPMA indicate zoning structures of the concentration of Mn, Zn and Mg negative correlation between Mg and (Mn + Zn) inside of a granule. Fluorescence XAFS analyses for Mn and Zn in the kidney granules, held at BL-7C, PF, KEK, shows that Mn and Zn exist as divalent cations in amorphous calcium phosphate matrix. It is considered that Mn and Zn have got a detoxication by substitution for Mg into amorphous calcium phosphate with flexible crystal structure. The teeth of chiton, which accumulate magnetite as a major substance of the teeth, have been also studied by SR-XRF and micro XAFS technique with microbeam focused in 6 μm φ from undulator at SPring-8, BL-39XU. In the early stage of the teeth formation, abrupt accumulation of Fe into a feeding plane of a tooth, while the concentration of Ca has been remained equally at the back of a tooth. Micro-XAFS measurement for Fe in the teeth indicates that a major material of the feeding plane is magnetite while trivalent iron compounds appears along the junction zone of the tooth and a base membrane. There is a complex scheme in the tooth formation of chiton, which is available to create some kinds of iron species and allocates those into different positions in a tooth. (author)

  10. Species-and stage-specific differences in trace element tissue concentrations in amphibians: implications for the disposal of coal-combustion wastes

    International Nuclear Information System (INIS)

    Roe, John H.; Hopkins, William A.; Jackson, Brian P.

    2005-01-01

    Information on species-and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged. - Results suggest that metamorphosed amphibians can transport trace elements from aquatic disposal basins to non-contaminated habitats

  11. Species-and stage-specific differences in trace element tissue concentrations in amphibians: implications for the disposal of coal-combustion wastes

    Energy Technology Data Exchange (ETDEWEB)

    Roe, John H. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States); Hopkins, William A. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States)]. E-mail: hopkins@srel.edu; Jackson, Brian P. [University of Georgia, Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802 (United States)

    2005-07-15

    Information on species-and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged. - Results suggest that metamorphosed amphibians can transport trace elements from aquatic disposal basins to non-contaminated habitats.

  12. Modeling and control of a hydraulically actuated flexible-prismatic link robot

    International Nuclear Information System (INIS)

    Love, L.; Kress, R.; Jansen, J.

    1996-12-01

    Most of the research related to flexible link manipulators to date has focused on single link, fixed length, single plane of vibration test beds. In addition, actuation has been predominantly based upon electromagnetic motors. Ironically, these elements are rarely found in the existing industrial long reach systems. This manuscript describes a new hydraulically actuated, long reach manipulator with a flexible prismatic link at Oak Ridge National Laboratory (ORNL). Focus is directed towards both modeling and control of hydraulic actuators as well as flexible links that have variable natural frequencies

  13. Earth-Space Link Attenuation Estimation via Ground Radar Kdp

    Science.gov (United States)

    Bolen, Steven M.; Benjamin, Andrew L.; Chandrasekar, V.

    2003-01-01

    A method of predicting attenuation on microwave Earth/spacecraft communication links, over wide areas and under various atmospheric conditions, has been developed. In the area around the ground station locations, a nearly horizontally aimed polarimetric S-band ground radar measures the specific differential phase (Kdp) along the Earth-space path. The specific attenuation along a path of interest is then computed by use of a theoretical model of the relationship between the measured S-band specific differential phase and the specific attenuation at the frequency to be used on the communication link. The model includes effects of rain, wet ice, and other forms of precipitation. The attenuation on the path of interest is then computed by integrating the specific attenuation over the length of the path. This method can be used to determine statistics of signal degradation on Earth/spacecraft communication links. It can also be used to obtain real-time estimates of attenuation along multiple Earth/spacecraft links that are parts of a communication network operating within the radar coverage area, thereby enabling better management of the network through appropriate dynamic routing along the best combination of links.

  14. Computationally efficient dynamic modeling of robot manipulators with multiple flexible-links using acceleration-based discrete time transfer matrix method

    DEFF Research Database (Denmark)

    Zhang, Xuping; Sørensen, Rasmus; RahbekIversen, Mathias

    2018-01-01

    This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations, and then is linea......This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations......, and then is linearized based on the acceleration-based state vector. The transfer matrices for each type of components/elements are developed, and used to establish the system equations of a flexible robot manipulator by concatenating the state vector from the base to the end-effector. With this strategy, the size...... manipulators, and only involves calculating and transferring component/element dynamic equations that have small size. The numerical simulations and experimental testing of flexible-link manipulators are conducted to validate the proposed methodologies....

  15. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation.

    Science.gov (United States)

    Wang, Lu; Peng, Qian; Zhao, Jianbo; Ren, Fei; Zhou, Hui; Wang, Wei; Liao, Liao; Owiti, Albert; Jiang, Quan; Han, Yuepeng

    2016-05-01

    Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.

  16. Species- and stage-specific differences in trace element tissue concentrations in amphibians: implications for the disposal of coal-combustion wastes

    Energy Technology Data Exchange (ETDEWEB)

    Roe, J.H.; Hopkins, W.A.; Jackson, B.P. [University of Georgia, Aiken, SC (US)

    2005-07-01

    Information on species- and stage-specific patterns of contaminant accumulation is generally lacking for amphibians, yet such information could provide valuable knowledge on how amphibians interact with contaminants. We assessed concentrations of As, Cd, Cu, Ni, Pb, Se, Sr, and Zn in whole bodies of larval, recently metamorphosed, and adult life stages in Bufo terrestris and Rana sphenocephala from a site that currently receives coal combustion waste (CCW) discharge, a site where CCW was formerly discharged that has undergone natural attenuation for 30 years, and a nearby reference site. For the majority of elements (As, Cd, Cu, Ni, Pb, Zn), concentrations were highest in larvae, but Se and Sr concentrations remained elevated in later life stages, likely because these elements are S and Ca analogs, respectively, and are thus retained throughout structural changes during metamorphosis. Element concentrations were generally higher in B. terrestris than in R. sphenocephala. Concentrations of As, Se, and Sr were up to 11-35 times higher in metamorphs emigrating from CCW-polluted wetlands compared to unpolluted wetlands, suggesting metamorphosed amphibians can transport trace elements from aquatic disposal basins to nearby uncontaminated terrestrial habitats. In addition, anurans utilizing naturally revegetated sites up to 30 years after CCW disposal ceases are exposed to trace elements, although to a lesser degree than sites where CCW is currently discharged.

  17. Children's 5-HTTLPR genotype moderates the link between maternal criticism and attentional biases specifically for facial displays of anger.

    Science.gov (United States)

    Gibb, Brandon E; Johnson, Ashley L; Benas, Jessica S; Uhrlass, Dorothy J; Knopik, Valerie S; McGeary, John E

    2011-09-01

    Theorists have proposed that negative experiences in childhood may contribute to the development of experience-specific information-processing biases, including attentional biases. There are also clear genetic influences on cognitive processes, with evidence that polymorphisms in specific candidate genes may moderate the impact of environmental stress on attentional biases (e.g., a functional polymorphism in the serotonin transporter gene; 5-HTTLPR). In the current study, we tested a gene×environment (G×E) model of risk for attentional biases. We hypothesised that children whose mothers exhibit high levels of expressed emotion criticism (EE-Crit) would display attentional biases specifically for angry, but not happy or sad, faces, and that this link would be stronger among children carrying one or two copies of the 5-HTTLPR short allele than among those homozygous for the long allele. Results generally supported these hypotheses, though we found that carriers of the 5-HTTLPR short allele who also had a critical mother exhibited attentional avoidance of angry faces rather than preferential attention.

  18. Elastic dynamic research of high speed multi-link precision press considering structural stiffness of rotation joints

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Feng Feng; Sun, Yu; Peng, Bin Bin [School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing (China)

    2016-10-15

    An elastic dynamic model of high-speed multi-link precision press considering structural stiffness of rotation joints was established by the finite element method. In the finite element model, rotation joint was established by four bar elements with equivalent stiffness, and connected link was established by beam element. Then, the elastic dynamics equation of the system was established, and modal superposition method was used to solve the dynamic response. Compared with the traditional elastic dynamic model with perfect constraint of the rotation joints, the elastic dynamic response value of the improved model is larger. To validate the presented new method of elastic dynamics analysis with stiffness of rotation joints, a related test of slider Bottom dead center (BDC) position in different speed was designed. The test shows that the model with stiffness of rotation joints is more reasonable. So it provides a reasonable theory and method for dynamic characteristics research of such a multi-link machine.

  19. Optimisation of the link volume for weakest link failure prediction in NBG-18 nuclear graphite

    International Nuclear Information System (INIS)

    Hindley, Michael P.; Groenwold, Albert A.; Blaine, Deborah C.; Becker, Thorsten H.

    2014-01-01

    This paper describes the process for approximating the optimal size of a link volume required for weakest link failure calculation in nuclear graphite, with NBG-18 used as an example. As part of the failure methodology, the link volume is defined in terms of two grouping criteria. The first criterion is a factor of the maximum grain size and the second criterion is a function of an equivalent stress limit. A methodology for approximating these grouping criteria is presented. The failure methodology employs finite element analysis (FEA) in order to predict the failure load, at 50% probability of failure. The average experimental failure load, as determined for 26 test geometries, is used to evaluate the accuracy of the weakest link failure calculations. The influence of the two grouping criteria on the failure load prediction is evaluated by defining an error in prediction across all test cases. Mathematical optimisation is used to find the minimum error across a range of test case failure predictions. This minimum error is shown to deliver the most accurate failure prediction across a whole range of components, although some test cases in the range predict conservative failure load. The mathematical optimisation objective function is penalised to account for non-conservative prediction of the failure load for any test case. The optimisation is repeated and a link volume found for conservative failure prediction. The failure prediction for each test case is evaluated, in detail, for the proposed link volumes. Based on the analysis, link design volumes for NBG-18 are recommended for either accurate or conservative failure prediction

  20. Simplified Qualitative Discrete Numerical Model to Determine Cracking Pattern in Brittle Materials by Means of Finite Element Method

    Directory of Open Access Journals (Sweden)

    J. Ochoa-Avendaño

    2017-01-01

    Full Text Available This paper presents the formulation, implementation, and validation of a simplified qualitative model to determine the crack path of solids considering static loads, infinitesimal strain, and plane stress condition. This model is based on finite element method with a special meshing technique, where nonlinear link elements are included between the faces of the linear triangular elements. The stiffness loss of some link elements represents the crack opening. Three experimental tests of bending beams are simulated, where the cracking pattern calculated with the proposed numerical model is similar to experimental result. The advantages of the proposed model compared to discrete crack approaches with interface elements can be the implementation simplicity, the numerical stability, and the very low computational cost. The simulation with greater values of the initial stiffness of the link elements does not affect the discontinuity path and the stability of the numerical solution. The exploded mesh procedure presented in this model avoids a complex nonlinear analysis and regenerative or adaptive meshes.

  1. The Importance of Memory Specificity and Memory Coherence for the Self: Linking Two Characteristics of Autobiographical Memory

    Directory of Open Access Journals (Sweden)

    Elien Vanderveren

    2017-12-01

    Full Text Available Autobiographical memory forms a network of memories about personal experiences that defines and supports well-being and effective functioning of the self in various ways. During the last three decades, there have been two characteristics of autobiographical memory that have received special interest regarding their role in psychological well-being and psychopathology, namely memory specificity and memory coherence. Memory specificity refers to the extent to which retrieved autobiographical memories are specific (i.e., memories about a particular experience that happened on a particular day. Difficulty retrieving specific memories interferes with effective functioning of the self and is related to depression and post-traumatic stress disorder. Memory coherence refers to the narrative expression of the overall structure of autobiographical memories. It has likewise been related to psychological well-being and the occurrence of psychopathology. Research on memory specificity and memory coherence has developed as two largely independent research domains, even though they show much overlap. This raises some important theoretical questions. How do these two characteristics of autobiographical memory relate to each other, both theoretically and empirically? Additionally, how can the integration of these two facilitate our understanding of the importance of autobiographical memory for the self? In this article, we give a critical overview of memory specificity and memory coherence and their relation to the self. We link both features of autobiographical memory by describing some important similarities and by formulating hypotheses about how they might relate to each other. By situating both memory specificity and memory coherence within Conway and Pleydell-Pearce’s Self-Memory System, we make a first attempt at a theoretical integration. Finally, we suggest some new and exciting research possibilities and explain how both research fields could benefit

  2. Deployment of a multi-link flexible structure

    Science.gov (United States)

    Na, Kyung-Su; Kim, Ji-Hwan

    2006-06-01

    Deployment of a multi-link beam structure undergoing locking is analyzed in the Timoshenko beam theory. In the modeling of the system, dynamic forces are assumed to be torques and restoring forces due to the torsion spring at each joint. Hamilton's principle is used to determine the equations of motion and the finite element method is adopted to analyze the system. Newmark time integration and Newton-Raphson iteration methods are used to solve for the non-linear equations of motion at each time step. The locking at the joints of the multi-link flexible structure is analyzed by the momentum balance method. Numerical results are compared with the previous experimental data. The angles and angular velocities of each joint, tip displacement, and velocity of each link are investigated to study the motions of the links at each time step. To analyze the effect of thickness on the motion of the link, the angle and the tip displacement of each link are compared according to the various slenderness ratios. Additionally, in order to investigate the effect of shear, the tip displacements of a Timoshenko beam are compared with those of an Euler-Bernoulli beam.

  3. A four-element based transposon system for allele specific tagging ...

    Indian Academy of Sciences (India)

    The four-element based construct would include both Ds and dSpm along with relevant marker genes and .... subsequent generations after transposition has taken place so as to ..... Cardon G H, Frey M, Seadler H and Gierl A 1993 Definition.

  4. Carbon Footprint Linked to transport infrastructures

    International Nuclear Information System (INIS)

    Crespo Garcia, L.; Jimenez Arroyo, F.

    2013-01-01

    Quantification of emissions of greenhouse effect gases associated to transport infrastructures has been addressed in different ways. The first tools for this purpose appeared with the application of ISO 14040 standards (Life cycle analysis) that, applied to the particular case of energetic resources, led to a new concept known as carbon footprint. There is a specific standard for this quantification (ISO 14064) according to which, for the case of infrastructures, emissions and environmental effects linked to the whole life cycle are assessed taking into account all the stages: building, exploitation, maintenance and dismantling. the key point to perform this analysis is the accurate definition of a calculation methodology to be applied to the inventory of activities covered, in order to avoid information lacks, overlaps or redundancies. Quantification tools for emissions are effectively a reality, but social and political will, supported by strong economical reasons recognizing energy as a vital resource, is necessary for these tools to be developed, enhanced and used in a systematic way as a key decision element to choice among different transport alternatives. (Author) 23 refs.

  5. Incompleteness as a link between obsessive-compulsive personality traits and specific symptom dimensions of obsessive-compulsive disorder.

    Science.gov (United States)

    Ecker, Willi; Kupfer, Jochen; Gönner, Sascha

    2014-01-01

    This paper examines the contribution of incompleteness/'not just right experiences' (NJREs) to an understanding of the relationship between obsessive-compulsive disorder (OCD) and obsessive-compulsive personality traits (OCPTs). It investigates the association of specific OCD symptom dimensions with OCPTs, conceptualized as continuous phenomena that are also observable below the diagnostic threshold. As empirical findings and clinical observation suggest that incompleteness feelings/NJREs may play a significant affective and motivational role for certain OCD subtypes, but also for patients with accentuated OCPTs, we hypothesized that OCPTs are selectively linked with incompleteness-associated OCD symptom dimensions (ordering, checking, hoarding and counting). Moreover, we assumed that this selective relationship cannot be demonstrated any more after statistical control of incompleteness, whereas it is preserved after statistical control of anxiety, depression, pathological worry and harm avoidance. Results from a study with a large clinical sample (n = 185) partially support these hypotheses and suggest that NJREs may be an important connecting link between specific OCD symptom dimensions, in particular ordering and checking, and accentuated OCPTs. Obsessive-compulsive personality traits (OCPTs) are positively related to obsessive-compulsive disorder symptom dimensions (ordering, checking, hoarding and counting) hypothesized or found to be associated with incompleteness/'not just right experiences' (NJREs), but not to washing and obsessions. This positive relationship, which is strongest for ordering and checking, is eliminated when NJREs are statistically controlled. Ordering, checking and accentuated OCPTs may share NJREs as a common affective-motivational underpinning.Dysfunctional behaviour patterns of people with accentuated OCPTs or obsessive-compulsive personality disorder (OCPD) may be viewed as efforts to avoid or reduce subjectively intolerable NJREs

  6. Competitive Enzyme-Linked Immunosorbent Assay Based on a Rhoptry-Associated Protein 1 Epitope Specifically Identifies Babesia bovis-Infected Cattle

    Science.gov (United States)

    Goff, Will L.; McElwain, Terry F.; Suarez, Carlos E.; Johnson, Wendell C.; Brown, Wendy C.; Norimine, Junzo; Knowles, Donald P.

    2003-01-01

    The competitive enzyme-linked immunosorbent assay (cELISA) format has proven to be an accurate, reliable, easily standardized, and high-throughput method for detecting hemoparasite infections. In the present study, a species-specific, broadly conserved, and tandemly repeated B-cell epitope within the C terminus of the rhoptry-associated protein 1 of the hemoparasite Babesia bovis was cloned and expressed as a histidine-tagged thioredoxin fusion peptide and used as antigen in a cELISA. The assay was optimized with defined negative and positive bovine sera, where positive sera inhibited the binding of the epitope-specific monoclonal antibody BABB75A4. The cELISA accurately differentiated animals with B. bovis-specific antibodies from uninfected animals and from animals with antibodies against other tick-borne hemoparasites (98.7% specificity). In addition, B. bovis-specific sera from Australia, Argentina, Bolivia, Puerto Rico, and Morocco inhibited the binding of BABB75A4, confirming conservation of the epitope. The assay first detected experimentally infected animals between 13 and 17 days postinfection, and with sera from naturally infected carrier cattle, was comparable to indirect immunofluorescence (98.3% concordance). The assay appears to have the characteristics necessary for an epidemiologic and disease surveillance tool. PMID:12522037

  7. Electronic structure and properties of superheavy elements

    International Nuclear Information System (INIS)

    Pershina, V.

    2015-01-01

    Spectacular developments in the relativistic quantum theory and computational algorithms in the last few decades allowed for accurate calculations of properties of the superheavy elements (SHE) and their compounds. Often conducted in a close link to the experimental research, these investigations helped predict and interpret an outcome of sophisticated and expensive experiments with single atoms. Most of the works, particularly those related to the experimental studies, are overviewed in this publication. The role of relativistic effects being of paramount importance for the heaviest elements is elucidated.

  8. Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087

    Science.gov (United States)

    Ciric, Lena; Mullany, Peter; Roberts, Adam P.

    2011-01-01

    Objectives Tn916-like elements are one of the most common types of integrative and conjugative element (ICE). In this study we aimed to determine whether novel accessory genes, i.e. genes whose products are not involved in mobility or regulation, were present on a Tn916-like element (Tn6087) isolated from Streptococcus oralis from the human oral cavity. Methods A minocycline-resistant isolate was analysed using restriction fragment length polymorphism (RFLP) analysis on amplicons derived from Tn916 and DNA sequencing to determine whether there were genetic differences in Tn6087 compared with Tn916. Mutational analysis was used to determine whether the novel accessory gene found was responsible for an observed extra phenotype. Results A novel Tn916-like element, Tn6087, is described that encodes both antibiotic and antiseptic resistance. The antiseptic resistance protein is encoded by a novel small multidrug resistance gene, designated qrg, that was shown to encode resistance to cetyltrimethylammonium bromide (CTAB), also known as cetrimide bromide. Conclusions This is the first Tn916-like element described that confers both antibiotic and antiseptic resistance, suggesting that selection of either antibiotic or antiseptic resistance will also select for the other and further highlights the need for prudent use of both types of compound. PMID:21816764

  9. Enzyme-linked immunosorbent serum assay specific for the 7S domain of Collagen Type IV (P4NP 7S)

    DEFF Research Database (Denmark)

    Leeming, Diana J; Nielsen, Mette J; Dai, Yueqin

    2012-01-01

    Aim:  The present study describes the ability of a newly developed N-terminal pro-peptides of type IV collagen 7S domain (P4NP 7S) competitive enzyme-linked immunosorbent assay (ELISA) for describing liver fibrosis. The assay applies a monoclonal antibody specific for a PIVNP 7S epitope 100...... were significantly elevated in rat with liver fibrosis as seen by histology (CCL4: 283% elevated in the highest quartile of total hepatic collagen compared with controls, P = 0.001; BDL: 183% elevated at week 4 compared with sham, P type IV collagen...... expression in BDL rats (r = 0.49, P serum assay specific for P4NP 7S was highly related to liver fibrosis...

  10. Design of in situ dispersible and calcium cross-linked alginate pellets as intestinal-specific drug carrier by melt pelletization technique.

    Science.gov (United States)

    Nurulaini, Harjoh; Wong, Tin Wui

    2011-06-01

    Conventional alginate pellets underwent rapid drug dissolution and loss of multiparticulate characteristics such as aggregation in acidic medium, thereby promoting oral dose dumping. This study aimed to design sustained-release dispersible alginate pellets through rapid in situ matrix dispersion and cross-linking by calcium salts during dissolution. Pellets made of alginate and calcium salts were prepared using a solvent-free melt pelletization technique that prevented reaction between processing materials during agglomeration and allowed such a reaction to occur only in dissolution phase. Drug release was remarkably retarded in acidic medium when pellets were formulated with water-soluble calcium acetate instead of acid-soluble calcium carbonate. Different from calcium salt-free and calcium carbonate-loaded matrices that aggregated or underwent gradual erosion, rapid in situ solvation of calcium acetate in pellets during dissolution resulted in burst of gas bubbles, fast pellet breakup, and dispersion. The dispersed fragments, though exhibiting a larger specific surface area for drug dissolution than intact matrix, were rapidly cross-linked by Ca(2+) from calcium acetate and had drug release retarded till a change in medium pH from 1.2 to 6.8. Being dispersible and pH-dependent in drug dissolution, these pellets are useful as multiparticulate intestinal-specific drug carrier without exhibiting dose dumping tendency of a "single-unit-like" system via pellet aggregation. Copyright © 2011 Wiley-Liss, Inc.

  11. The Versatile Link Demo Board (VLDB)

    International Nuclear Information System (INIS)

    Lesma, R. Martín; Alessio, F.; Barbosa, J.; Baron, S.; Caplan, C.; Leitao, P.; Porret, D.; Wyllie, K.; Pecoraro, C.

    2017-01-01

    The Versatile Link Demonstrator Board (VLDB) is the evaluation kit for the radiation-hard Optical Link ecosystem, which provides a 4.8 Gbps data transfer link for communication between front-end (FE) and back-end (BE) of the High Energy Physics experiments. It gathers the Versatile link main radiation-hard custom Application-Specific Integrated Circuits (ASICs) and modules: GBTx, GBT-SCA and VTRx/VTTx plus the FeastMP, a radiation-hard in-house designed DC-DC converter. This board is the first design allowing system-level tests of the Link with a complete interconnection of the constitutive components, allowing data acquisition, control and monitoring of FE devices with the GBT-SCA pair.

  12. Shuttle/TDRSS modelling and link simulation study

    Science.gov (United States)

    Braun, W. R.; Mckenzie, T. M.; Biederman, L.; Lindsey, W. C.

    1979-01-01

    A Shuttle/TDRSS S-band and Ku-band link simulation package called LinCsim was developed for the evaluation of link performance for specific Shuttle signal designs. The link models were described in detail and the transmitter distortion parameters or user constraints were carefully defined. The overall link degradation (excluding hardware degradations) relative to an ideal BPSK channel were given for various sets of user constraint values. The performance sensitivity to each individual user constraint was then illustrated. The effect of excessive Spacelab clock jitter on the return link BER performance was also investigated as was the problem of subcarrier recovery for the K-band Shuttle return link signal.

  13. Sleep and Cognition in Preschool Years: Specific Links to Executive Functioning

    Science.gov (United States)

    Bernier, Annie; Beauchamp, Miriam H.; Bouvette-Turcot, Andrée-Anne; Carlson, Stephanie M.; Carrier, Julie

    2013-01-01

    This study investigated the prospective links between sleep in infancy and preschoolers' cognitive performance. Mothers of 65 infants completed a sleep diary when infants were aged 1 year, and children completed two subscales of the Wechsler Preschool and Primary Scale of Intelligence at 4 years, indexing general cognitive ability and complex…

  14. Age-Associated ALU Element Instability in White Blood Cells Is Linked to Lower Survival in Elderly Adults: A Preliminary Cohort Study.

    Directory of Open Access Journals (Sweden)

    R Garrett Morgan

    Full Text Available ALU element instability could contribute to gene function variance in aging, and may partly explain variation in human lifespan.To assess the role of ALU element instability in human aging and the potential efficacy of ALU element content as a marker of biological aging and survival.Preliminary cohort study.We measured two high frequency ALU element subfamilies, ALU-J and ALU-Sx, by a single qPCR assay and compared ALU-J/Sx content in white blood cell (WBCs and skeletal muscle cell (SMCs biopsies from twenty-three elderly adults with sixteen healthy sex-balanced young adults; all-cause survival rates of elderly adults predicted by ALU-J/Sx content in both tissues; and cardiovascular disease (CVD- and cancer-specific survival rates of elderly adults predicted by ALU-J/Sx content in both tissues, as planned subgroup analyses.We found greater ALU-J/Sx content variance in WBCs from elderly adults than young adults (P < 0.001 with no difference in SMCs (P = 0.94. Elderly adults with low WBC ALU-J/Sx content had worse four-year all-cause and CVD-associated survival than those with high ALU-J/Sx content (both P = 0.03 and hazard ratios (HR ≥ 3.40, while WBC ALU-J/Sx content had no influence on cancer-associated survival (P = 0.42 and HR = 0.74. SMC ALU-J/Sx content had no influence on all-cause, CVD- or cancer -associated survival (all P ≥ 0.26; HR ≤ 2.07.These initial findings demonstrate that ALU element instability occurs with advanced age in WBCs, but not SMCs, and imparts greater risk of all-cause mortality that is likely driven by an increased risk for CVD and not cancer.

  15. Mapping 3D breast lesions from full-field digital mammograms using subject-specific finite element models

    Science.gov (United States)

    García, E.; Oliver, A.; Diaz, O.; Diez, Y.; Gubern-Mérida, A.; Martí, R.; Martí, J.

    2017-03-01

    Patient-specific finite element (FE) models of the breast have received increasing attention due to the potential capability of fusing images from different modalities. During the Magnetic Resonance Imaging (MRI) to X-ray mammography registration procedure, the FE model is compressed mimicking the mammographic acquisition. Subsequently, suspicious lesions in the MRI volume can be projected into the 2D mammographic space. However, most registration algorithms do not provide the reverse information, avoiding to obtain the 3D geometrical information from the lesions localized in the mammograms. In this work we introduce a fast method to localize the 3D position of the lesion within the MRI, using both cranio-caudal (CC) and medio-lateral oblique (MLO) mammographic projections, indexing the tetrahedral elements of the biomechanical model by means of an uniform grid. For each marked lesion in the Full-Field Digital Mammogram (FFDM), the X-ray path from source to the marker is calculated. Barycentric coordinates are computed in the tetrahedrons traversed by the ray. The list of elements and coordinates allows to localize two curves within the MRI and the closest point between both curves is taken as the 3D position of the lesion. The registration errors obtained in the mammographic space are 9.89 +/- 3.72 mm in CC- and 8.04 +/- 4.68 mm in MLO-projection and the error in the 3D MRI space is equal to 10.29 +/- 3.99 mm. Regarding the uniform grid, it is computed spending between 0.1 and 0.7 seconds. The average time spent to compute the 3D location of a lesion is about 8 ms.

  16. 1 kb of the lactase-phlorizin hydrolase promoter directs post-weaning decline and small intestinal-specific expression in transgenic mice

    DEFF Research Database (Denmark)

    Troelsen, J T; Mehlum, A; Spodsberg, N

    1994-01-01

    Adult-type hypolactasia is a genetic condition making approximately one half of the human population intolerant to milk because of abdominal symptoms. The cause is a post-weaning down-regulation of the intestinal-specific enzyme lactase-phlorizin hydrolase (LPH) reducing the intestinal capacity...... to hydrolyze lactose. We here demonstrate that the stretch -17 to -994 in the pig LPH-promoter carries cis-elements which direct a small intestinal-specific expression and a post-weaning decline of a linked rabbit beta-globin gene. These data demonstrate that the post-weaning decline of LPH is mainly due...

  17. Cell-cycle phase specificity of chloroethylnitrosoureas

    International Nuclear Information System (INIS)

    Linfoot, P.A.

    1986-01-01

    Although the cancer chemotherapeutic agent 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) is considered a non-cell cycle phase specific drug, it has been shown to produce differential cell killing in G 1 , S, and G 2 /M phase cells, with S phase cells appearing relatively resistant. Studies of cell cycle phase specific cell killing produced by nitrosoureas with different chemical reactivities, clearly indicated that the ability of compounds to cross-link DNA was important in determining their phase specificity. Cells that lacked guanine O 6 -alkytransferase activity showed similar patterns of BCNU phase specificity regardless of their intrinsic sensitivity to BCNU. DNA inter-strand cross-linking, as measured by alkaline elution, was similar in cells exposed to BCNU in G 1 or S phase. 3 H [1-chloroethyl-1nitrosourea] binding to DNA was the same in G 1 , S and G 2 /M phase cells indicating that phase-specific differences in drug uptake and intracellular drug dose were not responsible for phase specific cell kill. These studies suggest that cross-link lesions, other than DNA inter-strand cross-links, and/or effects on DNA repair, other than guanine O 6 -alkyltransferase, are additional important determinants of BCNU phase specific cell killing

  18. Links in a distributed database: Theory and implementation

    International Nuclear Information System (INIS)

    Karonis, N.T.; Kraimer, M.R.

    1991-12-01

    This document addresses the problem of extending database links across Input/Output Controller (IOC) boundaries. It lays a foundation by reviewing the current system and proposing an implementation specification designed to guide all work in this area. The document also describes an implementation that is less ambitious than our formally stated proposal, one that does not extend the reach of all database links across IOC boundaries. Specifically, it introduces an implementation of input and output links and comments on that overall implementation. We include a set of manual pages describing each of the new functions the implementation provides

  19. The major and trace element chemistry of fish and lake water within ...

    African Journals Online (AJOL)

    Chemical elements in lake water are incorporated into fish tissues through bioconcentration and biomagnification. Lake water and fish tissue samples from 23 lakes, located within 4 major South African catchments, were analysed to investigate the link between element concentrations in lake water and otolith, fin spine, ...

  20. Chemistry of superheavy elements

    International Nuclear Information System (INIS)

    Schaedel, M.

    2012-01-01

    The chemistry of superheavy elements - or transactinides from their position in the Periodic Table - is summarized. After giving an overview over historical developments, nuclear aspects about synthesis of neutron-rich isotopes of these elements, produced in hot-fusion reactions, and their nuclear decay properties are briefly mentioned. Specific requirements to cope with the one-atom-at-a-time situation in automated chemical separations and recent developments in aqueous-phase and gas-phase chemistry are presented. Exciting, current developments, first applications, and future prospects of chemical separations behind physical recoil separators ('pre-separator') are discussed in detail. The status of our current knowledge about the chemistry of rutherfordium (Rf, element 104), dubnium (Db, element 105), seaborgium (Sg, element 106), bohrium (Bh, element 107), hassium (Hs, element 108), copernicium (Cn, element 112), and element 114 is discussed from an experimental point of view. Recent results are emphasized and compared with empirical extrapolations and with fully-relativistic theoretical calculations, especially also under the aspect of the architecture of the Periodic Table. (orig.)

  1. Absorber element for fast breeder reactor

    International Nuclear Information System (INIS)

    Verset, L.

    1987-01-01

    This absorber element is characterized by a new head which avoids an accident disconnection of the mobil absorber. This head is made by a superior piece which can take shore up an adjusting ring on an adjusting bearing on the inferior piece. The intermediate piece is catched at the superior piece by a link of chain [fr

  2. Linking Quality and Spending to Measure Value for People with Serious Illness

    Science.gov (United States)

    Rodgers, Phillip E.

    2018-01-01

    Abstract Background: Healthcare payment is rapidly evolving to reward value by measuring and paying for quality and spending performance. Rewarding value for the care of seriously ill patients presents unique challenges. Objective: To evaluate the state of current efforts to measure and reward value for the care of seriously ill patients. Design: We performed a PubMed search of articles related to (1) measures of spending for people with serious illness and (2) linking spending and quality measures and rewarding performance for the care of people with serious illness. We limited our search to U.S.-based studies published in English between January 1, 1960, and March 31, 2017. We supplemented this search by identifying public programs and other known initiatives that linked quality and spending for the seriously ill and extracted key program elements. Results: Our search related to linking spending and quality measures and rewarding performance for the care of people with serious illness yielded 277 articles. We identified three current public programs that currently link measures of quality and spending—or are likely to within the next few years—the Oncology Care Model; the Comprehensive End-Stage Renal Disease Model; and Home Health Value-Based Purchasing. Models that link quality and spending consist of four core components: (1) measuring quality, (2) measuring spending, (3) the payment adjustment model, and (4) the linking/incentive model. We found that current efforts to reward value for seriously ill patients are targeted for specific patient populations, do not broadly encourage the use of palliative care, and have not closely aligned quality and spending measures related to palliative care. Conclusions: We develop recommendations for policymakers and stakeholders about how measures of spending and quality can be balanced in value-based payment programs. PMID:29091529

  3. Magnetic dichroism in photoemission: a new element-specific magnetometer with atomic-layer resolution

    International Nuclear Information System (INIS)

    Starke, K.; Arenholz, E.; Kaindl, G.

    1998-01-01

    Full text: Magnetic coupling in layered metallic structures has become a key issue in thin-film magnetism since the observation of oscillatory exchange coupling across non-ferromagnetic spacer layers. Although this phenomenon was discovered in rare earths (RE) superlattices, mostly transition-metal systems have been studied and are now applied in data-storage industry. An understanding of the coupling mechanisms has been reached after a fabrication of high-quality interfaces became possible. It allowed, in particular, the experimental finding of induced ferromagnetic order in 'nonmagnetic' atomic layers near an interface, using element-specific probes such as magnetic circular dichroism in x-ray absorption. - In layered RE systems, by contrast, the well known intermiscibility has prevented a preparation of atomically sharp interfaces, and all RE superlattices studied so far showed interdiffusion zones of several atomic layers. In the present overview, we report the first fabrication of atomically flat heteromagnetic RE interfaces, their structural characterization and their magnetic analysis using magnetic dichroism in photoemission (MDPE). This new tool gives access to the magnetization of individual atomic layers near interfaces in favourite cases. Merits of MDPE as a magnetometer are demonstrated at the example of Eu/Gd(0001), where chemical shifts of core-level photoemission lines allow to spectroscopically separate up to four different atomic layers. The high surface sensitivity of MDPE, together with the well known dependence of the core-level binding energies on the coordination number of the photo emitting atom, opens the door to future site-specific studies of magnetism in sub-monolayer systems such as 'nanowires'

  4. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.

    Science.gov (United States)

    Locati, Mauro D; Pagano, Johanna F B; Ensink, Wim A; van Olst, Marina; van Leeuwen, Selina; Nehrdich, Ulrike; Zhu, Kongju; Spaink, Herman P; Girard, Geneviève; Rauwerda, Han; Jonker, Martijs J; Dekker, Rob J; Breit, Timo M

    2017-04-01

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci. © 2017 Locati et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. A 3.0-kb deletion including an erythroid cell-specific regulatory element in intron 1 of the ABO blood group gene in an individual with the Bm phenotype.

    Science.gov (United States)

    Sano, R; Kuboya, E; Nakajima, T; Takahashi, Y; Takahashi, K; Kubo, R; Kominato, Y; Takeshita, H; Yamao, H; Kishida, T; Isa, K; Ogasawara, K; Uchikawa, M

    2015-04-01

    We developed a sequence-specific primer PCR (SSP-PCR) for detection of a 5.8-kb deletion (B(m) 5.8) involving an erythroid cell-specific regulatory element in intron 1 of the ABO blood group gene. Using this SSP-PCR, we performed genetic analysis of 382 individuals with Bm or ABm. The 5.8-kb deletion was found in 380 individuals, and disruption of the GATA motif in the regulatory element was found in one individual. Furthermore, a novel 3.0-kb deletion involving the element (B(m) 3.0) was demonstrated in the remaining individual. Comparisons of single-nucleotide polymorphisms and microsatellites in intron 1 between B(m) 5.8 and B(m) 3.0 suggested that these deletions occurred independently. © 2014 International Society of Blood Transfusion.

  6. Development of a prototype continuity of care record with context-specific links to meet the information needs of case managers for persons living with HIV.

    Science.gov (United States)

    Schnall, Rebecca; Cimino, James J; Bakken, Suzanne

    2012-08-01

    (1) To develop a prototype Continuity of Care Record (CCR) with context-specific links to electronic HIV information resources; and (2) to assess case managers' perceptions regarding the usability of the prototype. We integrated context-specific links to HIV case management information resources into a prototype CCR using the Infobutton Manager and Librarian Infobutton Tailoring Environment (LITE). Case managers (N=9) completed a think-aloud protocol and the Computer System Usability Questionnaire (CSUQ) to evaluate the usability of the prototype. Verbalizations from the think-aloud protocol were summarized using thematic analysis. CSUQ data were analyzed with descriptive statistics. Although participants expressed positive comments regarding the usability of the prototype, the think-aloud protocol also identified the need for improvement in resource labels and for additional resources. On a scale ranging from 1 (strongly agree) to 7 (strongly disagree), the average CSUQ overall satisfaction was 2.25 indicating that users (n=9) were generally satisfied with the system. Mean CSUQ factor scores were: System Usefulness (M=2.13), Information Quality (M=2.46), and Interface Quality (M=2.26). Our novel application of the Infobutton Manager and LITE in the context of case management for persons living with HIV in community-based settings resulted in a prototype CCR with infobuttons that met the majority of case managers' information needs and received relatively positive usability ratings. Findings from this study inform future integration of context-specific links into CCRs and electronic health records and support their use for meeting end-users information needs. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  7. Estimating Rain Attenuation In Satellite Communication Links

    Science.gov (United States)

    Manning, R. M.

    1991-01-01

    Attenuation computed with help of statistical model and meteorological data. NASA Lewis Research Center Satellite Link Attenuation Model (SLAM) program QuickBASIC computer program evaluating static and dynamic statistical assessment of impact of rain attenuation on communication link established between Earth terminal and geosynchronous satellite. Application in specification, design, and assessment of satellite communication links for any terminal location in continental United States. Written in Microsoft QuickBASIC.

  8. Spatially and time-resolved element-specific in situ corrosion investigations with an online hyphenated microcapillary flow injection inductively coupled plasma mass spectrometry set-up

    International Nuclear Information System (INIS)

    Homazava, N.; Ulrich, A.; Kraehenbuehl, U.

    2008-01-01

    A novel technique for in situ spatial, time-resolved element-specific investigations of corrosion processes is developed. The technique is based on an online hyphenation of a specially designed microflow-capillary set-up to inductively coupled plasma mass spectrometry (ICP-MS) using flow injection sample introduction. Detailed aspects of the method development, optimization of the sample microflow introduction and flow injection characteristics for the localized corrosion analysis are described. Moreover, specific challenges of the ICP-MS analysis as applied to the analysis of corrosion sample probes, e.g. high matrix load and limited sample volume, are discussed. The efficiency of the developed technique is proved by corrosion susceptibility analysis of a commercial Al alloy. Results of the corrosion experiments of the aluminum alloy AA 6111 are presented to demonstrate the influence of various factors such as exposure time and pH value of the corrosive medium on the element-specific dissolution rates of the alloy. This novel technique provides new aspects in corrosion science and sheds new light on corrosion mechanisms

  9. Chemistry of the actinide elements. Second edition

    International Nuclear Information System (INIS)

    Katz, J.J.; Seaborg, G.T.; Morss, L.R.

    1987-01-01

    This is an exhaustive, updated discourse on the chemistry of Actinides, Volume 1 contains a systematic coverage of the elements Ac, Th, Pa, U, Np, and Pu, which constitutes Part 1 of the work. The characterization of each element is discussed in terms of its nuclear properties, occurrence, preparation, atomic and metallic properties, chemistry of specific compounds, and solution chemistry. The first part of Volume 2 follows the same format as Volume 1 but is confined to the elements Am, Cm, Bk, Cf, and Es, plus a more condensed coverage of the Transeinsteinium elements (Fm, Md, No, Lw, and 104-109). Part 2 of this volume is devoted to a discussion of the actinide elements in general, with a specific focus on electronic spectra, thermodynamic and magnetic properties, the metallic state, structural chemistry, solution kinetics, organometallic chemistry for σ- and π-bonded compounds, and some concluding remarks on the superheavy elements

  10. Identification of an estrogen response element in the 3'-flanking region of the murine c-fos protooncogene.

    Science.gov (United States)

    Hyder, S M; Stancel, G M; Nawaz, Z; McDonnell, D P; Loose-Mitchell, D S

    1992-09-05

    We have used transient transfection assays with reporter plasmids expressing chloramphenicol acetyltransferase, linked to regions of mouse c-fos, to identify a specific estrogen response element (ERE) in this protooncogene. This element is located in the untranslated 3'-flanking region of the c-fos gene, 5 kilobases (kb) downstream from the c-fos promoter and 1.5 kb downstream of the poly(A) signal. This element confers estrogen responsiveness to chloramphenicol acetyltransferase reporters linked to both the herpes simplex virus thymidine kinase promoter and the homologous c-fos promoter. Deletion analysis localized the response element to a 200-base pair fragment which contains the element GGTCACCACAGCC that resembles the consensus ERE sequence GGTCACAGTGACC originally identified in Xenopus vitellogenin A2 gene. A synthetic 36-base pair oligodeoxynucleotide containing this c-fos sequence conferred estrogen inducibility to the thymidine kinase promoter. The corresponding sequence also induced reporter activity when present in the c-fos gene fragment 3 kb from the thymidine kinase promoter. Gel-shift experiments demonstrated that synthetic oligonucleotides containing either the consensus ERE or the c-fos element bind human estrogen receptor obtained from a yeast expression system. However, the mobility of the shifted band is faster for the fos-ERE-complex than the consensus ERE complex suggesting that the three-dimensional structure of the protein-DNA complexes is different or that other factors are differentially involved in the two reactions. When the 5'-GGTCA sequence present in the c-fos ERE is mutated to 5'-TTTCA, transcriptional activation and receptor binding activities are both lost. Mutation of the CAGCC-3' element corresponding to the second half-site of the c-fos sequence also led to the loss of receptor binding activity, suggesting that both half-sites of this element are involved in this function. The estrogen induction mediated by either the c-fos or

  11. Convenience of Statistical Approach in Studies of Architectural Ornament and Other Decorative Elements Specific Application

    Science.gov (United States)

    Priemetz, O.; Samoilov, K.; Mukasheva, M.

    2017-11-01

    An ornament is an actual phenomenon of the architecture modern theory, a common element in the practice of design and construction. It has been an important aspect of shaping for millennia. The description of the methods of its application occupies a large place in the studies on the theory and practice of architecture. However, the problem of the saturation of compositions with ornamentation, the specificity of its themes and forms have not been sufficiently studied yet. This aspect requires accumulation of additional knowledge. The application of quantitative methods for the plastic solutions types and a thematic diversity of facade compositions of buildings constructed in different periods creates another tool for an objective analysis of ornament development. It demonstrates the application of this approach for studying the features of the architectural development in Kazakhstan at the end of the XIX - XXI centuries.

  12. Die Areopagusrede (Hand. 17:22-31 – ’n verkenning van homiletiese elemente

    Directory of Open Access Journals (Sweden)

    C. J.H. Venter

    2005-07-01

    Full Text Available The Areopagus speech (Acts 17:22-31 – an exploration of homiletical elements In this article certain guidelines are developed from a selection of definitions for preaching and also from relevant data about the process of compiling and evaluating sermons. The aim in developing these guidelines was to establish parameters for the exploration of the Areopagus speech. It was established that the way in which listeners is addressed, and also the link-up with the situation of the listeners to the speech, can be considered as important homiletical elements. Together with these elements the structure of the speech as well as the transitions in the speech can be regarded as major homiletical elements in the body of the sermon. The trinitarian revelation of God in this speech and also the balance between indicative, imperative and promise mark this speech as a sermon. The elements of cohesion and progression are perceptibly present in this speech with the result that the introduction (God creates and grants life links up well with the climax (eternal life through the resurrection of Christ.

  13. Structural Elements in a Persistent Identifier Infrastructure and Resulting Benefits for the Earth Science Community

    Science.gov (United States)

    Weigel, T.; Toussaiant, F.; Stockhause, M.; Höck, H.; Kindermann, S.; Lautenschlager, M.; Ludwig, T.

    2012-12-01

    We propose a wide adoption of structural elements (typed links, collections, trees) in the Handle System to improve identification and access of scientific data, metadata and software as well as traceability of data provenance. Typed links target the issue of data provenance as a means to assess the quality of scientific data. Data provenance is seen here as a directed acyclic graph with nodes representing data and vertices representing derivative operations (Moreau 2010). Landing pages can allow a human user to explore the provenance graph back to the primary unprocessed data, thereby also giving credit to the original data producer. As in Earth System Modeling no single infrastructure with complete data lifecycle coverage exists, we propose to split the problem domain in two parts. Project-specific infrastructures such as the German project C3-Grid or the Earth System Grid Federation (ESGF) for CMIP5 data are aware of data and data operations (Toussaint et al. 2012) and can thus detect and accumulate single nodes and vertices in the provenance graph, assigning Handles to data, metadata and software. With a common schema for typed links, the provenance graph is established as downstream infrastructures refer incoming Handles. Data in this context is for example hierarchically structured Earth System model output data, which receives DataCite DOIs only for the most coarse-granular elements. Using Handle tree structures, the lower levels of the hierarchy can also receive Handles, allowing authors to more precisely identify the data they used (Lawrence et al. 2011). We can e.g. define a DOI for just the 2m-temperature variable of CMIP5 data across many CMIP5 experiments or a DOI for model and observational data coming from different sources. The structural elements should be implemented through Handle values at the Handle infrastructure level for two reasons. Handle values are more durable than downstream websites or databases, and thus the provenance chain does not

  14. Enzyme-linked immunosorbent assays for detection of equine antibodies specific to Sarcocystis neurona surface antigens.

    Science.gov (United States)

    Hoane, Jessica S; Morrow, Jennifer K; Saville, William J; Dubey, J P; Granstrom, David E; Howe, Daniel K

    2005-09-01

    Sarcocystis neurona is the primary causative agent of equine protozoal myeloencephalitis (EPM), a common neurologic disease of horses in the Americas. We have developed a set of enzyme-linked immunosorbent assays (ELISAs) based on the four major surface antigens of S. neurona (SnSAGs) to analyze the equine antibody response to S. neurona. The SnSAG ELISAs were optimized and standardized with a sample set of 36 equine sera that had been characterized by Western blotting against total S. neurona parasite antigen, the current gold standard for S. neurona serology. The recombinant SnSAG2 (rSnSAG2) ELISA showed the highest sensitivity and specificity at 95.5% and 92.9%, respectively. In contrast, only 68.2% sensitivity and 71.4% specificity were achieved with the rSnSAG1 ELISA, indicating that this antigen may not be a reliable serological marker for analyzing antibodies against S. neurona in horses. Importantly, the ELISA antigens did not show cross-reactivity with antisera to Sarcocystis fayeri or Neospora hughesi, two other equine parasites. The accuracy and reliability exhibited by the SnSAG ELISAs suggest that these assays will be valuable tools for examining the equine immune response against S. neurona infection, which may help in understanding the pathobiology of this accidental parasite-host interaction. Moreover, with modification and further investigation, the SnSAG ELISAs have potential for use as immunodiagnostic tests to aid in the identification of horses affected by EPM.

  15. Development and evaluation of a Sarcocystis neurona-specific IgM capture enzyme-linked immunosorbent assay.

    Science.gov (United States)

    Murphy, J E; Marsh, A E; Reed, S M; Meadows, C; Bolten, K; Saville, W J A

    2006-01-01

    Equine protozoal myeloencephalitis (EPM) is a serious neurologic disease of horses caused primarily by the protozoal parasite Sarcocystis neurona. Currently available antemortem diagnostic testing has low specificity. The hypothesis of this study was that serum and cerebrospinal fluid (CSF) of horses experimentally challenged with S neurona would have an increased S neurona-specific IgM (Sn-IgM) concentration after infection, as determined by an IgM capture enzyme linked immunoassay (ELISA). The ELISA was based on the S neurona low molecular weight protein SNUCD-1 antigen and the monoclonal antibody 2G5 labeled with horseradish peroxidase. The test was evaluated using serum and CSF from 12 horses experimentally infected with 1.5 million S neurona sporocysts and 16 horses experimentally infected with varying doses (100 to 100,000) of S neurona sporocysts, for which results of histopathologic examination of the central nervous system were available. For horses challenged with 1.5 million sporocysts, there was a significant increase in serum Sn-IgM concentrations compared with values before infection at weeks 2-6 after inoculation (P neurona, there were significant increases in serum Sn-IgM concentration at various points in time after inoculation, depending on the challenge dose (P < .01). In addition, there was a significant increase between the CSF Sn-IgM concentrations before and after inoculation (P < .0001). These results support further evaluation of the assay as a diagnostic test during the acute phase of EPM.

  16. Enzyme-Linked Immunosorbent Assays for Detection of Equine Antibodies Specific to Sarcocystis neurona Surface Antigens†

    Science.gov (United States)

    Hoane, Jessica S.; Morrow, Jennifer K.; Saville, William J.; Dubey, J. P.; Granstrom, David E.; Howe, Daniel K.

    2005-01-01

    Sarcocystis neurona is the primary causative agent of equine protozoal myeloencephalitis (EPM), a common neurologic disease of horses in the Americas. We have developed a set of enzyme-linked immunosorbent assays (ELISAs) based on the four major surface antigens of S. neurona (SnSAGs) to analyze the equine antibody response to S. neurona. The SnSAG ELISAs were optimized and standardized with a sample set of 36 equine sera that had been characterized by Western blotting against total S. neurona parasite antigen, the current gold standard for S. neurona serology. The recombinant SnSAG2 (rSnSAG2) ELISA showed the highest sensitivity and specificity at 95.5% and 92.9%, respectively. In contrast, only 68.2% sensitivity and 71.4% specificity were achieved with the rSnSAG1 ELISA, indicating that this antigen may not be a reliable serological marker for analyzing antibodies against S. neurona in horses. Importantly, the ELISA antigens did not show cross-reactivity with antisera to Sarcocystis fayeri or Neospora hughesi, two other equine parasites. The accuracy and reliability exhibited by the SnSAG ELISAs suggest that these assays will be valuable tools for examining the equine immune response against S. neurona infection, which may help in understanding the pathobiology of this accidental parasite-host interaction. Moreover, with modification and further investigation, the SnSAG ELISAs have potential for use as immunodiagnostic tests to aid in the identification of horses affected by EPM. PMID:16148170

  17. Link-topic model for biomedical abbreviation disambiguation.

    Science.gov (United States)

    Kim, Seonho; Yoon, Juntae

    2015-02-01

    The ambiguity of biomedical abbreviations is one of the challenges in biomedical text mining systems. In particular, the handling of term variants and abbreviations without nearby definitions is a critical issue. In this study, we adopt the concepts of topic of document and word link to disambiguate biomedical abbreviations. We newly suggest the link topic model inspired by the latent Dirichlet allocation model, in which each document is perceived as a random mixture of topics, where each topic is characterized by a distribution over words. Thus, the most probable expansions with respect to abbreviations of a given abstract are determined by word-topic, document-topic, and word-link distributions estimated from a document collection through the link topic model. The model allows two distinct modes of word generation to incorporate semantic dependencies among words, particularly long form words of abbreviations and their sentential co-occurring words; a word can be generated either dependently on the long form of the abbreviation or independently. The semantic dependency between two words is defined as a link and a new random parameter for the link is assigned to each word as well as a topic parameter. Because the link status indicates whether the word constitutes a link with a given specific long form, it has the effect of determining whether a word forms a unigram or a skipping/consecutive bigram with respect to the long form. Furthermore, we place a constraint on the model so that a word has the same topic as a specific long form if it is generated in reference to the long form. Consequently, documents are generated from the two hidden parameters, i.e. topic and link, and the most probable expansion of a specific abbreviation is estimated from the parameters. Our model relaxes the bag-of-words assumption of the standard topic model in which the word order is neglected, and it captures a richer structure of text than does the standard topic model by considering

  18. Genetic localisation of MRX27 to Xq24-26 defines another discrete gene for non-specific X-linked mental retardation

    Energy Technology Data Exchange (ETDEWEB)

    Gedeon, A.K.; Connor, J.M.; Mulley, J.C. [Univ. of Adelaide (Australia); Connor, J.M. [Duncan Guthrie Inst. of Medical Genetics, Yorkhill (United Kingdom); Glass, I.A. [Univ. of California, San Franciso, CA (United States)

    1996-07-12

    A large family with non-specific X-linked mental retardation (MRX) was first described in 1991, with a suggestion of linkage to Xq26-27. The maximum lod score was 1.60 ({theta} = 0.10) with the F9 locus. The localization of this MRX gene has now been established by linkage to microsatellite markers. Peak pairwise lod scores of 4.02 and 4.01 ({theta} = 0.00) were attained at the DXS1114 and DXS994 loci respectively. This MRX gene is now designated MRX27 and is localized to Xq24-26 by recombination events detected by DXS424 and DXS102. This regional localization spans 26.2 cM on the genetic background map and defines another distinct MRX interval by linkage to a specific region of the X chromosome. 25 refs., 1 fig., 1 tab.

  19. Front end data link processor

    International Nuclear Information System (INIS)

    Wallace, J.J.

    1988-01-01

    It is possible to expand the data acquisition capabilities of an existing process computer to include other dedicated computer based systems, provided each system has at least minimal data link capabilities. The following paper discusses the addition of three computer based acquisition systems to a Honeywell 4500C (also designated the 45000) running the SEER system. Only one data link port was required to support the link. Each of the three specialized systems implemented data link protocols used by their suppliers in previous projects: none of the three were compatible with Honeywell's protocol. Part one of the following provides a generic overview of the project and would be relevent to the operator of any process system interested in expansion. Part two provides specific details of this project and may serve to provide performance benchmarks to those who wish to consider a similar project

  20. Children’s 5-HTTLPR genotype moderates the link between maternal criticism and attentional biases specifically for facial displays of anger

    Science.gov (United States)

    Gibb, Brandon E.; Johnson, Ashley L.; Benas, Jessica S.; Uhrlass, Dorothy J.; Knopik, Valerie S.; McGeary, John E.

    2011-01-01

    Theorists have proposed that negative experiences in childhood may contribute to the development of experience-specific information-processing biases, including attentional biases. There are also clear genetic influences on cognitive processes, with evidence that polymorphisms in specific candidate genes may moderate the impact of environmental stress on attentional biases (e.g., a functional polymorphism in the serotonin transporter gene [5-HTTLPR]). In the current study, we tested a gene × environment (G × E) model of risk for attentional biases. We hypothesized that children whose mothers exhibit high levels of expressed emotion criticism (EE-Crit) would display attentional biases specifically for angry, but not happy or sad, faces, and that this link would be stronger among children carrying one or two copies of the 5-HTTLPR short allele than among those homozygous for the long allele. Results generally supported these hypotheses, though we found that carriers of the 5-HTTLPR short allele who also had a critical mother exhibited attentional avoidance of angry faces rather than preferential attention. PMID:21895572

  1. Banknote authentication using chaotic elements technology

    Science.gov (United States)

    Ambadiyil, Sajan; P. S., Krishnendu; Mahadevan Pillai, V. P.; Prabhu, Radhakrishna

    2017-10-01

    The counterfeit banknote is a growing threat to the society since the advancements in the field of computers, scanners and photocopiers, as they have made the duplication process for banknote much simpler. The fake note detection systems developed so far have many drawbacks such as high cost, poor accuracy, unavailability, lack of user-friendliness and lower effectiveness. One possible solution to this problem could be the use of a system uniquely linked to the banknote itself. In this paper, we present a unique identification and authentication process for the banknote using chaotic elements embedded in it. A chaotic element means that the physical elements are formed from a random process independent from human intervention. The chaotic elements used in this paper are the random distribution patterns of such security fibres set into the paper pulp. A unique ID is generated from the fibre pattern obtained from UV image of the note, which can be verified by any person who receives the banknote to decide whether the banknote is authentic or not. Performance analysis of the system is also studied in this paper.

  2. EarthCube GeoLink: Semantics and Linked Data for the Geosciences

    Science.gov (United States)

    Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Ji, P.; Jones, M. B.; Krisnadhi, A.; Lehnert, K. A.; Mickle, A.; Narock, T.; O'Brien, M.; Raymond, L. M.; Schildhauer, M.; Shepherd, A.; Wiebe, P. H.

    2015-12-01

    The NSF EarthCube initiative is building next-generation cyberinfrastructure to aid geoscientists in collecting, accessing, analyzing, sharing, and visualizing their data and knowledge. The EarthCube GeoLink Building Block project focuses on a specific set of software protocols and vocabularies, often characterized as the Semantic Web and "Linked Data", to publish data online in a way that is easily discoverable, accessible, and interoperable. GeoLink brings together specialists from the computer science, geoscience, and library science domains, and includes data from a network of NSF-funded repositories that support scientific studies in marine geology, marine ecosystems, biogeochemistry, and paleoclimatology. We are working collaboratively with closely-related Building Block projects including EarthCollab and CINERGI, and solicit feedback from RCN projects including Cyberinfrastructure for Paleogeosciences (C4P) and iSamples. GeoLink has developed a modular ontology that describes essential geoscience research concepts; published data from seven collections (to date) on the Web as geospatially-enabled Linked Data using this ontology; matched and mapped data between collections using shared identifiers for investigators, repositories, datasets, funding awards, platforms, research cruises, physical specimens, and gazetteer features; and aggregated the results in a shared knowledgebase that can be queried via a standard SPARQL endpoint. Client applications have been built around the knowledgebase, including a Web/map-based data browser using the Leaflet JavaScript library and a simple query service using the OpenSearch format. Future development will include extending and refining the GeoLink ontology, adding content from additional repositories, developing semi-automated algorithms to enhance metadata, and further work on client applications.

  3. Specific cross-linking of capsid proteins to virus RNA by ultraviolet irradiation of polio virus

    Energy Technology Data Exchange (ETDEWEB)

    Wetz, K.; Habermehl, K.O. (Freie Univ. Berlin (Germany, F.R.))

    1982-04-01

    Poliovirus was irradiated with u.v. light under conditions causing approx. 5% cross-linking of capsid protein to virus RNA. Cross-linked RNA-protein complexes, freed from unbound protein, were treated with nuclease, and then analysed on SDS-polyacrylamide gels. The smallest capsid polypeptide VP4 was found to be associated with the RNA to the greatest degree, followed by VP2 and VP1, while VP3 was attached only in trace amounts. Low radiation doses, which produced cross-linking of RNA to protein, did not cause breakdown of the virus particles or conformational changes of the capsid as examined physically and serologically. However, higher doses caused structural alterations of the virus capsid.

  4. Specific cross-linking of capsid proteins to virus RNA by ultraviolet irradiation of polio virus

    International Nuclear Information System (INIS)

    Wetz, K.; Habermehl, K.-O.

    1982-01-01

    Poliovirus was irradiated with u.v. light under conditions causing approx. 5% cross-linking of capsid protein to virus RNA. Cross-linked RNA-protein complexes, freed from unbound protein, were treated with nuclease, and then analysed on SDS-polyacrylamide gels. The smallest capsid polypeptide VP4 was found to be associated with the RNA to the greatest degree, followed by VP2 and VP1, while VP3 was attached only in trace amounts. Low radiation doses, which produced cross-linking of RNA to protein, did not cause breakdown of the virus particles or conformational changes of the capsid as examined physically and serologically. However, higher doses caused structural alterations of the virus capsid. (author)

  5. Two-Dimensional Nonlinear Finite Element Analysis of CMC Microstructures

    Science.gov (United States)

    Mital, Subodh K.; Goldberg, Robert K.; Bonacuse, Peter J.

    2012-01-01

    A research program has been developed to quantify the effects of the microstructure of a woven ceramic matrix composite and its variability on the effective properties and response of the material. In order to characterize and quantify the variations in the microstructure of a five harness satin weave, chemical vapor infiltrated (CVI) SiC/SiC composite material, specimens were serially sectioned and polished to capture images that detailed the fiber tows, matrix, and porosity. Open source quantitative image analysis tools were then used to isolate the constituents, from which two dimensional finite element models were generated which approximated the actual specimen section geometry. A simplified elastic-plastic model, wherein all stress above yield is redistributed to lower stress regions, is used to approximate the progressive damage behavior for each of the composite constituents. Finite element analyses under in-plane tensile loading were performed to examine how the variability in the local microstructure affected the macroscopic stress-strain response of the material as well as the local initiation and progression of damage. The macroscopic stress-strain response appeared to be minimally affected by the variation in local microstructure, but the locations where damage initiated and propagated appeared to be linked to specific aspects of the local microstructure.

  6. Expert communication link management: overview and progress

    Science.gov (United States)

    Dunkelberger, Kirk A.

    1998-08-01

    Consider the downsizing of our forces, the increasing complexity of our tactical platforms, and the ever widening array of communication options and the conclusion is inevitable. The need for automated support to reduce communication-related workload is critical to continued task force effectiveness. In a previous era, communication management expertise resided solely in the form of human experts. These experts flew with the pilots, providing the most effective means of communication in real time; they have since been removed from a great number of platforms due to force downsizing and real estate value in the cockpit. This burden has typically been shifted to the pilot, providing another set of tasks in an environment which is already far too taxing. An Expert Communication Link Manger (ECLM) is required -- a trusted, reliable assistant which can determine optimal link, channel, and waveform data for the communication requirements at hand and translate those requirements transparently into communication device control. Technologies are at hand which make ECLM possible; the mixture of these elements in the correct proportions can provide a capable, deployable, and cost effective ECLM in the near term. This paper describes specific applied ECLM research work in progress funded by the USAF under a four year effort. Operational objectives, technical objectives, a reference design, and technical excursions within the broad ECLM scope will be discussed in detail. Results of prototypes built to date in the area of communication inference from speech understanding, dynamic adaptive routing, and packet switching networks in the tactical environment will be presented.

  7. Predicting the Retention Behavior of Specific O-Linked Glycopeptides.

    Science.gov (United States)

    Badgett, Majors J; Boyes, Barry; Orlando, Ron

    2017-09-01

    O -Linked glycosylation is a common post-translational modification that can alter the overall structure, polarity, and function of proteins. Reverse-phase (RP) chromatography is the most common chromatographic approach to analyze O -glycosylated peptides and their unmodified counterparts, even though this approach often does not provide adequate separation of these two species. Hydrophilic interaction liquid chromatography (HILIC) can be a solution to this problem, as the polar glycan interacts with the polar stationary phase and potentially offers the ability to resolve the peptide from its modified form(s). In this paper, HILIC is used to separate peptides with O - N -acetylgalactosamine ( O -GalNAc), O - N -acetylglucosamine ( O -GlcNAc), and O -fucose additions from their native forms, and coefficients representing the extent of hydrophilicity were derived using linear regression analysis as a means to predict the retention times of peptides with these modifications.

  8. Noncoding Elements: Evolution and Epigenetic Regulation

    KAUST Repository

    Seridi, Loqmane

    2016-03-09

    When the human genome project was completed, it revealed a surprising result. 98% of the genome did not code for protein of which more than 50% are repeats— later known as ”Junk DNA”. However, comparative genomics unveiled that many noncoding elements are evolutionarily constrained; thus luckily to have a role in genome stability and regulation. Though, their exact functions remained largely unknown. Several large international consortia such as the Functional Annotation of Mammalian Genomes (FANTOM) and the Encyclopedia of DNA Elements (ENCODE) were set to understand the structure and the regulation of the genome. Specifically, these endeavors aim to measure and reveal the transcribed components and functional elements of the genome. One of the most the striking findings of these efforts is that most of the genome is transcribed, including non-conserved noncoding elements and repeat elements. Specifically, we investigated the evolution and epigenetic properties of noncoding elements. 1. We compared genomes of evolutionarily distant species and showed the ubiquity of constrained noncoding elements in metazoa. 2. By integrating multi-omic data (such as transcriptome, nucleosome profiling, histone modifications), I conducted a comprehensive analysis of epigenetic properties (chromatin states) of conserved noncoding elements in insects. We showed that those elements have distinct and protective sequence features, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. 3. I focused on the relationship between enhancers and repetitive elements. Using Cap Analysis of Gene Expression (CAGE) and RNASeq, I compiled a full catalog of active enhancers (a class of noncoding elements) during myogenesis of human primary cells of healthy donors and donors affected by Duchenne muscular dystrophy (DMD). Comparing the two time-courses, a significant change in the epigenetic

  9. A linked GeoData map for enabling information access

    Science.gov (United States)

    Powell, Logan J.; Varanka, Dalia E.

    2018-01-10

    OverviewThe Geospatial Semantic Web (GSW) is an emerging technology that uses the Internet for more effective knowledge engineering and information extraction. Among the aims of the GSW are to structure the semantic specifications of data to reduce ambiguity and to link those data more efficiently. The data are stored as triples, the basic data unit in graph databases, which are similar to the vector data model of geographic information systems (GIS); that is, a node-edge-node model that forms a graph of semantically related information. The GSW is supported by emerging technologies such as linked geospatial data, described below, that enable it to store and manage geographical data that require new cartographic methods for visualization. This report describes a map that can interact with linked geospatial data using a simulation of a data query approach called the browsable graph to find information that is semantically related to a subject of interest, visualized using the Data Driven Documents (D3) library. Such a semantically enabled map functions as a map knowledge base (MKB) (Varanka and Usery, 2017).A MKB differs from a database in an important way. The central element of a triple, alternatively called the edge or property, is composed of a logic formalization that structures the relation between the first and third parts, the nodes or objects. Node-edge-node represents the graphic form of the triple, and the subject-property-object terms represent the data structure. Object classes connect to build a federated graph, similar to a network in visual form. Because the triple property is a logical statement (a predicate), the data graph represents logical propositions or assertions accepted to be true about the subject matter. These logical formalizations can be manipulated to calculate new triples, representing inferred logical assertions, from the existing data.To demonstrate a MKB system, a technical proof-of-concept is developed that uses geographically

  10. Positive- and negative-acting regulatory elements contribute to the tissue-specific expression of INNER NO OUTER, a YABBY-type transcription factor gene in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Simon Marissa K

    2012-11-01

    Full Text Available Abstract Background The INNER NO OUTER (INO gene, which encodes a YABBY-type transcription factor, specifies and promotes the growth of the outer integument of the ovule in Arabidopsis. INO expression is limited to the abaxial cell layer of the developing outer integument of the ovule and is regulated by multiple regions of the INO promoter, including POS9, a positive element that when present in quadruplicate can produce low-level expression in the normal INO pattern. Results Significant redundancy in activity between different regions of the INO promoter is demonstrated. For specific regulatory elements, multimerization or the addition of the cauliflower mosaic virus 35S general enhancer was able to activate expression of reporter gene constructs that were otherwise incapable of expression on their own. A new promoter element, POS6, is defined and is shown to include sufficient positive regulatory information to reproduce the endogenous pattern of expression in ovules, but other promoter regions are necessary to fully suppress expression outside of ovules. The full-length INO promoter, but not any of the INO promoter deletions tested, is able to act as an enhancer-blocking insulator to prevent the ectopic activation of expression by the 35S enhancer. Sequence conservation between the promoter regions of Arabidopsis thaliana, Brassica oleracea and Brassica rapa aligns closely with the functional definition of the POS6 and POS9 regions, and with a defined INO minimal promoter. The B. oleracea INO promoter is sufficient to promote a similar pattern and level of reporter gene expression in Arabidopsis to that observed for the Arabidopsis promoter. Conclusions At least two independent regions of the INO promoter contain sufficient regulatory information to direct the specific pattern but not the level of INO gene expression. These regulatory regions act in a partially redundant manner to promote the expression in a specific pattern in the ovule and

  11. Detection of Francisella tularensis-Specific Antibodies in Patients with Tularemia by a Novel Competitive Enzyme-Linked Immunosorbent Assay

    Science.gov (United States)

    Sharma, Neekun; Hotta, Akitoyo; Yamamoto, Yoshie; Fujita, Osamu; Uda, Akihiko; Morikawa, Shigeru; Yamada, Akio

    2013-01-01

    A novel competitive enzyme-linked immunosorbent assay (cELISA) was developed and evaluated for detection of antibodies against Francisella tularensis in humans. The assay is based on the ability of serum antibodies to inhibit the binding of monoclonal antibodies (MAbs) directed against F. tularensis lipopolysaccharide antigens. The assay was evaluated using serum samples of tularemia patients, inactivated F. tularensis-immunized rabbits, and F. tularensis-infected mice. Antibodies against F. tularensis were successfully detected in serum samples of tularemia patients as well as the immunized and infected animals. The cELISA method was compared to indirect ELISA (iELISA) and the commonly used microagglutination test (MA) using serum samples of 19 tularemia patients and 50 healthy individuals. The sensitivity and specificity of cELISA were 93.9 and 96.1%, respectively, in comparison to the iELISA. MA was less sensitive than cELISA with a sensitivity and specificity of only 81.8 and 98.0%, respectively. A high degree of correlation (R2 = 0.8226) was observed between cELISA and iELISA results. The novel cELISA developed in this study appears to be highly sensitive and specific for serodiagnosis of human tularemia. The potential of the MAb-based cELISA to be used in both human and animal samples emphasizes its usefulness for serological survey of tularemia among multiple animal species. PMID:23114700

  12. Finite element computational fluid mechanics

    International Nuclear Information System (INIS)

    Baker, A.J.

    1983-01-01

    This book analyzes finite element theory as applied to computational fluid mechanics. It includes a chapter on using the heat conduction equation to expose the essence of finite element theory, including higher-order accuracy and convergence in a common knowledge framework. Another chapter generalizes the algorithm to extend application to the nonlinearity of the Navier-Stokes equations. Other chapters are concerned with the analysis of a specific fluids mechanics problem class, including theory and applications. Some of the topics covered include finite element theory for linear mechanics; potential flow; weighted residuals/galerkin finite element theory; inviscid and convection dominated flows; boundary layers; parabolic three-dimensional flows; and viscous and rotational flows

  13. Verklarende prediking. Basisteoretiese elemente uit Hebreërs

    Directory of Open Access Journals (Sweden)

    C.J.H. Venter

    2001-08-01

    Full Text Available Expository preaching. Basis-theoretical elements from Hebrews This article specifically focuses on basis-theoretical elements in the Letter to the Hebrews – a New Testament book that can actually be regarded as a sermon. In the introduction the point of departure, that is the focus on bais-theoretical elements, is justified. Furthermore, attention is paid to specific elements of preaching implied in this “sermon” in the Letter to the Hebrews: elements applicable to the practice of expository preaching, the structure in an expository sermon, that is the introduction, the body, and the conclusion. The purpose of the sermon is also touched upon. Issues like the spirituality of the preacher, his ministry of equipping by means of expository preaching, and his relationship to the congregation are also investigated, followed by final conclusions.

  14. Finite element approximation to the even-parity transport equation

    International Nuclear Information System (INIS)

    Lewis, E.E.

    1981-01-01

    This paper studies the finite element method, a procedure for reducing partial differential equations to sets of algebraic equations suitable for solution on a digital computer. The differential equation is cast into the form of a variational principle, the resulting domain then subdivided into finite elements. The dependent variable is then approximated by a simple polynomial, and these are linked across inter-element boundaries by continuity conditions. The finite element method is tailored to a variety of transport problems. Angular approximations are formulated, and the extent of ray effect mitigation is examined. Complex trial functions are introduced to enable the inclusion of buckling approximations. The ubiquitous curved interfaces of cell calculations, and coarse mesh methods are also treated. A concluding section discusses limitations of the work to date and suggests possible future directions

  15. LinkLights

    DEFF Research Database (Denmark)

    Grönvall, Erik; Kramp, Gunnar

    2011-01-01

    The project described in this paper aims to provide assistive tools to support elderly people affected by vestibular dysfunction (i.e. a form of balance disorder leading to dizziness and nausea) in their home-based rehabilitation activities. Challenges emerge as the rehabilitation moves from...... a supervised hospital setting to private homes. Our studies have shown that the elderly people are less motivated to perform the training at home. This paper presents a tangible, portable, two dimensional modular platform called LinkLights that has been developed to sustain the home-based rehabilitation......, giving clear guidelines what to do, adding motivational cues and elements of variation and surprise in the activity. Furthermore, a set of challenges for successful translocation of the therapeutic regimen from a supervised, hospital setting to an unsupervised home-based setting together with some early...

  16. Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

    Science.gov (United States)

    Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

    2017-07-01

    Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

  17. A Polymorphic Antioxidant Response Element Links NRF2/sMAF Binding to Enhanced MAPT Expression and Reduced Risk of Parkinsonian Disorders

    Directory of Open Access Journals (Sweden)

    Xuting Wang

    2016-04-01

    Full Text Available The NRF2/sMAF protein complex regulates the oxidative stress response by occupying cis-acting enhancers containing an antioxidant response element (ARE. Integrating genome-wide maps of NRF2/sMAF occupancy with disease-susceptibility loci, we discovered eight polymorphic AREs linked to 14 highly ranked disease-risk SNPs in individuals of European ancestry. Among these SNPs was rs242561, located within a regulatory region of the MAPT gene (encoding microtubule-associated protein Tau. It was consistently occupied by NRF2/sMAF in multiple experiments and its strong-binding allele associated with higher mRNA levels in cell lines and human brain tissue. Induction of MAPT transcription by NRF2 was confirmed using a human neuroblastoma cell line and a Nrf2-deficient mouse model. Most importantly, rs242561 displayed complete linkage disequilibrium with a highly protective allele identified in multiple GWASs of progressive supranuclear palsy, Parkinson’s disease, and corticobasal degeneration. These observations suggest a potential role for NRF2/sMAF in tauopathies and a possible role for NRF2 pathway activators in disease prevention.

  18. The ALICE detector data link

    CERN Document Server

    Rubin, G; Csató, P; Dénes, E; Kiss, T; Meggyesi, Z; Sulyán, J; Vesztergombi, G; Eged, B; Gerencsér, I; Novák, I; Soós, C; Tarján, D; Telegdy, A; Tóth, N

    1999-01-01

    The ALICE detector data link has been designed to cover all the needs for data transfer between the detector and the data-acquisition system. It is a 1 Gbit/s, full-duplex, multi-purpose fibre optic link that can be used as a medium for the bi-directional transmission of data blocks between the front-end electronics and the data- acquisition system and also for the remote control and test of the front-end electronics, In this paper the concept, the protocol, the specific test tools, the prototypes of the detector data link and the read-out receiver card, their application in the ALICE-TPC test system and the integration with the DATE software are presented. The test results on the performance are also shown. (14 refs).

  19. Using turbocodes on optical links

    Directory of Open Access Journals (Sweden)

    Glenn Claes

    2006-04-01

    Full Text Available The fast evolving telecommunication world is permanently in search for faster and better communication links. On one hand, turbo codes are like a dream come true. Due to their amazing performance, they have become the reference in the word of error detecting and correcting codes. On the other hand, broadband transmission channels like optical fibres can meet the need for higher transmission velocity. In this paper therefore we will bring these two elements together and thus the performance of turbocodes on optical links will be studied. First the turbocode will be optimised throughout an individual analysis of each of its design parameters. Moreover it wil be shown that turbocodes have much better performance than the well known Reed-Solomon codes. Finally we will show that the 8Bit/10Bit code, which is required to comply with the Gigabit Ethernet standard, becomes superfluous when working with turbocodes. All tests were carried out on multimode graded-index glass fibres.

  20. Cluster analysis to evaluate stable chemical elements and physical-chemical parameters behavior on uranium mining waste

    International Nuclear Information System (INIS)

    Pereira, Wagner de Souza; Py Junior, Delcy de Azevedo; Goncalves, Simone; Kelecom, Alphonse; Morais, Gustavo Ferrari de; Campelo, Emanuele Lazzaretti Cordova; Dores, Luis Augusto de Carvalho Bresser

    2011-01-01

    The Ore Treating Unit (UTM, in portuguese) is a deactivated uranium mine. A cluster analysis was used to evaluate the behavior of stable chemical elements and physical-chemical parameters in their effluents. The utilization of the cluster analysis proved itself effective in the assessment, allowing the identification of groups of chemical elements, physical-chemical parameters and their joint analysis (elements and parameters). As a result we may assert, based on data analysis, that there is a strong link between calcium and magnesium and between aluminum and rare-earth oxides on UTM's effluents. Sulphate was also identified as strongly linked to total and dissolved solids, and those to electrical conductivity. There were other associations, but not so strongly linked. Further gathering, to seasonal evaluation, are required in order to confirm those analysis. Additional statistical analysis (factor analysis) must be used to try to identify the origin of the identified groups on this analysis. (author)

  1. Cluster analysis to evaluate stable chemical elements and physical-chemical parameters behavior on uranium mining waste

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Wagner de Souza; Py Junior, Delcy de Azevedo; Goncalves, Simone, E-mail: wspereira@inb.gov.br [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Coordenacao de Protecao Radiologica. Grupo Multidisciplinar de Radioprotecao; Kelecom, Alphonse [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Biologia. Lab. de Radiobiologia e Radiometria Pedro Lopes dos Santos; Morais, Gustavo Ferrari de; Campelo, Emanuele Lazzaretti Cordova [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Coordenacao de Desenvolvimento de Processos; Dores, Luis Augusto de Carvalho Bresser [Unidade de Tratamento de Minerio (UTM/INB), Pocos de Caldas, MG (Brazil). Gerencia de Descomissionamento

    2011-07-01

    The Ore Treating Unit (UTM, in portuguese) is a deactivated uranium mine. A cluster analysis was used to evaluate the behavior of stable chemical elements and physical-chemical parameters in their effluents. The utilization of the cluster analysis proved itself effective in the assessment, allowing the identification of groups of chemical elements, physical-chemical parameters and their joint analysis (elements and parameters). As a result we may assert, based on data analysis, that there is a strong link between calcium and magnesium and between aluminum and rare-earth oxides on UTM's effluents. Sulphate was also identified as strongly linked to total and dissolved solids, and those to electrical conductivity. There were other associations, but not so strongly linked. Further gathering, to seasonal evaluation, are required in order to confirm those analysis. Additional statistical analysis (factor analysis) must be used to try to identify the origin of the identified groups on this analysis. (author)

  2. Stenotrophomonas maltophilia virulence and specific variations in trace elements during acute lung infection: implications in cystic fibrosis.

    Directory of Open Access Journals (Sweden)

    Arianna Pompilio

    Full Text Available Metal ions are necessary for the proper functioning of the immune system, and, therefore, they might have a significant influence on the interaction between bacteria and host. Ionic dyshomeostasis has been recently observed also in cystic fibrosis (CF patients, whose respiratory tract is frequently colonized by Stenotrophomonas maltophilia. For the first time, here we used an inductively mass spectrometry method to perform a spatial and temporal analysis of the pattern of changes in a broad range of major trace elements in response to pulmonary infection by S. maltophilia. To this, DBA/2 mouse lungs were comparatively infected by a CF strain and by an environmental one. Our results showed that pulmonary ionomic profile was significantly affected during infection. Infected mice showed increased lung levels of Mg, P, S, K, Zn, Se, and Rb. To the contrary, Mn, Fe, Co, and Cu levels resulted significantly decreased. Changes of element concentrations were correlated with pulmonary bacterial load and markers of inflammation, and occurred mostly on day 3 post-exposure, when severity of infection culminated. Interestingly, CF strain - significantly more virulent than the environmental one in our murine model - provoked a more significant impact in perturbing pulmonary metal homeostasis. Particularly, exposure to CF strain exclusively increased P and K levels, while decreased Fe and Mn ones. Overall, our data clearly indicate that S. maltophilia modulates pulmonary metal balance in a concerted and virulence-dependent manner highlighting the potential role of the element dyshomeostasis during the progression of S. maltophilia infection, probably exacerbating the harmful effects of the loss of CF transmembrane conductance regulator function. Further investigations are required to understand the biological significance of these alterations and to confirm they are specifically caused by S. maltophilia.

  3. Population specific absorption studies for some diet incorporated trace elements : comparison with ICRP data

    International Nuclear Information System (INIS)

    Parameswaran, M.; Dang, H.S.

    1999-01-01

    Daily intake and excretion can provide an important information regarding the absorption through the gastro-intestinal tract (f1 factor) of trace elements incorporated in diet. The absorption may depend upon the kind of diet consumed, the content of the fibre, protein etc and it could be quite different for two populations groups with entirely different food habits. ICRP has provided data on the intake and excretion of 63 trace elements by Caucasian population representing North American and European adults. This paper reports intake and excretion of twelve elements Na, K, Ca, Mg, Cu, Mn, Rb, Fe, Zn, Sr, Li and Cr for an urban adult Indian population group and compares with corresponding data on ICRP reference man. (author)

  4. Neuron-specific chromatin remodeling: a missing link in epigenetic mechanisms underlying synaptic plasticity, memory, and intellectual disability disorders.

    Science.gov (United States)

    Vogel-Ciernia, Annie; Wood, Marcelo A

    2014-05-01

    Long-term memory formation requires the coordinated regulation of gene expression. Until recently nucleosome remodeling, one of the major epigenetic mechanisms for controlling gene expression, had been largely unexplored in the field of neuroscience. Nucleosome remodeling is carried out by chromatin remodeling complexes (CRCs) that interact with DNA and histones to physically alter chromatin structure and ultimately regulate gene expression. Human exome sequencing and gene wide association studies have linked mutations in CRC subunits to intellectual disability disorders, autism spectrum disorder and schizophrenia. However, how mutations in CRC subunits were related to human cognitive disorders was unknown. There appears to be both developmental and adult specific roles for the neuron specific CRC nBAF (neuronal Brg1/hBrm Associated Factor). nBAF regulates gene expression required for dendritic arborization during development, and in the adult, contributes to long-term potentiation, a form of synaptic plasticity, and long-term memory. We propose that the nBAF complex is a novel epigenetic mechanism for regulating transcription required for long-lasting forms of synaptic plasticity and memory processes and that impaired nBAF function may result in human cognitive disorders. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Single-dilution enzyme-linked immunosorbent assay for quantification of antigen-specific salmonid antibody

    Science.gov (United States)

    Alcorn, S.W.; Pascho, R.J.

    2000-01-01

    An enzyme-linked immunosorbent assay (ELISA) was developed on the basis of testing a single dilution of serum to quantify the level of antibody to the p57 protein of Renibaclerium salmoninarum in sockeye salmon (Oncorhynchus nerka). The levels of antibody were interpolated from a standard curve constructed by relating the optical densities (OD) produced by several dilutions of a high-titer rainbow trout (O. mykiss) antiserum to the p57 protein. The ELISA OD values produced by as many as 36 test sera on each microplate were compared with the standard curve to calculate the antigen-specific antibody activity. Repeated measurements of 36 samples on 3 microplates on each of 6 assay dates indicated that the mean intraassay coefficient of variation (CV) was 6.68% (range, 0-23%) and the mean interassay CV was 8.29% (range, 4-16%). The antibody levels determined for the serum sample from 24 sockeye salmon vaccinated with a recombinant p57 protein generally were correlated with the levels determined by endpoint titration (r2 = 0.936) and with results from another ELISA that was based on extrapolation of antibody levels from a standard curve (r2 = 0.956). The single-dilution antibody ELISA described here increases the number of samples that can be tested on each microplate compared with immunoassays based on analysis of several dilutions of each test serum. It includes controls for interassay standardization and can be used to test fish weighing <3 g.

  6. Testing the ecological consequences of evolutionary change using elements.

    Science.gov (United States)

    Jeyasingh, Punidan D; Cothran, Rickey D; Tobler, Michael

    2014-02-01

    Understanding the ecological consequences of evolutionary change is a central challenge in contemporary biology. We propose a framework based on the ˜25 elements represented in biology, which can serve as a conduit for a general exploration of poorly understood evolution-to-ecology links. In this framework, known as ecological stoichiometry, the quantity of elements in the inorganic realm is a fundamental environment, while the flow of elements from the abiotic to the biotic realm is due to the action of genomes, with the unused elements excreted back into the inorganic realm affecting ecological processes at higher levels of organization. Ecological stoichiometry purposefully assumes distinct elemental composition of species, enabling powerful predictions about the ecological functions of species. However, this assumption results in a simplified view of the evolutionary mechanisms underlying diversification in the elemental composition of species. Recent research indicates substantial intraspecific variation in elemental composition and associated ecological functions such as nutrient excretion. We posit that attention to intraspecific variation in elemental composition will facilitate a synthesis of stoichiometric information in light of population genetics theory for a rigorous exploration of the ecological consequences of evolutionary change.

  7. An AU-rich element in the 3{prime} untranslated region of the spinach chloroplast petD gene participates in sequence-specific RNA-protein complex formation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Qiuyun; Adams, C.C.; Usack, L. [Cornell Univ., Ithaca, NY (United States)] [and others

    1995-04-01

    In chloroplasts, the 3{prime} untranslated regions of most mRNAs contain a stem-loop-forming inverted repeat (IR) sequence that is required for mRNA stability and correct 3{prime}-end formation. The IR regions of several mRNAs are also known to bind chloroplast proteins, as judged from in vitro gel mobility shift and UV cross-linking assays, and these RNA-protein interactions may be involved in the regulation of chloroplast mRNA processing and/or stability. Here we describe in detail the RNA and protein components that are involved in 3{prime} IR-containing RNA (3{prime} IR-RNA)-protein complex formation for the spinach chloroplast petD gene, which encodes subunit IV of the cytochrome b{sub 6}/f complex. We show that the complex contains 55-, 41-, and 29-kDa RNA-binding proteins (ribonucleoproteins [RNPs]). These proteins together protect a 90-nucleotide segment of RNA from RNase T{sub 1} digestion; this RNA contains the IR and downstream flanking sequences. Competition experiments using 3{prime} IR-RNAs from the psbA or rbcL gene demonstrate that the RNPs have a strong specificity for the petD sequence. Site-directed mutagenesis was carried out to define the RNA sequence elements required for complex formation. These studies identified an 8-nucleotide AU-rich sequence downstream of the IR; mutations within this sequence had moderate to severe effects on RNA-protein complex formation. Although other similar sequences are present in the petD 3{prime} untranslated region, only a single copy, which we have termed box II, appears to be essential for in vivo protein binding. In addition, the IR itself is necessary for optimal complex formation. These two sequence elements together with an RNP complex may direct correct 3{prime}-end processing and/or influence the stability of petD mRNA in chloroplasts. 48 refs., 9 figs., 2 tabs.

  8. Specificity in mediated pathways by anxiety symptoms linking adolescent stress profiles to depressive symptoms: Results of a moderated mediation approach.

    Science.gov (United States)

    Anyan, Frederick; Bizumic, Boris; Hjemdal, Odin

    2018-03-01

    We investigated the specificity in mediated pathways that separately link specific stress dimensions through anxiety to depressive symptoms and the protective utility of resilience. Thus, this study goes beyond lumping together potential mediating and moderating processes that can explain the relations between stress and (symptoms of) psychopathology and the buffering effect of resilience. Ghanaian adolescents between 13 and 17 years (female = 285; male = 244) completed the Adolescent Stress Questionnaire (ASQ), Spielberger State Anxiety Inventory (STAI), Short Mood Feeling Questionnaire (SMFQ) and the Resilience Scale for Adolescents (READ). Independent samples t-test, multivariate analysis of covariance with follow-up tests and moderated mediation analyses were performed. Evidences were found for specificity in the associations between dimensions of adolescent stressors and depressive symptoms independent of transient anxiety. Transient anxiety partly accounted for the indirect effects of eight stress dimensions on depressive symptoms. Except stress of school attendance and school/leisure conflict, resilience moderated the indirect effects of specific stress dimensions on depressive symptoms. Results suggested differences in how Ghanaian adolescents view the various stress dimensions, and mediated pathways associated with anxiety and depressive symptoms. Use of cross-sectional data does not show causal process and temporal changes over time. Findings support and clarify the specificity in the interrelations and mediated pathways among dimensions of adolescent stress, transient anxiety, and depressive symptoms. Conditional process analyses shows that resilience does not only buffer direct, but also indirect psychological adversities. Interventions for good mental health may focus on low resilience subgroups in specific stress dimensions while minimizing transient anxiety. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Associating uncertainty with datasets using Linked Data and allowing propagation via provenance chains

    Science.gov (United States)

    Car, Nicholas; Cox, Simon; Fitch, Peter

    2015-04-01

    With earth-science datasets increasingly being published to enable re-use in projects disassociated from the original data acquisition or generation, there is an urgent need for associated metadata to be connected, in order to guide their application. In particular, provenance traces should support the evaluation of data quality and reliability. However, while standards for describing provenance are emerging (e.g. PROV-O), these do not include the necessary statistical descriptors and confidence assessments. UncertML has a mature conceptual model that may be used to record uncertainty metadata. However, by itself UncertML does not support the representation of uncertainty of multi-part datasets, and provides no direct way of associating the uncertainty information - metadata in relation to a dataset - with dataset objects.We present a method to address both these issues by combining UncertML with PROV-O, and delivering resulting uncertainty-enriched provenance traces through the Linked Data API. UncertProv extends the PROV-O provenance ontology with an RDF formulation of the UncertML conceptual model elements, adds further elements to support uncertainty representation without a conceptual model and the integration of UncertML through links to documents. The Linked ID API provides a systematic way of navigating from dataset objects to their UncertProv metadata and back again. The Linked Data API's 'views' capability enables access to UncertML and non-UncertML uncertainty metadata representations for a dataset. With this approach, it is possible to access and navigate the uncertainty metadata associated with a published dataset using standard semantic web tools, such as SPARQL queries. Where the uncertainty data follows the UncertML model it can be automatically interpreted and may also support automatic uncertainty propagation . Repositories wishing to enable uncertainty propagation for all datasets must ensure that all elements that are associated with uncertainty

  10. Enzyme-linked immunosorbent assay using a virus type-specific peptide based on a subdomain of envelope protein e(rns) for serologic diagnosis of pestivirus infections in swine

    NARCIS (Netherlands)

    Langedijk, J.P.; Middel, W.G.; Meloen, R.H.; Kramps, J.A.; Smit, de J.A.

    2001-01-01

    Peptides deduced from the C-terminal end (residues 191 to 227) of pestivirus envelope protein Erns were used to develop enzyme-linked immunosorbent assays (ELISAs) to measure specifically antibodies against different types of pestiviruses. The choice of the peptide was based on the modular structure

  11. Linking CATHENA with other computer codes through a remote process

    Energy Technology Data Exchange (ETDEWEB)

    Vasic, A.; Hanna, B.N.; Waddington, G.M. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada); Sabourin, G. [Atomic Energy of Canada Limited, Montreal, Quebec (Canada); Girard, R. [Hydro-Quebec, Montreal, Quebec (Canada)

    2005-07-01

    'Full text:' CATHENA (Canadian Algorithm for THErmalhydraulic Network Analysis) is a computer code developed by Atomic Energy of Canada Limited (AECL). The code uses a transient, one-dimensional, two-fluid representation of two-phase flow in piping networks. CATHENA is used primarily for the analysis of postulated upset conditions in CANDU reactors; however, the code has found a wider range of applications. In the past, the CATHENA thermalhydraulics code included other specialized codes, i.e. ELOCA and the Point LEPreau CONtrol system (LEPCON) as callable subroutine libraries. The combined program was compiled and linked as a separately named code. This code organizational process is not suitable for independent development, maintenance, validation and version tracking of separate computer codes. The alternative solution to provide code development independence is to link CATHENA to other computer codes through a Parallel Virtual Machine (PVM) interface process. PVM is a public domain software package, developed by Oak Ridge National Laboratory and enables a heterogeneous collection of computers connected by a network to be used as a single large parallel machine. The PVM approach has been well accepted by the global computing community and has been used successfully for solving large-scale problems in science, industry, and business. Once development of the appropriate interface for linking independent codes through PVM is completed, future versions of component codes can be developed, distributed separately and coupled as needed by the user. This paper describes the coupling of CATHENA to the ELOCA-IST and the TROLG2 codes through a PVM remote process as an illustration of possible code connections. ELOCA (Element Loss Of Cooling Analysis) is the Industry Standard Toolset (IST) code developed by AECL to simulate the thermo-mechanical response of CANDU fuel elements to transient thermalhydraulics boundary conditions. A separate ELOCA driver program

  12. Linking CATHENA with other computer codes through a remote process

    International Nuclear Information System (INIS)

    Vasic, A.; Hanna, B.N.; Waddington, G.M.; Sabourin, G.; Girard, R.

    2005-01-01

    'Full text:' CATHENA (Canadian Algorithm for THErmalhydraulic Network Analysis) is a computer code developed by Atomic Energy of Canada Limited (AECL). The code uses a transient, one-dimensional, two-fluid representation of two-phase flow in piping networks. CATHENA is used primarily for the analysis of postulated upset conditions in CANDU reactors; however, the code has found a wider range of applications. In the past, the CATHENA thermalhydraulics code included other specialized codes, i.e. ELOCA and the Point LEPreau CONtrol system (LEPCON) as callable subroutine libraries. The combined program was compiled and linked as a separately named code. This code organizational process is not suitable for independent development, maintenance, validation and version tracking of separate computer codes. The alternative solution to provide code development independence is to link CATHENA to other computer codes through a Parallel Virtual Machine (PVM) interface process. PVM is a public domain software package, developed by Oak Ridge National Laboratory and enables a heterogeneous collection of computers connected by a network to be used as a single large parallel machine. The PVM approach has been well accepted by the global computing community and has been used successfully for solving large-scale problems in science, industry, and business. Once development of the appropriate interface for linking independent codes through PVM is completed, future versions of component codes can be developed, distributed separately and coupled as needed by the user. This paper describes the coupling of CATHENA to the ELOCA-IST and the TROLG2 codes through a PVM remote process as an illustration of possible code connections. ELOCA (Element Loss Of Cooling Analysis) is the Industry Standard Toolset (IST) code developed by AECL to simulate the thermo-mechanical response of CANDU fuel elements to transient thermalhydraulics boundary conditions. A separate ELOCA driver program starts, ends

  13. The challenges of translating culturally specific elements: the case of Mikhail Bulgakov’s The Master and Margarita

    Directory of Open Access Journals (Sweden)

    Natalia Kaloh Vid

    2016-12-01

    Full Text Available Mikhail Bulgakov’s novel The Master and Margarita, a highly complex and multi-levelled narrative, is a challenge for any translator. The emphasis in the current research is on the translation strategies used when translating culturally-specific elements, or historical realia, referred to as “Sovietisms,” in three English translations of the novel by Glenny (1967, Pevear and Volokhonsky (1997 and Aplin (2008. Sovietisms refer to items characteristic of the Soviet discourse of the 1930s: word-formations of the non-standard “Soviet Russian.” Bulgakov’s language is sated with Soviet vocabulary, which refers to various cultural and socio-political elements of Soviet reality. Sovietisms occur at various levels (lexical,syntactic, stylistic and rhetorical and should be carefully translated as a significant characteristic of Bulgakov’s style. A complete domestication of Sovietisms may lead to a loss of a connotative meaning essential for understanding the context, while a foreignisation of these terms, which are most likely unknown to western readers, may disturb fluidity of reading and cause confusion. The purpose of this analysis, thus, is to illustrate the use of domesticating/foreignising strategies employed by Bulgakov’s translators and to assess the translation choices. The comparative analysis employs the taxonomies suggested by Vlakhov and Florin (1995 and Vinay and Darbelnet (1958/1989 as the grounds for the case study.

  14. Specificity of the links between workplace harassment and PTSD: primary results using court decisions, a pilot study in France.

    Science.gov (United States)

    Bonafons, Claire; Jehel, Louis; Coroller-Béquet, Alain

    2009-04-01

    France is one of the first countries to have passed specific legislation concerning "mental harassment" (In French the term used in the legislation is "harcèlement moral" referring to harassment or bullying leading to mental or psychological distress.) in the workplace. However, the definition of mental harassment at work remains fairly vague. It is, indeed, a complex issue, since no objective and precise consensual definition has been given so far. The objective of this study is to clarify the criteria that French judges consider as characteristic of mental harassment, and to check whether the specific links between mental harassment at work and PTSD pointed to in recent international studies have been taken into account. This study proposes the main lines for debate in countries that have not yet adopted legal clauses on mental harassment at work. Our study is based on a sample of 22 people who were legally recognised as having been mentally harassed at work; this sample is taken as representative of all court decisions passed on harassment and published as such on the French Ministry of Justice website. To establish whether they were considering a case of harassment, the judges based their decisions on the nature of the accusations. In all cases (22/22), the charges brought against the defendant had to do with offences against the employee's dignity. Five cases out of 22 dealt with an offence infringing their rights, 10 cases out of 22 related to the employee's future within the company being compromised, while half of the cases (11/22) concerned a deterioration in the person's health. In more than half of the cases, the judges also looked for other factors, such as repetition and duration of the period of harassment. Whenever the judges noted a deterioration in the victim's mental health, they also referred to medical certificates reporting anxio-depressive syndromes or psychological disorders without providing further detail. No PTSD-like symptomatology was

  15. SPLAI: Computational Finite Element Model for Sensor Networks

    Directory of Open Access Journals (Sweden)

    Ruzana Ishak

    2006-01-01

    Full Text Available Wireless sensor network refers to a group of sensors, linked by a wireless medium to perform distributed sensing task. The primary interest is their capability in monitoring the physical environment through the deployment of numerous tiny, intelligent, wireless networked sensor nodes. Our interest consists of a sensor network, which includes a few specialized nodes called processing elements that can perform some limited computational capabilities. In this paper, we propose a model called SPLAI that allows the network to compute a finite element problem where the processing elements are modeled as the nodes in the linear triangular approximation problem. Our model also considers the case of some failures of the sensors. A simulation model to visualize this network has been developed using C++ on the Windows environment.

  16. New elements in production technology and operations

    International Nuclear Information System (INIS)

    Melberg, O.

    1995-01-01

    The title of this presentation embraces quite a wide scope, however, focus will be on Mobile Production Systems (MPSs) and in particular on Floating Production, Storage and Offloading Units (FPSOs), for which there is presently a remarkable boost in interest particularly in the North Sea area. Over the last 20 years, pioneered by the Argyll TW 58 in 1975, 11 mobile systems have been/are active in the North Sea, i.e. a growth of one for each second year. In 1994 alone a number of eight mobile production systems were contracted of which seven were FPSOs. This boost is following nine years of successful operation of the Petrojarl 1 and is also clearly linked to the success of the Kerr-McGee's Gryphon A project. The title of this presentation reflects new elements in this business; the upturn in interest for FPSOs introduces new ways of thinking and acting. In this paper, the new elements are divided into the general trends; new commercial elements and new technological elements

  17. A site-specific and multi-element isotopic approach to origin inference of sugars in foods and beverages

    International Nuclear Information System (INIS)

    Martin, M.L.; Martin, G.J.; Guillou, C.

    1991-01-01

    A strategy is presented for the characterization of sugars according to their botanical origin. The samples fermented in standardized conditions can be described in the multi-dimensional space of the overall carbon isotope ratio of ethanol measured by isotope ratio mass spectrometry (IRMS) and of the specific hydrogen isotope parameters of the methyl and methylene sites derived from nuclear magnetic resonance investigation of site-specific natural isotope fractionation (SNIF-NMR method). In the comparison of natural juices, the deuterium and oxygen-18 parameters of water extracted from the juice and from the end fermentation medium also contain information on the origin of the product. The isotopic effects of the concentration processes leading to concentrated juices, musts and syrups can be estimated and taken into account in interpreting the data. The classification power of this multi-element and multi-site approach is illustrated by discriminant analyses involving selected isotopic variables associated with pineapple, apple and barley sugars, compared to beet and cane sugars which are common sources of enrichment. The ability of the method to detect adulteration by exogenous sugars is improved when environmental conditions can be taken into account. (authors)

  18. TAL effectors specificity stems from negative discrimination.

    Directory of Open Access Journals (Sweden)

    Basile I M Wicky

    Full Text Available Transcription Activator-Like (TAL effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats with almost identical sequences. Most of the polymorphism is located at two consecutive amino acids termed Repeat Variable Diresidue (RVD. The discovery of a direct link between the RVD composition and the targeted nucleotide allowed the design of TAL-derived DNA-binding tools with programmable specificities that revolutionized the field of genome engineering. Despite structural data, the molecular origins of this specificity as well as the recognition mechanism have remained unclear. Molecular simulations of the recent crystal structures suggest that most of the protein-DNA binding energy originates from non-specific interactions between the DNA backbone and non-variable residues, while RVDs contributions are negligible. Based on dynamical and energetic considerations we postulate that, while the first RVD residue promotes helix breaks--allowing folding of TAL as a DNA-wrapping super-helix--the second provides specificity through a negative discrimination of matches. Furthermore, we propose a simple pharmacophore-like model for the rationalization of RVD-DNA interactions and the interpretation of experimental findings concerning shared affinities and binding efficiencies. The explanatory paradigm presented herein provides a better comprehension of this elegant architecture and we hope will allow for improved designs of TAL-derived biotechnological tools.

  19. Clinical Value of Specific Immunoglobulin E Detection by Enzyme-Linked Immunosorbent Assay in Cases of Acquired and Congenital Toxoplasmosis

    Science.gov (United States)

    Foudrinier, F.; Villena, I.; Jaussaud, R.; Aubert, D.; Chemla, C.; Martinot, F.; Pinon, J. M.

    2003-01-01

    The clinical value of immunoenzymatic (enzyme-linked immunosorbent assay) detection of anti-Toxoplasma immunoglobulin E (IgE) was assessed by studying 2,036 sera from 792 subjects, comprising seronegative controls and subjects with acute, active, reactivated, or congenital toxoplasmosis. Included were nonimmunized adults; pregnant women with recently acquired infection (acute toxoplasmosis); immunocompetent subjects with recently acquired severe infection (active toxoplasmosis) expressed as fever, adenopathies, splenomegaly, pneumonia, meningitis, or disseminated infection; subjects—some of them immunocompromised—whose previously moderate IgG antibody levels rose, suggesting a reactivation of quiescent toxoplasmosis; and infants born to seroconverted mothers and evaluated for diagnosis of congenital infection and therapeutic management. Specific IgE antibodies were never detected in seronegative subjects. They were present in 85.7% of asymptomatic seroconverters and in 100% of seroconverters with overt toxoplasmosis, following two different kinetics: in the former, the specific IgE titer generally presented a brief peak 2 to 3 months postinfection and then fell rapidly, whereas specific IgE persisted at a very high titer for several months in the latter. IgE emerged concomitantly with the increase in IgG during toxoplasmic reactivation. For neonatal diagnosis of congenital toxoplasmosis, IgE was less informative than IgM and IgA (sensitivities, 59.5, 64.3, and 76.2%, respectively) and had a specificity of 91.9%. Nevertheless, simultaneous measurement of the three isotypes at birth improved the diagnostic yield to 81% relative to the combination of IgA and IgM. Emergence of specific IgE during postnatal treatment for congenital toxoplasmosis is a sign of poor adherence or inadequate dosing. PMID:12682160

  20. APPLICATION OF RIGID LINKS IN STRUCTURAL DESIGN MODELS

    Directory of Open Access Journals (Sweden)

    Sergey Yu. Fialko

    2017-09-01

    Full Text Available A special finite element modelling rigid links is proposed for the linear static and buckling analysis. Unlike the classical approach based on the theorems of rigid body kinematics, the proposed approach preserves the similarity between the adjacency graph for a sparse matrix and the adjacency graph for nodes of the finite element model, which allows applying sparse direct solvers more effectively. Besides, the proposed approach allows significantly reducing the number of nonzero entries in the factored stiffness matrix in comparison with the classical one, which greatly reduces the duration of the solution. For buckling problems of structures containing rigid bodies, this approach gives correct results. Several examples demonstrate its efficiency.

  1. The EU network on trace element speciation in full swing

    DEFF Research Database (Denmark)

    Cornelis, R.; Camara, C.; Ebdon, L.

    2000-01-01

    health and hygiene. The network covers a number of important issues including organotin compounds, chromium and nickel species, chemical characterisation of environmental and industrial particulate samples, risk assessment, selenium and a series of other essential and toxic elements in food, as well......The EC-funded thematic network 'Speciation 21' links scientists in analytical chemistry working in method development for the chemical speciation of trace elements, and potential users from industry and representatives of legislative agencies, in the field of environment, food and occupational...

  2. A comparison of modern investment-linked pension savings products

    DEFF Research Database (Denmark)

    Linneman, Per; Bruhn, Kenneth; Steffensen, Mogens

    2015-01-01

    price changes in the financial market. Our results show that not only investment profiles define the stability of annuity benefits over time. In addition, more fundamental elements of the product design are important. The perspective on product design and development is Danish, but two of the compared......This paper is a continuation of and a supplement to the paper by Jørgensen & Linnemann. Both papers deal with TimePension – a (formula-based) smoothed investment-linked annuity pension scheme. Both papers compare TimePension with other pension savings products using stochastic financial simulation....... TimePension as well as the financial model and simulation concept being used in both papers were introduced in the paper op cit. Jørgensen & Linnemann compare TimePension with a traditional with-profits scheme involving bonus entitlement and an investment-linked Unit Link scheme with a fixed proportion...

  3. Traceability of Opuntia ficus-indica L. Miller by ICP-MS multi-element profile and chemometric approach.

    Science.gov (United States)

    Mottese, Antonio Francesco; Naccari, Clara; Vadalà, Rossella; Bua, Giuseppe Daniel; Bartolomeo, Giovanni; Rando, Rossana; Cicero, Nicola; Dugo, Giacomo

    2018-01-01

    Opuntia ficus-indica L. Miller fruits, particularly 'Ficodindia dell'Etna' of Biancavilla (POD), 'Fico d'india tradizionale di Roccapalumba' with protected brand and samples from an experimental field in Pezzolo (Sicily) were analyzed by inductively coupled plasma mass spectrometry in order to determine the multi-element profile. A multivariate chemometric approach, specifically principal component analysis (PCA), was applied to individuate how mineral elements may represent a marker of geographic origin, which would be useful for traceability. PCA has allowed us to verify that the geographical origin of prickly pear fruits is significantly influenced by trace element content, and the results found in Biancavilla PDO samples were linked to the geological composition of this volcanic areas. It was observed that two principal components accounted for 72.03% of the total variance in the data and, in more detail, PC1 explains 45.51% and PC2 26.52%, respectively. This study demonstrated that PCA is an integrated tool for the traceability of food products and, at the same time, a useful method of authentication of typical local fruits such as prickly pear. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  4. Modular verification of linked lists with views via separation logic

    DEFF Research Database (Denmark)

    Jensen, Jonas Braband; Birkedal, Lars; Sestoft, Peter

    2010-01-01

    We present a separation logic specification and verification of linked lists with views, a data structure from the C5 collection library for C#. A view is a generalization of the well-known concept of an iterator. Linked lists with views form an interesting case study for verification since...... mathematical model of lists with views, and formulate succinct modular abstract specifications of the operations on the data structure. To show that the concrete implementation realizes the specification, we use fractional permissions in a novel way to capture the sharing of data between views...

  5. Element-specific spectral imaging of multiple contrast agents: a phantom study

    Science.gov (United States)

    Panta, R. K.; Bell, S. T.; Healy, J. L.; Aamir, R.; Bateman, C. J.; Moghiseh, M.; Butler, A. P. H.; Anderson, N. G.

    2018-02-01

    This work demonstrates the feasibility of simultaneous discrimination of multiple contrast agents based on their element-specific and energy-dependent X-ray attenuation properties using a pre-clinical photon-counting spectral CT. We used a photon-counting based pre-clinical spectral CT scanner with four energy thresholds to measure the X-ray attenuation properties of various concentrations of iodine (9, 18 and 36 mg/ml), gadolinium (2, 4 and 8 mg/ml) and gold (2, 4 and 8 mg/ml) based contrast agents, calcium chloride (140 and 280 mg/ml) and water. We evaluated the spectral imaging performances of different energy threshold schemes between 25 to 82 keV at 118 kVp, based on K-factor and signal-to-noise ratio and ranked them. K-factor was defined as the X-ray attenuation in the K-edge containing energy range divided by the X-ray attenuation in the preceding energy range, expressed as a percentage. We evaluated the effectiveness of the optimised energy selection to discriminate all three contrast agents in a phantom of 33 mm diameter. A photon-counting spectral CT using four energy thresholds of 27, 33, 49 and 81 keV at 118 kVp simultaneously discriminated three contrast agents based on iodine, gadolinium and gold at various concentrations using their K-edge and energy-dependent X-ray attenuation features in a single scan. A ranking method to evaluate spectral imaging performance enabled energy thresholds to be optimised to discriminate iodine, gadolinium and gold contrast agents in a single spectral CT scan. Simultaneous discrimination of multiple contrast agents in a single scan is likely to open up new possibilities of improving the accuracy of disease diagnosis by simultaneously imaging multiple bio-markers each labelled with a nano-contrast agent.

  6. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms

    Directory of Open Access Journals (Sweden)

    Xin-Ping Wu

    2018-05-01

    Full Text Available Combined quantum mechanical and molecular mechanical (QM/MM methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

  7. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.

    Science.gov (United States)

    Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

    2018-05-30

    Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

  8. The substance use risk profile scale: a scale measuring traits linked to reinforcement-specific substance use profiles.

    Energy Technology Data Exchange (ETDEWEB)

    Woicik, P.A.; Stewart, S.H.; Pihl, R.O.; Conrod, P.J.

    2009-12-01

    The Substance Use Risk Profile Scale (SURPS) is based on a model of personality risk for substance abuse in which four personality dimensions (hopelessness, anxiety sensitivity, impulsivity, and sensation seeking) are hypothesized to differentially relate to specific patterns of substance use. The current series of studies is a preliminary exploration of the psychometric properties of the SURPS in two populations (undergraduate and high school students). In study 1, an analysis of the internal structure of two versions of the SURPS shows that the abbreviated version best reflects the 4-factor structure. Concurrent, discriminant, and incremental validity of the SURPS is supported by convergent/divergent relationships between the SURPS subscales and other theoretically relevant personality and drug use criterion measures. In Study 2, the factorial structure of the SURPS is confirmed and evidence is provided for its test-retest reliability and validity with respect to measuring personality vulnerability to reinforcement-specific substance use patterns. In Study 3, the SURPS was administered in a more youthful population to test its sensitivity in identifying younger problematic drinkers. The results from the current series of studies demonstrate support for the reliability and construct validity of the SURPS, and suggest that four personality dimensions may be linked to substance-related behavior through different reinforcement processes. This brief assessment tool may have important implications for clinicians and future research.

  9. Biocatalytic cross-linking of pectic polysaccharides for designed food functionality

    DEFF Research Database (Denmark)

    Zaidel, Dayang Norulfairuz Abang; Meyer, Anne S.

    2012-01-01

    the mechanisms of formation of functional pectic polysaccharide cross-links, including covalent cross-links (notably phenolic esters and uronyl ester linkages) and non-covalent, ionic cross-links (which involve calcium and borate ester links). The treatise examines how such cross-links can be designed via......Recent research has demonstrated how cross-linking of pectic polysaccharides to obtain gel formation can be promoted by enzymatic catalysis reactions, and provide opportunities for functional upgrading of pectic polysaccharides present in agro-industrial sidestreams. This review highlights...... specific enzymatic reactions, and highlights the most recent data concerning enzyme catalyzed engineering of cross-links for in situ structural design of functional properties of foods....

  10. Identification of hookworm DAF-16/FOXO response elements and direct gene targets.

    Directory of Open Access Journals (Sweden)

    Xin Gao

    2010-08-01

    Full Text Available The infective stage of the parasitic nematode hookworm is developmentally arrested in the environment and needs to infect a specific host to complete its life cycle. The canine hookworm (Ancylostoma caninum is an excellent model for investigating human hookworm infections. The transcription factor of A. caninum, Ac-DAF-16, which has a characteristic fork head or "winged helix" DNA binding domain (DBD, has been implicated in the resumption of hookworm development in the host. However, the precise roles of Ac-DAF-16 in hookworm parasitism and its downstream targets are unknown. In the present study, we combined molecular techniques and bioinformatics to identify a group of Ac-DAF-16 binding sites and target genes.The DNA binding domain of Ac-DAF-16 was used to select genomic fragments by in vitro genomic selection. Twenty four bound genomic fragments were analyzed for the presence of the DAF-16 family binding element (DBE and possible alternative Ac-DAF-16 bind motifs. The 22 genes linked to these genomic fragments were identified using bioinformatics tools and defined as candidate direct gene targets of Ac-DAF-16. Their developmental stage-specific expression patterns were examined. Also, a new putative DAF-16 binding element was identified.Our results show that Ac-DAF-16 is involved in diverse biological processes throughout hookworm development. Further investigation of these target genes will provide insights into the molecular basis by which Ac-DAF-16 regulates its downstream gene network in hookworm infection.

  11. Primary stability of a cementless acetabular cup in a cohort of patient-specific finite element models.

    Science.gov (United States)

    O'Rourke, Dermot; Al-Dirini, Rami Ma; Taylor, Mark

    2018-03-01

    The primary stability achieved during total hip arthroplasty determines the long-term success of cementless acetabular cups. Pre-clinical finite element testing of cups typically use a model of a single patient and assume the results can be extrapolated to the general population. This study explored the variability in predicted primary stability of a Pinnacle ® cementless acetabular cup in 103 patient-specific finite element models of the hemipelvis and examined the association between patient-related factors and the observed variability. Cups were inserted by displacement-control into the FE models and then a loading configuration simulating a complete level gait cycle was applied. The cohort showed a range of polar gap of 284-1112 μm and 95th percentile composite peak micromotion (CPM) of 18-624 μm. Regression analysis was not conclusive on the relationship between patient-related factors and primary stability. No relationship was found between polar gap and micromotion. However, when the patient-related factors were categorised into quartile groups, trends suggested higher polar gaps occurred in subjects with small and shallow acetabular geometries and cup motion during gait was affected most by low elastic modulus and high bodyweight. The variation in primary stability in the cohort for an acetabular cup with a proven clinical track record may provide benchmark data when evaluating new cup designs. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1012-1023, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  12. Cooperative action of multiple cis-acting elements is required for N-myc expression in branchial arches: specific contribution of GATA3.

    Science.gov (United States)

    Potvin, Eric; Beuret, Laurent; Cadrin-Girard, Jean-François; Carter, Marcelle; Roy, Sophie; Tremblay, Michel; Charron, Jean

    2010-11-01

    The precise expression of the N-myc proto-oncogene is essential for normal mammalian development, whereas altered N-myc gene regulation is known to be a determinant factor in tumor formation. Using transgenic mouse embryos, we show that N-myc sequences from kb -8.7 to kb +7.2 are sufficient to reproduce the N-myc embryonic expression profile in developing branchial arches and limb buds. These sequences encompass several regulatory elements dispersed throughout the N-myc locus, including an upstream limb bud enhancer, a downstream somite enhancer, a branchial arch enhancer in the second intron, and a negative regulatory element in the first intron. N-myc expression in the limb buds is under the dominant control of the limb bud enhancer. The expression in the branchial arches necessitates the interplay of three regulatory domains. The branchial arch enhancer cooperates with the somite enhancer region to prevent an inhibitory activity contained in the first intron. The characterization of the branchial arch enhancer has revealed a specific role of the transcription factor GATA3 in the regulation of N-myc expression. Together, these data demonstrate that correct N-myc developmental expression is achieved via cooperation of multiple positive and negative regulatory elements.

  13. Non-Linear Three Dimensional Finite Elements for Composite Concrete Structures

    Directory of Open Access Journals (Sweden)

    O. Kohnehpooshi

    Full Text Available Abstract The current investigation focused on the development of effective and suitable modelling of reinforced concrete component with and without strengthening. The modelling includes physical and constitutive models. New interface elements have been developed, while modified constitutive law have been applied and new computational algorithm is utilised. The new elements are the Truss-link element to model the interaction between concrete and reinforcement bars, the interface element between two plate bending elements and the interface element to represent the interfacial behaviour between FRP, steel plates and concrete. Nonlinear finite-element (FE codes were developed with pre-processing. The programme was written using FORTRAN language. The accuracy and efficiency of the finite element programme were achieved by analyzing several examples from the literature. The application of the 3D FE code was further enhanced by carrying out the numerical analysis of the three dimensional finite element analysis of FRP strengthened RC beams, as well as the 3D non-linear finite element analysis of girder bridge. Acceptable distributions of slip, deflection, stresses in the concrete and FRP plate have also been found. These results show that the new elements are effective and appropriate to be used for structural component modelling.

  14. Comparison of computed tomography based parametric and patient-specific finite element models of the healthy and metastatic spine using a mesh-morphing algorithm.

    Science.gov (United States)

    O'Reilly, Meaghan Anne; Whyne, Cari Marisa

    2008-08-01

    A comparative analysis of parametric and patient-specific finite element (FE) modeling of spinal motion segments. To develop patient-specific FE models of spinal motion segments using mesh-morphing methods applied to a parametric FE model. To compare strain and displacement patterns in parametric and morphed models for both healthy and metastatically involved vertebrae. Parametric FE models may be limited in their ability to fully represent patient-specific geometries and material property distributions. Generation of multiple patient-specific FE models has been limited because of computational expense. Morphing methods have been successfully used to generate multiple specimen-specific FE models of caudal rat vertebrae. FE models of a healthy and a metastatic T6-T8 spinal motion segment were analyzed with and without patient-specific material properties. Parametric and morphed models were compared using a landmark-based morphing algorithm. Morphing of the parametric FE model and including patient-specific material properties both had a strong impact on magnitudes and patterns of vertebral strain and displacement. Small but important geometric differences can be represented through morphing of parametric FE models. The mesh-morphing algorithm developed provides a rapid method for generating patient-specific FE models of spinal motion segments.

  15. LOD BIM Element specification for Railway Turnout Systems Risk Mitigation using the Information Delivery Manual

    Science.gov (United States)

    Gigante-Barrera, Ángel; Dindar, Serdar; Kaewunruen, Sakdirat; Ruikar, Darshan

    2017-10-01

    Railway turnouts are complex systems designed using complex geometries and grades which makes them difficult to be managed in terms of risk prevention. This feature poses a substantial peril to rail users as it is considered a cause of derailment. In addition, derailment deals to financial losses due to operational downtimes and monetary compensations in case of death or injure. These are fundamental drivers to consider mitigating risks arising from poor risk management during design. Prevention through design (PtD) is a process that introduces tacit knowledge from industry professionals during the design process. There is evidence that Building Information Modelling (BIM) can help to mitigate risk since the inception of the project. BIM is considered an Information System (IS) were tacit knowledge can be stored and retrieved from a digital database making easy to take promptly decisions as information is ready to be analysed. BIM at the model element level entails working with 3D elements and embedded data, therefore adding a layer of complexity to the management of information along the different stages of the project and across different disciplines. In order to overcome this problem, the industry has created a framework for model progression specification named Level of Development (LOD). The paper presents an IDM based framework for design risk mitigation through code validation using the LOD. This effort resulted on risk datasets which describe graphically and non-graphically a rail turnout as the model progresses. Thus, permitting its inclusion within risk information systems. The assignment of an LOD construct to a set of data, requires specialised management and process related expertise. Furthermore, the selection of a set of LOD constructs requires a purpose based analysis. Therefore, a framework for LOD constructs implementation within the IDM for code checking is required for the industry to progress in this particular field.

  16. Bit-error-rate testing of fiber optic data links for MMIC-based phased array antennas

    Science.gov (United States)

    Shalkhauser, K. A.; Kunath, R. R.; Daryoush, A. S.

    1990-01-01

    The measured bit-error-rate (BER) performance of a fiber optic data link to be used in satellite communications systems is presented and discussed. In the testing, the link was measured for its ability to carry high burst rate, serial-minimum shift keyed (SMSK) digital data similar to those used in actual space communications systems. The fiber optic data link, as part of a dual-segment injection-locked RF fiber optic link system, offers a means to distribute these signals to the many radiating elements of a phased array antenna. Test procedures, experimental arrangements, and test results are presented.

  17. Bit error rate testing of fiber optic data links for MMIC-based phased array antennas

    Science.gov (United States)

    Shalkhauser, K. A.; Kunath, R. R.; Daryoush, A. S.

    1990-01-01

    The measured bit-error-rate (BER) performance of a fiber optic data link to be used in satellite communications systems is presented and discussed. In the testing, the link was measured for its ability to carry high burst rate, serial-minimum shift keyed (SMSK) digital data similar to those used in actual space communications systems. The fiber optic data link, as part of a dual-segment injection-locked RF fiber optic link system, offers a means to distribute these signals to the many radiating elements of a phased array antenna. Test procedures, experimental arrangements, and test results are presented.

  18. A real-time PCR assay with improved specificity for detection and discrimination of all clinically relevant Bordetella species by the presence and distribution of three Insertion Sequence elements

    Directory of Open Access Journals (Sweden)

    Ossewaarde Jacobus M

    2011-01-01

    Full Text Available Abstract Background In Dutch laboratories molecular detection of B. pertussis and B. parapertussis is commonly based on insertion sequences IS481 and IS1001, respectively. Both IS elements are more widely spread among Bordetella species. Both Bordetella holmesii, and B. bronchiseptica can harbour IS481. Also, IS1001 is found among B. bronchiseptica. IS481, and IS1001 based PCR thus lacks specificity when used for detection of specific Bordetella spp. Findings We designed a PCR based on IS1002, another IS element that is present among Bordetella species, and exploited it as a template in combination with PCR for IS481, and IS1001. In combining the PCRs for IS481, IS1001, and IS1002, and including an inhibition control, we were able to detect and discriminate all clinically relevant Bordetella species. Conclusions We developed an improved PCR method for specific detection of B. pertussis, B. parapertussis, B. holmesii, and B. bronchiseptica.

  19. Is Case-Specificity Content-Specificity? An Analysis of Data from Extended-Matching Questions

    Science.gov (United States)

    Dory, Valerie; Gagnon, Robert; Charlin, Bernard

    2010-01-01

    Case-specificity, i.e., variability of a subject's performance across cases, has been a consistent finding in medical education. It has important implications for assessment validity and reliability. Its root causes remain a matter of discussion. One hypothesis, content-specificity, links variability of performance to variable levels of relevant…

  20. The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15.

    Science.gov (United States)

    Ahmed, Zubair M; Goodyear, Richard; Riazuddin, Saima; Lagziel, Ayala; Legan, P Kevin; Behra, Martine; Burgess, Shawn M; Lilley, Kathryn S; Wilcox, Edward R; Riazuddin, Sheikh; Griffith, Andrew J; Frolenkov, Gregory I; Belyantseva, Inna A; Richardson, Guy P; Friedman, Thomas B

    2006-06-28

    Sound and acceleration are detected by hair bundles, mechanosensory structures located at the apical pole of hair cells in the inner ear. The different elements of the hair bundle, the stereocilia and a kinocilium, are interconnected by a variety of link types. One of these links, the tip link, connects the top of a shorter stereocilium with the lateral membrane of an adjacent taller stereocilium and may gate the mechanotransducer channel of the hair cell. Mass spectrometric and Western blot analyses identify the tip-link antigen, a hitherto unidentified antigen specifically associated with the tip and kinocilial links of sensory hair bundles in the inner ear and the ciliary calyx of photoreceptors in the eye, as an avian ortholog of human protocadherin-15, a product of the gene for the deaf/blindness Usher syndrome type 1F/DFNB23 locus. Multiple protocadherin-15 transcripts are shown to be expressed in the mouse inner ear, and these define four major isoform classes, two with entirely novel, previously unidentified cytoplasmic domains. Antibodies to the three cytoplasmic domain-containing isoform classes reveal that each has a different spatiotemporal expression pattern in the developing and mature inner ear. Two isoforms are distributed in a manner compatible for association with the tip-link complex. An isoform located at the tips of stereocilia is sensitive to calcium chelation and proteolysis with subtilisin and reappears at the tips of stereocilia as transduction recovers after the removal of calcium chelators. Protocadherin-15 is therefore associated with the tip-link complex and may be an integral component of this structure and/or required for its formation.

  1. Patient-specific reconstruction plates are the missing link in computer-assisted mandibular reconstruction: A showcase for technical description.

    Science.gov (United States)

    Cornelius, Carl-Peter; Smolka, Wenko; Giessler, Goetz A; Wilde, Frank; Probst, Florian A

    2015-06-01

    Preoperative planning of mandibular reconstruction has moved from mechanical simulation by dental model casts or stereolithographic models into an almost completely virtual environment. CAD/CAM applications allow a high level of accuracy by providing a custom template-assisted contouring approach for bone flaps. However, the clinical accuracy of CAD reconstruction is limited by the use of prebent reconstruction plates, an analogue step in an otherwise digital workstream. In this paper the integration of computerized, numerically-controlled (CNC) milled, patient-specific mandibular plates (PSMP) within the virtual workflow of computer-assisted mandibular free fibula flap reconstruction is illustrated in a clinical case. Intraoperatively, the bone segments as well as the plate arms showed a very good fit. Postoperative CT imaging demonstrated close approximation of the PSMP and fibular segments, and good alignment of native mandible and fibular segments and intersegmentally. Over a follow-up period of 12 months, there was an uneventful course of healing with good bony consolidation. The virtual design and automated fabrication of patient-specific mandibular reconstruction plates provide the missing link in the virtual workflow of computer-assisted mandibular free fibula flap reconstruction. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  2. Defining the Sequence Elements and Candidate Genes for the Coloboma Mutation.

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Robb

    Full Text Available The chicken coloboma mutation exhibits features similar to human congenital developmental malformations such as ocular coloboma, cleft-palate, dwarfism, and polydactyly. The coloboma-associated region and encoded genes were investigated using advanced genomic, genetic, and gene expression technologies. Initially, the mutation was linked to a 990 kb region encoding 11 genes; the application of the genetic and genomic tools led to a reduction of the linked region to 176 kb and the elimination of 7 genes. Furthermore, bioinformatics analyses of capture array-next generation sequence data identified genetic elements including SNPs, insertions, deletions, gaps, chromosomal rearrangements, and miRNA binding sites within the introgressed causative region relative to the reference genome sequence. Coloboma-specific variants within exons, UTRs, and splice sites were studied for their contribution to the mutant phenotype. Our compiled results suggest three genes for future studies. The three candidate genes, SLC30A5 (a zinc transporter, CENPH (a centromere protein, and CDK7 (a cyclin-dependent kinase, are differentially expressed (compared to normal embryos at stages and in tissues affected by the coloboma mutation. Of these genes, two (SLC30A5 and CENPH are considered high-priority candidate based upon studies in other vertebrate model systems.

  3. Decreased N-TAF1 expression in X-linked dystonia-parkinsonism patient-specific neural stem cells

    Directory of Open Access Journals (Sweden)

    Naoto Ito

    2016-04-01

    Full Text Available X-linked dystonia-parkinsonism (XDP is a hereditary neurodegenerative disorder involving a progressive loss of striatal medium spiny neurons. The mechanisms underlying neurodegeneration are not known, in part because there have been few cellular models available for studying the disease. The XDP haplotype consists of multiple sequence variations in a region of the X chromosome containing TAF1, a large gene with at least 38 exons, and a multiple transcript system (MTS composed of five unconventional exons. A previous study identified an XDP-specific insertion of a SINE-VNTR-Alu (SVA-type retrotransposon in intron 32 of TAF1, as well as a neural-specific TAF1 isoform, N-TAF1, which showed decreased expression in post-mortem XDP brain compared with control tissue. Here, we generated XDP patient and control fibroblasts and induced pluripotent stem cells (iPSCs in order to further probe cellular defects associated with this disease. As initial validation of the model, we compared expression of TAF1 and MTS transcripts in XDP versus control fibroblasts and iPSC-derived neural stem cells (NSCs. Compared with control cells, XDP fibroblasts exhibited decreased expression of TAF1 transcript fragments derived from exons 32-36, a region spanning the SVA insertion site. N-TAF1, which incorporates an alternative exon (exon 34′, was not expressed in fibroblasts, but was detectable in iPSC-differentiated NSCs at levels that were ∼threefold lower in XDP cells than in controls. These results support the previous findings that N-TAF1 expression is impaired in XDP, but additionally indicate that this aberrant transcription might occur in neural cells at relatively early stages of development that precede neurodegeneration.

  4. Transcriptional activity of transposable elements in coelacanth.

    Science.gov (United States)

    Forconi, Mariko; Chalopin, Domitille; Barucca, Marco; Biscotti, Maria Assunta; De Moro, Gianluca; Galiana, Delphine; Gerdol, Marco; Pallavicini, Alberto; Canapa, Adriana; Olmo, Ettore; Volff, Jean-Nicolas

    2014-09-01

    The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity. © 2013 Wiley Periodicals, Inc.

  5. High resolution bone material property assignment yields robust subject specific finite element models of complex thin bone structures.

    Science.gov (United States)

    Pakdel, Amirreza; Fialkov, Jeffrey; Whyne, Cari M

    2016-06-14

    Accurate finite element (FE) modeling of complex skeletal anatomy requires high resolution in both meshing and the heterogeneous mapping of material properties onto the generated mesh. This study introduces Node-based elastic Modulus Assignment with Partial-volume correction (NMAP) as a new approach for FE material property assignment to thin bone structures. The NMAP approach incorporates point spread function based deblurring of CT images, partial-volume correction of CT image voxel intensities and anisotropic interpolation and mapping of CT intensity assignment to FE mesh nodes. The NMAP procedure combined with a derived craniomaxillo-facial skeleton (CMFS) specific density-isotropic elastic modulus relationship was applied to produce specimen-specific FE models of 6 cadaveric heads. The NMAP procedure successfully generated models of the complex thin bone structures with surface elastic moduli reflective of cortical bone material properties. The specimen-specific CMFS FE models were able to accurately predict experimental strains measured under in vitro temporalis and masseter muscle loading (r=0.93, slope=1.01, n=5). The strength of this correlation represents a robust validation for CMFS FE modeling that can be used to better understand load transfer in this complex musculoskeletal system. The developed methodology offers a systematic process-flow able to address the complexity of the CMFS that can be further applied to create high-fidelity models of any musculoskeletal anatomy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Study of Finite Element Number Influence over the Obtained Results in Finite Element Analyses of a Mechanical Structure

    Directory of Open Access Journals (Sweden)

    Ana-Maria Budai

    2013-05-01

    Full Text Available This paper present the results of a study that was made to establish the influence of finite element number used to determined the real load of a structure. Actually, the study represent a linear static analyze for a link gear control mechanism of a Kaplan turbine. The all analyze was made for the normal condition of functioning having like final scope to determine de life time duration of mentioned mechanism.

  7. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci.

    Science.gov (United States)

    Coetzee, Simon G; Shen, Howard C; Hazelett, Dennis J; Lawrenson, Kate; Kuchenbaecker, Karoline; Tyrer, Jonathan; Rhie, Suhn K; Levanon, Keren; Karst, Alison; Drapkin, Ronny; Ramus, Susan J; Couch, Fergus J; Offit, Kenneth; Chenevix-Trench, Georgia; Monteiro, Alvaro N A; Antoniou, Antonis; Freedman, Matthew; Coetzee, Gerhard A; Pharoah, Paul D P; Noushmehr, Houtan; Gayther, Simon A

    2015-07-01

    Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. Dynamic Training Elements in a Circuit Theory Course to Implement a Self-Directed Learning Process

    Science.gov (United States)

    Krouk, B. I.; Zhuravleva, O. B.

    2009-01-01

    This paper reports on the implementation of a self-directed learning process in a circuit theory course, incorporating dynamic training elements which were designed on the basis of a cybernetic model of cognitive process management. These elements are centrally linked in a dynamic learning frame, created on the monitor screen, which displays the…

  9. Elements of banking intermediation in the Algerian Banking system and the means to activate it

    Directory of Open Access Journals (Sweden)

    Habbar Abderezak, Dr.

    2014-06-01

    Banking intermediation raises several interrelated issues for banks, the central bank and the Treasury. It is linked to the gross domestic product, money supply and bank liquidity, etc. These elements will be examined in this article to learn the elements of bank intermediation in the Algerian banking system and ways of strengthening it.

  10. Chemistry of the transactinide elements

    International Nuclear Information System (INIS)

    Schaedel, M.

    1995-01-01

    The experimentally known chemical properties of the transactinide elements 104 and 105, and the experimental techniques used to study these properties on an atom-at-a-time base, are reviewed. The production of transactinides in heavy ion reactions and the specific aspects of chemical separations with single atoms is briefly discussed. The chemical properties of the first two transactinide elements are compared with the lighter element homologs in group 4 and 5 of the Periodic Table and with the expected behaviour obtained from most recent atomic and molecular calculations which take the increasingly strong relativistic effect into account. Elements 104 and 105 behave as transactinide elements and, in general, exhibit properties characteristic of their position in group 4 and 5 of the Periodic Table. However, surprising deviations of the chemical properties from expectations based on simple extrapolations have been observed. It is shown that the chemical properties of the heaviest elements cannot reliably be predicted by simple extrapolations. Prospects to extend our chemical knowledge at the top end of the Periodic Table are discussed. (orig.)

  11. Pemodelan Matematika Premi Tunggal Bersih Asuransi Unit Link Syariah

    Directory of Open Access Journals (Sweden)

    Nanang Supriadi

    2017-12-01

    Full Text Available The exact risk factor can be managed by transferring the risk to the other party (in this case the insurance company. In this paper will be discussed more life insurance, as the development now there are types of insurance combined with investment, which is popular with the term Unit Link insurance. Unit link Syariah began to be launched as one of the fulfilment of the high needs of the community, the privilege of the product Unit of Islamic links is actually located in the elements of the laws in accordance with Islamic Syariah. The issues that will be discussed are how to get a single premium model of life insurance unit link Syariah with life insurance and investment fund allocation invested in investment product with a big interest rate of risk (financial approach and investment product with the value of return maximum (actuarial approach. The resulting model is then implemented in case of examples by comparing the two approaches to see the shortcomings and advantages of Unit link lifetime life insurance when compared to life insurance. The result obtained from this research is the benefit obtained from Unit-linked sharia insurance on average will be greater if compared with life insurance for life, maximum benefit will be obtained Insurance Unit Link of sharia using actuarial approach compared to financial, but benefit with a relative financial approach more stable than actuarial approaches that tend to fluctuate.

  12. The High Rise Low Cost Housing : Sustainable Neighbourhood Elements (Green Elements) in Malaysia

    Science.gov (United States)

    Wahi, Noraziah; Mohamad, Ismail; Mohamad Zin, Rosli; Munikanan, Vikneswaran; Junaini, Syahrizan

    2018-03-01

    The sustainable development is a vital measure to alleviate the greenhouse gas effect, global warming and any other environment issues. The sustainable neighbourhood concept is not new in Malaysia, However, the concept still needs attention and awareness from the stakeholders. This paper discusses on the sustainable neighbourhood elements specifically green elements application on the high rise low cost housing in Malaysia. Malaysia should have focused sustainable neighbourhood planning and design especially on the high rise low cost housing therefore the future generation can be benefited from this type development.

  13. Semantic Web: Metadata, Linked Data, Open Data

    Directory of Open Access Journals (Sweden)

    Vanessa Russo

    2015-12-01

    Full Text Available What's the Semantic Web? What's the use? The inventor of the Web Tim Berners-Lee describes it as a research methodology able to take advantage of the network to its maximum capacity. This metadata system represents the innovative element through web 2.0 to web 3.0. In this context will try to understand what are the theoretical and informatic requirements of the Semantic Web. Finally will explain Linked Data applications to develop new tools for active citizenship.

  14. The evolution of ultraconserved elements with different phylogenetic origins

    KAUST Repository

    Ryu, Tae Woo

    2012-12-05

    Background: Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results: Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion: We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors. 2012 Ryu et al.; licensee BioMed Central Ltd.

  15. Novel IgG-Degrading Enzymes of the IgdE Protease Family Link Substrate Specificity to Host Tropism of Streptococcus Species.

    Science.gov (United States)

    Spoerry, Christian; Hessle, Pontus; Lewis, Melanie J; Paton, Lois; Woof, Jenny M; von Pawel-Rammingen, Ulrich

    2016-01-01

    Recently we have discovered an IgG degrading enzyme of the endemic pig pathogen S. suis designated IgdE that is highly specific for porcine IgG. This protease is the founding member of a novel cysteine protease family assigned C113 in the MEROPS peptidase database. Bioinformatical analyses revealed putative members of the IgdE protease family in eight other Streptococcus species. The genes of the putative IgdE family proteases of S. agalactiae, S. porcinus, S. pseudoporcinus and S. equi subsp. zooepidemicus were cloned for production of recombinant protein into expression vectors. Recombinant proteins of all four IgdE family proteases were proteolytically active against IgG of the respective Streptococcus species hosts, but not against IgG from other tested species or other classes of immunoglobulins, thereby linking the substrate specificity to the known host tropism. The novel IgdE family proteases of S. agalactiae, S. pseudoporcinus and S. equi showed IgG subtype specificity, i.e. IgdE from S. agalactiae and S. pseudoporcinus cleaved human IgG1, while IgdE from S. equi was subtype specific for equine IgG7. Porcine IgG subtype specificities of the IgdE family proteases of S. porcinus and S. pseudoporcinus remain to be determined. Cleavage of porcine IgG by IgdE of S. pseudoporcinus is suggested to be an evolutionary remaining activity reflecting ancestry of the human pathogen to the porcine pathogen S. porcinus. The IgG subtype specificity of bacterial proteases indicates the special importance of these IgG subtypes in counteracting infection or colonization and opportunistic streptococci neutralize such antibodies through expression of IgdE family proteases as putative immune evasion factors. We suggest that IgdE family proteases might be valid vaccine targets against streptococci of both human and veterinary medical concerns and could also be of therapeutic as well as biotechnological use.

  16. Automated Fuel Element Closure Welding System

    International Nuclear Information System (INIS)

    Wahlquist, D.R.

    1993-01-01

    The Automated Fuel Element Closure Welding System is a robotic device that will load and weld top end plugs onto nuclear fuel elements in a highly radioactive and inert gas environment. The system was developed at Argonne National Laboratory-West as part of the Fuel Cycle Demonstration. The welding system performs four main functions, it (1) injects a small amount of a xenon/krypton gas mixture into specific fuel elements, and (2) loads tiny end plugs into the tops of fuel element jackets, and (3) welds the end plugs to the element jackets, and (4) performs a dimensional inspection of the pre- and post-welded fuel elements. The system components are modular to facilitate remote replacement of failed parts. The entire system can be operated remotely in manual, semi-automatic, or fully automatic modes using a computer control system. The welding system is currently undergoing software testing and functional checkout

  17. Efficient Identification of Objects Carrying Elements of High-Order Symmetry By Using Correlated Orbital Angular Momentum (OAM States

    Directory of Open Access Journals (Sweden)

    Sergienko Alexander V.

    2014-01-01

    The potential for efficient identification of objects carrying elements of high-order symmetry using correlated orbital angular momentum (OAM states is demonstrated. The enhanced information capacity of this approach allows the recognition of specific spatial symmetry signatures present in objects with the use of fewer resources than in a conventional pixel-by-pixel imaging, representing the first demonstration of compressive sensing using OAM states. This approach demonstrates the capability to quickly evaluate multiple Fourier coefficients directly linked with the symmetry features of the object. The results suggest further application in small-scale biological contexts where symmetry and small numbers of noninvasive measurements are important.

  18. Chicken IgY Fc linked to Bordetella avium ompA and Taishan Pinus massoniana pollen polysaccharide adjuvant enhances macrophage function and specific immune responses

    Directory of Open Access Journals (Sweden)

    Zhu Ruiliang

    2016-11-01

    Full Text Available Fc-fusion technologies, in which immunoglobulin Fc is genetically fused to an antigenic protein, have been developed to confer antibody-like properties to proteins and peptides. Mammalian IgG Fc fusion exhibits improved antigen-induced immune responses by providing aggregates with high avidity for the IgG Fc receptor and salvaging the antigenic portion from endosomal degradation. However, whether the linked chicken IgY Fc fragment shares similar characteristics to mammalian IgG Fc remains unclear. In this study, we linked the chicken IgY Fc gene to the outer membrane protein A (ompA of Borderella avium through overlapping PCR. The fusion gene was cloned into the pPIC9 plasmid to construct the recombinant Pichia pastoris transformant expressing the ompA–Fc fusion protein. The effects of the linked Fc on macrophage vitality, activity, efficiency of antigen processing, and immune responses induced by the fused ompA were investigated. Furthermore, the effect of Taishan Pinus massoniana pollen polysaccharide (TPPPS, an immunomodulator, on chicken macrophage activation was evaluated. TPPPS was also used as an adjuvant to investigate its immunomodulatory effect on immunoresponses induced by the fused ompA–Fc in chickens. The pinocytosis, phagocytosis, secretion of nitric oxide and TNF-α, and MHC-II molecular expression of the macrophages treated with the fused ompA–Fc were significantly higher than those of the macrophages treated with ompA alone. The addition of TPPPS to the fused ompA–Fc further enhanced macrophage functions. The fused ompA–Fc elicited higher antigen-specific immune responses and protective efficacy compared with ompA alone. Moreover, the fused ompA–Fc conferred higher serum antibody titers, serum IL-2 and IL-4 concentrations, CD4+ and CD8+ T-lymphocyte counts, lymphocyte transformation rate, and protection rate compared with ompA alone. Notably, the prepared TPPPS adjuvant ompA–Fc vaccines induced high immune

  19. Local Type Checking for Linked Data Consumers

    Directory of Open Access Journals (Sweden)

    Gabriel Ciobanu

    2013-07-01

    Full Text Available The Web of Linked Data is the cumulation of over a decade of work by the Web standards community in their effort to make data more Web-like. We provide an introduction to the Web of Linked Data from the perspective of a Web developer that would like to build an application using Linked Data. We identify a weakness in the development stack as being a lack of domain specific scripting languages for designing background processes that consume Linked Data. To address this weakness, we design a scripting language with a simple but appropriate type system. In our proposed architecture some data is consumed from sources outside of the control of the system and some data is held locally. Stronger type assumptions can be made about the local data than external data, hence our type system mixes static and dynamic typing. Throughout, we relate our work to the W3C recommendations that drive Linked Data, so our syntax is accessible to Web developers.

  20. Statistic analysis of grouping in evaluation of the behavior of stable chemical elements and physical-chemical parameters in effluent from uranium mining

    International Nuclear Information System (INIS)

    Pereira, Wagner de S.

    2013-01-01

    The Ore Treatment Unit (UTM) is a uranium mine off. The statistical analysis of clustering was used to evaluate the behavior of stable chemical elements and physico-chemical variables in their effluents. The use of cluster analysis proved effective in the evaluation, allowing to identify groups of chemical elements in physico-chemical variables and group analyzes (element and variables ). As a result, we can say, based on the analysis of the data, a strong link between Ca and Mg and between Al and TR 2 O 3 (rare earth oxides) in the UTM effluents. The SO 4 was also identified as strongly linked to total solids and dissolved and these linked to electrical conductivity. Other associations existed, but were not as strongly linked. Additional collections for seasonal evaluation are required so that assessments can be confirmed. Additional statistics analysis (ordination techniques) should be used to help identify the origins of the groups identified in this analysis. (author)

  1. Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

    Science.gov (United States)

    Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

    2017-02-01

    Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  2. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  3. A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression.

    Directory of Open Access Journals (Sweden)

    Leonie Alten

    Full Text Available The vertebrate organizer and notochord have conserved, essential functions for embryonic development and patterning. The restricted expression of developmental regulators in these tissues is directed by specific cis-regulatory modules (CRMs whose sequence conservation varies considerably. Some CRMs have been conserved throughout vertebrates and likely represent ancestral regulatory networks, while others have diverged beyond recognition but still function over a wide evolutionary range. Here we identify and characterize a mammalian-specific CRM required for node and notochord specific (NNC expression of NOTO, a transcription factor essential for node morphogenesis, nodal cilia movement and establishment of laterality in mouse. A 523 bp enhancer region (NOCE upstream the Noto promoter was necessary and sufficient for NNC expression from the endogenous Noto locus. Three subregions in NOCE together mediated full activity in vivo. Binding sites for known transcription factors in NOCE were functional in vitro but dispensable for NOCE activity in vivo. A FOXA2 site in combination with a novel motif was necessary for NOCE activity in vivo. Strikingly, syntenic regions in non-mammalian vertebrates showed no recognizable sequence similarities. In contrast to its activity in mouse NOCE did not drive NNC expression in transgenic fish. NOCE represents a novel, mammal-specific CRM required for the highly restricted Noto expression in the node and nascent notochord and thus regulates normal node development and function.

  4. A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression.

    Science.gov (United States)

    Alten, Leonie; Schuster-Gossler, Karin; Eichenlaub, Michael P; Wittbrodt, Beate; Wittbrodt, Joachim; Gossler, Achim

    2012-01-01

    The vertebrate organizer and notochord have conserved, essential functions for embryonic development and patterning. The restricted expression of developmental regulators in these tissues is directed by specific cis-regulatory modules (CRMs) whose sequence conservation varies considerably. Some CRMs have been conserved throughout vertebrates and likely represent ancestral regulatory networks, while others have diverged beyond recognition but still function over a wide evolutionary range. Here we identify and characterize a mammalian-specific CRM required for node and notochord specific (NNC) expression of NOTO, a transcription factor essential for node morphogenesis, nodal cilia movement and establishment of laterality in mouse. A 523 bp enhancer region (NOCE) upstream the Noto promoter was necessary and sufficient for NNC expression from the endogenous Noto locus. Three subregions in NOCE together mediated full activity in vivo. Binding sites for known transcription factors in NOCE were functional in vitro but dispensable for NOCE activity in vivo. A FOXA2 site in combination with a novel motif was necessary for NOCE activity in vivo. Strikingly, syntenic regions in non-mammalian vertebrates showed no recognizable sequence similarities. In contrast to its activity in mouse NOCE did not drive NNC expression in transgenic fish. NOCE represents a novel, mammal-specific CRM required for the highly restricted Noto expression in the node and nascent notochord and thus regulates normal node development and function.

  5. Peptide binding specificity of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Sandhu, N.; Duus, K.; Jorgensen, C.S.

    2007-01-01

    Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composit......Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length...... than 5 amino acids showed binding and a clear correlation with hydrophobicity was demonstrated for oligomers of different hydrophobic amino acids. Insertion of hydrophilic amino acids in a hydrophobic sequence diminished or abolished binding. In conclusion our results show that calreticulin has...

  6. Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome

    Directory of Open Access Journals (Sweden)

    Caroline Y. Kuo

    2018-05-01

    Full Text Available X-linked hyper-immunoglobulin M (hyper-IgM syndrome (XHIM is a primary immunodeficiency due to mutations in CD40 ligand that affect immunoglobulin class-switch recombination and somatic hypermutation. The disease is amenable to gene therapy using retroviral vectors, but dysregulated gene expression results in abnormal lymphoproliferation in mouse models, highlighting the need for alternative strategies. Here, we demonstrate the ability of both the transcription activator-like effector nuclease (TALEN and clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9 platforms to efficiently drive integration of a normal copy of the CD40L cDNA delivered by Adeno-Associated Virus. Site-specific insertion of the donor sequence downstream of the endogenous CD40L promoter maintained physiologic expression of CD40L while overriding all reported downstream mutations. High levels of gene modification were achieved in primary human hematopoietic stem cells (HSCs, as well as in cell lines and XHIM-patient-derived T cells. Notably, gene-corrected HSCs engrafted in immunodeficient mice at clinically relevant frequencies. These studies provide the foundation for a permanent curative therapy in XHIM.

  7. Generation of an efficient artificial promoter of bovine skeletal muscle α-actin gene (ACTA1) through addition of cis-acting element.

    Science.gov (United States)

    Hu, Qian; Tong, Huili; Zhao, Dandan; Cao, Yunkao; Zhang, Weiwei; Chang, Shuwei; Yang, Yu; Yan, Yunqin

    2015-03-01

    The promoter of skeletal muscle α-actin gene (ACTA1) is highly muscle specific. The core of the bovine ACTA1 promoter extends from +29 to -233, about 262 base pairs (bp), which is sufficient to activate transcription in bovine muscle satellite cells. In this study, analysis by PCR site-specific mutagenesis showed that the cis-acting element SRE (serum response element binding factor) was processed as a transcriptional activator. In order to enhance the bovine ACTA1 promoter's activity, we used a strategy to modify it. We cloned a fragment containing three SREs from the promoter of ACTA1, and then one or two clones were linked upstream of the core promoter (262 bp) of ACTA1. One and two clones increased the activity of the ACTA1 promoter 3-fold and 10-fold, respectively, and maintained muscle tissue specificity. The modified promoter with two clones could increase the level of ACTA1 mRNA and protein 4-fold and 1.1-fold, respectively. Immunofluorescence results showed that green fluorescence of ACTA1 increased. Additionally, the number of total muscle microfilaments increased. These genetically engineered promoters might be useful for regulating gene expression in muscle cells and improving muscle mass in livestock.

  8. Identification of germline transcriptional regulatory elements in Aedes aegypti

    Science.gov (United States)

    Akbari, Omar S.; Papathanos, Philippos A.; Sandler, Jeremy E.; Kennedy, Katie; Hay, Bruce A.

    2014-02-01

    The mosquito Aedes aegypti is the principal vector for the yellow fever and dengue viruses, and is also responsible for recent outbreaks of the alphavirus chikungunya. Vector control strategies utilizing engineered gene drive systems are being developed as a means of replacing wild, pathogen transmitting mosquitoes with individuals refractory to disease transmission, or bringing about population suppression. Several of these systems, including Medea, UDMEL, and site-specific nucleases, which can be used to drive genes into populations or bring about population suppression, utilize transcriptional regulatory elements that drive germline-specific expression. Here we report the identification of multiple regulatory elements able to drive gene expression specifically in the female germline, or in the male and female germline, in the mosquito Aedes aegypti. These elements can also be used as tools with which to probe the roles of specific genes in germline function and in the early embryo, through overexpression or RNA interference.

  9. LinkedIn as a Learning Tool in Business Education

    Science.gov (United States)

    Cooper, Brett; Naatus, Mary Kate

    2014-01-01

    This article summarizes the existing research on social media as a learning tool in higher education and adds to the literature on incorporating social media tools into collegiate business education by suggesting specific course content areas of business where LinkedIn exercises and training can be incorporated. LinkedIn as a classroom tool cannot…

  10. High-temperature superconducting fault-current limiter - optimisation of superconducting elements

    International Nuclear Information System (INIS)

    2004-01-01

    This report summarises the findings of a study initiated to continue the work of a DTI-LINK Collaborative Research Programme 'Enhancing the Properties of Bulk High Temperature Superconductors and their Potential Application as Fault Current Limiters (FCL). Details are given of computer modelling of the quenching process involving the transition from superconducting to normal conducting states undergone by the material when large currents are present. The design of compound elements, and a multi-element model are described along with FCL design covering distribution bus-coupler, embedded generator connection, larger generator connection, hazardous area safety, and interconnection to fault-prone network. The evaluation of thermal loss, test equipment and schedule, the optimised element, installed cost data, and the UK market are considered

  11. Lumped Mass Modeling for Local-Mode-Suppressed Element Connectivity

    DEFF Research Database (Denmark)

    Joung, Young Soo; Yoon, Gil Ho; Kim, Yoon Young

    2005-01-01

    connectivity parameterization (ECP) is employed. On the way to the ultimate crashworthy structure optimization, we are now developing a local mode-free topology optimization formulation that can be implemented in the ECP method. In fact, the local mode-freeing strategy developed here can be also used directly...... experiencing large structural changes, appears to be still poor. In ECP, the nodes of the domain-discretizing elements are connected by zero-length one-dimensional elastic links having varying stiffness. For computational efficiency, every elastic link is now assumed to have two lumped masses at its ends....... Choosing appropriate penalization functions for lumped mass and link stiffness is important for local mode-free results. However, unless the objective and constraint functions are carefully selected, it is difficult to obtain clear black-and-white results. It is shown that the present formulation is also...

  12. Knowledge Representation and Management: a Linked Data Perspective.

    Science.gov (United States)

    Barros, M; Couto, F M

    2016-11-10

    Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management.

  13. Hypothetical link between infertility and genetically modified food.

    Science.gov (United States)

    Gao, Mingxia; Li, Bin; Yuan, Wenzhen; Zhao, Lihui; Zhang, Xuehong

    2014-01-01

    It is speculated that genetically modified food (GMF)/genetically modified organism (GMO) is responsible for infertility development. The risk linked with a wide use of GMFs/GMOs offers the basic elements for social criticism. However, to date, it has not been justified whether the bad effects are directly resulted from products of genetic modifications or trans-genesis process. Extensive experience with the risk assessment of whole foods has been applied recently on the safety and nutritional testing of GMFs/GMOs. Investigations have tested the safety of GMFs including sub-acute, chronic, reproductive, multi-generation and carcinogenicity studies. We extrapolated the potential risks associated with GMFs/GMOs on reproduction, and analyzed the multi-aspect linked between infertility and GMFs/GMOs. It could be conjectured that GMFs/GMOs could be potential hazard on reproduction, linking to the development of infertility through influencing the endocrine metabolism, endometriosis. However, little evidence shows the impaction on embryo or reproductive related tumor due to the limited literatures, and needs further research. The article presents some related patents on GMFs/GMOs, and some methods for tracking GMOs.

  14. Programming the finite element method

    CERN Document Server

    Smith, I M; Margetts, L

    2013-01-01

    Many students, engineers, scientists and researchers have benefited from the practical, programming-oriented style of the previous editions of Programming the Finite Element Method, learning how to develop computer programs to solve specific engineering problems using the finite element method. This new fifth edition offers timely revisions that include programs and subroutine libraries fully updated to Fortran 2003, which are freely available online, and provides updated material on advances in parallel computing, thermal stress analysis, plasticity return algorithms, convection boundary c

  15. Geometry reconstruction method for patient-specific finite element models for the assessment of tibia fracture risk in osteogenesis imperfecta.

    Science.gov (United States)

    Caouette, Christiane; Ikin, Nicole; Villemure, Isabelle; Arnoux, Pierre-Jean; Rauch, Frank; Aubin, Carl-Éric

    2017-04-01

    Lower limb deformation in children with osteogenesis imperfecta (OI) impairs ambulation and may lead to fracture. Corrective surgery is based on empirical assessment criteria. The objective was to develop a reconstruction method of the tibia for OI patients that could be used as input of a comprehensive finite element model to assess fracture risks. Data were obtained from three children with OI and tibia deformities. Four pQCT scans were registered to biplanar radiographs, and a template mesh was deformed to fit the bone outline. Cortical bone thickness was computed. Sensitivity of the model to missing slices of pQCT was assessed by calculating maximal von Mises stress for a vertical hopping load case. Sensitivity of the model to ±5 % of cortical thickness measurements was assessed by calculating loads at fracture. Difference between the mesh contour and bone outline on the radiographs was below 1 mm. Removal of one pQCT slice increased maximal von Mises stress by up to 10 %. Simulated ±5 % variation of cortical bone thickness leads to variations of up to 4.1 % on predicted fracture loads. Using clinically available tibia imaging from children with OI, the developed reconstruction method allowed the building of patient-specific finite element models.

  16. Is active participation in specific sport activities linked with back pain?

    DEFF Research Database (Denmark)

    Mogensen, A.M.; Gausel, AM; Wedderkopp, Niels

    2007-01-01

    A cross-sectional survey of 439 children/adolescents aged 12-13, living in Odense, Denmark, in the year 2001. To investigate (1) if there is any difference in back pain reporting among those practising specific sports as compared with non-performers and (2) if there is an association between...... specific kinds of sports and self-reported back problems. Back pain is a common complaint in young people and physical inactivity is generally thought to contribute to this. However, some specific sport activities may be detrimental or beneficial to the spine. Information was collected through a semi......-structured interview, a physical examination, and a questionnaire. Associations for back pain, low back pain, mid back pain and neck pain in the preceding month were investigated in relation to specific sports. Associations were controlled for body mass index, puberty stage and sex. There was no association between...

  17. Biotic elements of NPP techno-ecosystem

    International Nuclear Information System (INIS)

    Protasov, A.A.; Silaeva, A.A.

    2013-01-01

    Specific features of biotic elements in the NPP techno-ecosystems were considered and compared with natural ecosystems. Relationships between biotic communities and environmental factors that are specific to the techno-ecosystems were discussed, and the problems of limitation of biological hindrances in operation of equipment, principles of hydrobiological and environmental monitoring were considered.

  18. US HealthLink: a national information resource for health care professionals.

    Science.gov (United States)

    Yasnoff, W A

    1992-06-01

    US HealthLink is a new, comprehensive online medical information system designed specifically for health care professionals. Available to individuals for a fixed fee, it includes literature, news, diagnostic decision support, drug interactions, electronic mail, and bulletin boards. It also provides user-specific current awareness via clipping service, and fax delivery of both clipping and electronic mail information. US HealthLink can now be utilized to access a wide variety of medical information sources inexpensively.

  19. Processing Semblances Induced through Inter-Postsynaptic Functional LINKs, Presumed Biological Parallels of K-Lines Proposed for Building Artificial Intelligence

    Science.gov (United States)

    Vadakkan, Kunjumon I.

    2011-01-01

    The internal sensation of memory, which is available only to the owner of an individual nervous system, is difficult to analyze for its basic elements of operation. We hypothesize that associative learning induces the formation of functional LINK between the postsynapses. During memory retrieval, the activation of either postsynapse re-activates the functional LINK evoking a semblance of sensory activity arriving at its opposite postsynapse, nature of which defines the basic unit of internal sensation – namely, the semblion. In neuronal networks that undergo continuous oscillatory activity at certain levels of their organization re-activation of functional LINKs is expected to induce semblions, enabling the system to continuously learn, self-organize, and demonstrate instantiation, features that can be utilized for developing artificial intelligence (AI). This paper also explains suitability of the inter-postsynaptic functional LINKs to meet the expectations of Minsky’s K-lines, basic elements of a memory theory generated to develop AI and methods to replicate semblances outside the nervous system. PMID:21845180

  20. Table of specific activities of selected isotopes

    International Nuclear Information System (INIS)

    Shipley, G.

    The bulk of this publication consists of a table of the half-lives, decay modes, and specific activities of isotopes selected for their particular interest to the Environmental Health and Safety Department, LBL. The specific activities were calculated with a PDP 9/15 computer. Also included in the report is a table of stable isotopes, the Th and U decay chains, a chart of the nuclides for elements 101 through 106, the heavy element region of the periodic table, and a specific activity monograph. 5 figures, 2 tables

  1. Identification of a peroxisome proliferator responsive element (PPRE)-like cis-element in mouse plasminogen activator inhibitor-1 gene promoter

    International Nuclear Information System (INIS)

    Chen Jiegen; Li Xi; Huang Haiyan; Liu Honglei; Liu Deguo; Song Tanjing; Ma Chungu; Ma Duan; Song Houyan; Tang Qiqun

    2006-01-01

    PAI-1 is expressed and secreted by adipose tissue which may mediate the pathogenesis of obesity-associated cardiovascular complications. Evidence is presented in this report that PAI-1 is not expressed by preadipocyte, but significantly induced during 3T3-L1 adipocyte differentiation and the PAI-1 expression correlates with the induction of peroxisome proliferator-activated receptor γ (PPARγ). A peroxisome proliferator responsive element (PPRE)-like cis-element (-206TCCCCCATGCCCT-194) is identified in the mouse PAI-1 gene promoter by electrophoretic mobility shift assay (EMSA) combined with transient transfection experiments; the PPRE-like cis-element forms a specific DNA-protein complex only with adipocyte nuclear extracts, not with preadipocyte nuclear extracts; the DNA-protein complex can be totally competed away by non-labeled consensus PPRE, and can be supershifted with PPARγ antibody. Mutation of this PPRE-like cis-element can abolish the transactivation of mouse PAI-1 promoter mediated by PPARγ. Specific PPARγ ligand Pioglitazone can significantly induce the PAI-1 expression, and stimulate the secretion of PAI-1 into medium

  2. Integrated magnetics design for HF-link power converters

    Energy Technology Data Exchange (ETDEWEB)

    Ljusev, P.; Andersen, Michael A.E.

    2005-07-01

    This paper deals with the design of integrated magnetics for HF-link converters, where the two integrated magnetic components on the same core do not necessarily belong to the same voltage loop. Depending on the specific HF-link converter topology, the proposed integrated magnetics can either alleviate the derivation of independent auxiliary supply voltages from the main transformer or integrate other magnetic structures, thus saving board space and cutting costs. (au)

  3. Manifold-splitting regularization, self-linking, twisting, writhing numbers of space-time ribbons

    International Nuclear Information System (INIS)

    Tze, C.H.

    1988-01-01

    The authors present an alternative formulation of Polyakov's regularization of Gauss' integral formula for a single closed Feynman path. A key element in his proof of the D = 3 fermi-bose transmutations induced by topological gauge fields, this regularization is linked here with the existence and properties of a nontrivial topological invariant for a closed space ribbon. This self-linking coefficient, an integer, is the sum of two differential characteristics of the ribbon, its twisting and writhing numbers. These invariants form the basis for a physical interpretation of our regularization. Their connection to Polyakov's spinorization is discussed. The authors further generalize their construction to the self-linking, twisting and writhing of higher dimensional d = eta(odd) submanifolds in D = (2eta + 1) space-time

  4. Verification of Orthogrid Finite Element Modeling Techniques

    Science.gov (United States)

    Steeve, B. E.

    1996-01-01

    The stress analysis of orthogrid structures, specifically with I-beam sections, is regularly performed using finite elements. Various modeling techniques are often used to simplify the modeling process but still adequately capture the actual hardware behavior. The accuracy of such 'Oshort cutso' is sometimes in question. This report compares three modeling techniques to actual test results from a loaded orthogrid panel. The finite element models include a beam, shell, and mixed beam and shell element model. Results show that the shell element model performs the best, but that the simpler beam and beam and shell element models provide reasonable to conservative results for a stress analysis. When deflection and stiffness is critical, it is important to capture the effect of the orthogrid nodes in the model.

  5. Modular Verification of Linked Lists with Views via Separation Logic

    DEFF Research Database (Denmark)

    Jensen, Jonas Braband; Birkedal, Lars; Sestoft, Peter

    2011-01-01

    We present a separation logic specification and verification of linked lists with views, a data structure from the C5 collection library for .NET. A view is a generalization of the well-known concept of an iterator. Linked lists with views form an interesting case study for verification since...

  6. Trace element mapping of two Pyrenean chert deposits (SW Europe) by PIXE

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez de la Torre, Marta, E-mail: marta.sanchez-de-la-torre@u-bordeaux-montaigne.fr [IRAMAT-CRP2A (UMR 5060), CNRS/Université Bordeaux Montaigne, Maison de l’Archéologie, Esplanade des Antilles, 33607 Pessac Cedex (France); SERP-Universitat de Barcelona, Montalegre St 6-8, 08001 Barcelona (Spain); Angyal, Anikó; Kertész, Zsófia [MTA Atomki, Institute for Nuclear Research, Hungarian Academy of Sciences, H-4026 Debrecen (Hungary); Dubernet, Stéphan; Le Bourdonnec, François-Xavier [IRAMAT-CRP2A (UMR 5060), CNRS/Université Bordeaux Montaigne, Maison de l’Archéologie, Esplanade des Antilles, 33607 Pessac Cedex (France); Csedreki, László; Furu, Enikő; Papp, Enikő; Szoboszlai, Zoltán; Szikszai, Zita [MTA Atomki, Institute for Nuclear Research, Hungarian Academy of Sciences, H-4026 Debrecen (Hungary)

    2017-06-01

    The geochemical character of two chert formations from the Pyrenean mountain range (SW Europe) was established by PIXE analyses. While it was not possible to distinguish the formations through reference to major and minor elements, some variations were revealed at the trace elemental level. In order to determine if these elements are associated with the Si matrix or to the contents of a specific inclusion, elemental maps were acquired and the elemental composition of the identified inclusions were also determined. As a result, Sr, Ni and Zn are better represented in Montgaillard samples while Y, Hf, W and Zr are typical of Montsaunès cherts. Thanks to elemental maps it has been possible to determine that most of these characteristic elements are usually related to a specific inclusion content.

  7. Real and imaginary elements of fermion mass matrices

    International Nuclear Information System (INIS)

    Masina, I.; Savoy, C.A.

    2006-01-01

    Prompted by the recent better determination of the angles of the unitarity triangle, we re-appraise the problem of finding simple fermion mass textures, possibly linked to some symmetry principle and compatible with grand unification. In particular, the indication that the angle α is close to rectangle turns out to be the crucial ingredient leading us to single out fermion mass textures whose elements are either real or purely imaginary. In terms of the five parameters ascribed to the quark sector, these textures reproduce the eight experimental data on quark mass ratios and mixings within 1σ. When embedded in an SU(5) framework, these textures suggest a common origin for quark and lepton CP violations, also linked to the spontaneous breaking of the gauge group

  8. Finite Element Based Design and Optimization for Piezoelectric Accelerometers

    DEFF Research Database (Denmark)

    Liu, Bin; Kriegbaum, B.; Yao, Q.

    1998-01-01

    A systematic Finite Element design and optimisation procedure is implemented for the development of piezoelectric accelerometers. Most of the specifications of accelerometers can be obtained using the Finite Element simulations. The deviations between the simulated and calibrated sensitivities...

  9. Elements of non-relativistic quantum mechanics

    CERN Document Server

    Sobrino, Luis

    1996-01-01

    This book presents the basic structure of quantum mechanics, the elements needed to properly understand the subject and its applications. It is written at a level which is intermediate between the standard graduate textbooks, which it intends to supplement, and the more advanced mathematical writings in the subject. Particular attention is given to the concepts of kinematical and dynamical symmetries. The unifying thread that links the study of particles and systems of particles is the connection between Galilean invariance and the fundamental observables of a system. The mathematical appendic

  10. Multinetwork of international trade: A commodity-specific analysis

    Science.gov (United States)

    Barigozzi, Matteo; Fagiolo, Giorgio; Garlaschelli, Diego

    2010-04-01

    We study the topological properties of the multinetwork of commodity-specific trade relations among world countries over the 1992-2003 period, comparing them with those of the aggregate-trade network, known in the literature as the international-trade network (ITN). We show that link-weight distributions of commodity-specific networks are extremely heterogeneous and (quasi) log normality of aggregate link-weight distribution is generated as a sheer outcome of aggregation. Commodity-specific networks also display average connectivity, clustering, and centrality levels very different from their aggregate counterpart. We also find that ITN complete connectivity is mainly achieved through the presence of many weak links that keep commodity-specific networks together and that the correlation structure existing between topological statistics within each single network is fairly robust and mimics that of the aggregate network. Finally, we employ cross-commodity correlations between link weights to build hierarchies of commodities. Our results suggest that on the top of a relatively time-invariant “intrinsic” taxonomy (based on inherent between-commodity similarities), the roles played by different commodities in the ITN have become more and more dissimilar, possibly as the result of an increased trade specialization. Our approach is general and can be used to characterize any multinetwork emerging as a nontrivial aggregation of several interdependent layers.

  11. Storage and pre-neutron-activation-analysis treatment for trace-element analysis in urine

    International Nuclear Information System (INIS)

    Blotcky, A.J.; Rack, E.P.

    1985-01-01

    The problems regarding storage and pre-neutron-activation-analysis treatment for the elements aluminum, calcium, vanadium, selenium, copper, iodine, zinc, manganese, and magnesium in a urine matrix are reviewed. The type of collection and storage procedure and pre-neutron activation analysis treatment of urine depend on the specific trace element; that is, its inherent physical and chemical properties. Specifically polyethylene in teflon containers are the most suitable for general determinations. Whether any preservative is added would depend upon the stability of the trace element and its tendency for surface adsorption. Preferably, preservatives should contain no radioactivatable elements for maximum efficacy. Freeze drying or packing urine shipments under dry ice needs to be explored on an individual basis. Each pre- or post-neutron activation analysis treatment is specific and optimized for the trace element analyzed

  12. Derivation of the gauge link in light cone gauge

    International Nuclear Information System (INIS)

    Gao Jianhua

    2010-01-01

    In light cone gauge, a gauge link at light cone infinity is necessary for transverse momentum-dependent parton distribution to restore the gauge invariance in some specific boundary conditions. We derive such transverse gauge link in a more regular and general method. We find the gauge link at light cone infinity naturally arises from the contribution of the pinched poles: one is from the quark propagator and the other is hidden in the gauge vector field in light cone gauge. Actually, in the amplitude level, we have obtained a more general gauge link over the hypersurface at light cone infinity which is beyond the transverse direction. The difference of such gauge link between semi-inclusive deep inelastic scattering and Drell-Yan processes can also be obtained directly and clearly in our derivation.

  13. Preparation of spherical fuel elements for HTR-PM in INET

    International Nuclear Information System (INIS)

    Xiangwen, Zhou; Zhenming, Lu; Jie, Zhang; Bing, Liu; Yanwen, Zou; Chunhe, Tang; Yaping, Tang

    2013-01-01

    Highlights: • Modifications and optimizations in the manufacture of spherical fuel elements (SFE) for HTR-PM are presented. • A newly developed overcoater exhibits good stability and high efficiency in the preparation of overcoated particles. • The optimized carbonization process reduces the process time from 70 h in the period of HTR-10 to 20 h. • Properties of the prepared SFE and matrix graphite balls meet the design specifications for HTR-PM. • In particular the mean free uranium fraction of 5 consecutive batches is only 8.7 × 10 −6 . -- Abstract: The spherical fuel elements were successfully manufactured in the period of HTR-10. In order to satisfy the mass production of fuel elements for HTR-PM, several measures have been taken in modifying and optimizing the manufacture process of fuel elements. The newly developed overcoater system and its corresponding parameters exhibited good stability and high efficiency in the preparation of overcoated particles. The optimized carbonization process could reduce the carbonization time from more than 70 h to 20 h and improve the manufacturing efficiency. Properties of the manufactured spherical fuel elements and matrix graphite balls met the design specifications for HTR-PM. The mean free uranium fraction of 5 consecutive batches was 8.7 × 10 −6 . The optimized fuel elements manufacturing process could meet the requirements of design specifications of spherical fuel elements for HTR-PM

  14. Levels of house dust mite-specific serum immunoglobulin E (IgE) in different cat populations using a monoclonal based anti-IgE enzyme-linked immunosorbent assay.

    Science.gov (United States)

    Bexley, Jennifer; Hogg, Janice E; Hammerberg, Bruce; Halliwell, Richard E W

    2009-10-01

    Levels of serum immunoglobulin E (IgE) specific for the house dust mites (HDMs) Dermatophagoides farinae (DF) and Dermatophagoides pteronyssinus (DP) in 58 cats with clinical signs suggestive of atopic dermatitis (allergic dermatitis cats), 52 cats with no history of allergic or immunological disease (nonallergic cats) and 26 specific pathogen-free (SPF) cats were measured using a monoclonal anti-IgE enzyme-linked immunosorbent assay. Reactivity to both native and reduced HDM allergens was compared. SPF cats had significantly lower levels of HDM-specific serum IgE than cats with allergic dermatitis and nonallergic cats. The difference in levels of HDM-specific IgE in the serum of cats with allergic dermatitis and nonallergic cats was significant for native DF allergen, but not for native DP allergen or reduced HDM allergens. The results suggest that DF in its native form may be a significant allergen in cats with allergic dermatitis. The clinical relevance of these reactions, however, remains to be proven.

  15. SXT/R391 ICE elements encode a novel ‘trap-door’ strategy for mobile element escape

    Directory of Open Access Journals (Sweden)

    Michael P Ryan

    2016-05-01

    Full Text Available Integrative Conjugative Elements (ICEs are a class of bacterial mobile elements that have the ability to mediate their own integration, excision and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitisation function which results in stress induced killing of bacterial cells harbouring the ICE. This sensitisation has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer.

  16. Perturbation of N-linked oligosaccharide structure results in an altered incorporation of [3H]palmitate into specific proteins in Chinese hamster ovary cells

    International Nuclear Information System (INIS)

    Wellner, R.B.; Ghosh, P.C.; Roecklein, B.; Wu, H.C.

    1987-01-01

    Increased [ 3 H]palmitate incorporation into specific cellular proteins has been reported to occur in Chinese hamster ovary and yeast mutant cells. In this paper we report studies concerning the relationship between N-linked oligosaccharide structure and [ 3 H]palmitate incorporation into proteins of Chinese hamster ovary (CHO) cells. We have compared the incorporation of [ 3 H]palmitate into proteins of wild-type and four different mutant CHO cell lines defective in various steps of N-linked protein glycosylation. Sodium dodecyl sulfate-gel electrophoretic analysis showed that three of the mutants exhibited increased [ 3 H]palmitate incorporation into several CHO cellular proteins (approximately 30,000-38,000 molecular weight) as compared to the wild-type cells. One of the affected mutants which accumulates the Man5Gn2Asn intermediate structure was examined in detail. In agreement with earlier reports, virtually all of the [ 3 H] palmitate-labeled proteins of both wild-type and mutant cell lines are membrane-bound. Pretreatment of the mutant cell line with tunicamycin blocked the increased [ 3 H]palmitate incorporation into the two specific proteins (both of approximately 30,000 molecular weight) observed in untreated cells; the decreased incorporation of [ 3 H]palmitate into the 30,000 molecular weight species was accompanied by a concomitant increase in the incorporation of [ 3 H]palmitate into two proteins of approximately 20,000 molecular weight. Pretreatment of wild-type cells with tunicamycin also caused increased [ 3 H]palmitate incorporation into the 20,000 molecular weight species

  17. TAPIR, Thermal Analysis of HTGR with Graphite Sleeve Fuel Elements

    International Nuclear Information System (INIS)

    Weicht, U.; Mueller, W.

    1983-01-01

    1 - Nature of the physical problem solved: Thermal analysis of a reactor core containing internally and/or externally gas cooled prismatic fuel elements of various geometries, rating, power distribution, and material properties. 2 - Method of solution: A fuel element in this programme is regarded as a sector of a fuelled annulus with graphite sleeves of any shape on either side and optional annular gaps between fuel and graphite and/or within the graphite. It may have any centre angle and the fuelled annulus may become a solid cylindrical rod. Heat generation in the fuel is assumed to be uniform over the cross section and peripheral heat flux into adjacent sectors is ignored. Fuel elements and coolant channels are treated separately, then linked together to fit a specified pattern. 3 - Restrictions on the complexity of the problem: Maxima of: 50 fuel elements; 50 cooled channels; 25 fuel geometries; 25 coolant channel geometries; 10 axial power distributions; 10 graphite conductivities

  18. A Centerline Based Model Morphing Algorithm for Patient-Specific Finite Element Modelling of the Left Ventricle.

    Science.gov (United States)

    Behdadfar, S; Navarro, L; Sundnes, J; Maleckar, M; Ross, S; Odland, H H; Avril, S

    2017-09-20

    Hexahedral automatic model generation is a recurrent problem in computer vision and computational biomechanics. It may even become a challenging problem when one wants to develop a patient-specific finite-element (FE) model of the left ventricle (LV), particularly when only low resolution images are available. In the present study, a fast and efficient algorithm is presented and tested to address such a situation. A template FE hexahedral model was created for a LV geometry using a General Electric (GE) ultrasound (US) system. A system of centerline was considered for this LV mesh. Then, the nodes located over the endocardial and epicardial surfaces are respectively projected from this centerline onto the actual endocardial and epicardial surfaces reconstructed from a patient's US data. Finally, the position of the internal nodes is derived by finding the deformations with minimal elastic energy. This approach was applied to eight patients suffering from congestive heart disease. A FE analysis was performed to derive the stress induced in the LV tissue by diastolic blood pressure on each of them. Our model morphing algorithm was applied successfully and the obtained meshes showed only marginal mismatches when compared to the corresponding US geometries. The diastolic FE analyses were successfully performed in seven patients to derive the distribution of principal stresses. The original model morphing algorithm is fast and robust with low computational cost. This low cost model morphing algorithm may be highly beneficial for future patient-specific reduced-order modelling of the LV with potential application to other crucial organs.

  19. Performance and specificity of the covalently linked immunomagnetic separation-ATP method for rapid detection and enumeration of enterococci in coastal environments.

    Science.gov (United States)

    Zimmer-Faust, Amity G; Thulsiraj, Vanessa; Ferguson, Donna; Jay, Jennifer A

    2014-05-01

    The performance and specificity of the covalently linked immunomagnetic separation-ATP (Cov-IMS/ATP) method for the detection and enumeration of enterococci was evaluated in recreational waters. Cov-IMS/ATP performance was compared with standard methods: defined substrate technology (Enterolert; IDEXX Laboratories), membrane filtration (EPA Method 1600), and an Enterococcus-specific quantitative PCR (qPCR) assay (EPA Method A). We extend previous studies by (i) analyzing the stability of the relationship between the Cov-IMS/ATP method and culture-based methods at different field sites, (ii) evaluating specificity of the assay for seven ATCC Enterococcus species, (iii) identifying cross-reacting organisms binding the antibody-bead complexes with 16S rRNA gene sequencing and evaluating specificity of the assay to five nonenterococcus species, and (iv) conducting preliminary tests of preabsorption as a means of improving the assay. Cov-IMS/ATP was found to perform consistently and with strong agreement rates (based on exceedance/compliance with regulatory limits) of between 83% and 100% compared to the culture-based Enterolert method at a variety of sites with complex inputs. The Cov-IMS/ATP method is specific to five of seven different Enterococcus spp. tested. However, there is potential for nontarget bacteria to bind the antibody, which may be reduced by purification of the IgG serum with preabsorption at problematic sites. The findings of this study help to validate the Cov-IMS/ATP method, suggesting a predictable relationship between the Cov-IMS/ATP method and traditional culture-based methods, which will allow for more widespread application of this rapid and field-portable method for coastal water quality assessment.

  20. On the reliability of finite element solutions

    International Nuclear Information System (INIS)

    Prasad, K.S.R.K.

    1975-01-01

    The extent of reliability of the finite element method for analysis of nuclear reactor structures, and that of reactor vessels in particular and the need for the engineer to guard against the pitfalls that may arise out of both physical and mathematical models have been high-lighted. A systematic way of checking the model to obtain reasonably accurate solutions is presented. Quite often sophisticated elements are suggested for specific design and stress concentration problems. The desirability or otherwise of these elements, their scope and utility vis-a-vis the use of large stack of conventional elements are discussed from the view point of stress analysts. The methods of obtaining a check on the reliability of the finite element solutions either through modelling changes or an extrapolation technique are discussed. (author)

  1. The Compositional HJ-Biplot—A New Approach to Identifying the Links among Bioactive Compounds of Tomatoes

    Directory of Open Access Journals (Sweden)

    Marcos Hernández Suárez

    2016-11-01

    Full Text Available Tomatoes have been described as a functional food because of their particular composition of different bioactive compounds. In this study, the proximate composition, minerals and trace elements, and antioxidant compounds were determined in two tomato cultivars (Mariana and Dunkan that were grown in Gran Canaria (Spain either conventionally or hydroponically. Although compositional data of this type require being subjected to the specific statistical techniques of compositional analysis, this approach has not usually been considered in this context. In the present case, a compositional Mann–Whitney U test of the data showed significant differences for each factor (cultivar and cultivation system in several of the compositional variables studied. For the differences between cultivars, these parameters were the protein, Mg, lycopene, ascorbic acid, citric acid, and fumaric acid contents. For the differences between cultivation systems, they were mainly those of the mineral and trace elements group. Although one-year data are insufficient to make clear relationship among compounds because more repetitions in several localities and years are necessary, the compositional HJ-biplot (in which the links provide estimates of the linear relationship among variables results agreed with other scientific results about linear relationship among some compounds analyzed.

  2. A Radio-Frequency-over-Fiber link for large-array radio astronomy applications

    International Nuclear Information System (INIS)

    Mena, J; Bandura, K; Cliche, J-F; Dobbs, M; Gilbert, A; Tang, Q Y

    2013-01-01

    A prototype 425-850 MHz Radio-Frequency-over-Fiber (RFoF) link for the Canadian Hydrogen Intensity Mapping Experiment (CHIME) is presented. The design is based on a directly modulated Fabry-Perot (FP) laser, operating at ambient temperature, and a single-mode fiber. The dynamic performance, gain stability, and phase stability of the RFoF link are characterized. Tests on a two-element interferometer built at the Dominion Radio Astrophysical Observatory for CHIME prototyping demonstrate that RFoF can be successfully used as a cost-effective solution for analog signal transport on the CHIME telescope and other large-array radio astronomy applications

  3. Relationships over time of subjective and objective elements of recovery in persons with schizophreni

    DEFF Research Database (Denmark)

    Jørgensen, Rikke; Zoffmann, Vibeke; Munk-Jørgensen, Povl

    2015-01-01

    of symptoms with four assessments of self-reports of subjective aspects of recovery. Participants were 101 outpatients with schizophrenia. Symptoms were assessed with the Positive and Negative Syndrome Scale (PANSS) while subjective recovery was assessed with the Recovery Assessment Scale (RAS). Separate......Recovery from schizophrenia involves both subjective elements such as self-appraised wellness and objective elements such as symptom remission. Less is known about how they interact. To explore this issue, this study examined the relationship over the course of 1 year of four assessments...... Pearson׳s or Spearman׳s rank׳s correlation coefficients, calculated at all four measurement points, revealed the total symptom score was linked with lower levels of overall self-recovery at all four measurement points. The PANSS emotional discomfort subscale was linked with self-reported recovery at all...

  4. Linking DC together with TRSL

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Yong, X.

    2000-01-01

    in a method for real-time developments. An operational semantics with behavior is specified for TRSL. It is defined what its means for a TRSL process to satisfy a DC requirement, and a method for verifying whether the satisfaction relation holds or not is provided. Our contribution also demonstrates a general......Duration Calculus (DC) is an interval-based real-time logic, which can be used in capturing and eliciting users' real-time requirements. The Timed RAISE Specification Language (TRSL) is an extension of the RAISE Specification Language with real-time features. This paper links DC and TRSL together...

  5. Using pattern classification and nuclear forensic signatures to link UOC to source rocks and purification processes

    International Nuclear Information System (INIS)

    Marks, N.; Robel, M.; Borg, M.; Hutcheon, I.; Kristo, M.

    2014-01-01

    Nuclear forensics is a scientific discipline interfacing law enforcement, nuclear science and nonproliferation. Information on the history and on the potential origin of unknown nuclear material can be obtained through nuclear forensic analysis. Using commonly available techniques of mass spectrometry, microscopy and x-ray diffraction, we have gained insight into the processing and origin of a suite of uranium ore concentrate (UOC) samples. We have applied chemometric techniques to investigate the relationships between uranium ore deposits and UOC samples in order to identify chemical and isotopic signatures of nuclear forensic importance. We developed multivariate signatures based on elemental concentrations and isotope ratios using a database of characteristics of UOC originating throughout the world. By introducing detailed and specific information about the source rock geology for each sample, we improved our understanding of the preservation of forensic signatures in UOC. Improved characterization of sample processing and provenance allows us to begin to assess the statistical significance of different groupings of samples and identify underlying patterns. Initial results indicate the concentration of uranium in the ore body, the geochemical conditions associated with uranium emplacement, and host rock petrogenesis exert controlling influences on the impurities preserved in UOC. Specific ore processing techniques, particularly those related to In-Situ Recovery, are also reflected in UOC impurity signatures. Stable and radiogenic isotope geochemistry can be used in conjunction with rare earth element patterns and other characteristics to link UOCs to specific geologic deposits of origin. We will present a number of case studies illustrating the ways in which nuclear forensic analysis can provide insight into the ore geology and production and purification processes used to produce UOC. (author)

  6. Accuracy of specimen-specific nonlinear finite element analysis for evaluation of distal radius strength in cadaver material.

    Science.gov (United States)

    Matsuura, Yusuke; Kuniyoshi, Kazuki; Suzuki, Takane; Ogawa, Yasufumi; Sukegawa, Koji; Rokkaku, Tomoyuki; Takahashi, Kazuhisa

    2014-11-01

    Distal radius fracture, which often occurs in the setting of osteoporosis, can lead to permanent deformity and disability. Great effort has been directed toward developing noninvasive methods for evaluating the distal radius strength, with the goal of assessing fracture risk. The aim of this study was to evaluate distal radius strength using a finite element model and to gauge the accuracy of finite element model measurement using cadaver material. Ten wrists were obtained from cadavers with a mean age of 89.5 years at death. CT images of each wrist in an extended position were obtained. CT-based finite element models were prepared with Mechanical Finder software. Fracture on the models was simulated by applying a mechanical load to the palm in a direction parallel to the forearm axis, after which the fracture load and the site at which the fracture began were identified. For comparison, the wrists were fractured using a universal testing machine and the fracture load and the site of fracture were identified. The fracture load was 970.9 N in the finite element model group and 990.0 N in the actual measurement group. The site of the initial fracture was extra-articular to the distal radius in both groups. The finite element model was predictive for distal radius fracture when compared to the actual measurement. In this study, a finite element model for evaluation of distal radius strength was validated and can be used to predict fracture risk. We conclude that a finite element model is useful for the evaluation of distal radius strength. Knowing distal radius strength might avoid distal radius fracture because appropriate antiosteoporotic treatment can be initiated.

  7. Novel porcine repetitive elements

    Directory of Open Access Journals (Sweden)

    Nonneman Dan J

    2006-12-01

    Full Text Available Abstract Background Repetitive elements comprise ~45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals. Results We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI. These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute, covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats. Conclusion The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

  8. The elements of life and medicines.

    Science.gov (United States)

    Chellan, Prinessa; Sadler, Peter J

    2015-03-13

    Which elements are essential for human life? Here we make an element-by-element journey through the periodic table and attempt to assess whether elements are essential or not, and if they are, whether there is a relevant code for them in the human genome. There are many difficulties such as the human biochemistry of several so-called essential elements is not well understood, and it is not clear how we should classify elements that are involved in the destruction of invading microorganisms, or elements which are essential for microorganisms with which we live in symbiosis. In general, genes do not code for the elements themselves, but for specific chemical species, i.e. for the element, its oxidation state, type and number of coordinated ligands, and the coordination geometry. Today, the biological periodic table is in a position somewhat similar to Mendeleev's chemical periodic table of 1869: there are gaps and we need to do more research to fill them. The periodic table also offers potential for novel therapeutic and diagnostic agents, based on not only essential elements, but also non-essential elements, and on radionuclides. Although the potential for inorganic chemistry in medicine was realized more than 2000 years ago, this area of research is still in its infancy. Future advances in the design of inorganic drugs require more knowledge of their mechanism of action, including target sites and metabolism. Temporal speciation of elements in their biological environments at the atomic level is a major challenge, for which new methods are urgently needed.

  9. Analysis of Network Vulnerability Under Joint Node and Link Attacks

    Science.gov (United States)

    Li, Yongcheng; Liu, Shumei; Yu, Yao; Cao, Ting

    2018-03-01

    The security problem of computer network system is becoming more and more serious. The fundamental reason is that there are security vulnerabilities in the network system. Therefore, it’s very important to identify and reduce or eliminate these vulnerabilities before they are attacked. In this paper, we are interested in joint node and link attacks and propose a vulnerability evaluation method based on the overall connectivity of the network to defense this attack. Especially, we analyze the attack cost problem from the attackers’ perspective. The purpose is to find the set of least costs for joint links and nodes, and their deletion will lead to serious network connection damage. The simulation results show that the vulnerable elements obtained from the proposed method are more suitable for the attacking idea of the malicious persons in joint node and link attack. It is easy to find that the proposed method has more realistic protection significance.

  10. A novel whole-bacterial enzyme linked-immunosorbant assay to quantify Chlamydia trachomatis specific antibodies reveals distinct differences between systemic and genital compartments.

    Directory of Open Access Journals (Sweden)

    Hannah L Albritton

    Full Text Available Chlamydia trachomatis (CT is the leading sexually transmitted bacterial infection. The continued global burden of CT infection strongly predicates the need for a vaccine to supplement current chlamydial control programs. The correlates of protection against CT are currently unknown, but they must be carefully defined to guide vaccine design. The localized nature of chlamydial infection in columnar epithelial cells of the genital tract necessitates investigation of immunity at the site of infection. The purpose of this study was to develop a sensitive whole bacterial enzyme-linked immunosorbent assay (ELISA to quantify and compare CT-specific IgG and IgA in sera and genital secretions from CT-infected women. To achieve this, elementary bodies (EBs from two of the most common genital serovars (D and E were attached to poly-L-lysine-coated microtiter plates with glutaraldehyde. EB attachment and integrity were verified by the presence of outer membrane antigens and the absence of bacterial cytoplasmic antigens. EB-specific IgG and IgA standards were developed by pooling sera with high titers of CT-specific antibodies from infected women. Serum, endocervical and vaginal secretions, and endocervical cytobrush specimens from CT-infected women were used to quantify CT-specific IgG and IgA which were then normalized to total IgG and IgA, respectively. Analyses of paired serum and genital samples revealed significantly higher proportions of EB-specific antibodies in genital secretions compared to sera. Cervical and vaginal secretions and cytobrush specimens had similar proportions of EB-specific antibodies, suggesting any one of these genital sampling techniques could be used to quantify CT-specific antibodies when appropriate normalization methodologies are implemented. Overall, these results illustrate the need to investigate genital tract CT antibody responses, and our assay provides a useful quantitative tool to assess natural immunity in defined

  11. Rule representation using linked data technologies

    NARCIS (Netherlands)

    Zhang, C.; Beetz, J.

    2016-01-01

    In this paper, we report a prototype rule checking system based on Semantic Web and Linked Data technologies. This research aims to find a method to represent rules outside of specific systems, and can be used to integrate and share them among different organizations. In this system we propose to

  12. Specificity tests of an oligonucleotide probe against food-outbreak salmonella for biosensor detection

    Science.gov (United States)

    Chen, I.-H.; Horikawa, S.; Xi, J.; Wikle, H. C.; Barbaree, J. M.; Chin, B. A.

    2017-05-01

    Phage based magneto-elastic (ME) biosensors have been shown to be able to rapidly detect Salmonella in various food systems to serve food pathogen monitoring purposes. In this ME biosensor platform, the free-standing strip-shaped magneto-elastic sensor is the transducer and the phage probe that recognizes Salmonella in food serves as the bio-recognition element. According to Sorokulova et al. at 2005, a developed oligonucleotide probe E2 was reported to have high specificity to Salmonella enterica Typhimurium. In the report, the specificity tests were focused in most of Enterobacterace groups outside of Salmonella family. Here, to understand the specificity of phage E2 to different Salmonella enterica serotypes within Salmonella Family, we further tested the specificity of the phage probe to thirty-two Salmonella serotypes that were present in the major foodborne outbreaks during the past ten years (according to Centers for Disease Control and Prevention). The tests were conducted through an Enzyme linked Immunosorbent Assay (ELISA) format. This assay can mimic probe immobilized conditions on the magnetoelastic biosensor platform and also enable to study the binding specificity of oligonucleotide probes toward different Salmonella while avoiding phage/ sensor lot variations. Test results confirmed that this oligonucleotide probe E2 was high specific to Salmonella Typhimurium cells but showed cross reactivity to Salmonella Tennessee and four other serotypes among the thirty-two tested Salmonella serotypes.

  13. Diffractive elements performance in chromatic confocal microscopy

    International Nuclear Information System (INIS)

    Garzon, J; Duque, D; Alean, A; Toledo, M; Meneses, J; Gharbi, T

    2011-01-01

    The Confocal Laser Scanning Microscopy (CLSM) has been widely used in the semiconductor industry and biomedicine because of its depth discrimination capability. Subsequent to this technique has been developed in recent years Chromatic Confocal Microscopy. This method retains the same principle of confocal and offers the added advantage of removing the axial movement of the moving system. This advantage is usually accomplished with an optical element that generates a longitudinal chromatic aberration and a coding system that relates the axial position of each point of the sample with the wavelength that is focused on each. The present paper shows the performance of compact chromatic confocal microscope when some different diffractive elements are used for generation of longitudinal chromatic aberration. Diffractive elements, according to the process and manufacturing parameters, may have different diffraction efficiency and focus a specific wavelength in a specific focal position. The performance assessment is carried out with various light sources which exhibit an incoherent behaviour and a broad spectral width.

  14. Environmental mineralogy - Understanding element behavior in ecosystems; Mineralogie environnementale: comprendre le comportement des elements dans les ecosystemes

    Energy Technology Data Exchange (ETDEWEB)

    Brown Jr, G.E. [Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305-2115 (United States); Department of Photon Science and Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Calas, G. [Institut de mineralogie et de physique des milieux condenses (IMPMC), universite Paris-6 - universite Paris-7, IPGP, CNRS, case 115, 75252 Paris (France)

    2011-02-15

    Environmental Mineralogy has developed over the past decade in response to the recognition that minerals are linked in many important ways with the global ecosystem. Minerals are the main repositories of the chemical elements in Earth's crust and thus are the main sources of elements needed for the development of civilization, contaminant and pollutant elements that impact global and local ecosystems, and elements that are essential plant nutrients. These elements are released from minerals through natural processes, such as chemical weathering, and anthropogenic activities, such as mining and energy production, agriculture and industrial activities, and careless waste disposal. Minerals also play key roles in the biogeochemical cycling of the elements, sequestering elements and releasing them as the primary minerals in crustal rocks undergo various structural and compositional transformations in response to physical, chemical, and biological processes that produce secondary minerals and soils. These processes have resulted in the release of toxic elements such as arsenic in groundwater aquifers, which is having a major impact on the health of millions of people in South and Southeast Asia. The interfaces between mineral surfaces and aqueous solutions are the locations of most chemical reactions that control the composition of the natural environment, including the composition of natural waters. The nuclear fuel cycle, from uranium mining to the disposition of high-level nuclear waste, is also intimately related to minerals. A fundamental understanding of these processes requires molecular-scale information about minerals, their bulk structures and properties such as solubility, their surfaces, and their interactions with aqueous solutions, atmospheric and soil gases, natural organic matter, and biological organisms. Gaining this understanding is further complicated by the presence of natural, incidental, and manufactured nano-particles in the environment

  15. Fabrication of fuel elements interplay between typical SNR Mark Ia specifications and the fuel element fabrication

    International Nuclear Information System (INIS)

    Biermann, W.K.; Heuvel, H.J.; Pilate, S.; Vanderborck, Y.; Pelckmans, E.; Vanhellemont, G.; Roepenack, H.; Stoll, W.

    1987-01-01

    The core and fuel were designed for the SNR-300 first core by Interatom GmbH and Belgonucleaire. The fuel was fabricated by Alkem/RBU and Belgonucleaire. Based on the preparation of drawings and specifications and on the results of the prerun fabrication, an extensive interplay took place between design requirements, specifications, and fabrication processes at both fuel plants. During start-up of pellet and pin fabrication, this solved such technical questions as /sup 239/Pu equivalent linear weight, pellet density, stoichiometry of the pellets, and impurity content. Close cooperation of designers and manufacturers has allowed manufacture of 205 fuel assemblies without major problems

  16. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

    Science.gov (United States)

    Smith, Robin P; Riesenfeld, Samantha J; Holloway, Alisha K; Li, Qiang; Murphy, Karl K; Feliciano, Natalie M; Orecchia, Lorenzo; Oksenberg, Nir; Pollard, Katherine S; Ahituv, Nadav

    2013-07-18

    Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.

  17. Site specific study for possible ongoing salt dome movement

    International Nuclear Information System (INIS)

    Thoms, R.L.; Manning, T.A.; Paille, L.K.; Gehle, R.M.

    1977-01-01

    U.S. Gulf Coast salt domes, among other geologic structures, currently are being considered for storage of commercial radioactive wastes. A major concern with dome storage of long lived radioactive wastes lies with the possible tectonic movement of the host dome. Any ongoing movement of a salt dome can be monitored with a site specific complementary system of field instrumentation and finite element modelling. Field instrumentation and accompanying finite element analyses for a study dome in northwest Louisiana are described. Site specific data and early experience associated with tiltmeters over the dome are presented. Also, recommendations are made for modifications and extensions of the field instrumentation and finite element modelling appropriate to the specific site under study

  18. O-linked N-acetylglucosamine transferase enhances secretory clusterin expression via liver X receptors and sterol response element binding protein regulation in cervical cancer.

    Science.gov (United States)

    Kim, Min Jun; Choi, Mee Young; Lee, Dong Hoon; Roh, Gu Seob; Kim, Hyun Joon; Kang, Sang Soo; Cho, Gyeong Jae; Kim, Yoon Sook; Choi, Wan Sung

    2018-01-12

    O-linked N-acetylglucosamine transferase (OGT) expression is increased in various cancer types, indicating the potential importance of O-GlcNAcylation in tumorigenesis. Secretory clusterin (sCLU) is involved in cancer cell proliferation and drug resistance, and recently, liver X receptors (LXRs) and sterol response element binding protein-1 (SREBP-1) were reported to regulate sCLU transcription. Here, we found that sCLU is significantly increased in cervical cancer cell lines, which have higher expression levels of O-GlcNAc and OGT than keratinocytes. OGT knockdown decreased expression of LXRs, SREBP-1 and sCLU through hypo-O-GlcNAcylation of LXRs. Additionally, treatment with Thiamet G, O-GlcNAcase OGA inhibitor, increased expression of O-GlcNAcylation and sCLU, and high glucose increased levels of LXRs, SREBP-1 and sCLU in HeLa cells. Moreover, OGT knockdown induced G 0 /G 1 phase cell cycle arrest and late apoptosis in cisplatin-treated HeLa cells, and decreased viability compared to OGT intact HeLa cells. Taken together, these findings suggest that OGT, O-GlcNAcylated LXRs, and SREBP-1 increase sCLU expression in cervical cancer cells, which contributes to drug resistance.

  19. Culture-specific links between maternal executive function, parenting, and preschool children's executive function in South Korea.

    Science.gov (United States)

    Lee, Min Kyung; Baker, Sara; Whitebread, David

    2018-06-01

    Research on the relationships between parental factors and children's executive function (EF) has been conducted mainly in Western cultures. This study provides the first empirical test, in a non-Western context, of how maternal EF and parenting behaviours relate to child EF. South Korean mothers and their preschool children (N = 95 dyads) completed EF tasks. Two aspects of parental scaffolding were observed during a puzzle task: contingency (i.e., adjusting among levels of scaffolding according to the child's ongoing evidence of understanding) and intrusiveness (i.e., directive, mother-centred interactions). Maternal EF and maternal contingency each accounted for unique variance in child EF, above and beyond child age, child language and maternal education. Maternal intrusiveness, however, was not significantly related to child EF. Additionally, no mediating role of parenting was found in the maternal and child EF link. However, child language was found to partially mediate the link between maternal contingency and child EF. These results complement prior findings by revealing distinctive patterns in the link between maternal EF, parenting behaviours, and child EF in the Korean context. © 2018 The British Psychological Society.

  20. Trace element composition of hair in the Italian population

    International Nuclear Information System (INIS)

    Clemente, G.F.; Cigna Rossi, L.

    1979-01-01

    The content of the trace elements Ag, Co, Cr, Cs, Fe, Hg, Ni, Rb, Sb, Sc, Se and Zn has been evaluated in hair samples collected from five different groups of subjects in Italy. All the measurements were performed by means of non-destructive neutron activation analysis of the hair samples that were carefully washed before analysis. In most of the samples the Cs, Rb and Sc content was below the detection limit of the analytical method. Each population group was formed of about five individuals of each sex, selected to be representative of the adult population living in a well-defined community. The five groups were chosen from distinct regions with different socio-economical living habits in order to detect the variability, if any, of the trace element burden among the Italian population. The trace element hair concentration of each subject was correlated with the trace element blood concentration and daily urinary excretion in order to differentiate the trace element content due to exogenous deposition on hair from that due to endogenous absorption routes. The results obtained show that the variability of the hair content among the various groups is strongly linked to local environmental factors. The histograms of the individual values of the hair concentration are given for all trace elements measured, together with a statistical analysis of all data. (author)

  1. Patient-Specific Computational Modeling

    CERN Document Server

    Peña, Estefanía

    2012-01-01

    This book addresses patient-specific modeling. It integrates computational modeling, experimental procedures, imagine clinical segmentation and mesh generation with the finite element method (FEM) to solve problems in computational biomedicine and bioengineering. Specific areas of interest include cardiovascular problems, ocular and muscular systems and soft tissue modeling. Patient-specific modeling has been the subject of serious research over the last seven years and interest in the area is continually growing and this area is expected to further develop in the near future.

  2. A tetranucleotide repeat (D4S1652) is linked to facioscapulohumeral dystrophy and shows no linkage disequilibrium with the disease

    Energy Technology Data Exchange (ETDEWEB)

    Mathews, K.D.; Bailey, H.L.; Mills, K.A. [and others

    1994-09-01

    Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant dystrophy which is associated with a deletion in a subtelomeric repeat element on 4q35. The gene has not yet been identified. The probe detecting this deletion (D4F104S1) is not chromosome 4-specific, and at least one large family has been identified which is not linked to chromosome 4. Thus, persymptomatic/prenatal diagnosis can only be provided to families that are proven to be chromosome 4-linked or where a new mutation is demonstrated. The markers available to demonstrate linkage to chromosome 4, D4S139, D4S163, and D4F35S1, are VNTRs. We have used D4S1652, a tetranucleotide repeat recently identified by the Cooperative Human Linkage Center, in our FSHD families. We found it is completely linked to the 4q35 VNTRs and to the disease phenotype. Physical mapping, using radiation hybrids and somatic cell hybrids, places D4S1652 between D4S139, an interval of approximately 1 Mb. We have used D4S1652 to look for linkage disequilibrium in our FSHD patient population. This result is of interest because of our hypothesis that the deletion in the subtelomeric repeat element alters transcription of a more proximal gene through a position effect. Previously available markers have been unsatisfactory for this experiment because of difficulty comparing numerous VNTR alleles across families. We observed 4, easily distinguished, D4S1652 alleles in our families. We studied 14 chromosomes associated with disease phenotype and 55 chromosomes from nontransmitting parents. We found no evidence for linkage disequilibrium ({chi}{sup 2}=1.313, nonsignificant). This result will need confirmation with a larger patient population, but is consistent with the clinical observation that there is a high rate of a new mutation in this disorder.

  3. Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

    Directory of Open Access Journals (Sweden)

    Jiang Wei

    2008-08-01

    Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

  4. Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

    Science.gov (United States)

    Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

    2008-08-10

    With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

  5. Possible X linked congenital mitochondrial cardiomyopathy in three families.

    OpenAIRE

    Orstavik, K H; Skjörten, F; Hellebostad, M; Hågå, P; Langslet, A

    1993-01-01

    Familial cases of childhood congestive cardiomyopathy with X linked recessive inheritance and abnormalities of heart muscle mitochondria have been previously reported. We report here three families with possible X linked congestive cardiomyopathy and specific mitochondrial abnormalities. The heart disorder presented as endocardial fibroelastosis with neonatal death in two brothers in one family, and as heart failure and death in infancy in two brothers in the other two families. In one family...

  6. Quality assurance of fuel elements

    International Nuclear Information System (INIS)

    Hoerber, J.

    1980-01-01

    The quality assurance activities for reactor fuel elements are based on a quality assurance system which implies the requirements resulting from the specifications, regulations of the authorities, national standards and international rules and regulations. The quality assurance related to production of reactor fuel will be shown for PWR fuel elements in all typical fabrication steps as conversion into UO 2 -powder, pelletizing, rodmanufacture and assembling. A wide range of destructive and nondestructive techniques is applied. Quality assurance is not only verified by testing techniques but also by process monitoring by means of parameter control in production and testing procedures. (RW)

  7. Are Worry and Rumination Specific Pathways Linking Neuroticism and Symptoms of Anxiety and Depression in Patients with Generalized Anxiety Disorder, Major Depressive Disorder and Mixed Anxiety-Depressive Disorder?

    Science.gov (United States)

    Merino, Hipólito; Senra, Carmen; Ferreiro, Fátima

    2016-01-01

    This study examines the relationships between neuroticism (higher-order vulnerability factor), the cognitive styles of worry, brooding and reflection (second-order vulnerability factors) and symptoms of anxiety and depression in three groups of patients: patients with Generalized Anxiety Disorder (GAD), with Major Depressive Disorder (MDD) and with Mixed Anxiety-Depressive Disorder (MADD). One hundred and thirty four patients completed a battery of questionnaires including measures of neuroticism, worry, rumination (brooding and reflection), anxiety and depression. Multiple mediation analyses indicate that worry may act as a mediating mechanism linking neuroticism and anxiety symptoms in the three diagnostic groups, whereas brooding-rumination may play a mediating role between neuroticism and depressive symptoms in patients with MDD and MADD and, with less certainty, in patients with GAD. Overall, our findings suggest that neuroticism may increase the risk of anxious and depressive symptoms via specific links involving either worry or brooding, respectively, and that both worry and brooding may operate in the three groups examined, irrespectively of whether anxiety or depression are the main emotions or whether they coexist without any clear predominance; consequently, we hypothesize the existence of "specific transdiagnostic" mechanisms.

  8. Are Worry and Rumination Specific Pathways Linking Neuroticism and Symptoms of Anxiety and Depression in Patients with Generalized Anxiety Disorder, Major Depressive Disorder and Mixed Anxiety-Depressive Disorder?

    Science.gov (United States)

    Merino, Hipólito; Ferreiro, Fátima

    2016-01-01

    This study examines the relationships between neuroticism (higher-order vulnerability factor), the cognitive styles of worry, brooding and reflection (second-order vulnerability factors) and symptoms of anxiety and depression in three groups of patients: patients with Generalized Anxiety Disorder (GAD), with Major Depressive Disorder (MDD) and with Mixed Anxiety-Depressive Disorder (MADD). One hundred and thirty four patients completed a battery of questionnaires including measures of neuroticism, worry, rumination (brooding and reflection), anxiety and depression. Multiple mediation analyses indicate that worry may act as a mediating mechanism linking neuroticism and anxiety symptoms in the three diagnostic groups, whereas brooding-rumination may play a mediating role between neuroticism and depressive symptoms in patients with MDD and MADD and, with less certainty, in patients with GAD. Overall, our findings suggest that neuroticism may increase the risk of anxious and depressive symptoms via specific links involving either worry or brooding, respectively, and that both worry and brooding may operate in the three groups examined, irrespectively of whether anxiety or depression are the main emotions or whether they coexist without any clear predominance; consequently, we hypothesize the existence of "specific transdiagnostic" mechanisms. PMID:27243462

  9. Are Worry and Rumination Specific Pathways Linking Neuroticism and Symptoms of Anxiety and Depression in Patients with Generalized Anxiety Disorder, Major Depressive Disorder and Mixed Anxiety-Depressive Disorder?

    Directory of Open Access Journals (Sweden)

    Hipólito Merino

    Full Text Available This study examines the relationships between neuroticism (higher-order vulnerability factor, the cognitive styles of worry, brooding and reflection (second-order vulnerability factors and symptoms of anxiety and depression in three groups of patients: patients with Generalized Anxiety Disorder (GAD, with Major Depressive Disorder (MDD and with Mixed Anxiety-Depressive Disorder (MADD. One hundred and thirty four patients completed a battery of questionnaires including measures of neuroticism, worry, rumination (brooding and reflection, anxiety and depression. Multiple mediation analyses indicate that worry may act as a mediating mechanism linking neuroticism and anxiety symptoms in the three diagnostic groups, whereas brooding-rumination may play a mediating role between neuroticism and depressive symptoms in patients with MDD and MADD and, with less certainty, in patients with GAD. Overall, our findings suggest that neuroticism may increase the risk of anxious and depressive symptoms via specific links involving either worry or brooding, respectively, and that both worry and brooding may operate in the three groups examined, irrespectively of whether anxiety or depression are the main emotions or whether they coexist without any clear predominance; consequently, we hypothesize the existence of "specific transdiagnostic" mechanisms.

  10. Fabrication technology of spherical fuel element for HTR-10

    International Nuclear Information System (INIS)

    He Jun; Zou Yanwen; Liang Tongxiang; Qiu Xueliang

    2002-01-01

    R and D on the fabrication technology of the spherical fuel elements for the 10 MW HTR Test Module (HTR-10) began from 1986. Cold quasi-isostatic molding with a silicon rubber die is used for manufacturing the spherical fuel elements.The fabrication technology and the graphite matrix materials were investigated and optimized. Twenty five batches of fuel elements, about 11000 of the fuel elements, have been produced. The cold properties of the graphite matrix materials satisfied the design specifications. The mean free uranium fraction of 25 batches was 5 x 10 -5

  11. Integrator element as a promoter of active learning in engineering teaching

    Science.gov (United States)

    Oliveira, Paulo C.; Oliveira, Cristina G.

    2014-03-01

    In this paper, we present a teaching proposal used in an Introductory Physics course to civil engineering students from Porto's Engineering Institute/Instituto Superior de Engenharia do Porto (ISEP). The proposal was born from the need to change students' perception and motivation for learning physics. It consists in the use of an integrator element, called the physics elevator project. This integrator element allows us to use, in a single project, all the content taught in the course and uses several active learning strategies. In this paper, we analyse this project as: (i) a clarifying element of the contents covered in the course; (ii) a promoter element of motivation and active participation in class and finally and (iii) a link between the contents covered in the course and the 'real world'. The data were collected by a questionnaire and interviews to students. From the data collected, it seems that the integrator element improves students' motivation towards physics and develops several skills that they consider to be important to their professional future. It also acts as a clarifying element and makes the connection between the physics that is taught and the 'real world'.

  12. Linked data: un nuovo alfabeto del web semantico

    Directory of Open Access Journals (Sweden)

    Mauro Guerrini

    2013-01-01

    Full Text Available The paper defines the linked data as a set of best practices that are used to publish data on the web using a machine; the technology (or mode of realization of linked data is associated with the concept of the semantic web. It is the area of the semantic web, or web of data, as defined by Tim Berners-Lee "A web of things in the world, described by data on the web". The paper highlights the continuities and differences between semantic web and web traditional, or web documents. The analysis of linked data takes place within the world of libraries, archives and museums, traditionally committed to high standards for structuring and sharing of data. The data, in fact, assume the role of generating quality information for the network. The production of linked data requires compliance with rules and the use of specific technologies and languages, especially in the case of publication of linked data in open mode. The production cycle of linked data may be the track, or a guideline, for institutions that wish to join projects to publish their data. Data quality is assessed through a rating system designed by Tim Berners-Lee.

  13. An IFNG SNP with an estrogen-like response element selectively enhances promoter expression in peripheral but not lamina propria T cells.

    Science.gov (United States)

    Gonsky, R; Deem, R L; Bream, J H; Young, H A; Targan, S R

    2006-07-01

    This study examines mucosa-specific regulatory pathways involved in modulation of interferon-gamma (IFN-gamma) in lamina propria T cells. Previous studies identified mucosa-specific CD2 cis-elements within the -204 to -108 bp IFNG promoter. Within this region, a single-site nucleotide polymorphism, -179G/T, imparts tumor necrosis factor-alpha stimulation of IFNG in peripheral blood lymphocytes, and is linked with accelerated AIDS progression. We discovered a putative estrogen response element (ERE) introduced by the -179T, which displays selective activation in peripheral blood mononuclear cells (PBMC) vs lamina propria mononuclear cells (LPMC). Transfection of PBMC with constructs containing the -179G or -179T site revealed CD2-mediated enhancement of the -179T compared to -179G allele, although, in LPMC, a similar level of expression was detected. Electrophoretic mobility shift assay (EMSA) analysis demonstrated CD2-mediated nucleoprotein binding to the -179T but not the -179G in PBMC. In LPMC, binding is constitutive to both -179G and -179T regions. Sequence and EMSA analysis suggests that the -179T allele creates an ERE-like binding site capable of binding recombinant estrogen receptor. Estrogen response element transactivation is enhanced by CD2 signaling, but inhibited by estrogen in PBMC but not in LPMC, although expression of estrogen receptor was similar. This is the first report to describe a potential molecular mechanism responsible for selectively controlling IFN-gamma production in LPMC.

  14. Applications of Lagrangian Dispersion Modeling to the Analysis of Changes in the Specific Absorption of Elemental Carbon

    Energy Technology Data Exchange (ETDEWEB)

    Doran, J. C.; Fast, Jerome D.; Barnard, James C.; Laskin, Alexander; Desyaterik, Yury; Gilles, Marry K.; Hopkins, Rebecca J.

    2008-03-07

    We use a Lagrangian dispersion model driven by a mesoscale model with four-dimensional data assimilation to simulate the dispersion of elemental carbon (EC) over a region encompassing Mexico City and its surroundings, the study domain for the 2006 MAX-MEX experiment, which was a component of the MILAGRO campaign. The results are used to identify periods when biomass burning was likely to have had a significant impact on the concentrations of elemental carbon at two sites, T1 and T2, downwind of the city, and when emissions from the Mexico City Metropolitan Area (MCMA) were likely to have been more important. They are also used to estimate the median ages of EC affecting the specific absorption of light, aABS, at 870 nm as well as to identify periods when the urban plume from the MCMA was likely to have been advected over T1 and T2. Values of aABS at T1, the nearer of the two sites to Mexico City, were smaller at night and increased rapidly after mid-morning, peaking in the mid-afternoon. The behavior is attributed to the coating of aerosols with substances such as sulfate or organic carbon during daylight hours, but such coating appears to be limited or absent at night. Evidence for this is provided by scanning electron microscope images of aerosols collected at three sampling sites. During daylight hours the values of aABS did not increase with aerosol age for median ages in the range of 1-4 hours. There is some evidence for absorption increasing as aerosols were advected from T1 to T2 but the statistical significance of that result is not strong.

  15. Structural elements recognized by abacavir-induced T cells

    DEFF Research Database (Denmark)

    Yerly, Daniel; Pompeu, Yuri Andreiw; Schutte, Ryan J.

    2017-01-01

    of autoimmune destruction. The structural elements recognized by drug-specific T cell receptors (TCRs) in vivo are poorly defined. Drug-stimulated T cells express TCRs specific for peptide/HLA complexes, but the characteristics of peptides (sequence, or endogenous or exogenous origin) presented in the context...

  16. Visualizing Mutation-Specific Differences in the Trafficking-Deficient Phenotype of Kv11.1 Proteins Linked to Long QT Syndrome Type 2.

    Science.gov (United States)

    Hall, Allison R; Anderson, Corey L; Smith, Jennifer L; Mirshahi, Tooraj; Elayi, Claude S; January, Craig T; Delisle, Brian P

    2018-01-01

    KCNH2 encodes the Kv11.1 α-subunit that underlies the rapidly activating delayed-rectifier K + current in the heart. Loss-of-function KCNH2 mutations cause long QT syndrome type 2 (LQT2), and most LQT2-linked missense mutations inhibit the trafficking of Kv11.1 channel protein to the cell surface membrane. Several trafficking-deficient LQT2 mutations (e.g., G601S) generate Kv11.1 proteins that are sequestered in a microtubule-dependent quality control (QC) compartment in the transitional endoplasmic reticulum (ER). We tested the hypothesis that the QC mechanisms that regulate LQT2-linked Kv11.1 protein trafficking are mutation-specific. Confocal imaging analyses of HEK293 cells stably expressing the trafficking-deficient LQT2 mutation F805C showed that, unlike G601S-Kv11.1 protein, F805C-Kv11.1 protein was concentrated in several transitional ER subcompartments. The microtubule depolymerizing drug nocodazole differentially affected G601S- and F805C-Kv11.1 protein immunostaining. Nocodazole caused G601S-Kv11.1 protein to distribute into peripheral reticular structures, and it increased the diffuse immunostaining of F805C-Kv11.1 protein around the transitional ER subcompartments. Proteasome inhibition also affected the immunostaining of G601S- and F805C-Kv11.1 protein differently. Incubating cells in MG132 minimally impacted G601S-Kv11.1 immunostaining, but it dramatically increased the diffuse immunostaining of F805C-Kv11.1 protein in the transitional ER. Similar results were seen after incubating cells in the proteasome inhibitor lactacystin. Differences in the cellular distribution of G601S-Kv11.1 and F805C-Kv11.1 protein persisted in transfected human inducible pluripotent stem cell derived cardiomyocytes. These are the first data to visually demonstrate mutation-specific differences in the trafficking-deficient LQT2 phenotype, and this study has identified a novel way to categorize trafficking-deficient LQT2 mutations based on differences in intracellular

  17. Using Facebook and LinkedIn to Recruit Nurses for an Online Survey.

    Science.gov (United States)

    Stokes, Yehudis; Vandyk, Amanda; Squires, Janet; Jacob, Jean-Daniel; Gifford, Wendy

    2017-11-01

    Social media is an emerging tool used by researchers; however, limited information is available on its use for participant recruitment specifically. The purpose of this article is to describe the use of Facebook and LinkedIn social media sites in the recruitment of nurses for an online survey, using a 5-week modified online Dillman approach. Within 3 weeks, we exceeded our target sample size ( n = 170) and within 5 weeks recruited 267 English-speaking nurses ( n = 172, Facebook; n = 95, LinkedIn). Advantages included speed of recruitment, cost-efficiency, snowballing effects, and accessibility of the researcher to potential participants. However, an analysis of the recruited participants revealed significant differences when comparing the sociodemographics of participants recruited through Facebook and LinkedIn, specifically relating to the characteristics of sex, age, and level of education. Differences between Facebook and LinkedIn as recruitment platforms should be considered when incorporating these strategies.

  18. Trace Elements and Vitamin D in Gestational Diabetes

    Directory of Open Access Journals (Sweden)

    Genova Mariana

    2018-03-01

    Full Text Available Gestational diabetes mellitus (GDM, one of the most common pregnancy complications, is defined as glucose intolerance with onset or first recognition during pregnancy. Its prevalence varies worldwide in dependence on characteristics of the underlying population and applied diagnostic criteria. The etiology is multifactorial and not sufficiently elucidated. Available evidence suggests that the base of pathogenesis is relatively diminished insulin secretion coupled with pregnancy-induced insulin resistance. Modifiable and non-modifiable risk factors for development have been identified. Trace elements and vitamin D could be contributed to modifiable factors for prediction the risk in a large population. Essential trace elements in pregnancy are necessary to overcome systemic oxidative, metabolic and inflammatory stress. Evidence, still inconclusive, has been accumulated about the relation between higher incidence of vitamin D failure/deficiency during pregnancy and GDM. The lower level of 25-OH vitamin D could be associated with increased risk for anemia development, also including pregnant women. This review intends to provide an overview of the possible link between both vitamin D and trace elements as risk factors for GDM development.

  19. Elemental abundance analyses with coadded Dominion Astrophysical Observatory spectrograms: Pt. 3

    International Nuclear Information System (INIS)

    Adelman, S.J.

    1988-01-01

    Elemental abundance analyses were performed for three superficially normal main-sequence stars θ Leonis (A2V), τ Herculus (B5IV) and ο Pegasi (AlIV). These studies used coadded spectrograms produced from at least 12 2.4 A mm -1 IIaO Dominion Astrophysical Observatory spectrograms and show a greater degree of internal consistency and smaller microturbulent velocities than previous studies of these stars which used lower signal-to-noise data. Many lines not previously seen were identified including some of new atomic species whose analysis provide a more complete picture of the elemental abundances. The identification and analysis of La II lines in ο Peg link this star more closely with the classical metallic-lined (Am) stars, although there are considerable differences in abundances. Some of θ Leo's elemental abundances, particularly those of vanadium, strontium, and zirconium, are significantly different from solar in confirmation of previous analyses. τ Her's elemental abundances are typically a factor of 2 less than solar. (author)

  20. Rigid body formulation in a finite element context with contact interaction

    Science.gov (United States)

    Refachinho de Campos, Paulo R.; Gay Neto, Alfredo

    2018-03-01

    The present work proposes a formulation to employ rigid bodies together with flexible bodies in the context of a nonlinear finite element solver, with contact interactions. Inertial contributions due to distribution of mass of a rigid body are fully developed, considering a general pole position associated with a single node, representing a rigid body element. Additionally, a mechanical constraint is proposed to connect a rigid region composed by several nodes, which is useful for linking rigid/flexible bodies in a finite element environment. Rodrigues rotation parameters are used to describe finite rotations, by an updated Lagrangian description. In addition, the contact formulation entitled master-surface to master-surface is employed in conjunction with the rigid body element and flexible bodies, aiming to consider their interaction in a rigid-flexible multibody environment. New surface parameterizations are presented to establish contact pairs, permitting pointwise interaction in a frictional scenario. Numerical examples are provided to show robustness and applicability of the methods.

  1. SpEnD: Linked Data SPARQL Endpoints Discovery Using Search Engines

    OpenAIRE

    Yumusak, Semih; Dogdu, Erdogan; Kodaz, Halife; Kamilaris, Andreas

    2016-01-01

    In this study, a novel metacrawling method is proposed for discovering and monitoring linked data sources on the Web. We implemented the method in a prototype system, named SPARQL Endpoints Discovery (SpEnD). SpEnD starts with a "search keyword" discovery process for finding relevant keywords for the linked data domain and specifically SPARQL endpoints. Then, these search keywords are utilized to find linked data sources via popular search engines (Google, Bing, Yahoo, Yandex). By using this ...

  2. Director remuneration, corporate governance and performance: A comparison between government linked companies vs non government linked companies

    Directory of Open Access Journals (Sweden)

    Nazrul Hisyam Ab Razak

    2014-07-01

    Full Text Available This study has examined the relationship between director’s remuneration, corporate governance structure and performance of a sample of 150 companies listed on the Bursa Malaysia from year 2008 until 2013. The sample was selected to provide matched-pair of government linked companies (GLCs and non-government linked companies (non-GLCs, as it was anticipated that these group would have different governance structure, the key difference being government ownership. The result holds even when we control for company specific characteristic such as corporate governance, company size, leverage, director’s remuneration, board size and auditors. This study uses panel based regression model to examine the impact of government control mechanism on company performance using two important measurers. These are accounting based measure proxies by ROA and non-accounting based measures by Tobin’s Q. Statistically significant relationships were found across the groupings and for different performance measures. Findings appear to suggest that there is a significant impact of government ownership on company performance after controlling for company specific characteristics.

  3. Test bed for real-time image acquisition and processing systems based on FlexRIO, CameraLink, and EPICS

    International Nuclear Information System (INIS)

    Barrera, E.; Ruiz, M.; Sanz, D.; Vega, J.; Castro, R.; Juárez, E.; Salvador, R.

    2014-01-01

    Highlights: • The test bed allows for the validation of real-time image processing techniques. • Offers FPGA (FlexRIO) image processing that does not require CPU intervention. • Is fully compatible with the architecture of the ITER Fast Controllers. • Provides flexibility and easy integration in distributed experiments based on EPICS. - Abstract: Image diagnostics are becoming standard ones in nuclear fusion. At present, images are typically analyzed off-line. However, real-time processing is occasionally required (for instance, hot-spot detection or pattern recognition tasks), which will be the objective for the next generation of fusion devices. In this paper, a test bed for image generation, acquisition, and real-time processing is presented. The proposed solution is built using a Camera Link simulator, a Camera Link frame-grabber, a PXIe chassis, and offers software interface with EPICS. The Camera Link simulator (PCIe card PCIe8 DVa C-Link from Engineering Design Team) generates simulated image data (for example, from video-movies stored in fusion databases) using a Camera Link interface to mimic the frame sequences produced with diagnostic cameras. The Camera Link frame-grabber (FlexRIO Solution from National Instruments) includes a field programmable gate array (FPGA) for image acquisition using a Camera Link interface; the FPGA allows for the codification of ad-hoc image processing algorithms using LabVIEW/FPGA software. The frame grabber is integrated in a PXIe chassis with system architecture similar to that of the ITER Fast Controllers, and the frame grabber provides a software interface with EPICS to program all of its functionalities, capture the images, and perform the required image processing. The use of these four elements allows for the implementation of a test bed system that permits the development and validation of real-time image processing techniques in an architecture that is fully compatible with that of the ITER Fast Controllers

  4. Nuclide documentation. Element specific parameter values used in the biospheric models of the safety assessments SR 97 and SAFE

    International Nuclear Information System (INIS)

    Karlsson, Sara; Bergstroem, Ulla

    2002-05-01

    In this report the element and nuclide specific parameter values used in the biospheric models of the safety assessments SR 97 and SAFE are presented. The references used are presented and where necessary the process of estimation of data is described. The parameters treated in this report are distribution coefficients in soil, organic soil and suspended matter in freshwater and brackish water, root uptake factors for pasturage, cereals, root crops and vegetables, bioaccumulation factors for freshwater fish, brackish water fish, freshwater invertebrates and marine water plants, transfer coefficients for transfer to milk and meat, translocation factors and dose coefficients for external exposure, ingestion (age-dependent values) and inhalation (age-dependent values). The radionuclides treated are those which could be of interest in the two safety assessments. Physical data such as half-lives and type of decay are also presented

  5. Nuclide documentation. Element specific parameter values used in the biospheric models of the safety assessments SR 97 and SAFE

    Energy Technology Data Exchange (ETDEWEB)

    Karlsson, Sara; Bergstroem, Ulla [Studsvik Eco and Safety AB, Nykoeping (Sweden)

    2002-05-01

    In this report the element and nuclide specific parameter values used in the biospheric models of the safety assessments SR 97 and SAFE are presented. The references used are presented and where necessary the process of estimation of data is described. The parameters treated in this report are distribution coefficients in soil, organic soil and suspended matter in freshwater and brackish water, root uptake factors for pasturage, cereals, root crops and vegetables, bioaccumulation factors for freshwater fish, brackish water fish, freshwater invertebrates and marine water plants, transfer coefficients for transfer to milk and meat, translocation factors and dose coefficients for external exposure, ingestion (age-dependent values) and inhalation (age-dependent values). The radionuclides treated are those which could be of interest in the two safety assessments. Physical data such as half-lives and type of decay are also presented.

  6. Identification of a functional element in the promoter of the silkworm (Bombyx mori) fat body-specific gene Bmlp3.

    Science.gov (United States)

    Xu, Hanfu; Deng, Dangjun; Yuan, Lin; Wang, Yuancheng; Wang, Feng; Xia, Qingyou

    2014-08-01

    30K proteins are a group of structurally related proteins that play important roles in the life cycle of the silkworm Bombyx mori and are largely synthesized and regulated in a time-dependent manner in the fat body. Little is known about the upstream regulatory elements associated with the genes encoding these proteins. In the present study, the promoter of Bmlp3, a fat body-specific gene encoding a 30K protein family member, was characterized by joining sequences containing the Bmlp3 promoter with various amounts of 5' upstream sequences to a luciferase reporter gene. The results indicated that the sequences from -150 to -250bp and -597 to -675bp upstream of the Bmlp3 transcription start site were necessary for high levels of luciferase activity. Further analysis showed that a 21-bp sequence located between -230 and -250 was specifically recognized by nuclear factors from silkworm fat bodies and BmE cells, and could enhance luciferase reporter-gene expression 2.8-fold in BmE cells. This study provides new insights into the Bmlp3 promoter and contributes to the further clarification of the function and developmental regulation of Bmlp3. Copyright © 2014. Published by Elsevier B.V.

  7. Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer

    DEFF Research Database (Denmark)

    Zuber, Verena; Bettella, Francesco; Witoelar, Aree

    2017-01-01

    progression. Although previous approaches have been tried to explain risk associated with SNPs in regulatory DNA elements, so far epigenetic readers such as bromodomain containing protein 4 (BRD4) and super-enhancers have not been used to annotate SNPs. In prostate cancer (PC), androgen receptor (AR) binding......Background: Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA elements, acting to determine tissue or cell identity and driving tumor...... the differential enrichment of SNPs mapping to specific categories of enhancers. We find that BRD4 is the key discriminant of tissue-specific enhancers, showing that it is more powerful than AR binding information to capture PC specific risk loci, and can be used with similar effect in breast cancer (BC...

  8. Transcription factor trapping by RNA in gene regulatory elements.

    Science.gov (United States)

    Sigova, Alla A; Abraham, Brian J; Ji, Xiong; Molinie, Benoit; Hannett, Nancy M; Guo, Yang Eric; Jangi, Mohini; Giallourakis, Cosmas C; Sharp, Phillip A; Young, Richard A

    2015-11-20

    Transcription factors (TFs) bind specific sequences in promoter-proximal and -distal DNA elements to regulate gene transcription. RNA is transcribed from both of these DNA elements, and some DNA binding TFs bind RNA. Hence, RNA transcribed from regulatory elements may contribute to stable TF occupancy at these sites. We show that the ubiquitously expressed TF Yin-Yang 1 (YY1) binds to both gene regulatory elements and their associated RNA species across the entire genome. Reduced transcription of regulatory elements diminishes YY1 occupancy, whereas artificial tethering of RNA enhances YY1 occupancy at these elements. We propose that RNA makes a modest but important contribution to the maintenance of certain TFs at gene regulatory elements and suggest that transcription of regulatory elements produces a positive-feedback loop that contributes to the stability of gene expression programs. Copyright © 2015, American Association for the Advancement of Science.

  9. Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution

    Energy Technology Data Exchange (ETDEWEB)

    Kass, D.H. [Louisiana State Univ. Medical Center, New Orleans, LA (United States). Dept. of Biochemistry and Molecular Biology; Batzer, M.A. [Lawrence Livermore National Lab., CA (United States); Deininger, P.L. [Louisiana State Univ. Medical Center, New Orleans, LA (United States). Dept. of Biochemistry and Molecular Biology]|[Alton Ochsner Medical Foundation, New Orleans, LA (United States). Lab. of Molecular Genetics

    1995-01-01

    The Alu repetitive family of short interspersed elements (SINEs) in primates can be subdivided into distinct subfamilies by specific diagnostic nucleotide changes. The older subfamilies are generally very abundant, while the younger subfamilies have fewer copies. Some of the youngest Alu elements are absent in the orthologous loci of nonhuman primates, indicative of recent retroposition events, the primary mode of SINE evolutions. PCR analysis of one young Alu subfamily (Sb2) member found in the low-density lipoprotein receptor gene apparently revealed the presence of this element in the green monkey, orangutan, gorilla, and chimpanzee genomes, as well as the human genome. However, sequence analysis of these genomes revealed a highly mutated, older, primate-specific Alu element was present at this position in the nonhuman primates. Comparison of the flanking DNA sequences upstream of this Alu insertion corresponded to evolution expected for standard primate phylogeny, but comparison of the Alu repeat sequences revealed that the human element departed from this phylogeny. The change in the human sequence apparently occurred by a gene conversion event only within the Alu element itself, converting it from one of the oldest to one of the youngest Alu subfamilies. Although gene conversions of Alu elements are clearly very rare, this finding shows that such events can occur and contribute to specific cases of SINE subfamily evolution.

  10. Information Theoretical Limits of Free-Space Optical Links

    KAUST Repository

    Ansari, Imran Shafique; Al-Quwaiee, Hessa; Zedini, Emna; Alouini, Mohamed-Slim

    2016-01-01

    detection) over generalized atmospheric turbulence channels that account for generalized pointing errors is presented. Specifically, unified exact closed-form expressions for the moments of the end-to-end signal-to-noise ratio (SNR) of a single link FSO

  11. SXT/R391 Integrative and Conjugative Elements (ICEs) Encode a Novel 'Trap-Door' Strategy for Mobile Element Escape.

    Science.gov (United States)

    Ryan, Michael P; Armshaw, Patricia; Pembroke, J Tony

    2016-01-01

    Integrative conjugative elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision, and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation, and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitization function which results in stress induced killing of bacterial cells harboring the ICE. This sensitization has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer.

  12. Radiation tolerant optical links for the readout of the ATLAS experiment

    CERN Document Server

    Pearce, M

    2000-01-01

    The ATLAS experiment will use radiation tolerant optical links to transfer data to and from sub-detector systems. The link specifications can be broadly divided into two classes, represented by the inner tracking detectors and the electromagnetic calorimeter. A feature common to all the readout links is the use of vertical cavity surface emitting laser diodes coupled to multimode optical fibres. Results from the development for both of these environments are reviewed with particular attention bring paid to irradiation studies. (8 refs).

  13. Trace element quantification of lead based roof sheets of historical monuments by Laser Induced Breakdown Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Syvilay, D., E-mail: delphine.syvilay@culture.gouv.fr [LRMH USR 3224, 29 rue de Paris, 77420 Champs-sur-Marne (France); Texier, A. [LRMH USR 3224, 29 rue de Paris, 77420 Champs-sur-Marne (France); Arles, A.; Gratuze, B. [IRAMAT, 3D, rue de la Férollerie, 45071 Orléans Cedex 2 (France); Wilkie-Chancellier, N.; Martinez, L.; Serfaty, S. [SATIE, UMR CNRS 8029, Université de Cergy-Pontoise, ENS Cachan, 95000 Cergy-Pontoise Cedex (France); Detalle, V. [LRMH USR 3224, 29 rue de Paris, 77420 Champs-sur-Marne (France)

    2015-01-01

    The aim of this paper is to identify the different periods of construction or restoration of the lead roof of a historic monument. Trace elements in a lead matrix can be a signature of the metallurgical processes, allowing identification of a specific time period for the production of the lead used to build the roof. The ability of LIBS (Laser Induced Breakdown Spectroscopy) to detect such trace elements in a lead matrix is therefore explored and checked by comparing its results with LA-ICP-MS as a reference method (Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry). Concentrations of 263 samples were compared between LIBS and LA-ICP-MS data and their correlation was evaluated. Another way to compare their results is also suggested by combining PCA (Principal Component Analysis) and GIS (Geographic Information System). As a result statistical mappings were created, highlighting metallurgical groups of samples across the roof of the building. This innovative approach links concentration and spatial location resulting in an easily interpretable graphical presentation of the data. The results of both spectrometry methods lead to similar conclusions with distinctive areas of different lead compositions and by extension different lead dating across the roof. But since LIBS is portable we can conclude that it is a suitable and reliable instrument for in-situ applications on historic monuments. - Highlights: • Quantification of trace elements (Ag, Bi, Cu and Sn) in a lead matrix by LIBS and LA-ICP-MS • Low limit of detection for Ag, Bi, Cu and Sn by using LIBS portable instrumentation • Set up a specific data processing combining PCA and GIS for cultural heritage application • Comparison of LIBS and LA-ICP-MS results with 263 samples • 488 samples analyzed by LIBS.

  14. Transfer of Some Major and Trace Elements From Phosphate Rock to Super-Phosphate Fertilizers

    International Nuclear Information System (INIS)

    El-Reefya, H.I.; Bin-Jaz, A.A.; Zaied, M.E.; Badran, H.M.; Badran, H.M.

    2014-01-01

    This study assesses the transfer of some major and trace elements from phosphate rock (PR) to single (SSP) and triple (TSP) superphosphate fertilizers. Samples from a fertilizer plant and local market were collected and analyzed using inductively coupled plasma spectrometer. Cluster analysis indicated that the inner-relationship among the concentration of the elements in PR, SSP, and TSP are different. Only one element (Mo) has concentration in SSP higher than phosphate rock. The production process of these two types of superphosphate leads to transfer higher portion of Mn, B, Cu, Mo, Sr, and V present in the phosphate rock to SSP than TSP. The potentially hazardous element Cd is also transmitted more to SSP than TSP, and Cr is equally transferred to both types. The mean elemental concentrations normalized to the percentage of P 2 O 5 demonstrate that for most elements they are the higher concentrations in SSP are linked to the phosphate contents

  15. Processing semblances induced through inter-postsynaptic functional LINKs, presumed biological parallels of K-lines proposed for building artificial intelligence

    Directory of Open Access Journals (Sweden)

    Kunjumon I Vadakkan

    2011-07-01

    Full Text Available The internal sensation of memory, which is available only to the owner of an individual nervous system, is difficult to analyze for its basic elements of operation. We hypothesize that associative learning induces the formation of functional LINK between the postsynapses. During memory retrieval, the activation of either postsynapse re-activates the functional LINK evoking a semblance of sensory activity arriving at its opposite postsynapse, nature of which defines the basic unit of virtual internal sensation - namely, semblion. Neuronal networks that undergo continuous oscillatory activity at certain levels of their organization induce semblions enabling the system to continuously learn, self-organize, and demonstrate instantiation, features that can be utilized for developing artificial intelligence (AI. Suitability of the inter-postsynaptic functional LINKs to meet the expectations of Minsky’s K-lines, basic elements of a memory theory generated to develop AI and methods to replicate semblances outside the nervous system are explained.

  16. Too Many Links in the Horizon; What is Next? Linked Views and Linked History

    NARCIS (Netherlands)

    E. Liarou (Erietta); S. Idreos (Stratos)

    2011-01-01

    textabstractThe trend for more online linked data becomes stronger. Foreseeing a future where ``everything" will be online and linked, we ask the critical question; what is next? We envision that managing, querying and storing large amounts of links and data is far from yet another query

  17. Using linked data to evaluate collisions with fixed objects in Pennsylvania : Crash Outcome Data Evaluation System (CODES) linked data demonstration project

    Science.gov (United States)

    1998-10-01

    This report uses police-reported motor vehicle crash data linked to Emergency Medical Services data and hospital discharge data to evaluate the relative risk of injury posed by specific roadside objects in Pennsylvania. The report focuses primarily o...

  18. Reconceptualizing the motive/environment link in recreation choice behavior

    Science.gov (United States)

    Richard Schreyer; Richard C. Knopf; Daniel R. Williams

    1985-01-01

    Effective inventory, management, and planning for recreation resources depend upon knowing why persons choose certain environments to attain specific goals, and what elements in those environments facilitate goal-attainment. Research focused on relating motives for participation to specific components in the environment has had only limited success. This paper proposes...

  19. Evaluation of elemental profiling methods, including laser-induced breakdown spectroscopy (LIBS), for the differentiation of Cannabis plant material grown in different nutrient solutions.

    Science.gov (United States)

    El-Deftar, Moteaa M; Robertson, James; Foster, Simon; Lennard, Chris

    2015-06-01

    Laser-induced breakdown spectroscopy (LIBS) is an emerging atomic emission based solid sampling technique that has many potential forensic applications. In this study, the analytical performance of LIBS, as well as that of inductively coupled plasma mass spectrometry (ICP-MS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and X-ray microfluorescence (μXRF), was evaluated for the ability to conduct elemental analyses on Cannabis plant material, with a specific investigation of the possible links between hydroponic nutrients and elemental profiles from associated plant material. No such study has been previously published in the literature. Good correlation among the four techniques was observed when the concentrations or peak areas of the elements of interest were monitored. For Cannabis samples collected at the same growth time, the elemental profiles could be related to the use of particular commercial nutrients. In addition, the study demonstrated that ICP-MS, LA-ICP-MS and LIBS are suitable techniques for the comparison of Cannabis samples from different sources, with high discriminating powers being achieved. On the other hand, μXRF method was not suitable for the discrimination of Cannabis samples originating from different growth nutrients. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  20. Trace elements transport in western Siberia rivers across a permafrost gradient

    Science.gov (United States)

    Pokrovsky, O. S.; Manasypov, R. M.; Loiko, S.; Krickov, I. A.; Kopysov, S. G.; Kolesnichenko, L. G.; Vorobyev, S. N.; Kirpotin, S. N.

    2015-11-01

    Towards a better understanding of trace element transport in permafrost-affected Earth surface environments, we sampled ∼ 60 large and small rivers (important region. No statistically significant effect of the basin size on most TE concentration was evidenced. Three category of trace elements were distinguished according to their concentration - latitude pattern: (i) increasing northward in spring and winter (Fe, Al, Ga (only winter), Ti (only winter), REEs, Pb, Zr, Hf, Th (only winter)), linked to leaching from peat and/or redox processes and transport in the form of Fe-rich colloids, (ii) decreasing northward during all seasons (Sr, Mo, U, As, Sb) marking the underground water influence of river feeding and (iii) elements without distinct trend from S to N whose variations within each latitude range were higher than the difference between latitudinal ranges (B, Li, Ti (except summer), Cr, V, Mn, Zn, Cd, Cs, Hf, Th). In addition to these general features, specific, northward increase during spring period was mostly pronounced for Fe, Mn, Co, Zn and Ba and may stem from a combination of enhanced leaching from the topsoil and vegetation and bottom waters of the lakes (spring overturn). A spring time northward decrease was observed for Ni, Cu, Zr, Rb. The southward increase in summer was strongly visible for Fe, Ni, Ba, Rb and V, probably due to peat/moss release (Ni, Ba, Rb) or groundwater feeding (Fe, V). The Principal Component Analysis demonstrated two main factors potentially controlling the ensemble of TE concentration variation. The first factor, responsible for 16-20 % of overall variation, included trivalent and tetravalent hydrolysates, Cr, V, and DOC and presumably reflected the presence of organo-mineral colloids, as also confirmed by previous studies in Siberian rivers. The 2nd factor (8-14 % variation) was linked to the latitude of the watershed and acted on elements affected by the groundwater feeding (DIC, Sr, Mo, As, Sb, U), whose concentration

  1. Electrical engineering design using characterized elements; Conception en genie electrique a l'aide d'elements caracterises

    Energy Technology Data Exchange (ETDEWEB)

    Demni, H.E.

    2004-10-15

    This work treats systematic design of energy transformation structures used in Electrical Engineering. We propose an approach dedicated to design by association of characterized elements. Starting from a set of specifications, the designer has to define a coherent structure by assembling predefined elements. Within this framework, we adopt a characterization approach that takes into account various criteria necessary for design. Then, this approach allowed us to develop methodologies for designing electric energy transformation structures. These methodologies were used to implement a software application based on three tools: a data base as an elements library, a graphic tool allowing the construction of energy transformation structures, an expert module which helps the designer in his work. (author)

  2. Meta-path based heterogeneous combat network link prediction

    Science.gov (United States)

    Li, Jichao; Ge, Bingfeng; Yang, Kewei; Chen, Yingwu; Tan, Yuejin

    2017-09-01

    The combat system-of-systems in high-tech informative warfare, composed of many interconnected combat systems of different types, can be regarded as a type of complex heterogeneous network. Link prediction for heterogeneous combat networks (HCNs) is of significant military value, as it facilitates reconfiguring combat networks to represent the complex real-world network topology as appropriate with observed information. This paper proposes a novel integrated methodology framework called HCNMP (HCN link prediction based on meta-path) to predict multiple types of links simultaneously for an HCN. More specifically, the concept of HCN meta-paths is introduced, through which the HCNMP can accumulate information by extracting different features of HCN links for all the six defined types. Next, an HCN link prediction model, based on meta-path features, is built to predict all types of links of the HCN simultaneously. Then, the solution algorithm for the HCN link prediction model is proposed, in which the prediction results are obtained by iteratively updating with the newly predicted results until the results in the HCN converge or reach a certain maximum iteration number. Finally, numerical experiments on the dataset of a real HCN are conducted to demonstrate the feasibility and effectiveness of the proposed HCNMP, in comparison with 30 baseline methods. The results show that the performance of the HCNMP is superior to those of the baseline methods.

  3. The dynamic efficiency of feed-in tariffs: The impact of different design elements

    International Nuclear Information System (INIS)

    Río, Pablo del

    2012-01-01

    Dynamic efficiency has received much less attention than the effectiveness and static efficiency criteria to assess policies to support electricity from renewable energy sources (RES-E). On the other hand, the literature on RES-E support shows that the choice of design elements within RES-E support instruments is at least as important to successfully promote RES-E as the choice of specific instruments. The aim of this paper is to build a theoretical framework for dynamic efficiency analysis and assess the dynamic efficiency properties of the different design elements of feed-in tariffs. It is shown that, in fact, several design elements can have a significant impact on the different dimensions of dynamic efficiency. Particularly relevant design elements in this context are technology-specific fixed-tariffs, floor prices, degression, reductions of support over time for existing plants, long duration of support and support falling on consumers. In addition, it is shown than some design elements would be more appropriate than others to activate specific dimensions. - Highlights: ► A theoretical framework for dynamic efficiency analysis is built. ► The dynamic efficiency properties of feed-in tariffs design elements are assessed. ► Several design elements have a significant impact on the different dimensions of dynamic efficiency.

  4. Photoreactivities and thermal properties of psoralen cross-links

    International Nuclear Information System (INIS)

    Yeung, A.T.; Jones, B.K.; Chu, C.T.

    1988-01-01

    The authors have studied the photoreaction of 8-methoxypsoralen (8-MOP), 4,5',8-trimethylpsoralen (TMP), and 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) with a pair of 18-base-long oligonucleotides in which a 14-base region is complementary. Only one 5'TpA site, favored for both monoadduct and cross-link formation with psoralen, is present in this oligonucleotide pair. They have used this model system to demonstrate, for the first time, strand specificity in the photoreaction of psoralen with DNA. They found that the two types of cross-links which form at this site have large differences in thermal stabilities. In addition, the denaturation of each cross-links isomer duplex occurred in at least three stages, which can be visualized as three bands in thermal equilibrium under the conditions of a denaturing polyacrylamide gel. This novel observation suggests that there are several domains differing in thermal stability in a psoralen cross-link

  5. Transcriptome of pancreas-specific Bmpr1a-deleted islets links to TPH1–5-HT axis

    Directory of Open Access Journals (Sweden)

    Fang-Xu Jiang

    2015-08-01

    Full Text Available Bone morphogenetic protein (BMP signaling is crucial for the development and function of numerous organs, but its role on the function of pancreatic islets is not completely clear. To explore this question, we applied the high throughput transcriptomic analyses on the islets isolated from mice with a pancreas-specific deletion of the gene, Bmpr1a, encoding the type 1a BMP receptor. Consistently, these pBmpr1aKO mice had impaired glucose homeostasis at 3 months, and were more severely affected at 12 months of age. These had lower fasting blood insulin concentrations, with reduced expression of several key regulators of β-cell function. Importantly, transcriptomic profiling of 3-month pBmpr1aKO islets and bioinformatic analyses revealed abnormal expression of 203 metabolic genes. Critically among these, the tryptophan hydroxylase 1 gene (Tph1, encoding the rate-limiting enzyme for the production of 5-hydroxytryptamine (5-HT was the highest over-expressed one. 5-HT is an important regulator of insulin secretion from β cells. Treatment with excess 5-HT inhibited this secretion. Thus our transcriptomic analysis links two highly conserved molecular pathways the BMP signaling and the TPH1–5-HT axis on glucose homeostasis.

  6. Link Performance Analysis and monitoring - A unified approach to divergent requirements

    Science.gov (United States)

    Thom, G. A.

    Link Performance Analysis and real-time monitoring are generally covered by a wide range of equipment. Bit Error Rate testers provide digital link performance measurements but are not useful during real-time data flows. Real-time performance monitors utilize the fixed overhead content but vary widely from format to format. Link quality information is also present from signal reconstruction equipment in the form of receiver AGC, bit synchronizer AGC, and bit synchronizer soft decision level outputs, but no general approach to utilizing this information exists. This paper presents an approach to link tests, real-time data quality monitoring, and results presentation that utilizes a set of general purpose modules in a flexible architectural environment. The system operates over a wide range of bit rates (up to 150 Mbs) and employs several measurement techniques, including P/N code errors or fixed PCM format errors, derived real-time BER from frame sync errors, and Data Quality Analysis derived by counting significant sync status changes. The architecture performs with a minimum of elements in place to permit a phased update of the user's unit in accordance with his needs.

  7. Environmental mineralogy - Understanding element behavior in ecosystems

    International Nuclear Information System (INIS)

    Brown Jr, G.E.; Calas, G.

    2011-01-01

    Environmental Mineralogy has developed over the past decade in response to the recognition that minerals are linked in many important ways with the global ecosystem. Minerals are the main repositories of the chemical elements in Earth's crust and thus are the main sources of elements needed for the development of civilization, contaminant and pollutant elements that impact global and local ecosystems, and elements that are essential plant nutrients. These elements are released from minerals through natural processes, such as chemical weathering, and anthropogenic activities, such as mining and energy production, agriculture and industrial activities, and careless waste disposal. Minerals also play key roles in the biogeochemical cycling of the elements, sequestering elements and releasing them as the primary minerals in crustal rocks undergo various structural and compositional transformations in response to physical, chemical, and biological processes that produce secondary minerals and soils. These processes have resulted in the release of toxic elements such as arsenic in groundwater aquifers, which is having a major impact on the health of millions of people in South and Southeast Asia. The interfaces between mineral surfaces and aqueous solutions are the locations of most chemical reactions that control the composition of the natural environment, including the composition of natural waters. The nuclear fuel cycle, from uranium mining to the disposition of high-level nuclear waste, is also intimately related to minerals. A fundamental understanding of these processes requires molecular-scale information about minerals, their bulk structures and properties such as solubility, their surfaces, and their interactions with aqueous solutions, atmospheric and soil gases, natural organic matter, and biological organisms. Gaining this understanding is further complicated by the presence of natural, incidental, and manufactured nano-particles in the environment, which

  8. Transfer flask for hot active fuel elements

    International Nuclear Information System (INIS)

    Aubert, Roger; Moutard, Daniel.

    1980-01-01

    This invention concerns a flask for transporting active fuel elements removed from a nuclear reactor vessel, after only a few days storage and hence cooling, either within a nuclear power station itself or between such a station and a near-by storage area. This containment system is not a flask for conveyance over long and medium distances. Specifically, the invention concerns a transport flask that enables hot fuel elements to be cooled, even in the event of accidents [fr

  9. Links between geodiversity and cultural elements on three scale levels, a neglected part of geoconservation

    Science.gov (United States)

    van den Ancker, Hanneke; Jungerius, Pieter Dirk

    2015-04-01

    The best-known landscape map of The Netherlands is a simplified version of the first geological map of The Netherlands and was made between 1856 and 1867 by Winand Staring. It still is the basis of our vegetation districts. The main landscape units of this map are the sand landscape, the peat landscape, the river landscape, the marine landscape, the coastal dunes and the hills. On this scale level there is general awareness of the relationships between the geo aspects (geomorphology, geology, geohydrology and soil science) of the landscape and historical land use, e.g. in field patterns and other cultural elements (archaeology and historical geography). From three of these units, examples of interactions between geo-aspects and cultural elements are given for two different scale levels: first on a more regional scale level, then on site level. Especially the last level requires field study. The relationships between the geo and cultural aspects appear to be most intact and are most variable at the site level. Earth scientists as yet hardly involve themselves in geoconservation studies re these relationships, for which reason the geo-aspects of the cultural elements, especially those at the site level, often are not noticed and disappear during land development projects or gardening efforts. It also is a missed opportunity as these sites offer a chance to raise interest of a broader public for geomorphology and soils, which are in general more difficult to communicate. The development and management of cultural landscapes and sites, by Dutch law is the domain of land owners and landscape architects, who in the course of a project consult other experts. Our plea for future planning projects is to work with a team of experts including archaeologists, historical geographers, flora and fauna experts, geologists, geomorphologists and soil specialists. Although the costs of preparing a plan will be slightly higher, our experience is that it will improve the quality of

  10. Analytic analysis of auxetic metamaterials through analogy with rigid link systems

    OpenAIRE

    Rayneau-Kirkhope, Daniel; Zhang, Chengzhao; Theran, Louis; Dias, Marcelo A.

    2017-01-01

    Recent progress in advanced additive manufacturing techniques has stimulated the growth of the field of mechanical metamaterials. One area particular interest in this subject is the creation of auxetic material properties through elastic instability. This paper focuses on a novel methodology in the analysis of auxetic metamaterials through analogy with rigid link lattice systems. Our analytic methodology gives extremely good agreement with finite element simulations for both the onset of elas...

  11. Low-temperature-induced expression of rice ureidoglycolate amidohydrolase is mediated by a C-repeat/dehydration-responsive element that specifically interacts with rice C-repeat-binding factor 3

    Directory of Open Access Journals (Sweden)

    Juan eLi

    2015-11-01

    Full Text Available Nitrogen recycling and redistribution are important for the environmental stress response of plants. In non nitrogen-fixing plants, ureide metabolism is crucial to nitrogen recycling from organic sources. Various studies have suggested that the rate-limiting components of ureide metabolism respond to environmental stresses. However, the underlying regulation mechanism is not well understood. In this report, rice ureidoglycolate amidohydrolase (OsUAH, which is a recently identified enzyme catalyzing the final step of ureide degradation, was identified as low-temperature- (LT but not abscisic acid- (ABA regulated. To elucidate the LT regulatory mechanism at the transcriptional level, we isolated and characterized the promoter region of OsUAH (POsUAH. Series deletions revealed that a minimal region between -522 and -420 relative to the transcriptional start site was sufficient for the cold induction of POsUAH. Detailed analyses of this 103-bp fragment indicated that a C-repeat/dehydration-responsive (CRT/DRE element localized at position -434 was essential for LT-responsive expression. A rice C-repeat-binding factors/DRE-binding proteins 1 (CBFs/DREB1s subfamily member, OsCBF3, was screened to specifically bind to the CRT/DRE element in the minimal region both in yeast one-hybrid assays and in in vitro gel-shift analysis. Moreover, the promoter could be exclusively trans-activated by the interaction between the CRT/DRE element and OsCBF3 in vivo. These findings may help to elucidate the regulation mechanism of stress-responsive ureide metabolism genes and provide an example of the member-specific manipulation of the CBF/DREB1 subfamily.

  12. Nuclear fuel element and a method of manufacture thereof

    International Nuclear Information System (INIS)

    Wood, J.C.

    1975-01-01

    A nuclear fuel element having a sheath of zirconium or a zirconium alloy and a cross-linked siloxane lacquer coating on the inner surface of the sheath and separating the nuclear fuel material from the sheath is described. The siloxane lacquer coating retards cracking of the sheath by iodine vapor emitted by the fuel during burn-up, and acts as a lubricant for the fuel to prevent rupture of the sheath by thermal ratchetting of the fuel against the sheath and caused by differential thermal expansion between the fuel and the sheath. A silicone grease is applied as a thin layer in the sheath and then baked so that oxidative cleavage of the side chains of the grease occurs to form a cross-linked siloxane lacquer coating bonded to the sheath

  13. Depression and social anxiety in children: Differential links with coping strategies

    NARCIS (Netherlands)

    Wright, M.; Banerjee, R.; Hoek, W.; Rieffe, C.J.; Novin Farahbakhsh, S.

    2010-01-01

    Strategies that children use for coping with stressors are known to be related to emotional adjustment, but not enough is understood about specific links with social anxiety and depression. The present investigation tested differentiated associations of social anxiety and depression with specific

  14. Patient-specific stress analyses in the ascending thoracic aorta using a finite-element implementation of the constrained mixture theory.

    Science.gov (United States)

    Mousavi, S Jamaleddin; Avril, Stéphane

    2017-10-01

    It is now a rather common approach to perform patient-specific stress analyses of arterial walls using finite-element models reconstructed from gated medical images. However, this requires to compute for every Gauss point the deformation gradient between the current configuration and a stress-free reference configuration. It is technically difficult to define such a reference configuration, and there is actually no guarantee that a stress-free configuration is physically attainable due to the presence of internal stresses in unloaded soft tissues. An alternative framework was proposed by Bellini et al. (Ann Biomed Eng 42(3):488-502, 2014). It consists of computing the deformation gradients between the current configuration and a prestressed reference configuration. We present here the first finite-element results based on this concept using the Abaqus software. The reference configuration is set arbitrarily to the in vivo average geometry of the artery, which is obtained from gated medical images and is assumed to be mechanobiologically homeostatic. For every Gauss point, the stress is split additively into the contributions of each individual load-bearing constituent of the tissue, namely elastin, collagen, smooth muscle cells. Each constituent is assigned an independent prestretch in the reference configuration, named the deposition stretch. The outstanding advantage of the present approach is that it simultaneously computes the in situ stresses existing in the reference configuration and predicts the residual stresses that occur after removing the different loadings applied onto the artery (pressure and axial load). As a proof of concept, we applied it on an ideal thick-wall cylinder and showed that the obtained results were consistent with corresponding experimental and analytical results of the well-known literature. In addition, we developed a patient-specific model of a human ascending thoracic aneurysmal aorta and demonstrated the utility in predicting the

  15. Reducing Data Size Inequality during Finite Element Model Separation into Superelements

    Directory of Open Access Journals (Sweden)

    Yu. V. Berchun

    2015-01-01

    Full Text Available The work considers two methods of automatic separation of final element model into super-elements to decrease computing resource demand when solving the linearly - elastic problems of solid mechanics. The first method represents an algorithm to separate a final element grid into simply connected sub-regions according to the set specific number of nodes in the super-element. The second method is based on the generation of a super-element with the set specific data size of the coefficient matrix of the system of equations of the internal nodes balance, which are eliminated during super-element transformation. Both methods are based on the theory of graphs. The data size of a matrix of coefficients is assessed on the assumption that the further solution of a task will use Holetsky’s method. Before assessment of data size, a KatkhillaMackey's (Cuthill-McKee algorithm renumbers the internal nodes of a super-element both to decrease a profile width of the appropriate matrix of the system of equations of balance and to reduce the number of nonzero elements. Test examples show work results of abovementioned methods compared in terms of inequality of generated super-element separation according to the number of nodes and data size of the coefficient matrix of the system of equations of the internal nodes balance. It is shown that the offered approach provides smaller inequality of data size of super-element matrixes, with slightly increasing inequality by the number of tops.

  16. Specification of the surface figure and finish of optical elements in terms of system performance

    International Nuclear Information System (INIS)

    Church, E.L.; Takacs, P.Z.

    1992-09-01

    Brookhaven National Laboratory is the site of the National Synchrotron Light Source (NSLS); an electron synchrotron which is an intense source of hard and soft x-rays. Since there are no effective refracting elements for x rays, this radiation must be manipulated and focused by mirrors configured to give high reflectivity. This paper describes methods of predicting the degradation of the performance of a simple imaging system in terms of the statistics of the shape errors of the focusing element, and conversely, of specifying those statistics in terms of requirements on image quality. Results are illustrated for a normal-incidence x-ray mirrors having figure errors plus conventional and/or fractal finish errors

  17. Trace elements in blood samples of workers in Atbara railways foundry

    International Nuclear Information System (INIS)

    Mustafa, W. M.

    2013-09-01

    This study was conducted to determine trace elements and toxic substances in biological samples (blood samples) of humans. The aim of the current study was to determine the concentration of iron (Fe), copper (Cu), (Pb), lead, and zinc (Zn) in biological samples of workers employed in the industrial workshops in the River Nile state to assess the potential impact of exposure to the work environmental factors. For the purpose of comparison biological samples were collected from the same group of workers exposed to the elements of the work environment and workers not exposed to the elements of the work environment. The analysis of all elements in biological samples was done by x-ray fluorescence technique (X RF). There were no statistically significant differences between the analytical results for the exposed group and non-exposed group, using the same technique. The results showed that the concentrations of the four elements copper, lead, iron, and zinc in all biological samples from workers exposed were not much higher than those not exposed, it could be argued that there was a possible link between these elements with different causes of physiological disorder. The results also showed that need for an attention for improvements in hygiene practice in the workplace and industrial ventilation.(Author)

  18. Power-Aware Routing and Network Design with Bundled Links: Solutions and Analysis

    Directory of Open Access Journals (Sweden)

    Rosario G. Garroppo

    2013-01-01

    Full Text Available The paper deeply analyzes a novel network-wide power management problem, called Power-Aware Routing and Network Design with Bundled Links (PARND-BL, which is able to take into account both the relationship between the power consumption and the traffic throughput of the nodes and to power off both the chassis and even the single Physical Interface Card (PIC composing each link. The solutions of the PARND-BL model have been analyzed by taking into account different aspects associated with the actual applicability in real network scenarios: (i the time for obtaining the solution, (ii the deployed network topology and the resulting topology provided by the solution, (iii the power behavior of the network elements, (iv the traffic load, (v the QoS requirement, and (vi the number of paths to route each traffic demand. Among the most interesting and novel results, our analysis shows that the strategy of minimizing the number of powered-on network elements through the traffic consolidation does not always produce power savings, and the solution of this kind of problems, in some cases, can lead to spliting a single traffic demand into a high number of paths.

  19. Autonomy Level Specification for Intelligent Autonomous Vehicles

    Science.gov (United States)

    2003-09-01

    Autonomy Level Specification for Intelligent Autonomous Vehicles : Interim Progress Report Hui-Min Huang, Elena Messina, James Albus...Level Specification for Intelligent Autonomous Vehicles : Interim Progress Report 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

  20. A single cis element maintains repression of the key developmental regulator Gata2.

    Directory of Open Access Journals (Sweden)

    Jonathan W Snow

    2010-09-01

    Full Text Available In development, lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates. Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements. It is not understood whether these elements function collectively to confer transcriptional regulation, or individually to control specific aspects of activation or repression, such as initiation versus maintenance. Here, we have analyzed cis element regulation of the critical hematopoietic factor Gata2, which is expressed in early precursors and repressed as GATA-1 levels rise during terminal differentiation. We engineered mice lacking a single cis element -1.8 kb upstream of the Gata2 transcriptional start site. Although Gata2 is normally repressed in late-stage erythroblasts, the -1.8 kb mutation unexpectedly resulted in reactivated Gata2 transcription, blocked differentiation, and an aberrant lineage-specific gene expression pattern. Our findings demonstrate that the -1.8 kb site selectively maintains repression, confers a specific histone modification pattern and expels RNA Polymerase II from the locus. These studies reveal how an individual cis element establishes a normal developmental program via regulating specific steps in the mechanism by which a critical transcription factor is repressed.

  1. LOAD BEARING CAPACITY OF THE GLASS RAILING ELEMENT

    Directory of Open Access Journals (Sweden)

    Elizabeta Šamec

    2016-02-01

    Full Text Available In this paper some basic physical and mechanical properties of glass as structural material are presented. This research is about specifically manufactured glass railing element that will be a part of a pedestrian bridge construction in Zagreb, Croatia. Load bearing capacity test of the glass railing element is conducted within the Faculty of Civil Engineering in Zagreb and obtained experimental results are discussed and compared to the ones provided by the numerical model. Taking into account the behaviour of laminated glass and results of experimental and numerical testing, glass railing element can be regarded as safe.

  2. OpenSeesPy: Python library for the OpenSees finite element framework

    Science.gov (United States)

    Zhu, Minjie; McKenna, Frank; Scott, Michael H.

    2018-01-01

    OpenSees, an open source finite element software framework, has been used broadly in the earthquake engineering community for simulating the seismic response of structural and geotechnical systems. The framework allows users to perform finite element analysis with a scripting language and for developers to create both serial and parallel finite element computer applications as interpreters. For the last 15 years, Tcl has been the primary scripting language to which the model building and analysis modules of OpenSees are linked. To provide users with different scripting language options, particularly Python, the OpenSees interpreter interface was refactored to provide multi-interpreter capabilities. This refactoring, resulting in the creation of OpenSeesPy as a Python module, is accomplished through an abstract interface for interpreter calls with concrete implementations for different scripting languages. Through this approach, users are able to develop applications that utilize the unique features of several scripting languages while taking advantage of advanced finite element analysis models and algorithms.

  3. Seroprevalence study of Equine rhinitis B virus (ERBV) in Australian weanling horses using serotype-specific ERBV enzyme-linked immunosorbent assays.

    Science.gov (United States)

    Horsington, Jacquelyn; Hartley, Carol A; Gilkerson, James R

    2013-09-01

    Respiratory infections are a major burden in the performance horse industry. Equine rhinitis B virus (ERBV) has been isolated from horses displaying clinical respiratory disease, and ERBV-neutralizing antibodies have been detected in 50-80% of horses in reported surveys. Current ERBV isolation and detection methods may underestimate the number of ERBV-positive animals and do not identify multiple serotype infections. The aim of the current study was to develop a serotyping ERBV antibody-detection enzyme-linked immunosorbent assay (ELISA) and examine the seroprevalence of ERBV in a group of Australian weanling horses. ELISAs with high sensitivity and specificity were developed. The seroprevalence of ERBV in the weanling horses was high (74-86%); ERBV-3 antibodies were most prevalent (58-62%) and ERBV-2 antibodies were least prevalent (10-16%). Many horses were seropositive to 2 or more serotypes. All 3 serotypes of ERBV were detected, and concurrent positivity to multiple serotypes was common.

  4. Composition of cross-linked 125I-follitropin-receptor complexes

    Energy Technology Data Exchange (ETDEWEB)

    Shin, J.; Ji, T.H.

    1985-10-15

    Both of the alpha and beta subunits of intact human follitropin (FSH) were radioiodinated with SVI-sodium iodide and chloramine-T and could be resolved on sodium dodecyl sulfate-polyacrylamide gels. Radioiodinated FSH was affinity-cross-linked with a cleavable (nondisulfide) homobifunctional reagent to its membrane receptor on the porcine granulosa cell surface as well as to a Triton X-100-solubilized form of the receptor. Cross-linked samples revealed three additional bands of slower electrophoretic mobility, corresponding to 65, 83, and 117 kDa, in addition to the hormone bands. The hormone alpha beta dimer band corresponded to 43 kDa. Formation of the three bands requires the SVI-hormone to bind specifically to the receptor with subsequent cross-linking. Binding was prevented by an excess of the native hormone but not by other hormones. A monofunctional analog of the cross-linking reagent failed to produce the three bands. Reagent concentration-dependent cross-linking revealed that their formation was sequential; smaller complexes formed first and then larger ones. When gels of cross-linked complexes were treated to cleave covalent cross-links and then electrophoresed in a second dimension, 18-, 22-, and 34-kDa components were released, in addition to the alpha and beta subunits of the hormone.

  5. RARE EARTH ELEMENTS: A REVIEW OF PRODUCTION, PROCESSING, RECYCLING, AND ASSOCIATED ENVIRONMENTAL ISSUES

    Science.gov (United States)

    Rare earth elements (REEs) are a group of 15 chemical elements in the periodic table, specifically the lanthanides. Two other elements, scandium and yttrium, have a similar physiochemistry to the lanthanides, are commonly found in the same mineral assemblages, and are often refe...

  6. MESHREF, Finite Elements Mesh Combination with Renumbering

    International Nuclear Information System (INIS)

    1973-01-01

    1 - Nature of physical problem solved: The program can assemble different meshes stored on tape or cards. Renumbering is performed in order to keep band width low. Voids and/ or local refinement are possible. 2 - Method of solution: Topology and geometry are read according to input specifications. Abundant nodes and elements are eliminated. The new topology and geometry are stored on tape. 3 - Restrictions on the complexity of the problem: Maximum number of nodes = 2000. Maximum number of elements = 1500

  7. Towards an in-plane methodology to track breast lesions using mammograms and patient-specific finite-element simulations

    Science.gov (United States)

    Lapuebla-Ferri, Andrés; Cegoñino-Banzo, José; Jiménez-Mocholí, Antonio-José; Pérez del Palomar, Amaya

    2017-11-01

    In breast cancer screening or diagnosis, it is usual to combine different images in order to locate a lesion as accurately as possible. These images are generated using a single or several imaging techniques. As x-ray-based mammography is widely used, a breast lesion is located in the same plane of the image (mammogram), but tracking it across mammograms corresponding to different views is a challenging task for medical physicians. Accordingly, simulation tools and methodologies that use patient-specific numerical models can facilitate the task of fusing information from different images. Additionally, these tools need to be as straightforward as possible to facilitate their translation to the clinical area. This paper presents a patient-specific, finite-element-based and semi-automated simulation methodology to track breast lesions across mammograms. A realistic three-dimensional computer model of a patient’s breast was generated from magnetic resonance imaging to simulate mammographic compressions in cranio-caudal (CC, head-to-toe) and medio-lateral oblique (MLO, shoulder-to-opposite hip) directions. For each compression being simulated, a virtual mammogram was obtained and posteriorly superimposed to the corresponding real mammogram, by sharing the nipple as a common feature. Two-dimensional rigid-body transformations were applied, and the error distance measured between the centroids of the tumors previously located on each image was 3.84 mm and 2.41 mm for CC and MLO compression, respectively. Considering that the scope of this work is to conceive a methodology translatable to clinical practice, the results indicate that it could be helpful in supporting the tracking of breast lesions.

  8. Analisis Numerik Link Panjang dengan Penambahan Pelat Sayap Tepi terhadap Peningkatan Kinerja Struktur Rangka Baja Berpengaku Eksentrik

    Directory of Open Access Journals (Sweden)

    Musbar

    2015-04-01

    Full Text Available Conducting research in anticipating earthquake damage at building has been developed continuosly. One of it is Eccentrically Braced Frame (EBF for steel frame. EBF uses link element to absorb earthquake energy. Failure at long type link dominantly is caused by moment which make early failure because of fracture and buckling at the end of link such as in its flange. To tackle the early failure, stiffener at the end of the link has been added. The advantages of it are making easy of workmanship and minimizing the welding effort which can reduce residual stress because of welding process. This study does numerical study by using MSC Nastran/Patran program to measure the performance of long type link for several analysis types. Several parameters have been analyzed such as the length of the link, the edge addition of flange plate with its modeling configuration, the width of the plate, and the combination with vertical body stiffener. This study found that the addition of stiffener at the end of the link has increased the performance of long type link. Finally, the findings of this study are compared with that of standard link model. The variables that are compared between both of long type link and standard link are ductility, strength, energy dissipation and stiffness.

  9. Linked data management

    CERN Document Server

    Hose, Katja; Schenkel, Ralf

    2014-01-01

    Linked Data Management presents techniques for querying and managing Linked Data that is available on today’s Web. The book shows how the abundance of Linked Data can serve as fertile ground for research and commercial applications. The text focuses on aspects of managing large-scale collections of Linked Data. It offers a detailed introduction to Linked Data and related standards, including the main principles distinguishing Linked Data from standard database technology. Chapters also describe how to generate links between datasets and explain the overall architecture of data integration systems based on Linked Data. A large part of the text is devoted to query processing in different setups. After presenting methods to publish relational data as Linked Data and efficient centralized processing, the book explores lookup-based, distributed, and parallel solutions. It then addresses advanced topics, such as reasoning, and discusses work related to read-write Linked Data for system interoperation. Desp...

  10. Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea.

    Science.gov (United States)

    Kletzin, Arnulf; Urich, Tim; Müller, Fabian; Bandeiras, Tiago M; Gomes, Cláudio M

    2004-02-01

    The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.

  11. Advanced finite element simulation with MSC Marc application of user subroutines

    CERN Document Server

    Javanbakht, Zia

    2017-01-01

    This book offers an in-depth insight into the general-purpose finite element program MSC Marc, which is distributed by MSC Software Corporation. It is a specialized program for nonlinear problems (implicit solver) which is common in academia and industry. The primary goal of this book is to provide a comprehensive introduction to a special feature of this software: the user can write user-subroutines in the programming language Fortran, which is the language of all classical finite element packages. This subroutine feature allows the user to replace certain modules of the core code and to implement new features such as constitutive laws or new elements. Thus, the functionality of commercial codes (‘black box’) can easily be extended by linking user written code to the main core of the program. This feature allows to take advantage of a commercial software package with the flexibility of a ‘semi-open’ code. .

  12. Rigid Finite Element Method in Analysis of Dynamics of Offshore Structures

    CERN Document Server

    Wittbrodt, Edmund; Maczyński, Andrzej; Wojciech, Stanisław

    2013-01-01

    This book describes new methods developed for modelling dynamics of machines commonly used in the offshore industry. These methods are based both on the rigid finite element method, used for the description of link deformations, and on homogeneous transformations and joint coordinates, which is applied to the modelling of multibody system dynamics. In this monograph, the bases of the rigid finite element method  and homogeneous transformations are introduced. Selected models for modelling dynamics of offshore devices are then verified both by using commercial software, based on the finite element method, as well as by using additional methods. Examples of mathematical models of offshore machines, such as a gantry crane for Blowout-Preventer (BOP) valve block transportation, a pedestal crane with shock absorber, and pipe laying machinery are presented. Selected problems of control in offshore machinery as well as dynamic optimization in device control are also discussed. Additionally, numerical simulations of...

  13. Mapping queries to the Linking Open Data cloud: a case study using DBpedia

    NARCIS (Netherlands)

    Meij, E.; Bron, M.; Hollink, L.; Huurnink, B.; de Rijke, M.

    2011-01-01

    We introduce the task of mapping search engine queries to DBpedia, a major linking hub in the Linking Open Data cloud. We propose and compare various methods for addressing this task, using a mixture of information retrieval and machine learning techniques. Specifically, we present a supervised

  14. Managing Your Team's Weakest Link.

    Science.gov (United States)

    Hills, Laura

    2015-01-01

    Do you have a poor-performing employee on your medical practice team? If so, you're not alone. Unfortunately, this is a problem that many medical practice managers face. This article describes the best strategies for managing your team's weakest link. It explores common yet very difficult circumstances that cause low employee performance and that test the patience, heart, and skills of a practice manager. It guides readers through a process of self-discovery to determine whether their negative biases or grudges may be causing employees to perform poorly. It suggests several possible other reasons for weak employee performance, including problems with the job, practice, leadership, communication, and fit between the employee and the job. This article also suggests the best strategy for communicating concerns about performance to the weakest-link employee. It offers guidance to practice managers about protecting their time and energy when handling a poor performer. It provides a simple formula for calculating the cost of a low-performing employee, 10 possible personal reasons for the employee's poor work performance, specific questions to ask to uncover the reasons for poor performance, and an eight-rule strategy for confronting poor performance effectively. Finally, this article offers practice managers a practical strategy for handling resistance from their weakest link, illustrated with a sample dialogue.

  15. HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides

    DEFF Research Database (Denmark)

    Larsen, Malene Erup; Kloverpris, H.; Stryhn, A.

    2011-01-01

    ://www.cbs.dtu.dk/services/HLArestrictor ), which is based on the highly versatile and accurate NetMHCpan predictor, which here has been optimized for the identification of both the MHC restriction element and the corresponding minimal epitope of a T cell response in a given individual. As input, it requires high-resolution (i.e., 4-digit) HLA...... HLA restrictions and minimal epitopes for about 90% of the positive peptide/patient pairs while rejecting more than 95% of the negative peptide-HLA pairs. Furthermore, for 18 peptide/HLA tetramer validated responses, HLArestrictor in all cases predicted both the HLA restriction element and minimal...

  16. A study on the nonlinear finite element analysis of reinforced concrete structures: shell finite element formulation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sang Jin; Seo, Jeong Moon

    2000-08-01

    The main goal of this research is to establish a methodology of finite element analysis of containment building predicting not only global behaviour but also local failure mode. In this report, we summerize some existing numerical analysis techniques to be improved for containment building. In other words, a complete description of the standard degenerated shell finite element formulation is provided for nonlinear stress analysis of nuclear containment structure. A shell finite element is derived using the degenerated solid concept which does not rely on a specific shell theory. Reissner-Mindlin assumptions are adopted to consider the transverse shear deformation effect. In order to minimize the sensitivity of the constitutive equation to structural types, microscopic material model is adopted. The four solution algorithms based on the standard Newton-Raphson method are discussed. Finally, two numerical examples are carried out to test the performance of the adopted shell medel.

  17. A study on the nonlinear finite element analysis of reinforced concrete structures: shell finite element formulation

    International Nuclear Information System (INIS)

    Lee, Sang Jin; Seo, Jeong Moon

    2000-08-01

    The main goal of this research is to establish a methodology of finite element analysis of containment building predicting not only global behaviour but also local failure mode. In this report, we summerize some existing numerical analysis techniques to be improved for containment building. In other words, a complete description of the standard degenerated shell finite element formulation is provided for nonlinear stress analysis of nuclear containment structure. A shell finite element is derived using the degenerated solid concept which does not rely on a specific shell theory. Reissner-Mindlin assumptions are adopted to consider the transverse shear deformation effect. In order to minimize the sensitivity of the constitutive equation to structural types, microscopic material model is adopted. The four solution algorithms based on the standard Newton-Raphson method are discussed. Finally, two numerical examples are carried out to test the performance of the adopted shell medel

  18. Finite element bending behaviour of discretely delaminated ...

    African Journals Online (AJOL)

    user

    due to their light weight, high specific strength and stiffness properties. ... cylindrical shell roofs respectively using finite element method with centrally located .... where { }ε and { }γ are the direct and shear strains in midplane and { }κ denotes ...

  19. Performance of an optical encoder based on a nondiffractive beam implemented with a specific photodetection integrated circuit and a diffractive optical element.

    Science.gov (United States)

    Quintián, Fernando Perez; Calarco, Nicolás; Lutenberg, Ariel; Lipovetzky, José

    2015-09-01

    In this paper, we study the incremental signal produced by an optical encoder based on a nondiffractive beam (NDB). The NDB is generated by means of a diffractive optical element (DOE). The detection system is composed by an application specific integrated circuit (ASIC) sensor. The sensor consists of an array of eight concentric annular photodiodes, each one provided with a programmable gain amplifier. In this way, the system is able to synthesize a nonuniform detectivity. The contrast, amplitude, and harmonic content of the sinusoidal output signal are analyzed. The influence of the cross talk among the annular photodiodes is placed in evidence through the dependence of the signal contrast on the wavelength.

  20. Sex-linked dominant

    Science.gov (United States)

    Inheritance - sex-linked dominant; Genetics - sex-linked dominant; X-linked dominant; Y-linked dominant ... can be either an autosomal chromosome or a sex chromosome. It also depends on whether the trait ...

  1. Depression and Social Anxiety in Children: Differential Links with Coping Strategies

    Science.gov (United States)

    Wright, Mark; Banerjee, Robin; Hoek, Willemijn; Rieffe, Carolien; Novin, Sheida

    2010-01-01

    Strategies that children use for coping with stressors are known to be related to emotional adjustment, but not enough is understood about specific links with social anxiety and depression. The present investigation tested differentiated associations of social anxiety and depression with specific types of coping strategies, and evaluated the…

  2. Fabrication of chemically cross-linked porous gelatin matrices.

    Science.gov (United States)

    Bozzini, Sabrina; Petrini, Paola; Altomare, Lina; Tanzi, Maria Cristina

    2009-01-01

    The aim of this study was to chemically cross-link gelatin, by reacting its free amino groups with an aliphatic diisocyanate. To produce hydrogels with controllable properties, the number of reacting amino groups was carefully determined. Porosity was introduced into the gelatin-based hydrogels through the lyophilization process. Porous and non-porous matrices were characterized with respect to their chemical structure, morphology, water uptake and mechanical properties. The physical, chemical and mechanical properties of the porous matrices are related to the extent of their cross-linking, showing that they can be controlled by varying the reaction parameters. Water uptake values (24 hours) vary between 160% and 200% as the degree of cross-linking increases. The flexibility of the samples also decreases by changing the extent of cross-linking. Young's modulus shows values between 0.188 KPa, for the highest degree, and 0.142 KPa for the lowest degree. The matrices are potential candidates for use as tissue-engineering scaffolds by modulating their physical chemical properties according to the specific application.

  3. An Efficient Stepwise Statistical Test to Identify Multiple Linked Human Genetic Variants Associated with Specific Phenotypic Traits.

    Directory of Open Access Journals (Sweden)

    Iksoo Huh

    Full Text Available Recent advances in genotyping methodologies have allowed genome-wide association studies (GWAS to accurately identify genetic variants that associate with common or pathological complex traits. Although most GWAS have focused on associations with single genetic variants, joint identification of multiple genetic variants, and how they interact, is essential for understanding the genetic architecture of complex phenotypic traits. Here, we propose an efficient stepwise method based on the Cochran-Mantel-Haenszel test (for stratified categorical data to identify causal joint multiple genetic variants in GWAS. This method combines the CMH statistic with a stepwise procedure to detect multiple genetic variants associated with specific categorical traits, using a series of associated I × J contingency tables and a null hypothesis of no phenotype association. Through a new stratification scheme based on the sum of minor allele count criteria, we make the method more feasible for GWAS data having sample sizes of several thousands. We also examine the properties of the proposed stepwise method via simulation studies, and show that the stepwise CMH test performs better than other existing methods (e.g., logistic regression and detection of associations by Markov blanket for identifying multiple genetic variants. Finally, we apply the proposed approach to two genomic sequencing datasets to detect linked genetic variants associated with bipolar disorder and obesity, respectively.

  4. PlantCARE, a plant cis-acting regulatory element database

    OpenAIRE

    Rombauts, Stephane; Déhais, Patrice; Van Montagu, Marc; Rouzé, Pierre

    1999-01-01

    PlantCARE is a database of plant cis- acting regulatory elements, enhancers and repressors. Besides the transcription motifs found on a sequence, it also offers a link to the EMBL entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional. The information on these sites is given by matrices, consensus and individual site sequences on particular genes, depending on the available information. PlantCARE is a relational database avail...

  5. Assessment of Structural Behavior of Non-corroded and Corroded RCC Beams Using Finite Element Method

    Directory of Open Access Journals (Sweden)

    Anand Parande

    2008-09-01

    Full Text Available A three dimensional finite element model is developed to examine the structural behaviour of corroded reinforced concrete beam and non corroded reinforced concrete beam. Non linear finite element analysis is performed using the ANSYS program. SOLID 65, LINK 8 element represent concrete and discrete reinforcing steel bars, based on each component actual characteristics, non linear material properties are defined for both elements. The effect of corrosion in reinforced concrete is studied by finite element analysis; an approach is developed to model the corrosion product expansion causing concrete cover cracking for this, beam has been modeled using ANSYS and using this data the beam has been casted with M20 concrete after 28 days the beam will be tested for flexural strength. The comparison between ANSYS prediction and field data are made in terms of deflection, stress, strain, bond strength and crack pattern of concrete beam.

  6. Near-Earth Object Orbit Linking with the Large Synoptic Survey Telescope

    Science.gov (United States)

    Vereš, Peter; Chesley, Steven R.

    2017-07-01

    We have conducted a detailed simulation of the ability of the Large Synoptic Survey Telescope (LSST) to link near-Earth and main belt asteroid detections into orbits. The key elements of the study were a high-fidelity detection model and the presence of false detections in the form of both statistical noise and difference image artifacts. We employed the Moving Object Processing System (MOPS) to generate tracklets, tracks, and orbits with a realistic detection density for one month of the LSST survey. The main goals of the study were to understand whether (a) the linking of near-Earth objects (NEOs) into orbits can succeed in a realistic survey, (b) the number of false tracks and orbits will be manageable, and (c) the accuracy of linked orbits would be sufficient for automated processing of discoveries and attributions. We found that the overall density of asteroids was more than 5000 per LSST field near opposition on the ecliptic, plus up to 3000 false detections per field in good seeing. We achieved 93.6% NEO linking efficiency for H< 22 on tracks composed of tracklets from at least three distinct nights within a 12 day interval. The derived NEO catalog was comprised of 96% correct linkages. Less than 0.1% of orbits included false detections, and the remainder of false linkages stemmed from main belt confusion, which was an artifact of the short time span of the simulation. The MOPS linking efficiency can be improved by refined attribution of detections to known objects and by improved tuning of the internal kd-tree linking algorithms.

  7. Dictyostelium discoideum: mutants in the biosynthesis of the lipid-linked precursor of N-linked oligosaccharides

    International Nuclear Information System (INIS)

    Freeze, H.; Willies, L.; Hamilton, S.

    1986-01-01

    The lysosomal enzymes of Dictyostelium discoideum share highly immunogenic oligosaccharides which contain multiple Man-6-SO 4 residues. Two mutant strains which lack the shared antigenic determinant were analyzed in an attempt to identify the primary defect in each. [ 3 H]Man labelled N-linked oligosaccharides of secreted glycoproteins were released by Endo/PNGaseF digestion and analyzed. Both of the mutant strains produced smaller, less sulfated oligosaccharides compared to the wild-type, yet both still contained considerable amounts of Man-6-SO 4 . The size of the precursor lipid-linked oligosaccharide from the wild-type is consistent with a Glc 3 Man 9 GlcNAc 2 structure, while those from both of the mutants have an oligosaccharide the size of Man 5 GlcNAc 2 . The authors conclude that both of the mutants are defective in the biosynthesis of the precursor oligosaccharide. Both oligosaccharides from the mutants contain a tri-mannosyl core and are not glucosylated. Two of the five Man residues are released by a 1,2 specific α mannosidase. Based on the size and mannosidase digestions the authors conclude that 4/5 of the Man residues on the α1,6 branch of the β-linked Man residues are missing. Thus, these residues must be required to define the shared antigenic determinant

  8. Trace elements in natural drugs determined by INAA

    International Nuclear Information System (INIS)

    Chen Kehshaw; Tseng Chialiang; Lin Tehsien

    1993-01-01

    Natural drugs are widely used for diuretic, phlegm elimination and stomach invigoration purposes. Seventy-five of the most common remedies used by Chinese people have been subjected to trace element survey analysis by instrumental neutron activation. Within this large number of different natural products, fourteen trace elements (K, Sc, Cr, Fe, Co, Zn, Br, Rb, Cs, La, Sm, Eu, Au and Th) are commonly detected. Among these elements, Fe had the highest concentration followed by Zn, and Rb, Sm, Eu and Au were found to have the lowest concentrations. Although the three groups of natural drugs exhibit a widely different therapeutic action, the concentration ranges of the fourteen elements were very similar. While this suggests no apparent specific role for the trace elements in the drug function, parallels are drawn between the known drug related functions of Rb, Zn, Br, Fe, Co and K and the levels of elements found in the natural drugs. It is concluded that the various natural drugs also provide human benefits through supplements of essential elements such as Fe, Zn, Cr, Sc, Rb and Co. (author) 13 refs.; 5 tabs

  9. Regulatory elements in vivo in the promoter of the abscisic acid responsive gene rab17 from maize.

    Science.gov (United States)

    Busk, P K; Jensen, A B; Pagès, M

    1997-06-01

    The rab17 gene from maize is transcribed in late embryonic development and is responsive to abscisic acid and water stress in embryo and vegetative tissues. In vivo footprinting and transient transformation of rab17 were performed in embryos and vegetative tissues to characterize the cis-elements involved in regulation of the gene. By in vivo footprinting, protein binding was observed to nine elements in the promoter, which correspond to five putative ABREs (abscisic acid responsive elements) and four other sequences. The footprints indicated that distinct proteins interact with these elements in the two developmental stages. In transient transformation, six of the elements were important for high level expression of the rab17 promoter in embryos, whereas only three elements were important in leaves. The cis-acting sequences can be divided in embryo-specific, ABA-specific and leaf-specific elements on the basis of protein binding and the ability to confer expression of rab17. We found one positive, new element, called GRA, with the sequence CACTGGCCGCCC. This element was important for transcription in leaves but not in embryos. Two other non-ABRE elements that stimulated transcription from the rab17 promoter resemble previously described abscisic acid and drought-inducible elements. There were differences in protein binding and function of the five ABREs in the rab17 promoter. The possible reasons for these differences are discussed. The in vivo data obtained suggest that an embryo-specific pathway regulates transcription of the rab genes during development, whereas another pathway is responsible for induction in response to ABA and drought in vegetative tissues.

  10. Element Specific Versus Integral Structural and Magnetic Properties of Co:ZnO and Gd:GaN Probed with Hard X-ray Absorption Spectroscopy

    Directory of Open Access Journals (Sweden)

    Andreas Ney

    2010-06-01

    Full Text Available Dilute magnetic semiconductors (DMS are envisioned as sources of spin-polarized carriers for future semiconductor devices which simultaneously utilize spin and charge of the carriers. The hope of discovering a DMS with ferromagnetic order up to room temperature still motivates research on suitable DMS materials. Two candidate wide-band gap DMS are Gd:GaN and Co:ZnO. We have used hard X-ray absorption spectroscopy (XAS and in particular X-ray linear dichroism (XLD and X-ray magnetic circular dichroism (XMCD to study both DMS materials with element specificity and compare these findings with results from integral SQUID magnetometry as well as electron paramagnetic resonance (EPR.

  11. Links between N-modular redundancy and the theory of error-correcting codes

    Science.gov (United States)

    Bobin, V.; Whitaker, S.; Maki, G.

    1992-01-01

    N-Modular Redundancy (NMR) is one of the best known fault tolerance techniques. Replication of a module to achieve fault tolerance is in some ways analogous to the use of a repetition code where an information symbol is replicated as parity symbols in a codeword. Linear Error-Correcting Codes (ECC) use linear combinations of information symbols as parity symbols which are used to generate syndromes for error patterns. These observations indicate links between the theory of ECC and the use of hardware redundancy for fault tolerance. In this paper, we explore some of these links and show examples of NMR systems where identification of good and failed elements is accomplished in a manner similar to error correction using linear ECC's.

  12. The Chain-Link Fence Model: A Framework for Creating Security Procedures

    Science.gov (United States)

    Houghton, Robert F.

    2013-01-01

    A long standing problem in information technology security is how to help reduce the security footprint. Many specific proposals exist to address specific problems in information technology security. Most information technology solutions need to be repeatable throughout the course of an information systems lifecycle. The Chain-Link Fence Model is…

  13. In Vitro Selection of Single-Stranded DNA Molecular Recognition Elements against S. aureus Alpha Toxin and Sensitive Detection in Human Serum

    Directory of Open Access Journals (Sweden)

    Ka L. Hong

    2015-01-01

    Full Text Available Alpha toxin is one of the major virulence factors secreted by Staphylococcus aureus, a bacterium that is responsible for a wide variety of infections in both community and hospital settings. Due to the prevalence of S. aureus related infections and the emergence of methicillin-resistant S. aureus, rapid and accurate diagnosis of S. aureus infections is crucial in benefiting patient health outcomes. In this study, a rigorous Systematic Evolution of Ligands by Exponential Enrichment (SELEX variant previously developed by our laboratory was utilized to select a single-stranded DNA molecular recognition element (MRE targeting alpha toxin with high affinity and specificity. At the end of the 12-round selection, the selected MRE had an equilibrium dissociation constant (Kd of 93.7 ± 7.0 nM. Additionally, a modified sandwich enzyme-linked immunosorbent assay (ELISA was developed by using the selected ssDNA MRE as the toxin-capturing element and a sensitive detection of 200 nM alpha toxin in undiluted human serum samples was achieved.

  14. Features of spherical uranium-graphite HTGR fuel elements control

    International Nuclear Information System (INIS)

    Kreindlin, I.I.; Oleynikov, P.P.; Shtan, A.S.

    1985-01-01

    Control features of spherical HTGR uranium-graphite fuel elements with spherical coated fuel particles are mainly determined by their specific construction and fabrication technology. The technology is chiefly based on methods of ceramic fuel (fuel microspheres fabrication) and graphite production practice it is necessary to deal with a lot of problems from determination of raw materials properties to final fuel elements testing. These procedures are described

  15. Features of spherical uranium-graphite HTGR fuel elements control

    Energy Technology Data Exchange (ETDEWEB)

    Kreindlin, I I; Oleynikov, P P; Shtan, A S

    1985-07-01

    Control features of spherical HTGR uranium-graphite fuel elements with spherical coated fuel particles are mainly determined by their specific construction and fabrication technology. The technology is chiefly based on methods of ceramic fuel (fuel microspheres fabrication) and graphite production practice it is necessary to deal with a lot of problems from determination of raw materials properties to final fuel elements testing. These procedures are described.

  16. Determination of specificity influencing residues for key transcription factor families

    DEFF Research Database (Denmark)

    Patel, Ronak Y.; Garde, Christian; Stormo, Gary D.

    2015-01-01

    Transcription factors (TFs) are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly de...

  17. Improved Battery Charger Circuit Utilizing Reduced DC-link Capacitors

    Directory of Open Access Journals (Sweden)

    Vencislav Valchev

    2017-11-01

    Full Text Available The article presents a comparison of advantages and disadvantages of a battery charger circuit with and without the use of DC-link capacitors in it. The specific application requirements, namely ultra-light electric vehicles, are set as lightness, efficiency and robustness of the design. Prove of greater reliability and improvement on maintenance costs without significant decrease in the quality of charging process with the removal of DC-link capacitors in rectifier and boost converter circuits is accomplished. The proposed circuit parameters are analyzed by carried out simulations.

  18. Cis-regulatory RNA elements that regulate specialized ribosome activity.

    Science.gov (United States)

    Xue, Shifeng; Barna, Maria

    2015-01-01

    Recent evidence has shown that the ribosome itself can play a highly regulatory role in the specialized translation of specific subpools of mRNAs, in particular at the level of ribosomal proteins (RP). However, the mechanism(s) by which this selection takes place has remained poorly understood. In our recent study, we discovered a combination of unique RNA elements in the 5'UTRs of mRNAs that allows for such control by the ribosome. These mRNAs contain a Translation Inhibitory Element (TIE) that inhibits general cap-dependent translation, and an Internal Ribosome Entry Site (IRES) that relies on a specific RP for activation. The unique combination of an inhibitor of general translation and an activator of specialized translation is key to ribosome-mediated control of gene expression. Here we discuss how these RNA regulatory elements provide a new level of control to protein expression and their implications for gene expression, organismal development and evolution.

  19. Validation of the World Health Organization Enzyme-Linked Immunosorbent Assay for the Quantitation of Immunoglobulin G Serotype-Specific Anti-Pneumococcal Antibodies in Human Serum.

    Science.gov (United States)

    Lee, Hyunju; Lim, Soo Young; Kim, Kyung Hyo

    2017-10-01

    The World Health Organization (WHO) enzyme-linked immunosorbent assay (ELISA) guideline is currently accepted as the gold standard for the evaluation of immunoglobulin G (IgG) antibodies specific to pneumococcal capsular polysaccharide. We conducted validation of the WHO ELISA for 7 pneumococcal serotypes (4, 6B, 9V, 14, 18C, 19F, and 23F) by evaluating its specificity, precision (reproducibility and intermediate precision), accuracy, spiking recovery test, lower limit of quantification (LLOQ), and stability at the Ewha Center for Vaccine Evaluation and Study, Seoul, Korea. We found that the specificity, reproducibility, and intermediate precision were within acceptance ranges (reproducibility, coefficient of variability [CV] ≤ 15%; intermediate precision, CV ≤ 20%) for all serotypes. Comparisons between the provisional assignments of calibration sera and the results from this laboratory showed a high correlation > 94% for all 7 serotypes, supporting the accuracy of the ELISA. The spiking recovery test also fell within an acceptable range. The quantification limit, calculated using the LLOQ, for each of the serotypes was 0.05-0.093 μg/mL. The freeze-thaw stability and the short-term temperature stability were also within an acceptable range. In conclusion, we showed good performance using the standardized WHO ELISA for the evaluation of serotype-specific anti-pneumococcal IgG antibodies; the WHO ELISA can evaluate the immune response against pneumococcal vaccines with consistency and accuracy. © 2017 The Korean Academy of Medical Sciences.

  20. SpEnD: Linked Data SPARQL Endpoints Discovery Using Search Engines

    Science.gov (United States)

    Yumusak, Semih; Dogdu, Erdogan; Kodaz, Halife; Kamilaris, Andreas; Vandenbussche, Pierre-Yves

    In this study, a novel metacrawling method is proposed for discovering and monitoring linked data sources on the Web. We implemented the method in a prototype system, named SPARQL Endpoints Discovery (SpEnD). SpEnD starts with a "search keyword" discovery process for finding relevant keywords for the linked data domain and specifically SPARQL endpoints. Then, these search keywords are utilized to find linked data sources via popular search engines (Google, Bing, Yahoo, Yandex). By using this method, most of the currently listed SPARQL endpoints in existing endpoint repositories, as well as a significant number of new SPARQL endpoints, have been discovered. Finally, we have developed a new SPARQL endpoint crawler (SpEC) for crawling and link analysis.

  1. Soil-to-plant transfer of elements is not linear: Results for five elements relevant to radioactive waste in five boreal forest species

    Energy Technology Data Exchange (ETDEWEB)

    Tuovinen, Tiina S.; Roivainen, Paeivi, E-mail: paivi.roivainen@uef.fi; Makkonen, Sari; Kolehmainen, Mikko; Holopainen, Toini; Juutilainen, Jukka

    2011-12-01

    Element-specific concentration ratios (CRs) assuming that plant uptake of elements is linear are commonly used in radioecological modelling to describe the soil-to-plant transfer of elements. The goal of this study was to investigate the validity of the linearity assumption in boreal forest plants, for which only limited relevant data are available. The soil-to-plant transfer of three essential (Mo, Ni, Zn) and two non-essential (Pb, U) elements relevant to the safety of radioactive waste disposal was studied. Three understory species (blueberry, narrow buckler fern and May lily) and two tree species (Norway spruce and rowan) were included. Examining CRs as a function of soil concentration showed that CR was not constant but decreased with increasing soil concentrations for all elements and plant species. A non-linear equation fitted fairly well with the empirical data; the R{sup 2}-values for this equation were constantly higher than those for the linear fit. The difference between the two fits was most evident at low soil concentrations where the use of constant CRs underestimated transfer from soil to plants. Site-specific factors affected the transfer of Mo and Ni. The results suggested that systematic variation with soil concentrations explains a part of the large variation of empirically determined CRs, and the accuracy of modelling the soil-to-plant transfer might be improved by using non-linear methods. Non-linearity of soil-to-plant transfer has been previously reported for a few different species, elements and environments. The present study systematically tested the linearity assumption for five elements (both essential and non-essential) and in five boreal forest species representing different growth traits and phylogenies. The data supported non-linearity in all cases.

  2. Soil-to-plant transfer of elements is not linear: Results for five elements relevant to radioactive waste in five boreal forest species

    International Nuclear Information System (INIS)

    Tuovinen, Tiina S.; Roivainen, Päivi; Makkonen, Sari; Kolehmainen, Mikko; Holopainen, Toini; Juutilainen, Jukka

    2011-01-01

    Element-specific concentration ratios (CRs) assuming that plant uptake of elements is linear are commonly used in radioecological modelling to describe the soil-to-plant transfer of elements. The goal of this study was to investigate the validity of the linearity assumption in boreal forest plants, for which only limited relevant data are available. The soil-to-plant transfer of three essential (Mo, Ni, Zn) and two non-essential (Pb, U) elements relevant to the safety of radioactive waste disposal was studied. Three understory species (blueberry, narrow buckler fern and May lily) and two tree species (Norway spruce and rowan) were included. Examining CRs as a function of soil concentration showed that CR was not constant but decreased with increasing soil concentrations for all elements and plant species. A non-linear equation fitted fairly well with the empirical data; the R 2 -values for this equation were constantly higher than those for the linear fit. The difference between the two fits was most evident at low soil concentrations where the use of constant CRs underestimated transfer from soil to plants. Site-specific factors affected the transfer of Mo and Ni. The results suggested that systematic variation with soil concentrations explains a part of the large variation of empirically determined CRs, and the accuracy of modelling the soil-to-plant transfer might be improved by using non-linear methods. Non-linearity of soil-to-plant transfer has been previously reported for a few different species, elements and environments. The present study systematically tested the linearity assumption for five elements (both essential and non-essential) and in five boreal forest species representing different growth traits and phylogenies. The data supported non-linearity in all cases.

  3. Multi-element analyses of earthworms for radioecology

    International Nuclear Information System (INIS)

    Yoshida, Satoshi; Muramatsu, Yasuyuki; Peijnenburg, W.

    2004-01-01

    Increasing attention on the environmental radiation protection realizes that more information is required on the transfer and accumulation of radionuclides in the biological compartments of the ecosystems. Earthworms play an important role in ecosystems, and might be a good indicator of soil contamination and its effect on the ecosystem. The elemental composition of earthworms gives useful information on background levels and possible accumulation of metals as well as related radionuclides. However, data for the elemental composition of earthworms are limited except for some specific heavy metals such as Cd, Zn, Pb and Cu. In this study, earthworms and their growth media were analyzed for 35 elements, including radionuclide related elements such as Cs, Sr, Th and U, in order to obtain the basic information on the transfer parameters of the elements. The earthworms analyzed were fed in the laboratory or collected in the environment. The concentrations and transfer factors (TFs) of the elements were determined both for laboratory and natural conditions. Relatively high TFs were observed for Na, Mg, P, K, Ca, Co, Ni, Cu, Zn, As, Se, Rb, Mo and Cd. The TFs for Al, Sc, Ti, Y, Nb and lanthanide elements were low. The TFs of Cs were different depending on the medium (soil type), indicating that bioavailability of Cs in the medium might be one of the important controlling factors of Cs concentration in earthworm. (author)

  4. Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis.

    Science.gov (United States)

    Smith, Alias J; Chudnovsky, Lorissa; Simoes-Barbosa, Augusto; Delgadillo-Correa, Maria G; Jonsson, Zophonias O; Wohlschlegel, James A; Johnson, Patricia J

    2011-04-01

    A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5' untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif.

  5. Novel Core Promoter Elements and a Cognate Transcription Factor in the Divergent Unicellular Eukaryote Trichomonas vaginalis▿

    Science.gov (United States)

    Smith, Alias J.; Chudnovsky, Lorissa; Simoes-Barbosa, Augusto; Delgadillo-Correa, Maria G.; Jonsson, Zophonias O.; Wohlschlegel, James A.; Johnson, Patricia J.

    2011-01-01

    A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5′ untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif. PMID:21245378

  6. Endogenous retroviruses function as species-specific enhancer elements in the placenta.

    Science.gov (United States)

    Chuong, Edward B; Rumi, M A Karim; Soares, Michael J; Baker, Julie C

    2013-03-01

    The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers in mouse and rat trophoblast stem cells (TSCs) and found that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific histone H3 lysine 4 monomethylation (H3K4me1)- and histone H3 lysine 27 acetylation (H3K27ac)-defined enhancers that functionally bind Cdx2, Eomes and Elf5-core factors that define the TSC regulatory network. Furthermore, we show that RLTR13D5 is capable of driving gene expression in rat placental cells. Analysis in other tissues shows that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive for ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer co-option as a mechanism underlying the extensive evolutionary diversification of placental development.

  7. Role of special cross-links in structure formation of bacterial DNA polymer

    Science.gov (United States)

    Agarwal, Tejal; Manjunath, G. P.; Habib, Farhat; Lakshmi Vaddavalli, Pavana; Chatterji, Apratim

    2018-01-01

    Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain even of a simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify the large scale structure of a polymer chain with a few cross-links.

  8. Hip Hop Dance Experience Linked to Sociocognitive Ability.

    Science.gov (United States)

    Bonny, Justin W; Lindberg, Jenna C; Pacampara, Marc C

    2017-01-01

    Expertise within gaming (e.g., chess, video games) and kinesthetic (e.g., sports, classical dance) activities has been found to be linked with specific cognitive skills. Some of these skills, working memory, mental rotation, problem solving, are linked to higher performance in science, technology, math, and engineering (STEM) disciplines. In the present study, we examined whether experience in a different activity, hip hop dance, is also linked to cognitive abilities connected with STEM skills as well as social cognition ability. Dancers who varied in hip hop and other dance style experience were presented with a set of computerized tasks that assessed working memory capacity, mental rotation speed, problem solving efficiency, and theory of mind. We found that, when controlling for demographic factors and other dance style experience, those with greater hip hop dance experience were faster at mentally rotating images of hands at greater angle disparities and there was a trend for greater accuracy at identifying positive emotions displayed by cropped images of human faces. We suggest that hip hop dance, similar to other more technical activities such as video gameplay, tap some specific cognitive abilities that underlie STEM skills. Furthermore, we suggest that hip hop dance experience can be used to reach populations who may not otherwise be interested in other kinesthetic or gaming activities and potentially enhance select sociocognitive skills.

  9. Hip Hop Dance Experience Linked to Sociocognitive Ability.

    Directory of Open Access Journals (Sweden)

    Justin W Bonny

    Full Text Available Expertise within gaming (e.g., chess, video games and kinesthetic (e.g., sports, classical dance activities has been found to be linked with specific cognitive skills. Some of these skills, working memory, mental rotation, problem solving, are linked to higher performance in science, technology, math, and engineering (STEM disciplines. In the present study, we examined whether experience in a different activity, hip hop dance, is also linked to cognitive abilities connected with STEM skills as well as social cognition ability. Dancers who varied in hip hop and other dance style experience were presented with a set of computerized tasks that assessed working memory capacity, mental rotation speed, problem solving efficiency, and theory of mind. We found that, when controlling for demographic factors and other dance style experience, those with greater hip hop dance experience were faster at mentally rotating images of hands at greater angle disparities and there was a trend for greater accuracy at identifying positive emotions displayed by cropped images of human faces. We suggest that hip hop dance, similar to other more technical activities such as video gameplay, tap some specific cognitive abilities that underlie STEM skills. Furthermore, we suggest that hip hop dance experience can be used to reach populations who may not otherwise be interested in other kinesthetic or gaming activities and potentially enhance select sociocognitive skills.

  10. Enzyme-Linked Immunosorbent Assay Using a Virus Type-Specific Peptide Based on a Subdomain of Envelope Protein Erns for Serologic Diagnosis of Pestivirus Infections in Swine

    Science.gov (United States)

    Langedijk, J. P. M.; Middel, W. G. J.; Meloen, R. H.; Kramps, J. A.; de Smit, J. A.

    2001-01-01

    Peptides deduced from the C-terminal end (residues 191 to 227) of pestivirus envelope protein Erns were used to develop enzyme-linked immunosorbent assays (ELISAs) to measure specifically antibodies against different types of pestiviruses. The choice of the peptide was based on the modular structure of the Erns protein, and the peptide was selected for its probable independent folding and good exposure, which would make it a good candidate for an antigenic peptide to be used in a diagnostic test. A solid-phase peptide ELISA which was cross-reactive for several types of pestivirus antibodies and which can be used for the general detection of pestivirus antibodies was developed. To identify type-specific pestivirus antibodies, a liquid-phase peptide ELISA, with a labeled, specific classical swine fever virus (CSFV) peptide and an unlabeled bovine viral diarrhea virus peptide to block cross-reactivity, was developed. Specificity and sensitivity of the liquid-phase peptide ELISA for CSFV were 98 and 100%, respectively. Because the peptide is a fragment of the Erns protein, it can be used to differentiate between infected and vaccinated animals when a vaccine based on the E2 protein, which is another pestivirus envelope protein, is used. PMID:11230402

  11. Linking social capital and mortality in the elderly: a Swedish national cohort study.

    Science.gov (United States)

    Sundquist, Kristina; Hamano, Tsuyoshi; Li, Xinjun; Kawakami, Naomi; Shiwaku, Kuninori; Sundquist, Jan

    2014-07-01

    Our objective was to examine the association between neighborhood linking social capital (a concept describing the amount of trust between individuals and societal institutions) and all-cause and cause-specific mortality in the elderly. The entire Swedish population aged 65+, a total of 1,517,336 men and women, was followed from 1 January 2002 until death, emigration, or the end of the study on 31 December 2010. Small geographic units were used to define neighborhoods. The definition of linking social capital was based on neighborhood voting participation rates, categorized into three groups. Multilevel logistic regression was used to estimate odds ratios (ORs) and between-neighborhood variance in three different models. The results showed an overall association between linking social capital and all-cause mortality. The significant OR of 1.53 in the group with low linking social capital decreased, but remained significant (OR=1.27), after accounting for age, sex, family income, marital status, country of birth, education level, and region of residence. There were also significant associations between linking social capital and cause-specific mortality in coronary heart disease, psychiatric disorders, cancer, stroke, chronic lower respiratory diseases, type 2 diabetes, and suicide. There are associations between low linking social capital and mortality from chronic disorders and suicide in the elderly population. Community support for elderly people living in neighborhoods with low levels of linking social capital may need to be strengthened. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Linking project-based mechanisms with domestic greenhouse gas emissions trading schemes

    International Nuclear Information System (INIS)

    Bygrave, S.; Bosi, M.

    2004-01-01

    Although there are a number of possible links between emission trading and project-based mechanisms, the focus of this paper is on linking domestic GHG emission trading schemes with: (1) domestic; and, (2) international (JI and CDM) GHG reduction project activities. The objective is to examine some of the challenges in linking DETs and project-based mechanisms, as well as some possible solutions to address these challenges. The link between JI / CDM and intergovernmental international emissions trading (i.e. Article 17 of the Kyoto Protocol) is defined by the Kyoto Protocol, and therefore is not covered in this paper. The paper is written in the context of: (a) countries adhering to the Kyoto Protocol and elaborating their strategies to meet their GHG emission commitments, including through the use of the emissions trading and project-based mechanisms. For example, the European Union (EU) will be commencing a GHG Emissions Trading Scheme in January 2005, and recently, the Council of ministers and the European Parliament agreed on a text for an EU Linking Directive allowing the use of JI and CDM emission units in the EU Emission Trading Scheme (EU-ETS); and (b) all countries (and/or regions within countries) with GHG emission obligations that may choose to use domestic emissions trading and project-based mechanisms to meet their GHG commitments. The paper includes the following elements: (1) an overview of the different flexibility mechanisms (i.e. GHG emissions trading and PBMs), including a brief description and comparisons between the mechanisms (Section 3); (2) an exploration of the issues that emerge when project-based mechanisms link with domestic emissions trading schemes, as well as possible solutions to address some of the challenges raised (Section 4); (3) a case study examining the EU-ETS and the EU Linking Directive on project-based mechanisms, in particular on how the EU is addressing in a practical context relevant linking issues (Section 5); (4) a

  13. Molecular basis of coiled-coil oligomerization-state specificity.

    Science.gov (United States)

    Ciani, Barbara; Bjelic, Saša; Honnappa, Srinivas; Jawhari, Hatim; Jaussi, Rolf; Payapilly, Aishwarya; Jowitt, Thomas; Steinmetz, Michel O; Kammerer, Richard A

    2010-11-16

    Coiled coils are extensively and successfully used nowadays to rationally design multistranded structures for applications, including basic research, biotechnology, nanotechnology, materials science, and medicine. The wide range of applications as well as the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomerization. Here, we address the important and unresolved question why the presence of particular oligomerization-state determinants within a coiled coil does frequently not correlate with its topology. We found an unexpected, general link between coiled-coil oligomerization-state specificity and trigger sequences, elements that are indispensable for coiled-coil formation. By using the archetype coiled-coil domain of the yeast transcriptional activator GCN4 as a model system, we show that well-established trimer-specific oligomerization-state determinants switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence. We successfully confirmed our results in two other, unrelated coiled-coil dimers, ATF1 and cortexillin-1. We furthermore show that multiple topology determinants can coexist in the same trigger sequence, revealing a delicate balance of the resulting oligomerization state by position-dependent forces. Our experimental results should significantly improve the prediction of the oligomerization state of coiled coils. They therefore should have major implications for the rational design of coiled coils and consequently many applications using these popular oligomerization domains.

  14. Development of a scanning proton microprobe - computer-control, elemental mapping and applications

    International Nuclear Information System (INIS)

    Loevestam, Goeran.

    1989-08-01

    A scanning proton microprobe set-up has been developed at the Pelletron accelerator in Lund. A magnetic beam scanning system and a computer-control system for beam scanning and data aquisition is described. The computer system consists of a VMEbus front-end computer and a μVax-II host-computer, interfaced by means of a high-speed data link. The VMEbus computer controls data acquisition, beam charge monitoring and beam scanning while the more sophisticated work of elemental mapping and spectrum evaluations is left to the μVax-II. The calibration of the set-up is described as well as several applications. Elemental micro patterns in tree rings and bark has been investigated by means of elemental mapping and quantitative analysis. Large variations of elemental concentrations have been found for several elements within a single tree ring. An external beam set-up has been developed in addition to the proton microprobe set-up. The external beam has been used for the analysis of antique papyrus documents. Using a scanning sample procedure and particle induced X-ray emission (PIXE) analysis, damaged and missing characters of the text could be made visible by means of multivariate statistical data evaluation and elemental mapping. Also aspects of elemental mapping by means of scanning μPIXE analysis are discussed. Spectrum background, target thickness variations and pile-up are shown to influence the structure of elemental maps considerably. In addition, a semi-quantification procedure has been developed. (author)

  15. Rigid finite element method in analysis of dynamics of offshore structures

    Energy Technology Data Exchange (ETDEWEB)

    Wittbrodt, Edmund [Gdansk Univ. of Technology (Poland); Szczotka, Marek; Maczynski, Andrzej; Wojciech, Stanislaw [Bielsko-Biala Univ. (Poland)

    2013-07-01

    This book describes new methods developed for modelling dynamics of machines commonly used in the offshore industry. These methods are based both on the rigid finite element method, used for the description of link deformations, and on homogeneous transformations and joint coordinates, which is applied to the modelling of multibody system dynamics. In this monograph, the bases of the rigid finite element method and homogeneous transformations are introduced. Selected models for modelling dynamics of offshore devices are then verified both by using commercial software, based on the finite element method, as well as by using additional methods. Examples of mathematical models of offshore machines, such as a gantry crane for Blowout-Preventer (BOP) valve block transportation, a pedestal crane with shock absorber, and pipe laying machinery are presented. Selected problems of control in offshore machinery as well as dynamic optimization in device control are also discussed. Additionally, numerical simulations of pipe-laying operations taking active reel drive into account are shown.

  16. SAFETY CRITERION IN ASSESSING THE IMPORTANCE OF AN ELEMENT IN THE COMPLEX TECHNOLOGICAL SYSTEM RELIABILITY STRUCTURE

    Directory of Open Access Journals (Sweden)

    Leszek CHYBOWSKI

    2012-01-01

    Full Text Available The paper presents the need to develop a description of the importance of the technological systems reliability structure elements in terms of security of the system. Basic issues related to the exploration of weak links and important elements in the system as well as a proposal to develop the current approach to assessing the importance of the system components have been presented. Moreover, the differences between the unreliability of suitability and unreliability of safety have been pointed out.

  17. Generic linking of finite element models for non-linear static and global dynamic analyses for aircraft structures

    NARCIS (Netherlands)

    de Wit, A.J.; Akcay-Perdahcioglu, Didem; van den Brink, W.M.; de Boer, Andries; Rolfes, R.; Jansen, E.L.

    2011-01-01

    Depending on the type of analysis, Finite Element(FE) models of different fidelity are necessary. Creating these models manually is a labor intensive task. This paper discusses a generic approach for generating FE models of different fidelity from a single reference FE model. These different

  18. Trace elements in oral health and disease: An updated review

    Directory of Open Access Journals (Sweden)

    Noopur Kulkarni

    2014-01-01

    Full Text Available Enzymes of trace elements are an important part of certain biological and chemical reactions. They work in harmony with proteins and often with certain other co enzymes. They attract substrate molecules and enable their conversion to a specific end product. Some trace elements are involved in redox reactions. Modern day diet, comprising of refined foods is a cause of concern, as it may not have a sufficient amount of these trace elements. Dietary supplements may be of required to combat this shortage. The present paper has thoroughly discussed trace elements, as this area of research has not received the deserved attention. Thus, a comprehensive understanding of these trace elements is essential and significant for disease control and for maintaining optimal health.

  19. Peculiarities of rare-earth-element distribution in environmental objects

    International Nuclear Information System (INIS)

    Gorbunov, A.V.; Onischenko, T.L.; Gundorina, S.F.; Frontasyeva, M.V.

    1993-01-01

    The effect of the production of phosphorus fertilizers on the pollution of the environment by rare-earth elements is reviewed. The main sources of rare-earth element pollution in the environment are described. The levels of REEs in components of the environment - atmosphere, snow, different types of soil, native and agricultural types of vegetation - that provide evidence for their participation in the biological cycle of plants are considered. The high values of the correlation coefficients lead one to think that the REE distribution in vegetation occurs under specific laws true for this family of elements. (author) 9 refs.; 6 figs.; 5 tabs

  20. The missing link between values and behaviour

    DEFF Research Database (Denmark)

    Brunsø, Karen

    For a long time human values have been perceived as abstrat cognitions representing desired goals or end-states which motivate humnan behaviour. A number of studies have tried to explore the link between values and behaviour, but often different constructs are included as intermediate links between...... values and specific behaviour, since values may be too abstract to influence behaviour directly. We propose the concept of lifestyle as a mediator between values and behaviour, and present our approach to lifestyle based on principles from cognitive psychology, where we distinguish between values...... and lifestyle and behaviour. Based on this appraoch we collected data covering values, lifestyle and behaviour, and estimated the cogntiive hierarchy from values to lifestyle to behaviour by structural equation models....

  1. Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.

    Science.gov (United States)

    Petrotchenko, Evgeniy V; Borchers, Christoph H

    2014-09-01

    Cross-linking combined with MS involves enzymatic digestion of cross-linked proteins and identifying cross-linked peptides. Assignment of cross-linked peptide masses requires a search of all possible binary combinations of peptides from the cross-linked proteins' sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross-linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi et al., ), but has not previously been applied to cross-linking studies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Uptakes of trace elements in Zn-deficient mice

    International Nuclear Information System (INIS)

    Ohyama, T.; Yanaga, M.; Yoshida, T.; Maetsu, H.; Suganuma, H.; Omori, T.

    2002-01-01

    A multitracer technique was used to obtain uptake rates of essential trace elements in various organs and tissues in Zn-deficient mice. A multitracer solution, containing more than 20 radioisotopes, was injected intraperitoneally into Zn-deficient state mice and control ones. Uptake rates of the radioisotopes were compared with concentrations of trace elements determined by instrumental neutron activation analysis (INAA) in order to study a specific metabolism of Zn and other essential trace elements, such as Mn, Co, Se, Rb, and Sr. The result suggests that Zn is supplied from bone to other organs and tissues and an increase in Co concentration in all organs and tissues depends on its chemical form, under the Z-deficient state. (author)

  3. Biological toxicity of lanthanide elements on algae.

    Science.gov (United States)

    Tai, Peidong; Zhao, Qing; Su, Dan; Li, Peijun; Stagnitti, Frank

    2010-08-01

    The biological toxicity of lanthanides on marine monocellular algae was investigated. The specific objective of this research was to establish the relationship between the abundance in the seawater of lanthanides and their biological toxicities on marine monocellular algae. The results showed that all single lanthanides had similar toxic effects on Skeletonema costatum. High concentrations of lanthanides (29.04+/-0.61 micromol L(-1)) resulted in 50% reduction in growth of algae compared to the controls (0 micromol L(-1)) after 96 h (96 h-EC50). The biological toxicity of 13 lanthanides on marine monocellular algae was unrelated with the abundance of different lanthanide elements in nature, and the "Harkins rule" was not appropriate for the lanthanides. A mixed solution that contained equivalent concentrations of each lanthanide element had the same inhibition effect on algae cells as each individual lanthanide element at the same total concentration. This phenomenon is unique compared to the groups of other elements in the periodic table. Hence, we speculate that the monocellular organisms might not be able to sufficiently differentiate between the almost chemically identical lanthanide elements. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  4. Concentration of trace elements in marine organisms

    International Nuclear Information System (INIS)

    Ishii, Takaaki; Suzuki, Hamaji; Iimura, Mitsue; Koyanagi, Taku

    1976-01-01

    Information on the quality and quantity of stable trace elements in marine environments is frequently required to analyze the radioecological behavior of radionuclides released from nuclear facilities into the sea. In the present work, special attention was concentrated in determination of stable Mn, Fe, Co, Zn, Rb and Cs in marine organisms to estimate the concentration factors for these elements and corresponding radionuclides. Marine organisms (fishes, marine invertebrates and seaweeds) were collected at the seashore of Ibaragi prefecture and provided for chemical analysis after dry-ashing and wet-ashing. Atomic absorption spectrophotometry and neutron activation analysis were applied to determine the concentration of elements. The concentration of stable elements in fish muscle was independent on species of the fishes though slightly higher trends were observed in ''Usumebaru'', Sebastes nivosus for Cs, ''Ishimochi'', Nibea mitsukurii for Zn and Fe compared with other species. The concentration of Co, Zn and Fe in muscle of marine invertebrates was one order of magnitude higher than fish muscles especially in shellfishes for Co. Seaweeds showed peculiar species specificity for the concentration of stable trace elements and remarkable differences was observed between the species even among the same genus. (auth.)

  5. HIV-1 Infection of Primary CD4+ T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements.

    Science.gov (United States)

    Young, George R; Terry, Sandra N; Manganaro, Lara; Cuesta-Dominguez, Alvaro; Deikus, Gintaras; Bernal-Rubio, Dabeiba; Campisi, Laura; Fernandez-Sesma, Ana; Sebra, Robert; Simon, Viviana; Mulder, Lubbertus C F

    2018-01-01

    Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathological states, such as viral infections and certain cancers, coincide with ERV expression, suggesting that transcriptional reawakening is possible. HML-2 elements are reportedly induced during HIV-1 infection, but the conserved nature of these elements has, until recently, rendered their expression profiling problematic. Here, we provide comprehensive HERV-K HML-2 expression profiles specific for productively HIV-1-infected primary human CD4 + T cells. We combined enrichment of HIV-1 infected cells using a reporter virus expressing a surface reporter for gentle and efficient purification with long-read single-molecule real-time sequencing. We show that three HML-2 proviruses-6q25.1, 8q24.3, and 19q13.42-are upregulated on average between 3- and 5-fold in HIV-1-infected CD4 + T cells. One provirus, HML-2 12q24.33, in contrast, was repressed in the presence of active HIV replication. In conclusion, this report identifies the HERV-K HML-2 loci whose expression profiles differ upon HIV-1 infection in primary human CD4 + T cells. These data will help pave the way for further studies on the influence of endogenous retroviruses on HIV-1 replication. IMPORTANCE Endogenous retroviruses inhabit big portions of our genome. Moreover, although they are mainly inert, some of the evolutionarily younger members maintain the ability to express both RNA and proteins. We have developed an approach using long-read single-molecule real-time (SMRT) sequencing that produces long reads that

  6. Determination of trace elements in the human substantia nigra

    Energy Technology Data Exchange (ETDEWEB)

    Morawski, M. [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany)]. E-mail: morm@medizin.uni-leipzig.de; Meinecke, Ch. [Fakultaet fuer Physik und Geowissenschaften, Universitaet Leipzig, Linnestrasse 5, 04105 Leipzig (Germany); Reinert, T. [Fakultaet fuer Physik und Geowissenschaften, Universitaet Leipzig, Linnestrasse 5, 04105 Leipzig (Germany); Doerffel, A.C. [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany); Riederer, P. [Klin. Neurochemie, Abt. Psychiatrie, Universitaet Wuerzburg, Fuechsleinstrasse 15, 97080 Wuerzburg (Germany); Arendt, T. [Paul-Flechsig-Institut fuer Hirnforschung, Universitaet Leipzig, Jahnallee 59, 04109 Leipzig (Germany); Butz, T. [Fakultaet fuer Physik und Geowissenschaften, Universitaet Leipzig, Linnestrasse 5, 04105 Leipzig (Germany)

    2005-04-01

    'The gain in brain is mainly in the stain' was long time a key sentence for research in neurodegenerative disease. However, for a quantification of the element concentrations (especially iron) in brain tissue, standard staining methods are insufficient. Advanced physical methods allow a quantitative elemental analysis of brain tissue. The sophisticated ion beam analysis provides a quantitative determination of elemental concentrations with a subcellular spatial resolution using a scanning proton beam focussed down to below 1 {mu}m that induces characteristic X-rays in the specimen (PIXE - particle induced X-ray emission). Histochemical and biochemical determinations of total iron content in brain regions from idiopathic Parkinson's disease have demonstrated an increase of iron in parkinsonian substantia nigra pars compacta but not in the pars reticulata, however without a clear cellular classification. For the first time, we have differentially investigated the intra- and extraneuronal elemental concentrations (especially iron) of the human substantia nigra pars compacta versus pars reticulata with detection limits in the range of 50 {mu}mol/l. Thus, we could compare the neuronal iron concentration in human brain sections of healthy and parkinsonian brain tissue. Clear differences in the iron concentration and distribution could be disclosed. Additionally, we could show in situ that the increased intraneuronal iron content is linked to neuromelanin.

  7. Deploying Linked Open Vocabulary (LOV to Enhance Library Linked Data

    Directory of Open Access Journals (Sweden)

    Oh, Sam Gyun

    2015-06-01

    Full Text Available Since the advent of Linked Data (LD as a method for building webs of data, there have been many attempts to apply and implement LD in various settings. Efforts have been made to convert bibliographic data in libraries into Linked Data, thereby generating Library Linked Data (LLD. However, when memory institutions have tried to link their data with external sources based on principles suggested by Tim Berners-Lee, identifying appropriate vocabularies for use in describing their bibliographic data has proved challenging. The objective of this paper is to discuss the potential role of Linked Open Vocabularies (LOV in providing better access to various open datasets and facilitating effective linking. The paper will also examine the ways in which memory institutions can utilize LOV to enhance the quality of LLD and LLD-based ontology design.

  8. A specific family of interspersed repeats (SINEs facilitates meiotic synapsis in mammals

    Directory of Open Access Journals (Sweden)

    Johnson Matthew E

    2013-01-01

    Full Text Available Abstract Background Errors during meiosis that affect synapsis and recombination between homologous chromosomes contribute to aneuploidy and infertility in humans. Despite the clinical relevance of these defects, we know very little about the mechanisms by which homologous chromosomes interact with one another during mammalian meiotic prophase. Further, we remain ignorant of the way in which chromosomal DNA complexes with the meiosis-specific structure that tethers homologs, the synaptonemal complex (SC, and whether specific DNA elements are necessary for this interaction. Results In the present study we utilized chromatin immunoprecipitation (ChIP and DNA sequencing to demonstrate that the axial elements of the mammalian SC are markedly enriched for a specific family of interspersed repeats, short interspersed elements (SINEs. Further, we refine the role of the repeats to specific sub-families of SINEs, B1 in mouse and AluY in old world monkey (Macaca mulatta. Conclusions Because B1 and AluY elements are the most actively retrotransposing SINEs in mice and rhesus monkeys, respectively, our observations imply that they may serve a dual function in axial element binding; i.e., as the anchoring point for the SC but possibly also as a suppressor/regulator of retrotransposition.

  9. Why should we publish Linked Data?

    Science.gov (United States)

    Blower, Jon; Riechert, Maik; Koubarakis, Manolis; Pace, Nino

    2016-04-01

    publishing Linked Data will result in tangible user benefits. This presentation will address a number of these issues, using real-world experience gathered from four recent European projects: MELODIES (http://melodiesproject.eu), LEO (http://linkedeodata.eu), CHARMe (http://linkedeodata.eu) and TELEIOS (http://www.earthobservatory.eu). These projects have all applied Linked Data techniques in practical, real-world situations involving the use of diverse data (including earth science data) by both industrial and academic users. Specifically, we will: • Identify a set of practical and valuable uses for Linked Data, focusing on areas where Linked Data fills gaps left by other technologies. These uses include: enabling the discovery of earth science data using mass-market search engines, helping users to understand data and its uses, combining data from multiple sources and enabling the annotation of data by users. • Enumerate some common challenges faced by developers of data-driven services who wish to use Linked Data in their applications. • Describe a new suite of tools for managing, processing and visualising Linked Data in earth science applications (including geospatial Linked Data).

  10. Composing a Tumor Specific Bacterial Promoter.

    Directory of Open Access Journals (Sweden)

    Igor V Deyneko

    Full Text Available Systemically applied Salmonella enterica spp. have been shown to invade and colonize neoplastic tissues where it retards the growth of many tumors. This offers the possibility to use the bacteria as a vehicle for the tumor specific delivery of therapeutic molecules. Specificity of such delivery is solely depending on promoter sequences that control the production of a target molecule. We have established the functional structure of bacterial promoters that are transcriptionally active exclusively in tumor tissues after systemic application. We observed that the specific transcriptional activation is accomplished by a combination of a weak basal promoter and a strong FNR binding site. This represents a minimal set of control elements required for such activation. In natural promoters, additional DNA remodeling elements are found that alter the level of transcription quantitatively. Inefficiency of the basal promoter ensures the absence of transcription outside tumors. As a proof of concept, we compiled an artificial promoter sequence from individual motifs representing FNR and basal promoter and showed specific activation in a tumor microenvironment. Our results open possibilities for the generation of promoters with an adjusted level of expression of target proteins in particular for applications in bacterial tumor therapy.

  11. A guide to evaluating linkage quality for the analysis of linked data.

    Science.gov (United States)

    Harron, Katie L; Doidge, James C; Knight, Hannah E; Gilbert, Ruth E; Goldstein, Harvey; Cromwell, David A; van der Meulen, Jan H

    2017-10-01

    Linked datasets are an important resource for epidemiological and clinical studies, but linkage error can lead to biased results. For data security reasons, linkage of personal identifiers is often performed by a third party, making it difficult for researchers to assess the quality of the linked dataset in the context of specific research questions. This is compounded by a lack of guidance on how to determine the potential impact of linkage error. We describe how linkage quality can be evaluated and provide widely applicable guidance for both data providers and researchers. Using an illustrative example of a linked dataset of maternal and baby hospital records, we demonstrate three approaches for evaluating linkage quality: applying the linkage algorithm to a subset of gold standard data to quantify linkage error; comparing characteristics of linked and unlinked data to identify potential sources of bias; and evaluating the sensitivity of results to changes in the linkage procedure. These approaches can inform our understanding of the potential impact of linkage error and provide an opportunity to select the most appropriate linkage procedure for a specific analysis. Evaluating linkage quality in this way will improve the quality and transparency of epidemiological and clinical research using linked data. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

  12. Quench testing of HTS sub-elements for 13 kA and 600 A leads designed to the specifications for the CERN Large Hadron Collider project

    CERN Document Server

    Cowey, L; Krischel, D; Bock, J J

    2000-01-01

    Ability to safely withstand and survive self quench conditions is an important consideration in the design and utilisation of HTS current leads. The provision of a non superconducting shunt path allows current to be diverted in the event of a transition to the normal state. This shunt should allow very rapid transfer of current out of the HTS material and be able to safely support the full load current for the time required to detect the fault and reduce the current to zero. However, the shunt should also be designed to minimise the increased heat load which will result from it's addition to the lead. Test of leads based on melt cast BSCCO 2212 utilising a fully integrated silver gold alloy sheath are described. The HTS sub- elements form part of a full 13 kA lead, designed to the specifications of CERN for the LHC project. The sub-elements proved able to fully comply with and exceed the quench performance required by CERN. The HTS module was quenched at the full design current and continued to maintain this ...

  13. The Chromium is an essential element in the human

    International Nuclear Information System (INIS)

    Alvarado Gamez, A.; Blanco Saenz, R.; Mora Morales, E.

    2002-01-01

    The Chromium is an essential element for human and animals, because it a preponderant function in the insulin metabolism as a glucose tolerance factor (GTF). The deficiency of chromium engenders a deterioration in the glucose metabolism due to bad efficiency of insulin. Because the importance of this element an exhaustive reference review was made and this presents some studies realized in laboratory animals and in human beings where it is prove with resuits the effect of chromium over the improvement of patients with non-insulin dependant diabetes. Three substances are presented as chromium active biological forms: a material rich in chromium known as glucose tolerance factor, chromium picolinate and a substance of low molecular weight LMWCr in its forms of apo and holo that contains chromium and it links the insulin receptor and improves its activity. Also this paper presents information about the condition of diabetes in Costa Rica. (Author) [es

  14. Stoichiometry and Life-History Interact to Determine the Magnitude of Cross-Ecosystem Element and Biomass Fluxes

    Directory of Open Access Journals (Sweden)

    Thomas M. Luhring

    2017-05-01

    Full Text Available Ecosystems are linked through the transfer of materials and energy. Studies examining material fluxes across habitat boundaries frequently quantify unidirectional flows of nutrients and energy. However, material fluxes can be multidirectional, and we lack a conceptual framework to describe how their quantity and stoichiometry influence the net transfer of individual elements between ecosystems. Here we develop a zero net transfer isocline (ZNTI framework that integrates the relative mass and stoichiometry of fluxes into and out of an ecosystem. We then use case studies with amphibians and salmon to elucidate how life history, ontogenetic shifts in stoichiometry, and trophic interactions shape relative fluxes of nutrients between aquatic and terrestrial ecosystems. Because they increase in both size and Ca content from ova to metamorphs, amphibian life histories strongly bias them toward net Ca export into the terrestrial environment. Because amphibian biomass, C, P, and Ca ZNTIs do not overlap, there is no value of survivorship where the net flux of biomass, C, P, and Ca are simultaneously balanced between terrestrial and aquatic habitats. The degree of iteroparity and semelparity in salmon strongly affects both the magnitude of net biomass and P flux between riverine and marine environments. While the net direction of biomass flux generally remains strongly biased toward import into the riverine system, net P flux can reach net export into the marine environment because of increasing adult breeding survival leading to reduced mass and %P of what they deposit in rivers (e.g., ova vs. whole carcasses. These examples highlight how ontogenetic shifts in body size and stoichiometry result in asymmetric fluxes of elements and biomass that can lead to simultaneous net imports and exports of different elements within the same system. Furthermore, they demonstrate how changes in life-history characteristics and stage-specific survivorship can lead to

  15. Toward epigenetic and gene regulation models of specific language impairment: looking for links among growth, genes, and impairments

    Directory of Open Access Journals (Sweden)

    Rice Mabel L

    2012-11-01

    Full Text Available Abstract Children with specific language impairment (SLI are thought to have an inherited form of language impairment that spares other developmental domains. SLI shows strong heritability and recent linkage and association studies have replicated results for candidate genes. Regulatory regions of the genes may be involved. Behavioral growth models of language development of children with SLI reveal that the onset of language is delayed, and the growth trajectories of children with SLI parallel those of younger children without SLI. The rate of language acquisition decelerates in the pre-adolescent period, resulting in immature language levels for the children with SLI that persist into adolescence and beyond. Recent genetic and epigenetic discoveries and models relevant to language impairment are reviewed. T cell regulation of onset, acceleration, and deceleration signaling are described as potential conceptual parallels to the growth timing elements of language acquisition and impairment. A growth signaling disruption (GSD hypothesis is proposed for SLI, which posits that faulty timing mechanisms at the cellular level, intrinsic to neurocortical functioning essential for language onset and growth regulation, are at the core of the growth outcomes of SLI. The GSD highlights the need to document and account for growth patterns over childhood and suggests needed directions for future investigation.

  16. Automation of finite element methods

    CERN Document Server

    Korelc, Jože

    2016-01-01

    New finite elements are needed as well in research as in industry environments for the development of virtual prediction techniques. The design and implementation of novel finite elements for specific purposes is a tedious and time consuming task, especially for nonlinear formulations. The automation of this process can help to speed up this process considerably since the generation of the final computer code can be accelerated by order of several magnitudes. This book provides the reader with the required knowledge needed to employ modern automatic tools like AceGen within solid mechanics in a successful way. It covers the range from the theoretical background, algorithmic treatments to many different applications. The book is written for advanced students in the engineering field and for researchers in educational and industrial environments.

  17. Elemental analysis of traditional medicinal seeds by instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Khaled, S.; Mouzai, M.; Ararem, A.; Hamidatou, L.; Zouranen, B.

    2009-01-01

    Traditional medicinal seeds prescribed for specific treatment purposes, were purchased from local markets and analyzed by INAA. The samples were irradiated at Es-Salam research reactor, at a power of 5 MWfor 6 h. The accuracy of the method was established by analyzing reference materials. Twenty elements were measured, with good accuracy and reproducibility. The concentration of elements determined, was found to vary depending on the seeds. The daily intake of essential and toxic elements was determined, and compared with the recommended values. The probable cumulative intake of toxic elements is well below the tolerance limits. (author)

  18. The control of artificial radio-elements of medical use in France

    International Nuclear Information System (INIS)

    Cohen, Y.

    1960-01-01

    Artificial radio-elements are sometimes used in hospitals or laboratories possessing specific equipment and certified staff. These radio-elements are produced within the Saclay Nuclear Centre, and, if they are aimed to a medical use, are submitted to a pharmaceutical control which the issue is addressed in this report. After a recall of the preparation of these radio-elements, the author describes physical controls (determination of radioactivity, measurement of colloidal particle size, impurity content), and biological controls performed on these radio-elements. Reprint of a paper published in Annales pharmaceutiques francaises, tom. XVII, p. 250-260, 1959

  19. Test on large-scale seismic isolation elements

    International Nuclear Information System (INIS)

    Mazda, T.; Shiojiri, H.; Oka, Y.; Fujita, T.; Seki, M.

    1989-01-01

    Demonstration test of seismic isolation elements is considered as one of the most important items in the application of seismic isolation system to fast breeder reactor (FBR) plant. Facilities for testing seismic isolation elements have been built. This paper reports on tests for fullscale laminated rubber bearing and reduced scale models are conducted. From the result of the tests, the laminated rubber bearings turn out to satisfy the specification. Their basic characteristics are confirmed from the tests with fullscale and reduced scale models. The ultimate capacity of the bearings under the condition of ordinary temperature are evaluated

  20. Anatomically-specific intratubular and interstitial biominerals in the human renal medullo-papillary complex.

    Directory of Open Access Journals (Sweden)

    Ling Chen

    Full Text Available Limited information exists on the anatomically-specific early stage events leading to clinically detectable mineral aggregates in the renal papilla. In this study, quantitative multiscale correlative maps of structural, elemental and biochemical properties of whole medullo-papillary complexes from human kidneys were developed. Correlative maps of properties specific to the uriniferous and vascular tubules using high-resolution X-ray computed tomography, scanning and transmission electron microscopy, energy dispersive X-ray spectroscopy, and immunolocalization of noncollagenous proteins (NCPs along with their association with anatomy specific biominerals were obtained. Results illustrated that intratubular spherical aggregates primarily form at the proximal regions distant from the papillary tip while interstitial spherical and fibrillar aggregates are distally located near the papillary tip. Biominerals at the papillary tip were closely localized with 10 to 50 μm diameter vasa recta immunolocalized for CD31 inside the medullo-papillary complex. Abundant NCPs known to regulate bone mineralization were localized within nanoparticles, forming early pathologic mineralized regions of the complex. Based on the physical association between vascular and urothelial tubules, results from light and electron microscopy techniques suggested that these NCPs could be delivered from vasculature to prompt calcification of the interstitial regions or they might be synthesized from local vascular smooth muscle cells after transdifferentiation into osteoblast-like phenotypes. In addition, results provided insights into the plausible temporal events that link the anatomically specific intratubular mineral aggregates with the interstitial biomineralization processes within the functional unit of the kidney.