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Sample records for core domain bound

  1. Critical SQG in bounded domains

    OpenAIRE

    Constantin, Peter; Ignatova, Mihaela

    2016-01-01

    We consider the critical dissipative SQG equation in bounded domains, with the square root of the Dirichlet Laplacian dissipation. We prove global a priori interior $C^{\\alpha}$ and Lipschitz bounds for large data.

  2. A Characterization of Complete Bounded Domain

    Institute of Scientific and Technical Information of China (English)

    殷慰萍; 苏简兵; 赵振刚

    2002-01-01

    @@ 1 IntroductionThis paper is concerned with biholomorphic mappings between two bounded domains D and G both in Cn.Consequently,an important question is whether the domain D is biholomorphic to G? We give an answer for this question under a very weak condition.

  3. Qp-spaces on bounded symmetric domains

    Directory of Open Access Journals (Sweden)

    Jonathan Arazy

    2008-01-01

    Full Text Available We generalize the theory of Qp spaces, introduced on the unit disc in 1995 by Aulaskari, Xiao and Zhao, to bounded symmetric domains in Cd, as well as to analogous Moebius-invariant function spaces and Bloch spaces defined using higher order derivatives; the latter generalization contains new results even in the original context of the unit disc.

  4. Dynamics of Nonlinear Waves on Bounded Domains

    CERN Document Server

    Maliborski, Maciej

    2016-01-01

    This thesis is concerned with dynamics of conservative nonlinear waves on bounded domains. In general, there are two scenarios of evolution. Either the solution behaves in an oscillatory, quasiperiodic manner or the nonlinear effects cause the energy to concentrate on smaller scales leading to a turbulent behaviour. Which of these two possibilities occurs depends on a model and the initial conditions. In the quasiperiodic scenario there exist very special time-periodic solutions. They result for a delicate balance between dispersion and nonlinear interaction. The main body of this dissertation is concerned with construction (by means of perturbative and numerical methods) of time-periodic solutions for various nonlinear wave equations on bounded domains. While turbulence is mainly associated with hydrodynamics, recent research in General Relativity has also revealed turbulent phenomena. Numerical studies of a self-gravitating massless scalar field in spherical symmetry gave evidence that anti-de Sitter space ...

  5. Preservation under Substructures modulo Bounded Cores

    CERN Document Server

    Sankaran, Abhisekh; Madan, Vivek; Kamath, Pritish; Chakraborty, Supratik

    2012-01-01

    We investigate a model-theoretic property that generalizes the classical notion of "preservation under substructures". We call this property \\emph{preservation under substructures modulo bounded cores}, and present a syntactic characterization via $\\Sigma_2^0$ sentences for properties of arbitrary structures definable by FO sentences. Towards a sharper characterization, we conjecture that the count of existential quantifiers in the $\\Sigma_2^0$ sentence equals the size of the smallest bounded core. While we do not have a proof of the conjecture yet, we show that it holds for special fragments of FO and also over special classes of structures. We present a (not FO-definable) class of finite structures for which the conjecture fails, but for which the classical {\\L}o\\'s-Tarski preservation theorem holds. As a fallout of our studies, we have obtained combinatorial proofs of the {\\L}o\\'s-Tarski theorem for some of the aforementioned cases.

  6. Singular integral on bounded strictly pseudoconvex domain

    Institute of Scientific and Technical Information of China (English)

    GONG Ding-dong

    2008-01-01

    Kytmanov and Myslivets gave a special Cauchy principal value of the singular integral on the bounded strictly pseudoconvex domain with smooth boundary. By means of this Cauchy integral principal value, the corresponding singular integral and a composition formula are obtained. This composition formula is quite different from usual ones in form. As an application, the corresponding singular integral equation and the system of singular integral equations are discussed as well.

  7. Lateral diffusion of peripheral membrane proteins on supported lipid bilayers is controlled by the additive frictional drags of (1) bound lipids and (2) protein domains penetrating into the bilayer hydrocarbon core.

    Science.gov (United States)

    Ziemba, Brian P; Falke, Joseph J

    2013-01-01

    Peripheral membrane proteins bound to lipids on bilayer surfaces play central roles in a wide array of cellular processes, including many signaling pathways. These proteins diffuse in the plane of the bilayer and often undergo complex reactions involving the binding of regulatory and substrate lipids and proteins they encounter during their 2D diffusion. Some peripheral proteins, for example pleckstrin homology (PH) domains, dock to the bilayer in a relatively shallow position with little penetration into the bilayer. Other peripheral proteins exhibit more complex bilayer contacts, for example classical protein kinase C isoforms (PKCs) bind as many as six lipids in stepwise fashion, resulting in the penetration of three PKC domains (C1A, C1B, C2) into the bilayer headgroup and hydrocarbon regions. A molecular understanding of the molecular features that control the diffusion speeds of proteins bound to supported bilayers would enable key molecular information to be extracted from experimental diffusion constants, revealing protein-lipid and protein-bilayer interactions difficult to study by other methods. The present study investigates a range of 11 different peripheral protein constructs comprised by 1-3 distinct domains (PH, C1A, C1B, C2, anti-lipid antibody). By combining these constructs with various combinations of target lipids, the study measures 2D diffusion constants on supported bilayers for 17 different protein-lipid complexes. The resulting experimental diffusion constants, together with the known membrane interaction parameters of each complex, are used to analyze the molecular features correlated with diffusional slowing and bilayer friction. The findings show that both (1) individual bound lipids and (2) individual protein domains that penetrate into the hydrocarbon core make additive contributions to the friction against the bilayer, thereby defining the 2D diffusion constant. An empirical formula is developed that accurately estimates the diffusion

  8. Jackson's Theorem on Bounded Symmetric Domains

    Institute of Scientific and Technical Information of China (English)

    Ming Zhi WANG; Guang Bin REN

    2007-01-01

    Polynomial approximation is studied on bounded symmetric domain Ω in C n for holo-morphic function spaces X ,such as Bloch-type spaces,Bergman-type spaces,Hardy spaces,Ω algebra and Lipschitz space.We extend the classical Jackson ’s theorem to several complex variables:E k f,X ) ω (1 /k,f,X ),where E k f,X )is the deviation of the best approximation of f ∈X by polynomials of degree at mostk with respect to the X -metric and ω (1/k,f,X )is the corresponding modulus of continuity.

  9. One Health Core Competency Domains.

    Science.gov (United States)

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  10. One Health Core Competency Domains

    Science.gov (United States)

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting “One Health” approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches. PMID:27679794

  11. One Health Core Competency Domains

    Directory of Open Access Journals (Sweden)

    Rebekah Frankson

    2016-09-01

    Full Text Available The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting ‘One Health’ approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education as they describe the knowledge, skills and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  12. Bound or free: interaction of the C-terminal domain of Escherichia coli single-stranded DNA-binding protein (SSB) with the tetrameric core of SSB.

    Science.gov (United States)

    Su, Xun-Cheng; Wang, Yao; Yagi, Hiromasa; Shishmarev, Dmitry; Mason, Claire E; Smith, Paul J; Vandevenne, Marylène; Dixon, Nicholas E; Otting, Gottfried

    2014-04-01

    Single-stranded DNA (ssDNA)-binding protein (SSB) protects ssDNA from degradation and recruits other proteins for DNA replication and repair. Escherichia coli SSB is the prototypical eubacterial SSB in a family of tetrameric SSBs. It consists of a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain). The eight-residue C-terminal segment of SSB (C-peptide) mediates the binding of SSB to many different SSB-binding proteins. Previously published nuclear magnetic resonance (NMR) data of the monomeric state at pH 3.4 showed that the C-peptide binds to the OB-domain at a site that overlaps with the ssDNA binding site, but investigating the protein at neutral pH is difficult because of the high molecular mass and limited solubility of the tetramer. Here we show that the C-domain is highly mobile in the SSB tetramer at neutral pH and that binding of the C-peptide to the OB-domain is so weak that most of the C-peptides are unbound even in the absence of ssDNA. We address the problem of determining intramolecular binding affinities in the situation of fast exchange between two states, one of which cannot be observed by NMR and cannot be fully populated. The results were confirmed by electron paramagnetic resonance spectroscopy and microscale thermophoresis. The C-peptide-OB-domain interaction is shown to be driven primarily by electrostatic interactions, so that binding of 1 equiv of (dT)35 releases practically all C-peptides from the OB-domain tetramer. The interaction is much more sensitive to NaCl than to potassium glutamate, which is the usual osmolyte in E. coli. As the C-peptide is predominantly in the unbound state irrespective of the presence of ssDNA, long-range electrostatic effects from the C-peptide may contribute more to regulating the activity of SSB than any engagement of the C-peptide by the OB-domain.

  13. Properties of squeezing functions and geometry of bounded domains

    CERN Document Server

    Deng, Fusheng; Zhang, Liyou

    2012-01-01

    In this article we continue the study of properties of squeezing functions and geometry of bounded domains. The limit of squeezing functions of a sequence of bounded domains is studied. We give comparisons of intrinsic positive forms and metrics on bounded domains in terms of squeezing functions. To study the boundary behavior of squeezing functions, we introduce the notions of (intrinsic) ball pinching radius, and give boundary estimate of squeezing functions in terms of these datum. Finally, we use these results to study geometric and analytic properties of some interesting domains, including planar domains, Cartan-Hartogs domains, and a strongly pseudoconvex Reinhardt domain which is not convex. As a corollary, all Cartan-Hartogs domains are homogenous regular, i.e., their squeezing functions admit positive lower bounds.

  14. Classification of billiard motions in domains bounded by confocal parabolas

    Energy Technology Data Exchange (ETDEWEB)

    Fokicheva, V V [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2014-08-01

    We consider the billiard dynamical system in a domain bounded by confocal parabolas. We describe such domains in which the billiard problem can be correctly stated. In each such domain we prove the integrability for the system, analyse the arising Liouville foliation, and calculate the invariant of Liouville equivalence--the so-called marked molecule. It turns out that billiard systems in certain parabolic domains have the same closures of solutions (integral trajectories) as the systems of Goryachev-Chaplygin-Sretenskii and Joukowski at suitable energy levels. We also describe the billiard motion in noncompact domains bounded by confocal parabolas, namely, we describe the topology of the Liouville foliation in terms of rough molecules. Bibliography: 16 titles.

  15. Bloch spaces on bounded symmetric domains in complex Banach spaces

    Institute of Scientific and Technical Information of China (English)

    DENG; Fangwen

    2006-01-01

    We give a definition of Bloch space on bounded symmetric domains in arbitrary complex Banach space and prove such function space is a Banach space. The properties such as boundedness, compactness and closed range of composition operators on such Bloch space are studied.

  16. Extreme Growth of Enstrophy on 2D Bounded Domains

    Science.gov (United States)

    Protas, Bartosz; Sliwiak, Adam

    2016-11-01

    We study the vortex states responsible for the largest instantaneous growth of enstrophy possible in viscous incompressible flow on 2D bounded domain. The goal is to compare these results with estimates obtained using mathematical analysis. This problem is closely related to analogous questions recently considered in the periodic setting on 1D, 2D and 3D domains. In addition to systematically characterizing the most extreme behavior, these problems are also closely related to the open question of the finite-time singularity formation in the 3D Navier-Stokes system. We demonstrate how such extreme vortex states can be found as solutions of constrained variational optimization problems which in the limit of small enstrophy reduce to eigenvalue problems. Computational results will be presented for circular and square domains emphasizing the effect of geometric singularities (corners of the domain) on the structure of the extreme vortex states. Supported by an NSERC (Canada) Discovery Grant.

  17. Linguistic Explanation and Domain Specialization: a case study in bound variable anaphora

    Directory of Open Access Journals (Sweden)

    David eAdger

    2015-09-01

    Full Text Available The core question behind this Frontiers research topic is whether explaining linguistic phenomena requires appeal to properties of human cognition that are specialised to language. We argue here that investigating this issue requires taking linguistic research results seriously, and evaluating these for domain-specificity. We present a particular empirical phenomenon, bound variable interpretations of pronouns dependent on a quantifier phrase, and argue for a particular theory of this empirical domain that is couched at a level of theoretical depth which allows its principles to be evaluated for domain-specialisation. We argue that the relevant principles are specialised when they apply in the domain of language, even if analogues of them are plausibly at work elsewhere in cognition or the natural world more generally. So certain principles may be specialised to language, though not, ultimately, unique to it. Such specialisation is underpinned by ultimately biological factors, hence part of UG.

  18. On the automorphism groups of algebraic bounded domains

    CERN Document Server

    Zaitsev, D

    1994-01-01

    Let D be a bounded domain in C^n. By the theorem of H.~Cartan, the group Aut(D) of all biholomorphic automorphisms of D has a unique structure of a real Lie group such that the action Aut(D)\\times D\\to D is real analytic. This structure is defined by the embedding C_v\\colon Aut(D)\\hookrightarrow D\\times Gl_n(C), f\\mapsto (f(v), f_{*v}), where v\\in D is arbitrary. Here we restrict our attention to the class of domains D defined by finitely many polynomial inequalities. The appropriate category for studying automorphism of such domains is the Nash category. Therefore we consider the subgroup Aut_a(D)\\subset Aut(D) of all algebraic biholomorphic automorphisms which in many cases coincides with Aut(D). Assume that n>1 and D has a boundary point where the Levi form is non-degenerate. Our main result is theat the group Aut_a(D) carries a unique structure of an affine Nash group such that the action Aut_a(D)\\times D\\to D is Nash. This structure is defined by the embedding C_v\\colon Aut_a(D)\\hookrightarrow D\\times Gl...

  19. Smooth Contractive Embeddings and Application to Feynman Formula for Parabolic Equations on Smooth Bounded Domains

    OpenAIRE

    Baur, Benedict; Conrad, Florian; Grothaus, Martin

    2010-01-01

    We prove two assumptions made in an article by Ya.A. Butko, M. Grothaus, O.G. Smolyanov concerning the existence of a strongly continuous operator semigroup solving a Cauchy-Dirichlet problem for an elliptic differential operator in a bounded domain and the existence of a smooth contractive embedding of a core of the generator of the semigroup into the space $C_c^{2,\\alpha}(\\R^n)$. Based on these assumptions a Feynman formula for the solution of the Cauchy-Dirichlet problem is constructed in ...

  20. Eigenproblems of large powers of the Laplacian in bounded domains

    Energy Technology Data Exchange (ETDEWEB)

    Ramani, A [CPT, Ecole Polytechnique, CNRS, UMR 7644, 91128 Palaiseau (France); Grammaticos, B [IMNC, Universite Paris VII-Paris XI, CNRS, UMR 8165, Bat. 104, 91406 Orsay (France); Pomeau, Y [Laboratoire de Physique Statistique de l' Ecole normale superieure, 24 Rue Lhomond, 75231 Paris Cedex 05 (France)

    2007-05-18

    We present a method for computing the spectrum of large powers of the Laplacian in a bounded domain restricting ourselves to the one- and three-dimensional cases. Since it does not seem possible to obtain information on the eigenvalues directly from the transcendental equation that gives the spectrum, we introduce a Wallis-inspired method. We obtain the expansion of the eigenfunction and the eigenvalues in power series where the inverse of the power at which the Laplacian is raised plays the role of the small parameter. We compare these eigenvalues to those obtained through a simple variational approach and remark that the latter offers an excellent approximation to the exact result. (fast track communication)

  1. Positive blowup solutions for some fractional systems in bounded domains

    Directory of Open Access Journals (Sweden)

    Ramzi Alsaedi

    2013-01-01

    Full Text Available Using some potential theory tools and the Schauder fixed point theorem, we prove the existence of a positive continuous weak solution for the fractional system $$ ( -Delta ^{alpha/2}u+ p(xu^{sigma }v^{r}=0,quad (-Delta^{alpha/2}v+q(xu^{s}v^{eta }=0 $$ in a bounded $ C^{1,1}$-domain D in $mathbb{R}^{n}$ $(ngeq 3$, subject to Dirichlet conditions, where $0

  2. Smooth Contractive Embeddings and Application to Feynman Formula for Parabolic Equations on Smooth Bounded Domains

    CERN Document Server

    Baur, Benedict; Grothaus, Martin

    2010-01-01

    We prove two assumptions made in an article by Ya.A. Butko, M. Grothaus, O.G. Smolyanov concerning the existence of a strongly continuous operator semigroup solving a Cauchy-Dirichlet problem for an elliptic differential operator in a bounded domain and the existence of a smooth contractive embedding of a core of the generator of the semigroup into the space $C_c^{2,\\alpha}(\\R^n)$. Based on these assumptions a Feynman formula for the solution of the Cauchy-Dirichlet problem is constructed in the article mentioned above. In this article we show that the assumptions are fulfilled for domains with $C^{4,\\alpha}$-smooth boundary and coefficients in $C^{2,\\alpha}$.

  3. Lower Bound for the Radiation $Q$ of Electrically Small Magnetic Dipole Antennas With Solid Magnetodielectric Core

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Breinbjerg, Olav

    2011-01-01

    A new lower bound for the radiation $Q$ of electrically small spherical magnetic dipole antennas with solid magnetodielectric core is derived in closed form using the exact theory. The new bound approaches the Chu lower bound from above as the antenna electrical size decreases. For $ka, the new...

  4. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Bradley R.; Drake, Eric J.; Shi, Ce; Aldrich, Courtney C.; Gulick, Andrew M.

    2016-09-05

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.

  5. Coexistence of bound and virtual-bound states in shallow-core to valence x-ray spectroscopies

    Science.gov (United States)

    Sen Gupta, Subhra; Bradley, J. A.; Haverkort, M. W.; Seidler, G. T.; Tanaka, A.; Sawatzky, G. A.

    2011-08-01

    With the example of the non-resonant inelastic x-ray scattering (NIXS) at the O45 edges (5d→5f) of the actinides, we develop the theory for shallow-core to valence excitations, where the multiplet spread is larger than the core-hole attraction, such as if the core and valence orbitals have the same principal quantum number. This involves very strong final state configuration interaction (CI), which manifests itself as huge reductions in the Slater-Condon integrals, needed to explain the spectral shapes within a simple renormalized atomic multiplet theory. But more importantly, this results in a cross-over from bound (excitonic) to virtual-bound excited states with increasing energy, within the same core-valance multiplet structure, and in large differences between the dipole and high-order multipole transitions, as observed in NIXS. While the bound states (often higher multipole allowed) can still be modeled using local cluster-like models, the virtual-bound resonances (often dipole-allowed) cannot be interpreted within such local approaches. This is in stark contrast to the more familiar core-valence transitions between different principal quantum number shells, where all the final excited states almost invariably form bound core-hole excitons and can be modeled using local approaches. The possibility of observing giant multipole resonances for systems with high angular momentum ground states is also predicted. The theory is important to obtain ground state information from core-level x-ray spectroscopies of strongly correlated transition metal, rare-earth, and actinide systems.

  6. Ribosomal small subunit domains radiate from a central core

    Science.gov (United States)

    Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O’Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

    2016-01-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2′OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit. PMID:26876483

  7. Ribosomal small subunit domains radiate from a central core

    Science.gov (United States)

    Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O'Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

    2016-02-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2‧OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.

  8. Transient domain formation in membrane-bound organelles undergoing maturation

    Science.gov (United States)

    Dmitrieff, Serge; Sens, Pierre

    2013-12-01

    The membrane components of cellular organelles have been shown to segregate into domains as the result of biochemical maturation. We propose that the dynamical competition between maturation and lateral segregation of membrane components regulates domain formation. We study a two-component fluid membrane in which enzymatic reaction irreversibly converts one component into another and phase separation triggers the formation of transient membrane domains. The maximum domain size is shown to depend on the maturation rate as a power law similar to the one observed for domain growth with time in the absence of maturation, despite this time dependence not being verified in the case of irreversible maturation. This control of domain size by enzymatic activity could play a critical role in regulating exchange between organelles or within compartmentalized organelles such as the Golgi apparatus.

  9. Establishing a core domain set to measure rheumatoid arthritis flares

    DEFF Research Database (Denmark)

    Bykerk, Vivian P; Lie, Elisabeth; Bartlett, Susan J;

    2014-01-01

    agenda for OMERACT 12. CONCLUSION: At OMERACT 11, a core domain set to measure RA flare was ratified and endorsed by attendees. Domain validation aligning with Filter 2.0 is ongoing in new randomized controlled clinical trials and longitudinal observational studies using existing and new instruments......OBJECTIVE: The OMERACT Rheumatoid Arthritis (RA) Flare Group (FG) is developing a data-driven, patient-inclusive, consensus-based RA flare definition for use in clinical trials, longterm observational studies, and clinical practice. At OMERACT 11, we sought endorsement of a proposed core domain set....... At OMERACT 11, breakout groups discussed key domains and instruments to measure them, and proposed a research agenda. Patients were active research partners in all focus groups and domain identification activities. Processes for domain selection and patient partner involvement were case studies for OMERACT...

  10. DECAY ESTIMATES FOR ISENTROPIC COMPRESSIBLE MAGNETOHYDRODYNAMIC EQUATIONS IN BOUNDED DOMAIN

    Institute of Scientific and Technical Information of China (English)

    Mohamed Ahmed Abdallah; Jiang Fei; Tan Zhong

    2012-01-01

    In this paper,under the hypothesis that (o) is upper bounded,we construct a Lyapunov functional for the multidimensional isentropic compressible magnetohydrodynamic equations and show that the weak solutions decay exponentially to the equilibrium state in L2 norm.Our result verifies that the method of Daoyuan Fang,Ruizhao Zi and Ting Zhang [1] can be adapted to magnetohydrodynamic equations.

  11. POSITIVE SOLUTIONS OF FULLY NONLINEAR ELLIPTIC EQUATIONS ON GENERAL BOUNDED DOMAINS

    Institute of Scientific and Technical Information of China (English)

    Li Meisheng; Bao Jiguang

    2001-01-01

    We prove the refined ABP maximum principle, comparison principle, and related existence and uniqueness theorem for the positive solutions of the Dirich let problems of second order fully nonlinear elliptic equations on arbitrary bounded domains.

  12. Weighted Composition Operators between Different Bergman Spaces of Bounded Symmetric Domains

    Indian Academy of Sciences (India)

    Xiaofen Lv; Xiaomin Tang

    2009-09-01

    In this paper, we consider the boundedness and compactness of the weighted composition operators between different Bergman spaces of bounded symmetric domains in terms of the Carleson measure. As an application, we study the multipliers between different Bergman spaces.

  13. Stationary Solutions for a Generalized Kadomtsev-Petviashvili Equation in Bounded Domain

    Institute of Scientific and Technical Information of China (English)

    Zhang Ke-yu; Xu Jia-fa; Li Yong(Communicated)

    2014-01-01

    In this work, we are mainly concerned with the existence of stationary solutions for a generalized Kadomtsev-Petviashvili equation in bounded domain of Rn. We utilize variational method and critical point theory to establish our main results.

  14. Characterization of Amyloid Cores in Prion Domains

    Science.gov (United States)

    Sant’Anna, Ricardo; Fernández, Maria Rosario; Batlle, Cristina; Navarro, Susanna; de Groot, Natalia S.; Serpell, Louise; Ventura, Salvador

    2016-01-01

    Amyloids consist of repetitions of a specific polypeptide chain in a regular cross-β-sheet conformation. Amyloid propensity is largely determined by the protein sequence, the aggregation process being nucleated by specific and short segments. Prions are special amyloids that become self-perpetuating after aggregation. Prions are responsible for neuropathology in mammals, but they can also be functional, as in yeast prions. The conversion of these last proteins to the prion state is driven by prion forming domains (PFDs), which are generally large, intrinsically disordered, enriched in glutamines/asparagines and depleted in hydrophobic residues. The self-assembly of PFDs has been thought to rely mostly on their particular amino acid composition, rather than on their sequence. Instead, we have recently proposed that specific amyloid-prone sequences within PFDs might be key to their prion behaviour. Here, we demonstrate experimentally the existence of these amyloid stretches inside the PFDs of the canonical Sup35, Swi1, Mot3 and Ure2 prions. These sequences self-assemble efficiently into highly ordered amyloid fibrils, that are functionally competent, being able to promote the PFD amyloid conversion in vitro and in vivo. Computational analyses indicate that these kind of amyloid stretches may act as typical nucleating signals in a number of different prion domains. PMID:27686217

  15. SCHWARZ-PICK ESTIMATES FOR BOUNDED HOLOMORPHIC FUNCTIONS ON CLASSICAL DOMAINS

    Institute of Scientific and Technical Information of China (English)

    Liu Yang; Chen Zhihua

    2011-01-01

    In this paper,Schwarz-Pick estimates for high order Fréchet derivatives of bounded holomorphic functions on three kinds of classical domains are presented.We generalize the early work on Schwarz-Pick estimates of higher order partial derivatives for bounded holomorphic functions on the disk and unit ball.

  16. Weighted Composition Operators on Weighted Bergman Spaces of Bounded Symmetric Domains

    Indian Academy of Sciences (India)

    Sanjay Kumar; Kanwar Jatinder Singh

    2007-05-01

    In this paper, we study the weighted compositon operators on weighted Bergman spaces of bounded symmetric domains. The necessary and sufficient conditions for a weighted composition operator $W_{\\varphi,\\psi}$ to be bounded and compact are studied by using the Carleson measure techniques. In the last section, we study the Schatten -class weighted composition operators.

  17. A topological classification of billiards in locally planar domains bounded by arcs of confocal quadrics

    Energy Technology Data Exchange (ETDEWEB)

    Fokicheva, V V [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2015-10-31

    A new class of integrable billiard systems, called generalized billiards, is discovered. These are billiards in domains formed by gluing classical billiard domains along pieces of their boundaries. (A classical billiard domain is a part of the plane bounded by arcs of confocal quadrics.) On the basis of the Fomenko-Zieschang theory of invariants of integrable systems, a full topological classification of generalized billiards is obtained, up to Liouville equivalence. Bibliography: 18 titles.

  18. Re-refinement of the spliceosomal U4 snRNP core-domain structure.

    Science.gov (United States)

    Li, Jade; Leung, Adelaine K; Kondo, Yasushi; Oubridge, Chris; Nagai, Kiyoshi

    2016-01-01

    The core domain of small nuclear ribonucleoprotein (snRNP), comprised of a ring of seven paralogous proteins bound around a single-stranded RNA sequence, functions as the assembly nucleus in the maturation of U1, U2, U4 and U5 spliceosomal snRNPs. The structure of the human U4 snRNP core domain was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed by density modification using untwinned data recently led to a structure of the minimal U1 snRNP at 3.3 Å resolution. With the latter structure providing a search model for molecular replacement, the U4 core-domain structure has now been re-refined. The U4 Sm site-sequence AAUUUUU has been shown to bind to the seven Sm proteins SmF-SmE-SmG-SmD3-SmB-SmD1-SmD2 in an identical manner as the U1 Sm-site sequence AAUUUGU, except in SmD1 where the bound U replaces G. The progression from the initial to the re-refined structure exemplifies a tortuous route to accuracy: where well diffracting crystals of complex assemblies are initially unavailable, the early model errors are rectified by exploiting preliminary interpretations in further experiments involving homologous structures. New insights are obtained from the more accurate model.

  19. Updating the Psoriatic Arthritis (PsA) Core Domain Set

    DEFF Research Database (Denmark)

    Orbai, Ana-Maria; de Wit, Maarten; Mease, Philip J

    2017-01-01

    OBJECTIVE: To include the patient perspective in accordance with the Outcome Measures in Rheumatology (OMERACT) Filter 2.0 in the updated Psoriatic Arthritis (PsA) Core Domain Set for randomized controlled trials (RCT) and longitudinal observational studies (LOS). METHODS: At OMERACT 2016, research...

  20. Interaction dynamics of multiple autonomous mobile robots in bounded spatial domains

    Science.gov (United States)

    Wang, P. K. C.

    1989-01-01

    A general navigation strategy for multiple autonomous robots in a bounded domain is developed analytically. Each robot is modeled as a spherical particle (i.e., an effective spatial domain about the center of mass); its interactions with other robots or with obstacles and domain boundaries are described in terms of the classical many-body problem; and a collision-avoidance strategy is derived and combined with homing, robot-robot, and robot-obstacle collision-avoidance strategies. Results from homing simulations involving (1) a single robot in a circular domain, (2) two robots in a circular domain, and (3) one robot in a domain with an obstacle are presented in graphs and briefly characterized.

  1. New representation of the non-symmetric homogeneous bounded domains in ℂ4 and ℂ5

    Directory of Open Access Journals (Sweden)

    Gr. Tsagas

    1992-01-01

    Full Text Available This paper deals with the corresponding solvable Lie algebra to each of non-symmetric homogeneous bounded domains in ℂ4 and ℂ5 by special set of matrices. Some interesting properties of Kähler manifolds are found. The theory of s-structure on a complete Riemann manifold is also studied.

  2. Time domain reflectometry waveform analysis with second order bounded mean oscillation

    Science.gov (United States)

    Tangent-line methods and adaptive waveform interpretation with Gaussian filtering (AWIGF) have been proposed for determining reflection positions of time domain reflectometry (TDR) waveforms. However, the accuracy of those methods is limited for short probe TDR sensors. Second order bounded mean osc...

  3. A new Leray formula for smooth functions on bounded domains in Cn

    Institute of Scientific and Technical Information of China (English)

    YAO; Zongyuan(姚宗元); QIU; Chunhui(邱春晖); ZHONG; Chunping

    2002-01-01

    By means of a new technique of integral representations in Cn given by the authors, we establish a new abstract formula with a vector function W for smooth functions on bounded domains in Cn, which is different from the well-known Leray formula, This new formula eliminates the term that contains the parameter λ from the classical Leray formula, and especially on some domains the uniform estimates for the -equation are very simple. From the new Leray formula, we can obtain correspondingly many new formulas for smooth functions on many domains in Cn, which are different from the classical ones, when we properly select the vector function W.

  4. Strict lower bounds with separation of sources of error in non-overlapping domain decomposition methods

    CERN Document Server

    Rey, Valentine; Rey, Christian

    2016-01-01

    This article deals with the computation of guaranteed lower bounds of the error in the framework of finite element (FE) and domain decomposition (DD) methods. In addition to a fully parallel computation, the proposed lower bounds separate the algebraic error (due to the use of a DD iterative solver) from the discretization error (due to the FE), which enables the steering of the iterative solver by the discretization error. These lower bounds are also used to improve the goal-oriented error estimation in a substructured context. Assessments on 2D static linear mechanic problems illustrate the relevance of the separation of sources of error and the lower bounds' independence from the substructuring. We also steer the iterative solver by an objective of precision on a quantity of interest. This strategy consists in a sequence of solvings and takes advantage of adaptive remeshing and recycling of search directions.

  5. A Proof of Bobkov's Spectral Bound For Convex Domains via Gaussian Fitting and Free Energy Estimation

    CERN Document Server

    Milman, Emanuel

    2012-01-01

    We obtain a new proof of Bobkov's lower bound on the first positive eigenvalue of the (negative) Neumann Laplacian (or equivalently, the Cheeger constant) on a bounded convex domain $K$ in Euclidean space. Our proof avoids employing the localization method or any of its geometric extensions. Instead, we deduce the lower bound by invoking a spectral transference principle for log-concave measures, comparing the uniform measure on $K$ with an appropriately scaled Gaussian measure which is conditioned on $K$. The crux of the argument is to establish a good overlap between these two measures (in say the relative-entropy or total-variation distances), which boils down to obtaining sharp lower bounds on the free energy of the conditioned Gaussian measure.

  6. Electric Dipole Antennas With Magnetic-Coated PEC Cores: Reaching the Chu Lower Bound on Q

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.

    2012-01-01

    The radiation properties of spherical electric dipole antennas with electric current excitation and material-coated perfectly electrically conducting (PEC) cores are investigated analytically using vector spherical wave functions. Closed-form expressions for electric and magnetic stored energy as...... as well as the radiation quality factor $Q$ are derived. Using these, it is shown that properly selected magnetic coating and radius of the PEC core vastly reduce the internal stored energy, and thus make the $Q$ of an electric dipole antenna approach the Chu lower bound....

  7. A Priori Estimates for Fractional Nonlinear Degenerate Diffusion Equations on Bounded Domains

    Science.gov (United States)

    Bonforte, Matteo; Vázquez, Juan Luis

    2015-10-01

    We investigate quantitative properties of the nonnegative solutions to the nonlinear fractional diffusion equation, , posed in a bounded domain, , with m > 1 for t > 0. As we use one of the most common definitions of the fractional Laplacian , 0 zero Dirichlet boundary conditions. We consider a general class of very weak solutions of the equation, and obtain a priori estimates in the form of smoothing effects, absolute upper bounds, lower bounds, and Harnack inequalities. We also investigate the boundary behaviour and we obtain sharp estimates from above and below. In addition, we obtain similar estimates for fractional semilinear elliptic equations. Either the standard Laplacian case s = 1 or the linear case m = 1 are recovered as limits. The method is quite general, suitable to be applied to a number of similar problems.

  8. Finite time blow-up for a reaction-diffusion system in bounded domain

    Science.gov (United States)

    Bai, Xueli

    2014-02-01

    This paper mainly considers the coupled parabolic system in a bounded domain: u t = Δ u + u α v p , v t = Δ v + u q v β in Ω × (0, T) with null Dirichlet boundary value condition which had been discussed by Wang in (Z Angew Math Phys 51:160-167, 2000). The aim of this paper is to solve the open problem mentioned in the Remark of Wang (Z Angew Math Phys 51:160-167, 2000).

  9. The spectrum of large powers of the Laplacian in bounded domains

    Energy Technology Data Exchange (ETDEWEB)

    Katzav, E; Adda-Bedia, M [Laboratoire de Physique Statistique de l' Ecole Normale Superieure, CNRS UMR 8550, 24 rue Lhomond, 75231 Paris Cedex 05 (France)

    2008-01-18

    We present exact results for the spectrum of the Nth power of the Laplacian in a bounded domain. We begin with the one-dimensional case and show that the whole spectrum can be obtained in the limit of large N. We also show that it is a useful numerical approach valid for any N. Finally, we discuss implications of this work and present its possible extensions for non-integer N and for 3D Laplacian problems. (fast track communication)

  10. Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality.

    Science.gov (United States)

    Bronson, Jonathan R; Levine, Joshua A; Whitaker, Ross T

    2013-01-01

    We introduce a new algorithm for generating tetrahedral meshes that conform to physical boundaries in volumetric domains consisting of multiple materials. The proposed method allows for an arbitrary number of materials, produces high-quality tetrahedral meshes with upper and lower bounds on dihedral angles, and guarantees geometric fidelity. Moreover, the method is combinatoric so its implementation enables rapid mesh construction. These meshes are structured in a way that also allows grading, in order to reduce element counts in regions of homogeneity.

  11. Automorphism groups of causal symmetric spaces of Cayley type and bounded symmetric domains

    Institute of Scientific and Technical Information of China (English)

    Soji; Kaneyuki

    2005-01-01

    Symmetric spaces of Cayley type are a higher dimensional analogue of a onesheeted hyperboloid in R3. They form an important class of causal symmetric spaces. To a symmetric space of Cayley type M, one can associate a bounded symmetric domain of tube type D. We determine the full causal automorphism group of M. This clarifies the relation between the causal automorphism group and the holomorphic automorphism group of D.

  12. Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

    Energy Technology Data Exchange (ETDEWEB)

    Simonetti, Angelita [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Marzi, Stefano [Architecture et Réactivité de l’ARN, UPR 9002 CNRS, IBMC (Institute of Molecular and Cellular Biology), 15 Rue R. Descartes, 67084 Strasbourg, France, Université de Strasbourg, 67000 Strasbourg (France); Fabbretti, Attilio [University of Camerino, 62032 Camerino (Monaco) (Italy); Hazemann, Isabelle; Jenner, Lasse [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale -INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Urzhumtsev, Alexandre [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France); Université de Lorraine, 54506 Vandoeuvre-lès-Nancy (France); Gualerzi, Claudio O. [University of Camerino, 62032 Camerino (Monaco) (Italy); Klaholz, Bruno P., E-mail: klaholz@igbmc.fr [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale - INSERM U964/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch (France)

    2013-06-01

    The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2 is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.

  13. An improved convergence bound for aggregation-based domain decomposition preconditioners.

    Energy Technology Data Exchange (ETDEWEB)

    Shadid, John Nicolas; Sala, Marzio; Tuminaro, Raymond Stephen

    2005-06-01

    In this paper we present a two-level overlapping domain decomposition preconditioner for the finite-element discretization of elliptic problems in two and three dimensions. The computational domain is partitioned into overlapping subdomains, and a coarse space correction, based on aggregation techniques, is added. Our definition of the coarse space does not require the introduction of a coarse grid. We consider a set of assumptions on the coarse basis functions to bound the condition number of the resulting preconditioned system. These assumptions involve only geometrical quantities associated with the aggregates and the subdomains. We prove that the condition number using the two-level additive Schwarz preconditioner is O(H/{delta} + H{sub 0}/{delta}), where H and H{sub 0} are the diameters of the subdomains and the aggregates, respectively, and {delta} is the overlap among the subdomains and the aggregates. This extends the bounds presented in [C. Lasser and A. Toselli, Convergence of some two-level overlapping domain decomposition preconditioners with smoothed aggregation coarse spaces, in Recent Developments in Domain Decomposition Methods, Lecture Notes in Comput. Sci. Engrg. 23, L. Pavarino and A. Toselli, eds., Springer-Verlag, Berlin, 2002, pp. 95-117; M. Sala, Domain Decomposition Preconditioners: Theoretical Properties, Application to the Compressible Euler Equations, Parallel Aspects, Ph.D. thesis, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland, 2003; M. Sala, Math. Model. Numer. Anal., 38 (2004), pp. 765-780]. Numerical experiments on a model problem are reported to illustrate the performance of the proposed preconditioner.

  14. THE PARAMETRIC REPRESENTATION FOR SPIRAL-LIKE MAPPINGS OF TYPE α ON BOUNDED BALANCED PSEUDOCONVEX DOMAINS

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Let Ω be a bounded balanced pseudoconvex domain in Cn that admits a plurisubhamonic defining function of class C2. The authors prove that if f is a spiral-like mapping of type α on Ω, then f can be expressed as a limiting form concerning a Schwarz mapping. Moreover, the characteristics for star-like mappings and spiral-like mappings of type α are obtained. As a direct application, the growth theorem for spiral-like mappings of type α is set up.

  15. Coefficient multipliers of H~p spaces over bounded symmetric domains in C

    Institute of Scientific and Technical Information of China (English)

    肖建斌

    1995-01-01

    One way to give information about the Taylor coefficients of Hp functions is to describe the multipliers of Hp into various spaces. In the case of one complex variable, Duren and Shields described the multipliers of Hp into lq (0bounded symmetric domains in Cn are generalized. The results are sharp if q≥2. A sufficient condition of Hp into Hq is given for any p and q, 0

  16. EXISTENCE AND UNIQUENESS OF STRONG PERIODIC SOLUTION OF THE EVOLUTION SYSTEM DESCRIBING GEOPHYSICAL FLOW PART I: IN BOUNDED DOMAINS

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The existence and uniqueness of a strong periodic solution of the evolution system describing geophysical flow in bounded domains of RN(N = 3, 4) are proven if external forces are periodic in time and sufficiently small.

  17. Super-Grid Modeling of the Elastic Wave Equation in Semi-Bounded Domains

    Energy Technology Data Exchange (ETDEWEB)

    Petersson, N. Anders; Sjögreen, Björn

    2014-10-01

    Abstract

    We develop a super-grid modeling technique for solving the elastic wave equation in semi-bounded two- and three-dimensional spatial domains. In this method, waves are slowed down and dissipated in sponge layers near the far-field boundaries. Mathematically, this is equivalent to a coordinate mapping that transforms a very large physical domain to a significantly smaller computational domain, where the elastic wave equation is solved numerically on a regular grid. To damp out waves that become poorly resolved because of the coordinate mapping, a high order artificial dissipation operator is added in layers near the boundaries of the computational domain. We prove by energy estimates that the super-grid modeling leads to a stable numerical method with decreasing energy, which is valid for heterogeneous material properties and a free surface boundary condition on one side of the domain. Our spatial discretization is based on a fourth order accurate finite difference method, which satisfies the principle of summation by parts. We show that the discrete energy estimate holds also when a centered finite difference stencil is combined with homogeneous Dirichlet conditions at several ghost points outside of the far-field boundaries. Therefore, the coefficients in the finite difference stencils need only be boundary modified near the free surface. This allows for improved computational efficiency and significant simplifications of the implementation of the proposed method in multi-dimensional domains. Numerical experiments in three space dimensions show that the modeling error from truncating the domain can be made very small by choosing a sufficiently wide super-grid damping layer. The numerical accuracy is first evaluated against analytical solutions of Lamb’s problem, where fourth order accuracy is observed with a sixth order artificial dissipation. We then use successive grid refinements to study the numerical accuracy in the more

  18. Structure of RCC1 chromatin factor bound to the nucleosome core particle

    Energy Technology Data Exchange (ETDEWEB)

    Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song (Penn)

    2010-11-11

    The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin-bound RCC1 (regulator of chromosome condensation) protein, which recruits Ran to nucleosomes and activates Ran's nucleotide exchange activity. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 {angstrom} resolution, providing an atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.

  19. Isotropic model of fractional transport in two-dimensional bounded domains.

    Science.gov (United States)

    Kullberg, A; del-Castillo-Negrete, D; Morales, G J; Maggs, J E

    2013-05-01

    A two-dimensional fractional Laplacian operator is derived and used to model nonlocal, nondiffusive transport. This integro-differential operator appears in the long-wavelength, fluid description of quantities undergoing non-Brownian random walks without characteristic length scale. To study bounded domains, a mask function is introduced that modifies the kernel in the fractional Laplacian and removes singularities at the boundary. Green's function solutions to the fractional diffusion equation are presented for the unbounded domain and compared to the one-dimensional Cartesian approximations. A time-implicit numerical integration scheme is presented to study fractional diffusion in a circular disk with azimuthal symmetry. Numerical studies of steady-state reveal temperature profiles in which the heat flux and temperature gradient are in the same direction, i.e., uphill transport. The response to off-axis heating, scaling of confinement time with system size, and propagation of cold pulses are investigated.

  20. NMR backbone dynamics of VEK-30 bound to the human plasminogen kringle 2 domain.

    Science.gov (United States)

    Wang, Min; Prorok, Mary; Castellino, Francis J

    2010-07-07

    To gain insights into the mechanisms for the tight and highly specific interaction of the kringle 2 domain of human plasminogen (K2(Pg)) with a 30-residue internal peptide (VEK-30) from a group A streptococcal M-like protein, the dynamic properties of free and bound K2(Pg) and VEK-30 were investigated using backbone amide (15)N-NMR relaxation measurements. Dynamic parameters, namely the generalized order parameter, S(2), the local correlation time, tau(e), and the conformational exchange contribution, R(ex), were obtained for this complex by Lipari-Szabo model-free analysis. The results show that VEK-30 displays distinctly different dynamic behavior as a consequence of binding to K2(Pg), manifest by decreased backbone flexibility, particularly at the binding region of the peptide. In contrast, the backbone dynamics parameters of K2(Pg) displayed similar patterns in the free and bound forms, but, nonetheless, showed interesting differences. Based on our previous structure-function studies of this interaction, we also made comparisons of the VEK-30/K2(Pg) dynamics results from different kringle modules complexed with small lysine analogs. The differences in dynamics observed for kringles with different ligands provide what we believe to be new insights into the interactions responsible for protein-ligand recognition and a better understanding of the differences in binding affinity and binding specificity of kringle domains with various ligands.

  1. Structure of Protein Phosphatase 2A Core Enzyme Bound to Tumor-Inducing Toxins

    Energy Technology Data Exchange (ETDEWEB)

    Xing,Y.; Xu, Y.; Chen, Y.; Jeffrey, P.; Chao, Y.; Lin, Z.; Li, Z.; Strack, S.; Stock, J.; Shi, Y.

    2006-01-01

    The serine/threonine phosphatase protein phosphatase 2A (PP2A) plays an essential role in many aspects of cellular functions and has been shown to be an important tumor suppressor. The core enzyme of PP2A comprises a 65 kDa scaffolding subunit and a 36 kDa catalytic subunit. Here we report the crystal structures of the PP2A core enzyme bound to two of its inhibitors, the tumor-inducing agents okadaic acid and microcystin-LR, at 2.6 and 2.8 {angstrom} resolution, respectively. The catalytic subunit recognizes one end of the elongated scaffolding subunit by interacting with the conserved ridges of HEAT repeats 11-15. Formation of the core enzyme forces the scaffolding subunit to undergo pronounced structural rearrangement. The scaffolding subunit exhibits considerable conformational flexibility, which is proposed to play an essential role in PP2A function. These structures, together with biochemical analyses, reveal significant insights into PP2A function and serve as a framework for deciphering the diverse roles of PP2A in cellular physiology.

  2. Two optical bistability domains in composites of metal nanoparticles with nonlinear dielectric core

    Energy Technology Data Exchange (ETDEWEB)

    Shewamare, Sisay, E-mail: sisayshewa20@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia); Mal' nev, V.N., E-mail: vadimnmalnev@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia)

    2012-12-15

    It is shown that the local field in metal spherical particles with a dielectric core in an external varying electric field has two maxima at two different frequencies. The second maximum becomes more important with an increment in the metal fraction. Due to the nonlinear dielectric function of the core, the composite of these inclusions may have two optically induced bistability domains at different frequencies. At rather high metal fraction, two bistability domains merge and form one entire bistability domain. The parameters of these domains are studied numerically. The paper focuses on the second bistability domain, which has not been discussed in the literature so far. This domain exists in a comparatively narrow frequency range and its onset fields are lower than those of the first bistability domain. The lowest bistability onset fields are obtained in the entire domain. This peculiarity of the optical induced bistability in the metal composite with small dielectric cores can be attractive for possible applications.

  3. Existence and asymptotic behavior of positive solutions of a semilinear elliptic system in a bounded domain

    Directory of Open Access Journals (Sweden)

    Majda Chaieb

    2016-01-01

    Full Text Available Let \\(\\Omega\\ be a bounded domain in \\(\\mathbb{R}^{n}\\ (\\(n\\geq 2\\ with a smooth boundary \\(\\partial \\Omega\\. We discuss in this paper the existence and the asymptotic behavior of positive solutions of the following semilinear elliptic system \\[\\begin{aligned} -\\Delta u&=a_{1}(xu^{\\alpha}v^{r}\\quad\\text{in}\\;\\Omega ,\\;\\;\\,u|_{\\partial\\Omega}=0,\\\\ -\\Delta v&=a_{2}(xv^{\\beta}u^{s}\\quad\\text{in}\\;\\Omega ,\\;\\;\\,v|_{\\partial\\Omega }=0.\\end{aligned}\\] Here \\(r,s\\in \\mathbb{R}\\, \\(\\alpha,\\beta \\lt 1\\ such that \\(\\gamma :=(1-\\alpha(1-\\beta-rs\\gt 0\\ and the functions \\(a_{i}\\ (\\(i=1,2\\ are nonnegative and satisfy some appropriate conditions with reference to Karamata regular variation theory.

  4. Vector tomography for reconstructing electric fields with non-zero divergence in bounded domains

    Science.gov (United States)

    Koulouri, Alexandra; Brookes, Mike; Rimpiläinen, Ville

    2017-01-01

    In vector tomography (VT), the aim is to reconstruct an unknown multi-dimensional vector field using line integral data. In the case of a 2-dimensional VT, two types of line integral data are usually required. These data correspond to integration of the parallel and perpendicular projection of the vector field along the integration lines and are called the longitudinal and transverse measurements, respectively. In most cases, however, the transverse measurements cannot be physically acquired. Therefore, the VT methods are typically used to reconstruct divergence-free (or source-free) velocity and flow fields that can be reconstructed solely from the longitudinal measurements. In this paper, we show how vector fields with non-zero divergence in a bounded domain can also be reconstructed from the longitudinal measurements without the need of explicitly evaluating the transverse measurements. To the best of our knowledge, VT has not previously been used for this purpose. In particular, we study low-frequency, time-harmonic electric fields generated by dipole sources in convex bounded domains which arise, for example, in electroencephalography (EEG) source imaging. We explain in detail the theoretical background, the derivation of the electric field inverse problem and the numerical approximation of the line integrals. We show that fields with non-zero divergence can be reconstructed from the longitudinal measurements with the help of two sparsity constraints that are constructed from the transverse measurements and the vector Laplace operator. As a comparison to EEG source imaging, we note that VT does not require mathematical modeling of the sources. By numerical simulations, we show that the pattern of the electric field can be correctly estimated using VT and the location of the source activity can be determined accurately from the reconstructed magnitudes of the field.

  5. Behaviour near extinction for the Fast Diffusion Equation on bounded domains

    CERN Document Server

    Bonforte, Matteo; Vazquez, Juan Luis

    2010-01-01

    We consider the Fast Diffusion Equation $u_t=\\Delta u^m$ posed in a bounded smooth domain $\\Omega\\subset \\RR^d$ with homogeneous Dirichlet conditions; the exponent range is $m_s=(d-2)_+/(d+2)bounded positive solutions $u(t,x)$ of such problem extinguish in a finite time $T$, and also that such solutions approach a separate variable solution $u(t,x)\\sim (T-t)^{1/(1-m)}S(x)$, as $t\\to T^-$. Here we are interested in describing the behaviour of the solutions near the extinction time. We first show that the convergence $u(t,x)\\,(T-t)^{-1/(1-m)}$ to $S(x)$ takes place uniformly in the relative error norm. Then, we study the question of rates of convergence of the rescaled flow. For $m$ close to 1 we get such rates by means of entropy methods and weighted Poincar\\'e inequalities. The analysis of the latter point makes an essential use of fine properties of the associated stationary elliptic problem $-\\Delta S^m= {\\bf c} S$ in the limit $m\\to 1$, and such a study has an independent inte...

  6. A statistical model of the wave field in a bounded domain

    Science.gov (United States)

    Hellsten, T.

    2017-02-01

    Numerical simulations of plasma heating with radiofrequency waves often require repetitive calculations of wave fields as the plasma evolves. To enable effective simulations, bench marked formulas of the power deposition have been developed. Here, a statistical model applicable to waves with short wavelengths is presented, which gives the expected amplitude of the wave field as a superposition of four wave fields with weight coefficients depending on the single pass damping, as. The weight coefficient for the wave field coherent with that calculated in the absence of reflection agrees with the coefficient for strong single pass damping of an earlier developed heuristic model, for which the weight coefficients were obtained empirically using a full wave code to calculate the wave field and power deposition. Antennas launching electromagnetic waves into bounded domains are often designed to produce localised wave fields and power depositions in the limit of strong single pass damping. The reflection of the waves changes the coupling that partly destroys the localisation of the wave field, which explains the apparent paradox arising from the earlier developed heuristic formula that only a fraction as2(2-as) and not as of the power is absorbed with a profile corresponding to the power deposition for the first pass of the rays. A method to account for the change in the coupling spectrum caused by reflection for modelling the wave field with ray tracing in bounded media is proposed, which should be applicable to wave propagation in non-uniform media in more general geometries.

  7. On the Dirichlet Problem for First Order Linear Hyperbolic PDEs on Bounded Domains with Mere Inflow Boundary

    CERN Document Server

    März, Thomas

    2010-01-01

    Here we study the Dirichlet problem for first order linear and quasi-linear hyperbolic PDEs on a simply connected bounded domain of $\\R^2$, where the domain has an interior outflow set and a mere inflow boundary. By means of a Lyapunov function we show the existence of a unique solution in the space of functions of bounded variation and its continuous dependence on all the data of the linear problem. Finally, we conclude the existence of a solution to the quasi-linear case by utilizing the Schauder fixed point theorem. This type of problems considered here appears in applications such as transport based image inpainting.

  8. Vector tomography for reconstructing electric fields with non-zero divergence in bounded domains

    Energy Technology Data Exchange (ETDEWEB)

    Koulouri, Alexandra, E-mail: koulouri@uni-muenster.de [Institute for Computational and Applied Mathematics, University of Münster, Einsteinstrasse 62, D-48149 Münster (Germany); Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, London SW7 2BT (United Kingdom); Brookes, Mike [Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, London SW7 2BT (United Kingdom); Rimpiläinen, Ville [Institute for Biomagnetism and Biosignalanalysis, University of Münster, Malmedyweg 15, D-48149 Münster (Germany); Department of Mathematics, University of Auckland, Private bag 92019, Auckland 1142 (New Zealand)

    2017-01-15

    In vector tomography (VT), the aim is to reconstruct an unknown multi-dimensional vector field using line integral data. In the case of a 2-dimensional VT, two types of line integral data are usually required. These data correspond to integration of the parallel and perpendicular projection of the vector field along the integration lines and are called the longitudinal and transverse measurements, respectively. In most cases, however, the transverse measurements cannot be physically acquired. Therefore, the VT methods are typically used to reconstruct divergence-free (or source-free) velocity and flow fields that can be reconstructed solely from the longitudinal measurements. In this paper, we show how vector fields with non-zero divergence in a bounded domain can also be reconstructed from the longitudinal measurements without the need of explicitly evaluating the transverse measurements. To the best of our knowledge, VT has not previously been used for this purpose. In particular, we study low-frequency, time-harmonic electric fields generated by dipole sources in convex bounded domains which arise, for example, in electroencephalography (EEG) source imaging. We explain in detail the theoretical background, the derivation of the electric field inverse problem and the numerical approximation of the line integrals. We show that fields with non-zero divergence can be reconstructed from the longitudinal measurements with the help of two sparsity constraints that are constructed from the transverse measurements and the vector Laplace operator. As a comparison to EEG source imaging, we note that VT does not require mathematical modeling of the sources. By numerical simulations, we show that the pattern of the electric field can be correctly estimated using VT and the location of the source activity can be determined accurately from the reconstructed magnitudes of the field. - Highlights: • Vector tomography is used to reconstruct electric fields generated by dipole

  9. Blow-up criterion for 2-D Boussinesq equations in bounded domain

    Institute of Scientific and Technical Information of China (English)

    HU Langhua; JIAN Huaiyu

    2007-01-01

    We extend the results for 2-D Boussinesq equations from R2 to a bounded domain Ω.First, as for the existence of weak solutions, we trans form Boussinesq equations to a nonlinear evolution equation Ut + A(t, U) = O.In stead of using the methods of fundamental solutions in the case of entire R2, we study the qualities of F(u,v) = (u.▽)v to get some useful estimates for A(t, U), which helps us to conclude the local-in-time existence and uniqueness of solutions.Second, as for blow-up criterions, we use energy methods, Sobolev inequalities and Gronwall inequality to con trol‖θ‖Hs(Ω) and ‖u‖H8(Ω) by ‖▽θ‖L∞(Ω) and‖▽u‖L∞(Ω).Furthermore,‖▽θ‖L∞(Ω) can control ‖▽u‖L∞(Ω) by using vorticity transportation equations.At last, ‖▽θ‖Mφ(Ω) can control ‖▽θ‖L∞(Ω).Thus, we can find a blow up criterion in the form of limt→T* ∫to‖▽θ(.,τ)‖Mφ(Ω)dτ= ∞.

  10. On the Inviscid Limit for the Compressible Navier-Stokes System in an Impermeable Bounded Domain

    Science.gov (United States)

    Sueur, Franck

    2014-03-01

    In this paper we investigate the issue of the inviscid limit for the compressible Navier-Stokes system in an impermeable fixed bounded domain. We consider two kinds of boundary conditions. The first one is the no-slip condition. In this case we extend the famous conditional result (Kato, T.: Remarks on zero viscosity limit for nonstationary Navier-Stokes flows with boundary. In: Seminar on nonlinear partial differential equations, vol. 2, pp. 85-98. Math. Sci. Res. Inst. Publ., Berkeley 1984) obtained by Kato in the homogeneous incompressible case. Kato proved that if the energy dissipation rate of the viscous flow in a boundary layer of width proportional to the viscosity vanishes then the solutions of the incompressible Navier-Stokes equations converge to some solutions of the incompressible Euler equations in the energy space. We provide here a natural extension of this result to the compressible case. The other case is the Navier condition which encodes that the fluid slips with some friction on the boundary. In this case we show that the convergence to the Euler equations holds true in the energy space, as least when the friction is not too large. In both cases we use in a crucial way some relative energy estimates proved recently by Feireisl et al. in J. Math. Fluid Mech. 14:717-730 (2012).

  11. On the inviscid limit for the compressible Navier-Stokes system in an impermeable bounded domain

    CERN Document Server

    Sueur, Franck

    2012-01-01

    In this paper we investigate the issue of the inviscid limit for the compressible Navier-Stokes system in an impermeable fixed bounded domain. We consider two kinds of boundary conditions. The first one is the no-slip condition. In this case we extend the famous conditional result obtained by Kato in the homogeneous incompressible case. Kato proved that if the energy dissipation rate of the viscous flow in a boundary layer of width proportional to the viscosity vanishes then the solutions of the incompressible Navier-Stokes equations converge to some solutions of the incompressible Euler equations in the energy space. We provide here a natural extension of this result to the compressible case. The other case is the Navier condition which encodes that the fluid slips with some friction on the boundary. In this case we show that the convergence to the Euler equations holds true in the energy space, as least when the friction is not too large. In both cases we use in a crucial way some relative energy estimates ...

  12. Microbial starch binding domains are superior to granule bound starch synthase 1 for anchoring luciferase to potato starch granules

    NARCIS (Netherlands)

    Ji, Q.; Vincken, J.P.; Suurs, L.C.J.M.; Visser, R.G.F.

    2006-01-01

    Microbial starch-binding domains (SBD) and granule-bound starch synthase I (GBSSI) are proteins which are accumulated in potato starch granules. The efficiency of SBD and GBSSI for targeting active luciferase reporter proteins to granules during starch biosynthesis was compared. GBSSI or SBD sequenc

  13. Slp4-a/granuphilin-a inhibits dense-core vesicle exocytosis through interaction with the GDP-bound form of Rab27A in PC12 cells.

    Science.gov (United States)

    Fukuda, Mitsunori

    2003-04-25

    Slp4-a (synaptotagmin-like protein 4-a)/granuphilin-a is specifically localized on dense-core vesicles in PC12 cells and negatively controls dense-core vesicle exocytosis through specific interaction with Rab27A via the N-terminal Slp homology domain (SHD) (Fukuda, M., Kanno, E., Saegusa, C., Ogata, Y., and Kuroda, T. S. (2002) J. Biol. Chem. 277, 39673-39678). However, the mechanism of the inhibition by Slp4-a has never been elucidated at the molecular level and is still a matter of controversy. In this study, I discovered an unexpected biochemical property of Slp4-a, that Slp4-a, but not other Rab27 effectors reported thus far, is capable of interacting with both Rab27A(T23N), a dominant negative form that mimics the GDP-bound form, and Rab27A(Q78L), a dominant active form that mimics the GTP-bound form, whereas Slp4-a specifically recognizes the GTP-bound form of Rab3A and Rab8A and does not recognize their GDP-bound form. I show by deletion and mutation analyses that the TGDWFY sequence in SHD2 is essential for Rab27A(T23N) binding, whereas SHD1 is involved in Rab27A(Q78L) binding. I further show by immunoprecipitation and cotransfection assays that Munc18-1, but not syntaxin IA, directly interacts with the C-terminal domain of Slp4-a in a Rab27A-independent manner. Expression of Slp4-a mutants that lack Rab27A(T23N) binding activity (i.e. specific binding to Rab27A(Q78L)) completely reverses the inhibitory effect of the wild-type Slp4-a on high KCl-dependent neuropeptide Y secretion in PC12 cells. The results strongly indicate that interaction of Slp4-a with the GDP-bound form of Rab27A, not with syntaxin IA or Munc18-1, is the primary reason that Slp4-a expression inhibits dense core vesicle exocytosis in PC12 cells.

  14. Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member with calcium bound at the fifth EF-hand

    Energy Technology Data Exchange (ETDEWEB)

    Partha, Sarathy K.; Ravulapalli, Ravikiran; Allingham, John S.; Campbell, Robert L.; Davies, Peter L. [Queens

    2014-08-21

    Calpains are Ca2+dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca2+ signaling in the cell. The major isoforms of this enzyme family, calpain-1 and calpain-2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C-terminal penta-EF hand (PEF) domains. Calpain-3, or p94, is a skeletal muscle-specific isoform that is genetically linked to limb-girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain-3 support the suggestion that full-length calpain-3 exists as a homodimer. Here, we report the crystallization of calpain-3's PEF domain and its crystal structure in the presence of Ca2+, which provides evidence for the homodimer architecture of calpain-3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain-3 PEF domain contains a Ca2+ bound at the EF5-hand used for homodimer association. Three of the four Ca2+-binding EF-hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca2+ signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain-3 large subunit were to try to pair with a calpain small subunit.

  15. Measuring and Reporting Leadership and Core Competency Domains

    Science.gov (United States)

    2015-09-04

    Project LLC Auditors , 2004, http://www.projectauditors.com/Papers/DIMHRS.PDF; Defense Business Board, “Transforming DoD’s Core Business Processes...RET DATE: 00000000 DEPLOY STAT: GEO LOC DCTB:199810 ROTATION TOUR DATE: 00000000 COMBAT SERV CODE: OVERSEAS CONTROL DATE: 00000000 LAST COMBAT

  16. Identifying core domains to assess flare in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Hewlett, Sarah; Bingham, Clifton O

    2012-01-01

    For rheumatoid arthritis (RA), there is no consensus on how to define and assess flare. Variability in flare definitions impairs understanding of findings across studies and limits ability to pool results. The OMERACT RA Flare Group sought to identify domains to define RA flares from patient...

  17. Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

    Science.gov (United States)

    Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

    2012-01-01

    The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

  18. A Constructive Approach to Regularity of Lagrangian Trajectories for Incompressible Euler Flow in a Bounded Domain

    Science.gov (United States)

    Besse, Nicolas; Frisch, Uriel

    2017-04-01

    The 3D incompressible Euler equations are an important research topic in the mathematical study of fluid dynamics. Not only is the global regularity for smooth initial data an open issue, but the behaviour may also depend on the presence or absence of boundaries. For a good understanding, it is crucial to carry out, besides mathematical studies, high-accuracy and well-resolved numerical exploration. Such studies can be very demanding in computational resources, but recently it has been shown that very substantial gains can be achieved first, by using Cauchy's Lagrangian formulation of the Euler equations and second, by taking advantage of analyticity results of the Lagrangian trajectories for flows whose initial vorticity is Hölder-continuous. The latter has been known for about 20 years (Serfati in J Math Pures Appl 74:95-104, 1995), but the combination of the two, which makes use of recursion relations among time-Taylor coefficients to obtain constructively the time-Taylor series of the Lagrangian map, has been achieved only recently (Frisch and Zheligovsky in Commun Math Phys 326:499-505, 2014; Podvigina et al. in J Comput Phys 306:320-342, 2016 and references therein). Here we extend this methodology to incompressible Euler flow in an impermeable bounded domain whose boundary may be either analytic or have a regularity between indefinite differentiability and analyticity. Non-constructive regularity results for these cases have already been obtained by Glass et al. (Ann Sci Éc Norm Sup 45:1-51, 2012). Using the invariance of the boundary under the Lagrangian flow, we establish novel recursion relations that include contributions from the boundary. This leads to a constructive proof of time-analyticity of the Lagrangian trajectories with analytic boundaries, which can then be used subsequently for the design of a very high-order Cauchy-Lagrangian method.

  19. A Constructive Approach to Regularity of Lagrangian Trajectories for Incompressible Euler Flow in a Bounded Domain

    Science.gov (United States)

    Besse, Nicolas; Frisch, Uriel

    2017-01-01

    The 3D incompressible Euler equations are an important research topic in the mathematical study of fluid dynamics. Not only is the global regularity for smooth initial data an open issue, but the behaviour may also depend on the presence or absence of boundaries. For a good understanding, it is crucial to carry out, besides mathematical studies, high-accuracy and well-resolved numerical exploration. Such studies can be very demanding in computational resources, but recently it has been shown that very substantial gains can be achieved first, by using Cauchy's Lagrangian formulation of the Euler equations and second, by taking advantage of analyticity results of the Lagrangian trajectories for flows whose initial vorticity is Hölder-continuous. The latter has been known for about 20 years (Serfati in J Math Pures Appl 74:95-104, 1995), but the combination of the two, which makes use of recursion relations among time-Taylor coefficients to obtain constructively the time-Taylor series of the Lagrangian map, has been achieved only recently (Frisch and Zheligovsky in Commun Math Phys 326:499-505, 2014; Podvigina et al. in J Comput Phys 306:320-342, 2016 and references therein). Here we extend this methodology to incompressible Euler flow in an impermeable bounded domain whose boundary may be either analytic or have a regularity between indefinite differentiability and analyticity. Non-constructive regularity results for these cases have already been obtained by Glass et al. (Ann Sci Éc Norm Sup 45:1-51, 2012). Using the invariance of the boundary under the Lagrangian flow, we establish novel recursion relations that include contributions from the boundary. This leads to a constructive proof of time-analyticity of the Lagrangian trajectories with analytic boundaries, which can then be used subsequently for the design of a very high-order Cauchy-Lagrangian method.

  20. On the Domain of the Triangle on the Spaces of Null, Convergent, and Bounded Sequences

    Directory of Open Access Journals (Sweden)

    Naim L. Braha

    2013-01-01

    Full Text Available We introduce the spaces of -null, -convergent, and -bounded sequences. We examine some topological properties of the spaces and give some inclusion relations concerning these sequence spaces. Furthermore, we compute -, -, and -duals of these spaces. Finally, we characterize some classes of matrix transformations from the spaces of -bounded and -convergent sequences to the spaces of bounded, almost convergent, almost null, and convergent sequences and present a Steinhaus type theorem.

  1. Global classical solutions to the 3D isentropic compressible Navier-Stokes equations in a bounded domain

    Science.gov (United States)

    Yu, Haibo; Zhao, Junning

    2017-01-01

    In this paper, we study the global existence for classical solutions to the 3D isentropic compressible Navier-Stokes equations in a cuboid domain. Compared to the Cauchy problem studied in Hoff (1995 J. Differ. Equ. 120 215-54), Hoff (2005 J. Math. Fluid Mech. 7 315-38), Huang et al (2012 Commun. Pure Appl. Math. 65 549-85), some new thoughts are applied to obtain upper bounds for density. Precisely, through piecewise estimation and some time-depending a priori estimates, we establish time-uniform upper bounds for density under the assumption that the initial energy is small. The initial vacuum is allowed.

  2. Open Core Protocol (OCP) Clock Domain Crossing Interfaces

    DEFF Research Database (Denmark)

    Herlev, Mathias; Poulsen, Christian Keis; Sparsø, Jens

    2014-01-01

    The open core protocol (OCP) is an openly licensed configurable and scalable interface protocol for on-chip subsystem communications. The protocol defines read and write transactions from a master towards a slave across a point-to-point connection and the protocol assumes a single common clock. T...... of synchronizing a simple streaming interface is well described in the literature and often solved using bi-synchronous FIFOs we found surprisingly little published material addressing synchronization of bus-style read-write transaction interfaces....

  3. One-pot synthesis of iniferter-bound polystyrene core nanoparticles for the controlled grafting of multilayer shells

    Science.gov (United States)

    Marchyk, Nataliya; Maximilien, Jacqueline; Beyazit, Selim; Haupt, Karsten; Sum Bui, Bernadette Tse

    2014-02-01

    A novel approach using one-pot synthesis for the production of uniform, iniferter-bound polystyrene core nanoparticles of size 30-40 nm is described. Conventional oil-in-water emulsion polymerisation of styrene and divinylbenzene, combining a hybrid initiation system (thermal and UV), triggered sequentially, was employed to form the surface-bound thiocarbamate iniferters in situ. The iniferter cores were then used as seeds for re-initiating further polymerisation by UV irradiation to produce water-compatible core-shell nanoparticles. Grafting of various shell-types is demonstrated: linear polymers of poly(N-isopropylacrylamide) brushes, crosslinked polymers bearing different surface charges and molecularly imprinted polymers. The shell thickness was readily tuned by varying the monomers' concentration and polymerisation time. Our method is straightforward and in addition, gives access to the preparation of fluorescent seeds and the possibility of grafting nanosized multiple shells. The core-shell nanoparticles were fully characterised by dynamic light scattering, transmission electron microscopy, Fourier transform infrared spectroscopy and microelemental analysis.A novel approach using one-pot synthesis for the production of uniform, iniferter-bound polystyrene core nanoparticles of size 30-40 nm is described. Conventional oil-in-water emulsion polymerisation of styrene and divinylbenzene, combining a hybrid initiation system (thermal and UV), triggered sequentially, was employed to form the surface-bound thiocarbamate iniferters in situ. The iniferter cores were then used as seeds for re-initiating further polymerisation by UV irradiation to produce water-compatible core-shell nanoparticles. Grafting of various shell-types is demonstrated: linear polymers of poly(N-isopropylacrylamide) brushes, crosslinked polymers bearing different surface charges and molecularly imprinted polymers. The shell thickness was readily tuned by varying the monomers' concentration and

  4. ENTROPY SOLUTIONS FOR FIRST-ORDER QUASILINEAR EQUATIONS RELATED TO A BILATERAL OBSTACLE CONDITION IN A BOUNDED DOMAIN

    Institute of Scientific and Technical Information of China (English)

    L.LEVI; G.VALLET

    2001-01-01

    This paper is devoted to the existence and the uniqueness of the entropy solution for a general scalar conservation law associated with a forced bilateral obstacle condition in a bounded domain of RP, p ≥ 1. The method of penalization is used with a view to obtaining an existence result. How-ever, the former only gives uniform L∞-estimates and so leads in fact to look for an Entropy Measure-Valued Solution, according to the specific properties of bounded sequences in L∞. The uniqueness of this EMVS is proved. Classically, it first ensures the existence of a bounded and measurable function U entropy solution and then the strong convergence in La of approximate solutions to U.

  5. ENTROPY SOLUTIONS FOR FIRST-ORDER QUASILINEAR EQUATIONS RELATED TO A BILATERAL OBSTACLE CONDITION IN A BOUNDED DOMAIN

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper is devoted to the existence and the uniqueness of the entropy solution for a general scalar conservation law associated with a forced bilateral obstacle condition in a bounded domain of Rp, p 1. The method of penalization is used with a view to obtaining an existence result. However, the former only gives uniform L∞-estimates and so leads in fact to look for an Entropy Measure-Valued Solution, according to the specific properties of bounded sequences in L∞. The uniqueness of this EMVS is proved. Classically, it first ensures the existence of a bounded and measurable function U entropy solution and then the strong convergence in Lq of approximate solutions to U.

  6. Jump dynamics due to jump datum of compressible viscous Navier-Stokes flows in a bounded plane domain

    Science.gov (United States)

    Kweon, Jae Ryong

    2016-09-01

    In this paper, when the initial density has a jump across an interior curve in a bounded domain, we show unique existence, piecewise regularity and jump discontinuity dynamics for the density and the velocity vector governed by the Navier-Stokes equations of compressible viscous barotropic flows. A critical difficulty is in controlling the gradient of the pressure across the jump curve. This is resolved by constructing a vector function associated with the pressure jump value on the convecting curve and extending it to the whole domain.

  7. What are the most common domains of the core competencies of disaster nursing? A scoping review.

    Science.gov (United States)

    Al Thobaity, Abdullelah; Plummer, Virginia; Williams, Brett

    2017-03-01

    Scoping review was conducted to identify the most common domains of the core competencies of disaster nursing. Nurses play an essential role in all phases of disaster management. For nurses to respond competently, they must be equipped with the skills to provide comprehensive and holistic care to the populations affected by or at risk of disasters. A scoping review was conducted using the Joanna Briggs Institute methodology. The review used information from six databases: the Cumulative Index to Nursing and Allied Health Literature, Ovid MEDLINE, ScienceDirect, ProQuest, Scopus and the Education Resources Information Center. Keywords and inclusion and exclusion criteria were identified as strategies to use in this review. Twelve studies were eligible for result extraction, as they listed domains of the core competencies. These domains varied among studies. However, the most common domains were related to communication, planning, decontamination and safety, the Incident Command System and ethics. Knowledge of the domains of the core competencies, such as understanding the content and location of the disaster plan, communication during disaster and ethical issues is fundamental for nurses. Including these domains in the planning and provision of training for nurses, such as disaster drills, will strengthen their preparedness to respond competently to disaster cases. Nurses must be involved in future research in this area to explore and describe their fundamental competencies in each domain. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. A Preliminary Core Domain Set for Clinical Trials of Shoulder Disorders: A Report from the OMERACT 2016 Shoulder Core Outcome Set Special Interest Group.

    Science.gov (United States)

    Buchbinder, Rachelle; Page, Matthew J; Huang, Hsiaomin; Verhagen, Arianne P; Beaton, Dorcas; Kopkow, Christian; Lenza, Mario; Jain, Nitin B; Richards, Bethan; Richards, Pamela; Voshaar, Marieke; van der Windt, Danielle; Gagnier, Joel J

    2017-01-15

    The Outcome Measures in Rheumatology (OMERACT) Shoulder Core Outcome Set Special Interest Group (SIG) was established to develop a core outcome set (COS) for clinical trials of shoulder disorders. In preparation for OMERACT 2016, we systematically examined all outcome domains and measurement instruments reported in 409 randomized trials of interventions for shoulder disorders published between 1954 and 2015. Informed by these data, we conducted an international Delphi consensus study including shoulder trial experts, clinicians, and patients to identify key domains that should be included in a shoulder disorder COS. Findings were discussed at a stakeholder premeeting of OMERACT. At OMERACT 2016, we sought consensus on a preliminary core domain set and input into next steps. There were 13 and 15 participants at the premeeting and the OMERACT 2016 SIG meeting, respectively (9 attended both meetings). Consensus was reached on a preliminary core domain set consisting of an inner core of 4 domains: pain, physical function/activity, global perceived effect, and adverse events including death. A middle core consisted of 3 domains: emotional well-being, sleep, and participation (recreation and work). An outer core of research required to inform the final COS was also formulated. Our next steps are to (1) analyze whether participation (recreation and work) should be in the inner core, (2) conduct a third Delphi round to finalize definitions and wording of domains and reach final endorsement for the domains, and (3) determine which instruments fulfill the OMERACT criteria for measuring each domain.

  9. Development of a Draft Core Set of Domains for Measuring Shared Decision Making in Osteoarthritis

    DEFF Research Database (Denmark)

    Toupin-April, Karine; Barton, Jennifer; Fraenkel, Liana;

    2015-01-01

    the decision into practice, and (7) assessing the effect of the decision. Contextual factors were also suggested. CONCLUSION: We proposed a draft core set of shared decision-making domains for OA intervention research studies. Next steps include a workshop at OMERACT 13 to reach consensus on these proposed......OBJECTIVE: Despite the importance of shared decision making for delivering patient-centered care in rheumatology, there is no consensus on how to measure its process and outcomes. The aim of this Outcome Measures in Rheumatology (OMERACT) working group is to determine the core set of domains...... for measuring shared decision making in intervention studies in adults with osteoarthritis (OA), from the perspectives of patients, health professionals, and researchers. METHODS: We followed the OMERACT Filter 2.0 method to develop a draft core domain set by (1) forming an OMERACT working group; (2) conducting...

  10. Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ.

    Science.gov (United States)

    Schumacher, Maria A; Zeng, Wenjie

    2016-05-03

    Cell division in most prokaryotes is mediated by FtsZ, which polymerizes to create the cytokinetic Z ring. Multiple FtsZ-binding proteins regulate FtsZ polymerization to ensure the proper spatiotemporal formation of the Z ring at the division site. The DNA-binding protein SlmA binds to FtsZ and prevents Z-ring formation through the nucleoid in a process called "nucleoid occlusion" (NO). As do most FtsZ-accessory proteins, SlmA interacts with the conserved C-terminal domain (CTD) that is connected to the FtsZ core by a long, flexible linker. However, SlmA is distinct from other regulatory factors in that it must be DNA-bound to interact with the FtsZ CTD. Few structures of FtsZ regulator-CTD complexes are available, but all reveal the CTD bound as a helix. To deduce the molecular basis for the unique SlmA-DNA-FtsZ CTD regulatory interaction and provide insight into FtsZ-regulator protein complex formation, we determined structures of Escherichia coli, Vibrio cholera, and Klebsiella pneumonia SlmA-DNA-FtsZ CTD ternary complexes. Strikingly, the FtsZ CTD does not interact with SlmA as a helix but binds as an extended conformation in a narrow, surface-exposed pocket formed only in the DNA-bound state of SlmA and located at the junction between the DNA-binding and C-terminal dimer domains. Binding studies are consistent with the structure and underscore key interactions in complex formation. Combined, these data reveal the molecular basis for the SlmA-DNA-FtsZ interaction with implications for SlmA's NO function and underscore the ability of the FtsZ CTD to adopt a wide range of conformations, explaining its ability to bind diverse regulatory proteins.

  11. Structural insights into calcium-bound S100P and the V domain of the RAGE complex.

    Directory of Open Access Journals (Sweden)

    Srinivasa R Penumutchu

    Full Text Available The S100P protein is a member of the S100 family of calcium-binding proteins and possesses both intracellular and extracellular functions. Extracellular S100P binds to the cell surface receptor for advanced glycation end products (RAGE and activates its downstream signaling cascade to meditate tumor growth, drug resistance and metastasis. Preventing the formation of this S100P-RAGE complex is an effective strategy to treat various disease conditions. Despite its importance, the detailed structural characterization of the S100P-RAGE complex has not yet been reported. In this study, we report that S100P preferentially binds to the V domain of RAGE. Furthermore, we characterized the interactions between the RAGE V domain and Ca(2+-bound S100P using various biophysical techniques, including isothermal titration calorimetry (ITC, fluorescence spectroscopy, multidimensional NMR spectroscopy, functional assays and site-directed mutagenesis. The entropy-driven binding between the V domain of RAGE and Ca(+2-bound S100P was found to lie in the micromolar range (Kd of ∼ 6 µM. NMR data-driven HADDOCK modeling revealed the putative sites that interact to yield a proposed heterotetrameric model of the S100P-RAGE V domain complex. Our study on the spatial structural information of the proposed protein-protein complex has pharmaceutical relevance and will significantly contribute toward drug development for the prevention of RAGE-related multifarious diseases.

  12. Structural Insights into Calcium-Bound S100P and the V Domain of the RAGE Complex

    Science.gov (United States)

    Penumutchu, Srinivasa R.; Chou, Ruey-Hwang; Yu, Chin

    2014-01-01

    The S100P protein is a member of the S100 family of calcium-binding proteins and possesses both intracellular and extracellular functions. Extracellular S100P binds to the cell surface receptor for advanced glycation end products (RAGE) and activates its downstream signaling cascade to meditate tumor growth, drug resistance and metastasis. Preventing the formation of this S100P-RAGE complex is an effective strategy to treat various disease conditions. Despite its importance, the detailed structural characterization of the S100P-RAGE complex has not yet been reported. In this study, we report that S100P preferentially binds to the V domain of RAGE. Furthermore, we characterized the interactions between the RAGE V domain and Ca2+-bound S100P using various biophysical techniques, including isothermal titration calorimetry (ITC), fluorescence spectroscopy, multidimensional NMR spectroscopy, functional assays and site-directed mutagenesis. The entropy-driven binding between the V domain of RAGE and Ca+2-bound S100P was found to lie in the micromolar range (Kd of ∼6 µM). NMR data-driven HADDOCK modeling revealed the putative sites that interact to yield a proposed heterotetrameric model of the S100P-RAGE V domain complex. Our study on the spatial structural information of the proposed protein-protein complex has pharmaceutical relevance and will significantly contribute toward drug development for the prevention of RAGE-related multifarious diseases. PMID:25084534

  13. Feasibility and Domain Validation of Rheumatoid Arthritis (RA) Flare Core Domain Set

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Bykerk, Vivian P; Cooksey, Roxanne

    2015-01-01

    OBJECTIVE: The Outcome Measures in Rheumatology (OMERACT) Rheumatoid Arthritis (RA) Flare Group was established to develop an approach to identify and measure RA flares. An overview of our OMERACT 2014 plenary is provided. METHODS: Feasibility and validity of flare domains endorsed at OMERACT 11...... (2012) were described based on initial data from 3 international studies collected using a common set of questions specific to RA flare. Mean flare frequency, severity, and duration data were presented, and domain scores were compared by flare status to examine known-groups validity. Breakout groups......, and stiffness scores averaged ≥ 2 times higher (2 of 11 points) in flaring individuals. Correlations between flare domains and corresponding legacy instruments were obtained: r = 0.46 to 0.93. A combined definition (patient report of flare and 28-joint Disease Activity Score increase) was evaluated in 2 other...

  14. Design of synthetic autonomous VH domain libraries and structural analysis of a VH domain bound to vascular endothelial growth factor.

    Science.gov (United States)

    Ma, Xiaolei; Barthelemy, Pierre A; Rouge, Lionel; Wiesmann, Christian; Sidhu, Sachdev S

    2013-06-26

    We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can tolerate significant diversity within all three complementarity-determining regions (CDRs) and also within framework 3, and thus, VH-B1a and the Fab are similar in terms of the regions of the antigen-binding site that can tolerate diversity without compromising stability. We constructed libraries of synthetic VH domains and isolated binders with moderate affinity for vascular endothelial growth factor (VEGF) from a library in which only CDR3 was randomized. One binder was subjected to affinity maturation to derive an autonomous VH domain (VH-V1a) that recognized both human and mouse VEGF with high affinity (KD=16nM or 10nM, respectively). Structural analysis revealed that VH-V1a binds to an epitope that is distinct from the epitopes of a natural VEGF receptor and six different anti-VEGF Fabs. Moreover, VH-V1a recognizes VEGF by using an unusual paratope consisting predominantly of CDR3 but with significant contributions from framework residues within the former light chain interface. These results suggest that VH-B1a and other autonomous VH domains may be useful scaffolds to support both conventional libraries with antigen-binding sites built from the three CDR loops and, also, nonconventional libraries with antigen-binding sites built from CDR3 and the former light chain interface.

  15. Identification of preliminary core outcome domains for communication about childhood vaccination: An online Delphi survey.

    Science.gov (United States)

    Kaufman, Jessica; Ryan, Rebecca; Lewin, Simon; Bosch-Capblanch, Xavier; Glenton, Claire; Cliff, Julie; Oyo-Ita, Angela; Muloliwa, Artur Manuel; Oku, Afiong; Ames, Heather; Rada, Gabriel; Cartier, Yuri; Hill, Sophie

    2017-08-20

    Communication interventions for childhood vaccination are promising strategies to address vaccine hesitancy, but current research is limited by the outcomes measured. Most studies measure only vaccination-related outcomes, with minimal consideration of vaccine hesitancy-relevant intermediate outcomes. This impedes understanding of which interventions or elements are effective. It is also unknown which outcomes are important to the range of stakeholders affected by vaccine hesitancy. Outcome selection shapes the evidence base, informing future interventions and trials, and should reflect stakeholder priorities. Therefore, our aim was to identify which outcome domains (i.e. broad outcome categories) are most important to different stakeholders, identifying preliminary core outcome domains to inform evaluation of three common vaccination communication types: (i) communication to inform or educate, (ii) remind or recall, and (iii) enhance community ownership. We conducted a two-stage online Delphi survey, involving four stakeholder groups: parents or community members, healthcare providers, researchers, and government or non-governmental organisation representatives. Participants rated the importance of eight outcome domains for each of the three communication types. They also rated specific outcomes within one domain ("attitudes or beliefs") and provided feedback about the survey. Collectively, stakeholder groups prioritised outcome domains differently when considering the effects of different communication types. For communication that aims to (i) inform or educate, the most important outcome domain is "knowledge or understanding"; for (ii) reminder communication, "vaccination status and behaviours"; and for (iii) community engagement communication, "community participation". All stakeholder groups rated most outcome domains as very important or critical. The highest rated specific outcome within the "attitudes or beliefs" domain was "trust". This Delphi survey

  16. High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.

    Science.gov (United States)

    Klumpp, Klaus; Lam, Angela M; Lukacs, Christine; Vogel, Robert; Ren, Suping; Espiritu, Christine; Baydo, Ruth; Atkins, Kateri; Abendroth, Jan; Liao, Guochun; Efimov, Andrey; Hartman, George; Flores, Osvaldo A

    2015-12-01

    The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010-001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010-001-E2 binds at the dimer-dimer interface of the core proteins, forms a new interaction surface promoting protein-protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010-001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein-protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties.

  17. High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein

    Science.gov (United States)

    Klumpp, Klaus; Lam, Angela M.; Lukacs, Christine; Vogel, Robert; Ren, Suping; Espiritu, Christine; Baydo, Ruth; Atkins, Kateri; Abendroth, Jan; Liao, Guochun; Efimov, Andrey; Hartman, George; Flores, Osvaldo A.

    2015-01-01

    The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010–001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010–001-E2 binds at the dimer–dimer interface of the core proteins, forms a new interaction surface promoting protein–protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010–001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein–protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties. PMID:26598693

  18. Stabilization and control of subcritical semilinear wave equation in bounded domain with Cauchy-Ventcel boundary conditions

    Institute of Scientific and Technical Information of China (English)

    A.Kanoune; N.Mehidi

    2008-01-01

    We analyze the exponential decay property of solutions of the semilinear wave equation in bounded domain Q of RN with a damping term which is effective on the exterior of a ball and boundary conditions of the Cauchy-ventcel type.Under suitable and natural assumptions on the nonlinearity,we prove that the exponential decay holds locally uniformly for finite energy solutions provided the nonlinearity is subcritical at infinity.Subcriticality means,roughly speaking,that the nonlinearity grows at infinity at most as a power P<5.The results obtained in R3 and RN by B.Dehman,G.Lebeau and E.Zuazua on the inequalities of the classical energv(which estimate the total energy of solutions in terms of the energy localized in the exterior of a ball)and on Strichartz's estimates,allow us to give an application to the stabilization controllability of the semilinear wave equation in a bounded domain of RN with a subcritical nonlinearity on the domain and its boundary,and conditions on the boundary of Cauchy-Vlentcel type.

  19. Out-of-core Interactive Display of Large Meshes Using an Oriented Bounding Box-based Hardware Depth Query

    Energy Technology Data Exchange (ETDEWEB)

    Ha, H; Gregorski, B; Joy, K I

    2004-06-24

    In this paper we present an occlusion culling method that uses hardware-based depth queries on oriented bounding boxes to cull unseen geometric primitives efficiently. An out-of-core design enables this method to interactively display data sets that are too large to fit into main memory. During a preprocessing phase, a spatial subdivision (such as an octree or BSP tree) of a given data set is constructed where, for each node, an oriented bounding box containing mesh primitives is computed using principal component analysis (PCA). At runtime, the tree indicated by the spatial subdivision is traversed in front-to-back order, and only nodes that are determined to be visible, based on a hardware accelerated depth query, are rendered.

  20. Uniform Regularity and Vanishing Dissipation Limit for the Full Compressible Navier-Stokes System in Three Dimensional Bounded Domain

    Science.gov (United States)

    Wang, Yong

    2016-09-01

    In the present paper, we study the uniform regularity and vanishing dissipation limit for the full compressible Navier-Stokes system whose viscosity and heat conductivity are allowed to vanish at different orders. The problem is studied in a three dimensional bounded domain with Navier-slip type boundary conditions. It is shown that there exists a unique strong solution to the full compressible Navier-Stokes system with the boundary conditions in a finite time interval which is independent of the viscosity and heat conductivity. The solution is uniformly bounded in {W^{1,infty}} and is a conormal Sobolev space. Based on such uniform estimates, we prove the convergence of the solutions of the full compressible Navier-Stokes to the corresponding solutions of the full compressible Euler system in {L^infty(0,T; L^2)}, {L^infty(0,T; H1)} and {L^infty([0,T]×Ω)} with a rate of convergence.

  1. Sharp Estimates in Bergman and Besov Spaces on Bounded Symmetric Domains

    Institute of Scientific and Technical Information of China (English)

    Guang Bin REN; Ji Huai SHI

    2002-01-01

    Sharp estimates of the point-evaluation functional in weighted Bergman spaces Lpa(Ω, dva)and for the point-evaluation derivalive functional in Besov spaces BP(Ω) are obtained for boundedsymmetric domains Ω in Cn.

  2. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sukosd, Zsuzsanna; Andersen, Ebbe S.; Seemann, Stefan E.

    2015-01-01

    protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential...

  3. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan;

    2015-01-01

    of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...

  4. The redefinition of Helicobacter pylori lipopolysaccharide O-antigen and core-oligosaccharide domains

    Science.gov (United States)

    Debowski, Aleksandra W.; Nilsson, Hans-Olof; Fulurija, Alma; Dell, Anne; Stubbs, Keith A.; Marshall, Barry J.

    2017-01-01

    Helicobacter pylori lipopolysaccharide promotes chronic gastric colonisation through O-antigen host mimicry and resistance to mucosal antimicrobial peptides mediated primarily by modifications of the lipid A. The structural organisation of the core and O-antigen domains of H. pylori lipopolysaccharide remains unclear, as the O-antigen attachment site has still to be identified experimentally. Here, structural investigations of lipopolysaccharides purified from two wild-type strains and the O-antigen ligase mutant revealed that the H. pylori core-oligosaccharide domain is a short conserved hexasaccharide (Glc-Gal-DD-Hep-LD-Hep-LD-Hep-KDO) decorated with the O-antigen domain encompassing a conserved trisaccharide (-DD-Hep-Fuc-GlcNAc-) and variable glucan, heptan and Lewis antigens. Furthermore, the putative heptosyltransferase HP1284 was found to be required for the transfer of the third heptose residue to the core-oligosaccharide. Interestingly, mutation of HP1284 did not affect the ligation of the O-antigen and resulted in the attachment of the O-antigen onto an incomplete core-oligosaccharide missing the third heptose and the adjoining Glc-Gal residues. Mutants deficient in either HP1284 or O-antigen ligase displayed a moderate increase in susceptibility to polymyxin B but were unable to colonise the mouse gastric mucosa. Finally, mapping mutagenesis and colonisation data of previous studies onto the redefined organisation of H. pylori lipopolysaccharide revealed that only the conserved motifs were essential for colonisation. In conclusion, H. pylori lipopolysaccharide is missing the canonical inner and outer core organisation. Instead it displays a short core and a longer O-antigen encompassing residues previously assigned as the outer core domain. The redefinition of H. pylori lipopolysaccharide domains warrants future studies to dissect the role of each domain in host-pathogen interactions. Also enzymes involved in the assembly of the conserved core structure

  5. The redefinition of Helicobacter pylori lipopolysaccharide O-antigen and core-oligosaccharide domains.

    Science.gov (United States)

    Li, Hong; Yang, Tiandi; Liao, Tingting; Debowski, Aleksandra W; Nilsson, Hans-Olof; Fulurija, Alma; Haslam, Stuart M; Mulloy, Barbara; Dell, Anne; Stubbs, Keith A; Marshall, Barry J; Benghezal, Mohammed

    2017-03-01

    Helicobacter pylori lipopolysaccharide promotes chronic gastric colonisation through O-antigen host mimicry and resistance to mucosal antimicrobial peptides mediated primarily by modifications of the lipid A. The structural organisation of the core and O-antigen domains of H. pylori lipopolysaccharide remains unclear, as the O-antigen attachment site has still to be identified experimentally. Here, structural investigations of lipopolysaccharides purified from two wild-type strains and the O-antigen ligase mutant revealed that the H. pylori core-oligosaccharide domain is a short conserved hexasaccharide (Glc-Gal-DD-Hep-LD-Hep-LD-Hep-KDO) decorated with the O-antigen domain encompassing a conserved trisaccharide (-DD-Hep-Fuc-GlcNAc-) and variable glucan, heptan and Lewis antigens. Furthermore, the putative heptosyltransferase HP1284 was found to be required for the transfer of the third heptose residue to the core-oligosaccharide. Interestingly, mutation of HP1284 did not affect the ligation of the O-antigen and resulted in the attachment of the O-antigen onto an incomplete core-oligosaccharide missing the third heptose and the adjoining Glc-Gal residues. Mutants deficient in either HP1284 or O-antigen ligase displayed a moderate increase in susceptibility to polymyxin B but were unable to colonise the mouse gastric mucosa. Finally, mapping mutagenesis and colonisation data of previous studies onto the redefined organisation of H. pylori lipopolysaccharide revealed that only the conserved motifs were essential for colonisation. In conclusion, H. pylori lipopolysaccharide is missing the canonical inner and outer core organisation. Instead it displays a short core and a longer O-antigen encompassing residues previously assigned as the outer core domain. The redefinition of H. pylori lipopolysaccharide domains warrants future studies to dissect the role of each domain in host-pathogen interactions. Also enzymes involved in the assembly of the conserved core structure

  6. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar

    2011-12-31

    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  7. Tracking the Interplay between Bound Peptide and the Lid Domain of DnaK, Using Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Yossi Tsfadia

    2013-06-01

    Full Text Available Hsp70 chaperones consist of two functional domains: the 44 kDa Nucleotide Binding Domain (NBD, that binds and hydrolyses ATP, and the 26 kDa Substrate Binding Domain (SBD, which binds unfolded proteins and reactivates them, utilizing energy obtained from nucleotide hydrolysis. The structure of the SBD of the bacterial Hsp70, DnaK, consists of two sub-domains: A β-sandwich part containing the hydrophobic cavity to which the hepta-peptide NRLLLTG (NR is bound, and a segment made of 5 α-helices, called the “lid” that caps the top of the β-sandwich domain. In the present study we used the Escherichia coli Hsp70, DnaK, as a model for Hsp70 proteins, focusing on its SBD domain, examining the changes in the lid conformation. We deliberately decoupled the NBD from the SBD, limiting the study to the structure of the SBD section, with an emphasis on the interaction between the charges of the peptide with the residues located in the lid. Molecular dynamics simulations of the complex revealed significant mobility within the lid structure; as the structure was released from the forces operating during the crystallization process, the two terminal helices established a contact with the positive charge at the tip of the peptide. This contact is manifested only in the presence of electrostatic attraction. The observed internal motions within the lid provide a molecular role for the function of this sub-domain during the reaction cycle of Hsp 70 chaperones.

  8. Tevatron Higgs Mass Bounds: Projecting U(1)' Models to LHC Domain

    CERN Document Server

    Sert, Hale; Demir, Durmus A; Solmaz, Levent

    2010-01-01

    We study Higgs boson masses in supersymmetric models with an extra U(1) symmetry to be called U(1)$^{\\prime}$. Such extra gauge symmetries are urged by the $\\mu$ problem of the MSSM, and they also arise frequently in low-energy supersymmetric models stemming from GUTs and strings. We analyze mass of the lightest Higgs boson and various other particle masses and couplings by taking into account the LEP bounds as well as the recent bounds from Tevatron experiments. We find that the $\\mu$-problem motivated generic low-energy U(1)$^{\\prime}$ model yields Higgs masses as large as $\\sim 200\\ {\\rm GeV}$ and violate the Tevatron bounds for certain ranges of parameters. We analyze correlations among various model parameters, and determine excluded regions by both scanning the parameter space and by examining certain likely parameter values. We also make educated projections for LHC measurements in light of the Tevatron restrictions on the parameter space. We further analyze certain benchmark models stemming from E(6) ...

  9. Photonic realization of topologically protected bound states in domain-wall waveguide arrays

    CERN Document Server

    Lee-Thorp, James P; Xu, Xinan; Yang, Jinghui; Fefferman, Charles L; Wong, Chee Wei; Weinstein, Michael I

    2016-01-01

    We present an analytical theory of topologically protected photonic states for the two-dimensional Maxwell equations for a class of continuous periodic dielectric structures, modulated by a domain wall. We further numerically confirm the applicability of this theory for three-dimensional structures.

  10. Improved bounds on the phase transition for the hard-core model in 2 dimensions

    NARCIS (Netherlands)

    Vera, Juan C.; Vigoda, E.; Yang, L.

    2015-01-01

    For the hard-core lattice gas model defined on independent sets weighted by an activity $\\lambda$, we study the critical activity $\\lambda_c(\\mathbb{Z}^2)$ for the uniqueness/nonuniqueness threshold on the 2-dimensional integer lattice $\\mathbb{Z}^2$. The conjectured value of the critical activity i

  11. A New Boundary Model for Simulating Complex and Flexible Wall Bounded Domain in Dissipative Particle Dynamics

    Directory of Open Access Journals (Sweden)

    Saeid Mokhtarian

    2014-01-01

    Full Text Available Despite extensive area of applications, simulation of complex wall bounded problems or any deformable boundary is still a challenge in a Dissipative Particle Dynamics simulation. This limitation is rooted in the soft force nature of DPD and the fact that we need to use an antipenetration model for escaped particles. In the present paper, we propose a new model of antipenetration which preserves the conservation of linear momentum on the boundaries and enables us to simulate complex and flexible boundaries. Finally by performing numerical simulations, we demonstrate the validity of our new model.

  12. Exponential attractors for a Cahn-Hilliard model in bounded domains with permeable walls

    Directory of Open Access Journals (Sweden)

    Ciprian G. Gal

    2006-11-01

    Full Text Available In a previous article [7], we proposed a model of phase separation in a binary mixture confined to a bounded region which may be contained within porous walls. The boundary conditions were derived from a mass conservation law and variational methods. In the present paper, we study the problem further. Using a Faedo-Galerkin method, we obtain the existence and uniqueness of a global solution to our problem, under more general assumptions than those in [7]. We then study its asymptotic behavior and prove the existence of an exponential attractor (and thus of a global attractor with finite dimension.

  13. Asymptotic Expansions of the Heat Kernel of the Laplacian for General Annular Bounded Domains with Robin Boundary Conditions: Further Results

    Institute of Scientific and Technical Information of China (English)

    E. M. E. ZAYED

    2003-01-01

    The asymptotic expansions of the trace of the heat kernel Θ(t) = ∑∞ν=1 exp(-tλν) for smallpositive t, where {λν} are the eigenvalues of the negative Laplacian -△n = - ∑n i=1 ( / xi )2 in Rn(n= 2or 3), are studied for a general annular bounded domain Ω with a smooth inner boundary (e)Ω1 and asmooth outer boundary (e)Ω2, where a finite number of piecewise smooth Robin boundary conditions((e)/(e)nj+rj)φ=0 on the components γj(j = 1, ..., k)of (e)Ω1 and on teh components γj(j = 1, ..., m) of (e)Ω2 are considered such that( (e)Ω1+ukj=1 Fj and (e)Ω2=Umj=k+1Fj )and where the coefficients (rj(j=1,…,m))are piecewise smooth positive functions. Some applications of Θ(t) for an ideal gasenclosed in the general annular bounded domain Ω are given. Further results are also obtained.

  14. Effects of Heat Treatment on the Magnetic Properties of Polymer-Bound Iron Particle Cores

    Science.gov (United States)

    Namkung, M.; Wincheski, B.; Bryant, R. G.; Buchman, A.

    1998-01-01

    Spherical iron particles of three different size distributions, 6-10 micrometers in diameter, 100 mesh and 30-80 mesh, were mixed with 2.0 wt % of soluble imide and compression molded at 300 C under 131 MPa. Post-fabrication heat treatments were performed at 960 C for 6 h resulting in a significant enhancement of the permeability in low field region for all the specimens except for the one made of 30-80 mesh particles. The rate of core loss of these specimens at a magnetic induction of 5 kG measured up to 1 kHz shows a noticeable. increase after heat treatment which, along with the permeability enhancement, can be explained by the coalescence of particles forming a network of conductivity paths in the specimens. ne scanning electron micrographs taken for the 6-10 micrometer particle specimens show no evidence of heat treatment-induced grain growth. The untreated specimens show a very weak f(sup 2) -dependence of the core loss which clearly indicates a negligible contribution from the eddy current loss. In particular, an almost perfect linearity was found in the frequency dependence of the core loss of the untreated specimen made of 100 mesh iron particles.

  15. Expression of Core Domain of Porcine Zona Pellucida 3β in E. coli

    Institute of Scientific and Technical Information of China (English)

    Qiu-ling XIE; Xiao-jia CHEN; Wei-jie ZHU; Ling ZHANG; Wan-xiang XU; An HONG; Jing LI; Si-hong GAO

    2005-01-01

    Objective To obtain the recombinant core domain of porcine zone pellucida 3β (cZP3β)for the further research on its functions Methods The nucleotide sequence region from 44 to 306 codons of pZP3β entire cDNA was obtained by PCR and then was cloned into pET-3c vector. After being identified, recon was transformed into E. coli BL21 (DE3) pLysS and then induced by IPTG.Results The recombinant cZP3β was expressed in E. coli up to 15% of total cellular proteins, and was made sure by Western blot analysis.Conclusion The research on expression of core domain of pZP3β could benefit to further investigation of its immunogenicity and the development of antigen preparation.

  16. Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of adhesion molecule CD44

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Tomoyuki; Kitano, Ken; Terawaki, Shin-ichi; Maesaki, Ryoko; Hakoshima, Toshio, E-mail: hakosima@bs.naist.jp [Structural Biology Laboratory, Nara Institute of Science and Technology, Keihanna Science City, Nara 630-0192 (Japan)

    2007-10-01

    The radixin FERM domain complexed with the CD44 cytoplasmic tail peptide has been crystallized. A diffraction data set from the complex was collected to 2.1 Å. CD44 is an important adhesion molecule that specifically binds hyaluronic acid and regulates cell–cell and cell–matrix interactions. Increasing evidence has indicated that CD44 is assembled in a regulated manner into the membrane–cytoskeletal junction, a process that is mediated by ERM (ezrin/radixin/moesin) proteins. Crystals of a complex between the radixin FERM domain and the C-terminal cytoplasmic region of CD44 have been obtained. The crystal of the radixin FERM domain bound to the CD44 cytoplasmic tail peptide belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.70, b = 66.18, c = 86.22 Å, and contain one complex in the crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.1 Å.

  17. Software-Defined Radio FPGA Cores: Building towards a Domain-Specific Language

    Directory of Open Access Journals (Sweden)

    Lekhobola Tsoeunyane

    2017-01-01

    Full Text Available This paper reports on the design and implementation of an open-source library of parameterizable and reusable Hardware Description Language (HDL Intellectual Property (IP cores designed for the development of Software-Defined Radio (SDR applications that are deployed on FPGA-based reconfigurable computing platforms. The library comprises a set of cores that were chosen, together with their parameters and interfacing schemas, based on recommendations from industry and academic SDR experts. The operation of the SDR cores is first validated and then benchmarked against two other cores libraries of a similar type to show that our cores do not take much more logic elements than existing cores and that they support a comparable maximum clock speed. Finally, we propose our design for a Domain-Specific Language (DSL and supporting tool-flow, which we are in the process of building using our SDR library and the Delite DSL framework. We intend to take this DSL and supporting framework further to provide a rapid prototyping system for SDR application development to programmers not experienced in HDL coding. We conclude with a summary of the main characteristics of our SDR library and reflect on how our DSL tool-flow could assist other developers working in SDR field.

  18. Mixed first- and second-order transport method using domain decomposition techniques for reactor core calculations

    Energy Technology Data Exchange (ETDEWEB)

    Girardi, E.; Ruggieri, J.M. [CEA Cadarache, CEA/DEN/CAD/DER/SPRC/LEPH, 13 - Saint-Paul Lez Durance (France)

    2003-07-01

    The aim of this paper is to present the last developments made on a domain decomposition method applied to reactor core calculations. In this method, two kind of balance equation with two different numerical methods dealing with two different unknowns are coupled. In the first part the two balance transport equations (first order and second order one) are presented with the corresponding following numerical methods: Variational Nodal Method and Discrete Ordinate Nodal Method. In the second part, the Multi-Method/Multi-Domain algorithm is introduced by applying the Schwarz domain decomposition to the multigroup eigenvalue problem of the transport equation. The resulting algorithm is then provided. The projection operators used to coupled the two methods are detailed in the last part of the paper. Finally some preliminary numerical applications on benchmarks are given showing encouraging results. (authors)

  19. Fabrication of hydrogel-encapsulated silica core bound with chitosan chains for efficient drug delivery

    Science.gov (United States)

    Byeol Bae, Saet; Lee, Sang Wha

    2016-06-01

    In this study, hydrogel-encapsulated silica nanoparticles were facilely prepared through the following three consecutive steps: i) silica nanoparticles (SNPs) were synthesized via a sol-gel reaction of tetraethyl orthosilicate (TEOS) with ammonium hydroxide, ii) the resulting SNPs were functionalized with 3-(trimethoxysilyl)-propylmethacrylate (TPM) ligand with an olefin group, and iii) the TPM-functionalized SNPs were encapsulated with poly(N-isopropylacrylamide-co-acrylic acid), NIPAM-co-AAc hydrogels by using a radical polymerization reaction of the co-monomers at the following ratio: \\text{NIPAM}:\\text{AAc} = 91:9 wt %. The lower critical solution temperature (LCST) of the encapsulated hydrogels with a moiety of carboxylic groups was slightly above physiological temperature and they demonstrated a thermo-sensitive variation of particle size. The hydrogel-encapsulated SNPs (SNPs@Hyd) were finally bound with chitosan chains, which are bio-friendly and non-toxic polymers. When compared to SNPs@Hyd, chitosan-coated SNPs@Hyd (SNPs@Hyd@Chi) exhibited prolonged drug (ibuprofen) release and stable structural integrity during the release test.

  20. Reaching the Chu Lower Bound on Q With Magnetic Dipole Antennas Using a Magnetic-Coated PEC Core

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Breinbjerg, Olav

    2011-01-01

    We analytically solve the radiation problem for a spherical magnetic dipole antenna with a material-coated perfectly electrically conducting core. Using the closed-form expressions derived for the internal and external stored energies as well as for the radiation quality factor $Q$, we determine...... the optimal geometrical and material parameters of the antenna. We show that the optimal permeability of the coating increases as the coating becomes thinner; as a result, the energy stored in it and the radiation quality factor $Q$ reduce. In the limit of an infinitely thin coating, the optimal permeability...... tends to infinity, the internal stored energy vanishes, and the $Q$ reaches the Chu lower bound, irrespective of the antenna electrical size $ka$ and permittivity of the coating....

  1. Determination of free and bound phenolic compounds in soy isoflavone concentrate using a PFP fused core column.

    Science.gov (United States)

    Verardo, Vito; Riciputi, Ylenia; Garrido-Frenich, Antonia; Caboni, Maria Fiorenza

    2015-10-15

    In the last years, the consumption of soy-based foods has increased due to the health benefits related to soy bioactives like phenolic compounds. Thus, in the present study, a new chromatographic method using reverse-phase high performance liquid chromatography coupled to diode array detection (RP-HPLC/DAD) was developed using a fused core pentafluorophenyl (PFP) column. The established method allowed the determination of twenty-one free phenolic compounds and eleven bound phenolics in a soy isoflavone concentrate. The method was validated in terms of precision and recovery. Intra and inter-day precision were less than 5% (% RSD) and the recovery was between 97.4% and 103.6%. Limits of quantification (LOQs) ranged between 0.093 and 0.443 μg/mL. Because of that, PFP stationary phase can be easily applied for routine determination of phenolic compounds in soy based foods.

  2. Parabolic equations and Feynman_Kac formula on general bounded domains

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Gongqing

    2001-01-01

    [1]Berestycki, H., Nirenberg, L., Varadhan, S. V. R., The principal eigenvalue and maximum principle for second order elliptic operators in general domains, Comm. Pure and Appl. Math., 1994, 47: 47.[2]Chen, Y. Z., Alexandrov's maximum principle and Bony's maximum principle for parabolic equations, Acta Mathematica Applicae Sinica, 1985, 2: 309.[3]Dong, G. C., Nonlinear Second Order Partial Differential Equations, AMS Translations, Providence: AMS, 1991.[4]Krylov, N. V., Nonlinear Elliptic and Parabolic Equations of Second Order, Mathematics and Its Applications, Dordrecht: D. Reidel Publication Company, 1987.[5]Tso, K. S., On the Alexandrov_Bakel'man type maximum principle for second order parabolic equations, Comm. PDE, 1985, 10: 543.[6]Miller, K., Barriers on cones for uniformly elliptic operators, Ann. Mat. Pura e Appl., 1967, 76: 93.[7]Strook, D., Varadhan, S. V. R., Multidimensional Diffusion Process, New York, Berlin: Springer_Verlag, 1979.[8]Pinsky, R. G., Positive Harmonic Functions and Diffusions, Cambridge: Cambridge University Press, 1995.[9]Friedman, A., Partial Differential Equations of Parabolic Type, Englewood Cliffs: Prentice_Hall Inc., 1964.

  3. Crystal Structure of the MAP3K TAO2 Kinase Domain Bound by an Inhibitor Staurosporine

    Institute of Scientific and Technical Information of China (English)

    Tian-Jun ZHOU; Li-Guang SUN; Yan GAO; Elizabeth J. GOLDSMITH

    2006-01-01

    Mitogen-activated protein kinase (MAPK) signal transduction pathways are ubiquitous in eukaryotic cells, which transfer signals from the cell surface to the nucleus, controlling multiple cellular programs. MAPKs are activated by MAPK kinases [MAP2Ks or MAP/extracellular signal-regulated kinase (ERK) kinases (MEK)], which in turn are activated by MAPK kinase kinases (MAP3Ks). TAO2 is a MAP3K level kinase that activates the MAP2Ks MEK3 and MEK6 to activate p38 MAPKs. Because p38 MAPKs are key regulators of expression of inflammatory cytokines, they appear to be involved in human diseases such as asthma and autoimmunity. As an upstream activator of p38s, TAO2 represents a potential drug target. Here we report the crystal structure of active TAO2 kinase domain in complex with staurosporine, a broadrange protein kinase inhibitor that inhibits TAO2 with an IC50 of 3 μM. The structure reveals that staurosporine occupies the position where the adenosine of ATP binds in TAO2, and the binding of the inhibitor mimics many features of ATP binding. Both polar and nonpolar interactions contribute to the enzyme-inhibitor recognition. Staurosporine induces conformational changes in TAO2 residues that surround the inhibitor molecule, but causes very limited global changes in the kinase. The structure provides atomic details for TAO2-staurosporine interactions, and explains the relatively low potency of staurosporine against TAO2. The structure presented here should aid in the design of inhibitors specific to TAO2 and related kinases.

  4. Characterization of Solanum tuberosum multicystatin and the significance of core domains.

    Science.gov (United States)

    Green, Abigail R; Nissen, Mark S; Kumar, G N Mohan; Knowles, N Richard; Kang, Chulhee

    2013-12-01

    Potato (Solanum tuberosum) multicystatin (PMC) is a unique cystatin composed of eight repeating units, each capable of inhibiting cysteine proteases. PMC is a composite of several cystatins linked by trypsin-sensitive (serine protease) domains and undergoes transitions between soluble and crystalline forms. However, the significance and the regulatory mechanism or mechanisms governing these transitions are not clearly established. Here, we report the 2.2-Å crystal structure of the trypsin-resistant PMC core consisting of the fifth, sixth, and seventh domains. The observed interdomain interaction explains PMC's resistance to trypsin and pH-dependent solubility/aggregation. Under acidic pH, weakening of the interdomain interactions exposes individual domains, resulting in not only depolymerization of the crystalline form but also exposure of cystatin domains for inhibition of cysteine proteases. This in turn allows serine protease-mediated fragmentation of PMC, producing ∼ 10-kD domains with intact inhibitory capacity and faster diffusion, thus enhancing PMC's inhibitory ability toward cysteine proteases. The crystal structure, light-scattering experiments, isothermal titration calorimetry, and site-directed mutagenesis confirmed the critical role of pH and N-terminal residues in these dynamic transitions between monomer/polymer of PMC. Our data support a notion that the pH-dependent structural regulation of PMC has defense-related implications in tuber physiology via its ability to regulate protein catabolism.

  5. Characterization of Solanum tuberosum Multicystatin and the Significance of Core Domains[C

    Science.gov (United States)

    Green, Abigail R.; Nissen, Mark S.; Kumar, G.N. Mohan; Knowles, N. Richard; Kang, ChulHee

    2013-01-01

    Potato (Solanum tuberosum) multicystatin (PMC) is a unique cystatin composed of eight repeating units, each capable of inhibiting cysteine proteases. PMC is a composite of several cystatins linked by trypsin-sensitive (serine protease) domains and undergoes transitions between soluble and crystalline forms. However, the significance and the regulatory mechanism or mechanisms governing these transitions are not clearly established. Here, we report the 2.2-Å crystal structure of the trypsin-resistant PMC core consisting of the fifth, sixth, and seventh domains. The observed interdomain interaction explains PMC’s resistance to trypsin and pH-dependent solubility/aggregation. Under acidic pH, weakening of the interdomain interactions exposes individual domains, resulting in not only depolymerization of the crystalline form but also exposure of cystatin domains for inhibition of cysteine proteases. This in turn allows serine protease–mediated fragmentation of PMC, producing ∼10-kD domains with intact inhibitory capacity and faster diffusion, thus enhancing PMC’s inhibitory ability toward cysteine proteases. The crystal structure, light-scattering experiments, isothermal titration calorimetry, and site-directed mutagenesis confirmed the critical role of pH and N-terminal residues in these dynamic transitions between monomer/polymer of PMC. Our data support a notion that the pH-dependent structural regulation of PMC has defense-related implications in tuber physiology via its ability to regulate protein catabolism. PMID:24363310

  6. Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Young Do; Finzi, Andrés; Wu, Xueling; Dogo-Isonagie, Cajetan; Lee, Lawrence K.; Moore, Lucas R.; Schmidt, Stephen D.; Stuckey, Jonathan; Yang, Yongping; Zhou, Tongqing; Zhu, Jiang; Vicic, David A.; Debnath, Asim K.; Shapiro, Lawrence; Bewley, Carole A.; Mascola, John R.; Sodroski, Joseph G.; Kwong, Peter D. (Harvard-Med); (NIH); (Hawaii); (L.F. Kimball); (Columbia); (VCCRI); (Arkansas); (DFCI)

    2013-03-04

    The HIV-1 envelope (Env) spike (gp120{sub 3}/gp41{sub 3}) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation and primes Env for entry. The CD4-bound state, however, is prone to spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1 maintain CD4-binding capacity and regulate transitions to the CD4-bound state? To define this mechanistically, we determined crystal structures of unliganded core gp120 from HIV-1 clades B, C, and E. Notably, all of these unliganded HIV-1 structures resembled the CD4-bound state. Conformational fixation with ligand selection and thermodynamic analysis of full-length and core gp120 interactions revealed that the tendency of HIV-1 gp120 to adopt the CD4-bound conformation was restrained by the V1/V2- and V3-variable loops. In parallel, we determined the structure of core gp120 in complex with the small molecule, NBD-556, which specifically recognizes the CD4-bound conformation of gp120. Neutralization by NBD-556 indicated that Env spikes on primary isolates rarely assume the CD4-bound conformation spontaneously, although they could do so when quaternary restraints were loosened. Together, the results suggest that the CD4-bound conformation represents a 'ground state' for the gp120 core, with variable loop and quaternary interactions restraining unliganded gp120 from 'snapping' into this conformation. A mechanism of control involving deformations in unliganded structure from a functionally critical state (e.g., the CD4-bound state) provides advantages in terms of HIV-1 Env structural diversity and resistance to antibodies and inhibitors, while maintaining elements essential for entry.

  7. Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A.

    Directory of Open Access Journals (Sweden)

    Jer-Wei Chang

    Full Text Available BACKGROUND: Tumor suppressor gene (TSG RASSF1A and candidate TSG BLU are two tandem head-to-tail genes located at 3p21.3. We hypothesized that there may be a concordance on their gene expression and promoter methylation status. If not, then there may be an insulator located between RASSF1A and BLU genes that provides a barrier activity. METHODOLOGY/PRINCIPAL FINDINGS: We first identified potential transcriptionally important CpG sites using the methylation-specific oligonucleotide array in relation to mRNA expression of RASSF1A and BLU genes in primary lung tumors. We demonstrated that E2F1 bound to the potential transcriptionally important CpG sites in RASSF1A gene of a normal lung cell line expressing RASSF1A transcripts, whereas loss of E2F1 binding to RASSF1A in A549 cancer cell line was the result of DNA methylation. Both RASSF1A and BLU genes had their own potential transcriptionally important CpG regions. However, there was no correlation of methylation status between RASSF1A and BLU. Using gel shift assay and chromatin immunoprecipitation-PCR (ChIP-PCR, we found that CCCTC-binding factor (CTCF bound to insulator sequences located between these two genes. Bisulfite sequencing and ChIP-PCR revealed distinct methylation and chromatin boundaries separated by the CTCF binding domains in normal cells, whereas such distinct epigenetic domains were not observed in cancer cells. Note that demethylation reagent and histone deacetylase inhibitor treatments led to CTCF binding and recovery of barrier effect for RASSF1A and BLU genes in cancer cells. CONCLUSIONS/SIGNIFICANCE: Our study dissects the potential transcriptionally important CpG sites for RASSF1A and BLU genes at the sequence level and demonstrates that CTCF binding to the insulator of BLU gene provides a barrier activity within separate epigenetic domains of the juxtaposed BLU and RASSF1A loci in the 3p21.3 gene cluster region.

  8. A strict error bound with separated contributions of the discretization and of the iterative solver in non-overlapping domain decomposition methods

    CERN Document Server

    Rey, Valentine; Gosselet, Pierre

    2013-01-01

    This paper deals with the estimation of the distance between the solution of a static linear mechanic problem and its approximation by the finite element method solved with a non-overlapping domain decomposition method (FETI or BDD). We propose a new strict upper bound of the error which separates the contribution of the iterative solver and the contribution of the discretization. Numerical assessments show that the bound is sharp and enables us to define an objective stopping criterion for the iterative solver

  9. On the existence of weak solutions to the three-dimensional steady compressible Navier-Stokes equations in bounded domains

    CERN Document Server

    Jiang, Song

    2011-01-01

    We prove the existence of a weak solution to the three-dimensional steady compressible isentropic Navier-Stokes equations in bounded domains for any specific heat ratio \\gamma > 1. Generally speaking, the proof is based on the new weighted estimates of both pressure and kinetic energy for the approximate system which result in some higher integrability of the density, and the method of weak convergence. Comparing with [12] where the spatially periodic case was studied, here we have to control the additional integral terms of both pressure and kinetic energy involving with the points near the boundary which become degenerate when the points approach the boundary. Such integral terms are estimated using some new techniques, i.e., we use the techniques of the mirror image and boundary straightening to prove that the weighted estimates of both pressure and kinetic energy for the points near the boundary can be controlled by the weighted estimates for the points on the boundary. Moreover, we prove that once the we...

  10. Membrane docking geometry of GRP1 PH domain bound to a target lipid bilayer: an EPR site-directed spin-labeling and relaxation study.

    Directory of Open Access Journals (Sweden)

    Huai-Chun Chen

    Full Text Available The second messenger lipid PIP(3 (phosphatidylinositol-3,4,5-trisphosphate is generated by the lipid kinase PI3K (phosphoinositide-3-kinase in the inner leaflet of the plasma membrane, where it regulates a broad array of cell processes by recruiting multiple signaling proteins containing PIP(3-specific pleckstrin homology (PH domains to the membrane surface. Despite the broad importance of PIP(3-specific PH domains, the membrane docking geometry of a PH domain bound to its target PIP(3 lipid on a bilayer surface has not yet been experimentally determined. The present study employs EPR site-directed spin labeling and relaxation methods to elucidate the membrane docking geometry of GRP1 PH domain bound to bilayer-embedded PIP(3. The model target bilayer contains the neutral background lipid PC and both essential targeting lipids: (i PIP(3 target lipid that provides specificity and affinity, and (ii PS facilitator lipid that enhances the PIP(3 on-rate via an electrostatic search mechanism. The EPR approach measures membrane depth parameters for 18 function-retaining spin labels coupled to the PH domain, and for calibration spin labels coupled to phospholipids. The resulting depth parameters, together with the known high resolution structure of the co-complex between GRP1 PH domain and the PIP(3 headgroup, provide sufficient constraints to define an optimized, self-consistent membrane docking geometry. In this optimized geometry the PH domain engulfs the PIP(3 headgroup with minimal bilayer penetration, yielding the shallowest membrane position yet described for a lipid binding domain. This binding interaction displaces the PIP(3 headgroup from its lowest energy position and orientation in the bilayer, but the headgroup remains within its energetically accessible depth and angular ranges. Finally, the optimized docking geometry explains previous biophysical findings including mutations observed to disrupt membrane binding, and the rapid lateral

  11. Crystal structure of the yeast TSC1 core domain and implications for tuberous sclerosis pathological mutations.

    Science.gov (United States)

    Sun, Wei; Zhu, Ye Julia; Wang, Zhizhi; Zhong, Qiang; Gao, Feng; Lou, Jizhong; Gong, Weimin; Xu, Wenqing

    2013-01-01

    Tuberous sclerosis complex is a disease caused by mutations in two tumor-suppressor genes, TSC1 and TSC2. The TSC1 protein, also known as hamartin, has a critical role in controlling mTOR signalling. TSC1 does not bear apparent sequence homology with other proteins. Here we show that the N-terminal half of yeast TSC1 forms a protease-resistant domain, which is evolutionarily conserved. The crystal structure of this yeast TSC1 core domain shows that it contains a pseudo-HEAT repeat fold with its C-terminal end capped by a helical subdomain. This allows us to model the three-dimensional structure of the human TSC1 N-terminal domain (TSC1-NTD), which anchors essentially all pathogenic TSC1 missense mutations found in tuberous sclerosis patients. Interestingly, most pathogenic mutations map inside of the folded TSC1-NTD structure, whereas most non-pathogenic variants are on the structural surface. This indicates that the disruption of the TSC1-NTD globular structure is a major cause of tuberous sclerosis.

  12. 一类有界Reinhardt域上的函数论%Function Theory of a Class of Bounded Reinhardt Domains

    Institute of Scientific and Technical Information of China (English)

    李娴

    2006-01-01

    In this paper, we consider a class of bounded Reinhardt domains Dα(m,n1,…,nm). The Bergman kernel function K(z,(z)), the Bergman metric matrix T(z,(z)), the Cauchy-Szeg(o) kernel function S(z,(ζ)) are obtained. Then we prove that the formal Poisson kernel function is not a Poisson kernel function. At last, we prove that Dα is a quasiconvex domain and Dα is a stronger quasiconvex domain if and only if Dα is a hypersphere.

  13. Elucidating the domain architecture and functions of non-core RAG1: The capacity of a non-core zinc-binding domain to function in nuclear import and nucleic acid binding

    Directory of Open Access Journals (Sweden)

    Zhao Shuying

    2011-05-01

    Full Text Available Abstract Background The repertoire of the antigen-binding receptors originates from the rearrangement of immunoglobulin and T-cell receptor genetic loci in a process known as V(DJ recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. The majority of studies on RAG1 and RAG2 have focused on the minimal, core regions required for catalytic activity. Though not absolutely required, non-core regions of RAG1 and RAG2 have been shown to influence the efficiency and fidelity of the recombination reaction. Results Using a partial proteolysis approach in combination with bioinformatics analyses, we identified the domain boundaries of a structural domain that is present in the 380-residue N-terminal non-core region of RAG1. We term this domain the Central Non-core Domain (CND; residues 87-217. Conclusions We show how the CND alone, and in combination with other regions of non-core RAG1, functions in nuclear localization, zinc coordination, and interactions with nucleic acid. Together, these results demonstrate the multiple roles that the non-core region can play in the function of the full length protein.

  14. Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition.

    Science.gov (United States)

    Gautam, Gunjan; Rehman, Syed Arif Abdul; Pandey, Preeti; Gourinath, Samudrala

    2017-08-01

    The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction. Molecular-docking studies combined with various comparisons revealed structural similarity between EhMySH3 and the SH3 domain of β-Pix, and this similarity led to the prediction that EhMySH3 preferentially binds targets containing type II-like PXXP motifs. These studies expand the understanding of the EhMySH3 domain and provide extensive structural knowledge, which is expected to help in predicting the interacting partners which function together with myosin IB during phagocytosis in E. histolytica infections.

  15. Structural Analysis of the Carboxy Terminal PH Domain of Pleckstrin Bound to D-myo-Inositol 1,2,3,5,6-pentakisphosphate

    Energy Technology Data Exchange (ETDEWEB)

    Jackson,S.; Zhang, Y.; Haslam, R.; Junop, M.

    2007-01-01

    Pleckstrin homology (PH) domains are one of the most prevalent domains in the human proteome and represent the major phosphoinositide-binding module. These domains are often found in signaling proteins and function predominately by targeting their host proteins to the cell membrane. Inositol phosphates, which are structurally similar to phosphoinositides, are not only known to play a role as signaling molecules but are also capable of being bound by PH domains. In the work presented here it is shown that the addition of commercial myo-inositol hexakisphosphate (IP6) inhibited the binding of the carboxy terminal PH domain of pleckstrin (C-PH) to phosphatidylinositol 3, 4-bisphosphate with an IC50 of 7.5 {mu}M. In an attempt to characterize this binding structurally, C-PH was crystallized in the presence of IP6 and the structure was determined to 1.35 Angstroms . Examination of the resulting electron density unexpectedly revealed the bound ligand to be D-myo-inositol 1, 2,3, 5,6-pentakisphosphate. The discovery of D-myo-inositol 1, 2,3, 5,6-pentakisphosphate in the crystal structure suggests that the inhibitory effects observed in the binding studies may be due to this ligand rather than IP6. Analysis of the protein-ligand interaction demonstrated that this myo-inositol pentakisphosphate isomer interacts specifically with protein residues known to be involved in phosphoinositide binding. In addition to this, a structural alignment of other PH domains bound to inositol phosphates containing either four or five phosphate groups revealed that the majority of phosphate groups occupy conserved locations in the binding pockets of PH domains. These findings, taken together with other recently reported studies suggest that myo-inositol pentakisphosphates could act to regulate PH domain-phosphoinositide interactions by directly competing for binding, thus playing an important role as signaling molecules.

  16. Domain Decomposition strategy for pin-wise full-core Monte Carlo depletion calculation with the reactor Monte Carlo Code

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Jingang; Wang, Kan; Qiu, Yishu [Dept. of Engineering Physics, LiuQing Building, Tsinghua University, Beijing (China); Chai, Xiao Ming; Qiang, Sheng Long [Science and Technology on Reactor System Design Technology Laboratory, Nuclear Power Institute of China, Chengdu (China)

    2016-06-15

    Because of prohibitive data storage requirements in large-scale simulations, the memory problem is an obstacle for Monte Carlo (MC) codes in accomplishing pin-wise three-dimensional (3D) full-core calculations, particularly for whole-core depletion analyses. Various kinds of data are evaluated and quantificational total memory requirements are analyzed based on the Reactor Monte Carlo (RMC) code, showing that tally data, material data, and isotope densities in depletion are three major parts of memory storage. The domain decomposition method is investigated as a means of saving memory, by dividing spatial geometry into domains that are simulated separately by parallel processors. For the validity of particle tracking during transport simulations, particles need to be communicated between domains. In consideration of efficiency, an asynchronous particle communication algorithm is designed and implemented. Furthermore, we couple the domain decomposition method with MC burnup process, under a strategy of utilizing consistent domain partition in both transport and depletion modules. A numerical test of 3D full-core burnup calculations is carried out, indicating that the RMC code, with the domain decomposition method, is capable of pin-wise full-core burnup calculations with millions of depletion regions.

  17. Harmonic Domain Modelling of Transformer Core Nonlinearities Using the DIgSILENT PowerFactory Software

    DEFF Research Database (Denmark)

    Bak, Claus Leth; Bak-Jensen, Birgitte; Wiechowski, Wojciech

    2008-01-01

    This paper demonstrates the results of implementation and verification of an already existing algorithm that allows for calculating saturation characteristics of singlephase power transformers. The algorithm was described for the first time in 1993. Now this algorithm has been implemented using...... the DIgSILENT Programming Language (DPL) as an external script in the harmonic domain calculations of a power system analysis tool PowerFactory [10]. The algorithm is verified by harmonic measurements on a single-phase power transformer. A theoretical analysis of the core nonlinearities phenomena...... in single and three-phase transformers is also presented. This analysis leads to the conclusion that the method can be applied for modelling nonlinearities of three-phase autotransformers....

  18. Data for ion and seed dependent fibril assembly of a spidroin core domain

    Directory of Open Access Journals (Sweden)

    Martin Humenik

    2015-09-01

    Full Text Available This data article includes size exclusion chromatography data of soluble eADF4(C16, an engineered spider silk variant based on the core domain sequence of the natural dragline silk protein ADF4 of Araneus diadematus, in combination with light scattering; the protein is monomeric before assembly. The assembled mature fibrils were visualized by transmission electron microscopy (TEM and atomic force microscopy (AFM. Sonicated fibrils were used as seeds to by-pass the nucleation lag phase in eADF4(C16 assembly. We also provide data on the sedimentation kinetics of spider silk in the presence of different NaCl concentrations revealing very slow protein aggregation in comparison to the fast assembly triggered by phosphate ions published previously [1]. Experiments in the Data article represent supporting material for our work published recently [1], which described the assembly mechanism of recombinant eADF4(C16 fibrils.

  19. Quanty for core level spectroscopy - excitons, resonances and band excitations in time and frequency domain

    Science.gov (United States)

    Haverkort, Maurits W.

    2016-05-01

    Depending on the material and edge under consideration, core level spectra manifest themselves as local excitons with multiplets, edge singularities, resonances, or the local projected density of states. Both extremes, i.e., local excitons and non-interacting delocalized excitations are theoretically well under control. Describing the intermediate regime, where local many body interactions and band-formation are equally important is a challenge. Here we discuss how Quanty, a versatile quantum many body script language, can be used to calculate a variety of different core level spectroscopy types on solids and molecules, both in the frequency as well as the time domain. The flexible nature of Quanty allows one to choose different approximations for different edges and materials. For example, using a newly developed method merging ideas from density renormalization group and quantum chemistry [1-3], Quanty can calculate excitons, resonances and band-excitations in x-ray absorption, photoemission, x-ray emission, fluorescence yield, non-resonant inelastic x-ray scattering, resonant inelastic x-ray scattering and many more spectroscopy types. Quanty can be obtained from: http://www.quanty.org.

  20. 代数L-domain和强core紧空间的刻画%Characterization Algebraic L-domains and Strong Core Compact Space

    Institute of Scientific and Technical Information of China (English)

    吴耀强

    2012-01-01

    给出代数L-domain和强core紧空间以及连续L-domain和core紧空间的刻画.%In this paper.the characterization algebraic L-domains and strong core compact space is provided sfuthermore, the continuous L-domains algebraic L-domains between core compact space also provided.

  1. RAG2's non-core domain contributes to the ordered regulation of V(D)J recombination.

    Science.gov (United States)

    Curry, John D; Schlissel, Mark S

    2008-10-01

    Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recombinatorial order. In mice lacking the non-core domain of RAG2 the ordered rearrangement is disturbed and direct V to D rearrangements are 10- to 1000-times increased in tri-partite immune gene loci. Some forms of inter-chromosomal translocations between TCRbeta and TCRdelta D gene segments are also increased in the core RAG2 animals as compared with their wild-type (WT) counterparts. In addition, the concise use of proper recombination signal sequences (RSSs) appears to be disturbed in the core RAG2 mice as compared with WT RAG2 animals.

  2. Modeling of absorption and scattering properties of core -shell nanoparticles for application as nanoantenna in optical domain

    Science.gov (United States)

    Devi, Jutika; Saikia, Rashmi; Datta, Pranayee

    2016-10-01

    The present paper describes the study of core-shell nanoparticles for application as nanoantenna in the optical domain. To obtain the absorption and extinction efficiencies as well as the angular distribution of the far field radiation pattern and the resonance wavelengths for these metal-dielectric, dielectric-metal and metal-metal core-shell nanoparticles in optical domain, we have used Finite Element Method based COMSOL Multiphysics Software and Mie Theory. From the comparative study of the extinction efficiencies of core-shell nanoparticles of different materials, it is found that for silica - gold core - shell nanoparticles, the resonant wavelength is greater than that of the gold - silver, silver-gold and gold-silica core - shell nanoparticles and also the radiation pattern of the silica-gold core-shell nanoparticle is the most suitable one from the point of view of directivity. The dielectric functions of the core and shell material as well as of the embedded matrix are extremely important and plays a very major role to tune the directivity and resonance wavelength. Such highly controllable parameters of the dielectric - metal core - shell nanoparticles make them suitable for efficient coupling of optical radiation into nanoscale structures for a broad range of applications in the field of communications.

  3. The Topographic Torque on a Bounding Surface of a Rotating Gravitating Fluid and the Excitation by Core Motions of Decadal Fluctuations in the Earth's Rotation

    Science.gov (United States)

    Hide, Raymond

    1995-01-01

    General expressions (with potential applications in several areas of geophysical fluid dynamics) are derived for all three components of the contribution made by the geostrophic part of the pressure field associated with flow in a rotating gravitating fluid to the topographic torque exerted by the fluid on a rigid impermeable bounding surface of any shape. When applied to the Earth's liquid metallic core, which is bounded by nearly spherical surfaces and can be divided into two main regions, the "torosphere" and "polosphere," the expressions reduce to formulae given previously by the author, thereby providing further support for his work and that of others on the role of topographic coupling at the core-mantle boundary in the excitation by core motions of Earth rotation fluctuations on decadal time scales. They also show that recent criticisms of that work are vitiated by mathematical and physical errors. Contrary to these criticisms, the author's scheme for exploiting Earth rotation and other geophysical data (either real or simulated in computer models) in quantitative studies of the topography of the core-mantle boundary (CMB) by intercomparing various models of (a) motions in the core based on geomagnetic secular variation data and (b) CMB topography based on seismological and gravity data has a sound theoretical basis. The practical scope of the scheme is of course limited by the accuracy of real data, but this is a matter for investigation, not a priori assessment.

  4. Global Regularity and Long-time Behavior of the Solutions to the 2D Boussinesq Equations without Diffusivity in a Bounded Domain

    Science.gov (United States)

    Ju, Ning

    2017-03-01

    New results are obtained for global regularity and long-time behavior of the solutions to the 2D Boussinesq equations for the flow of an incompressible fluid with positive viscosity and zero diffusivity in a smooth bounded domain. Our first result for global boundedness of the solution {(u, θ)} in {D(A)× H^1} improves considerably the main result of the recent article (Hu et al. in J Math Phys 54(8):081507, 2013). Our second result on global boundedness of the solution {(u, θ)} in {V× H^1} for both bounded domain and the whole space R2 is a new one. It has been open and also seems much more challenging than the first result. Global regularity of the solution {(u, θ)} in {D(A)× H2} is also proved.

  5. Global Regularity and Long-time Behavior of the Solutions to the 2D Boussinesq Equations without Diffusivity in a Bounded Domain

    Science.gov (United States)

    Ju, Ning

    2016-07-01

    New results are obtained for global regularity and long-time behavior of the solutions to the 2D Boussinesq equations for the flow of an incompressible fluid with positive viscosity and zero diffusivity in a smooth bounded domain. Our first result for global boundedness of the solution {(u, θ)} in {D(A)× H^1} improves considerably the main result of the recent article (Hu et al. in J Math Phys 54(8):081507, 2013). Our second result on global boundedness of the solution {(u, θ)} in {V× H^1} for both bounded domain and the whole space {{R}2} is a new one. It has been open and also seems much more challenging than the first result. Global regularity of the solution {(u, θ)} in {D(A)× H2} is also proved.

  6. 有界完备的domain范畴是monadic范畴%The category of bounded complete k-domains is monadic

    Institute of Scientific and Technical Information of China (English)

    张巍

    2011-01-01

    A continuous lattice is a complete continuous partially ordered set (poset),while a bounded complete domain is a continuous poset that has directed joins and nonempty meets.In 1975,Day proved that the category of continuous lattices is monadic over the category of sets and that of T0 spaces.In this paper this conclusion is extended to bounded complete g-domains for any infinite cardinal k.First,the concepts of bounded complete k-domain and Scott k topology are introduced; Then,it is showed that the category of bounded complete g-domains is monadic over the category of sets and that of T0 g-spaces.%一个连续格就是一个完备的连续偏序集,一个有界完备domain则是一个有定向并与非空交的连续偏序集.1975年,Day证明了连续格范畴是集合范畴和T0拓扑空间范畴上的monadic范畴.本文作者把这一结论推广到了有界完备domain范畴:对任意无限基数κ,作者引入了有界完备的κ-domain以及相应的Scott κ拓扑的概念,并证明了有界完备的κ-domain范畴是集合范畴和T0的κ拓扑空间范畴上的monadic范畴.

  7. Global existence and asymptotic behavior for the 3D compressible Navier-Stokes equations without heat conductivity in a bounded domain

    Science.gov (United States)

    Wu, Guochun

    2017-01-01

    In this paper, we investigate the global existence and uniqueness of strong solutions to the initial boundary value problem for the 3D compressible Navier-Stokes equations without heat conductivity in a bounded domain with slip boundary. The global existence and uniqueness of strong solutions are obtained when the initial data is near its equilibrium in H2 (Ω). Furthermore, the exponential convergence rates of the pressure and velocity are also proved by delicate energy methods.

  8. Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization.

    Science.gov (United States)

    Saridakis, Vivian; Sheng, Yi; Sarkari, Feroz; Holowaty, Melissa N; Shire, Kathy; Nguyen, Tin; Zhang, Rongguang G; Liao, Jack; Lee, Weontae; Edwards, Aled M; Arrowsmith, Cheryl H; Frappier, Lori

    2005-04-01

    USP7/HAUSP is a key regulator of p53 and Mdm2 and is targeted by the Epstein-Barr nuclear antigen 1 (EBNA1) protein of Epstein-Barr virus (EBV). We have determined the crystal structure of the p53 binding domain of USP7 alone and bound to an EBNA1 peptide. This domain is an eight-stranded beta sandwich similar to the TRAF-C domains of TNF-receptor associated factors, although the mode of peptide binding differs significantly from previously observed TRAF-peptide interactions in the sequence (DPGEGPS) and the conformation of the bound peptide. NMR chemical shift analyses of USP7 bound by EBNA1 and p53 indicated that p53 binds the same pocket as EBNA1 but makes less extensive contacts with USP7. Functional studies indicated that EBNA1 binding to USP7 can protect cells from apoptotic challenge by lowering p53 levels. The data provide a structural and conceptual framework for understanding how EBNA1 might contribute to the survival of Epstein-Barr virus-infected cells.

  9. The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD).

    Science.gov (United States)

    Bateman, A; Bycroft, M

    2000-06-16

    The LysM domain is a widespread protein module. It was originally identified in enzymes that degrade bacterial cell walls but is also present in many other bacterial proteins. Several proteins that contain the domain, such as Staphylococcal IgG binding proteins and Escherichia coli intimin, are involved in bacterial pathogenesis. LysM domains are also found in some eukaryotic proteins, apparently as a result of horizontal gene transfer from bacteria. The available evidence suggests that the LysM domain is a general peptidoglycan-binding module. We have determined the structure of this domain from E. coli membrane-bound lytic murein transglycosylase D. The LysM domain has a betaalphaalphabeta secondary structure with the two helices packing onto the same side of an anti- parallel beta sheet. The structure shows no similarity to other bacterial cell surface domains. A potential binding site in a shallow groove on surface of the protein has been identified. Copyright 2000 Academic Press.

  10. Core outcome domains and measures for pediatric acute and chronic/recurrent pain clinical trials : PedIMMPACT recommendations

    NARCIS (Netherlands)

    McGrath, Patrick J.; Walco, Gary A.; Turk, Dennis C.; Dworkin, Robert H.; Brown, Mark T.; Davidson, Karina; Eccleston, Christopher; Finley, G. Allen; Goldschneider, Kenneth; Haverkos, Lynne; Hertz, Sharon H.; Ljungman, Gustaf; Palermo, Tonya; Rappaport, Bob A.; Rhodes, Thomas; Schechter, Neil; Scott, Jane; Sethna, Navil; Svensson, Ola K.; Stinson, Jennifer; von Baeyer, Carl L.; Walker, Lynn; Weisman, Steven; White, Richard E.; Zajicek, Anne; Zeltzer, Lonnie

    2008-01-01

    Under the auspices of the Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (IMMPACT), 26 professionals from academia, governmental agencies, and the pharmaceutical industry participated in a 2-stage Delphi poll and a consensus meeting that identified core outcome domains an

  11. Highly retentive core domains in K-feldspar preserve argon ages from high temperature stages of granite exhumation

    Science.gov (United States)

    Forster, Marnie; Lister, Gordon

    2016-04-01

    Retentive core domains are characterized by diffusion parameters that imply K-feldspar should be able to retain argon even at temperatures near or above the granite solidus. In this case it should be possible to date granite emplacement using argon geochronology, and the same answer should be obtained as by using other methods. We present one case study where this is the case, from the elevated Capoas granite stock on Palawan, in the Philippines, and another where it is not, from the South Cyclades Shear Zone, on Ios, Greece. We attempt to determine the factors such as the role of fluid ingress in triggering the in situ recrystallization that can eliminate and/or modify the core domains, leading to relatively youthful ages. Thermochronology is still possible, because less retentive diffusion domains exist, but different methods need to be applied to interpret the data. The work also demonstrates that K-feldspar can be sufficiently retentive as to allow direct dating of processes that reduce the dimensions of diffusion domains, e.g., cataclased and/or recrystallized K-feldspar in fault rock and/or mylonite. These are important developments in the methodology of 40Ar/39Ar geochronology, but to further advance we need to clarify the nature of these highly retentive core domains. In particular, we need better understand how they are modified by microstructural processes during deformation and metamorphism. We need also to assess the role of any crystal structural changes during step-heating in vacuo.

  12. Purification and biophysical characterization of the core protease domain of anthrax lethal factor.

    Science.gov (United States)

    Gkazonis, Petros V; Dalkas, Georgios A; Chasapis, Christos T; Vlamis-Gardikas, Alexios; Bentrop, Detlef; Spyroulias, Georgios A

    2010-06-04

    Anthrax lethal toxin (LeTx) stands for the major virulence factor of the anthrax disease. It comprises a 90kDa highly specific metalloprotease, the anthrax lethal factor (LF). LF possesses a catalytic Zn(2+) binding site and is highly specific against MAPK kinases, thus representing the most potent native biomolecule to alter and inactivate MKK [MAPK (mitogen-activated protein kinase) kinases] signalling pathways. Given the importance of the interaction between LF and substrate for the development of anti-anthrax agents as well as the potential treatment of nascent tumours, the analysis of the structure and dynamic properties of the LF catalytic site are essential to elucidate its enzymatic properties. Here we report the recombinant expression and purification of a C-terminal part of LF (LF(672-776)) that harbours the enzyme's core protease domain. The biophysical characterization and backbone assignments ((1)H, (13)C, (15)N) of the polypeptide revealed a stable, well folded structure even in the absence of Zn(2+), suitable for high resolution structural analysis by NMR.

  13. Preparation and reactivity of a tetranuclear Fe(II) core in the metallothionein α-domain.

    Science.gov (United States)

    Sano, Yohei; Onoda, Akira; Sakurai, Rie; Kitagishi, Hiroaki; Hayashi, Takashi

    2011-05-01

    Metallothioneins (MTs) are small cysteine-rich proteins which exhibit high affinities for various metal ions and play roles in storage of essential metals and detoxification of toxic metals. Studies on the redox properties of MTs have been quite limited. Recently, we focused on the α-domain of MT (MTα) as a protein matrix and incorporated a tetranuclear metal cluster as a reductant. UV-visible, CD and MS data indicate the formation of the stable tetranuclear metal-cysteine cluster in the MTα matrix with Fe(II)(4)-MTα and Co(II)(4)-MTα species existing in water. Furthermore, the Fe(II)(4)-MTα species was found to promote the reduction of met-myoglobin and azobenzene derivatives under mild conditions. Particularly, the stoichiometric reduction of methyl red with Fe(II)(4)-MTα (1:1) was found to proceed with a conversion of 98% over a period of 6h at 25°C. This indicates that all of the four Fe(II) cores contribute to the reduction. In this paper, we describe the preparation and reactivity of the tetranuclear iron cluster in the protein matrix.

  14. C-terminal domain of hepatitis C virus core protein is essential for secretion

    Institute of Scientific and Technical Information of China (English)

    Soo-Ho Choi; Kyu-Jin Park; So-Yeon Kim; Dong-Hwa Choi; Jung-Min Park; Soon B. Hwang

    2005-01-01

    AIM: We have previously demonstrated that hepatitis C virus (HCV) core protein is efficiently released into the culture medium in insect cells. The objective of this study is to characterize the HCV core secretion in insect cells.METHODS: We constructed recombinant baculoviruses expressing various-length of mutant core proteins, expressed these proteins in insect cells, and examined core protein secretion in insect cells.RESULTS: Only wild type core was efficiently released into the culture medium, although the protein expression level of wild type core was lower than those of other mutant core proteins. We found that the shorter form of the core construct expressed the higher level of protein. However, if more than 18 amino acids of the core were truncated at the C-terminus,core proteins were no longer seareted into the culture medium.Membrane flotation data show that the secreted core proteins are associated with the cellular membrane protein, indicating that HCV core is secreted as a membrane complex.CONCLUSION: The C-terminal 18 amino acids of HCV core were crucial for core secretion into the culture media.Since HCV replication occurs on lipid raft membrane structure,these results suggest that HCV may utilize a unique core release mechanism to escape immune surveillance, thereby potentially representing the feature of HCV morphogenesis.

  15. Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

    Energy Technology Data Exchange (ETDEWEB)

    Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira; Tan, Martha; Senear, Donald F. [University of California, Irvine, Irvine, CA 92697 (United States); Luecke, Hartmut, E-mail: hudel@uci.edu [University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); University of California, Irvine, Irvine, CA 92697 (United States); Universidad del Pais Vasco, 48940 Leioa (Spain)

    2013-10-01

    X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol{sup −1} (15.1 kJ mol{sup −1}). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the

  16. Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe (UPENN)

    2012-05-08

    We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

  17. Crystal Structures of the S. cerevisiae Spt6 Core and C-terminal Tandem SH2 Domain

    Energy Technology Data Exchange (ETDEWEB)

    D Close; S Johnson; M Sdano; S McDonald; H Robinson; T Formosa; C Hill

    2011-12-31

    The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the {approx} 900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.

  18. Crystal Structures of the S. cerevisiae Spt6 Core and C-Terminal Tandem SH2 Domain

    Energy Technology Data Exchange (ETDEWEB)

    Close, D.; Robinson, H.; Johnson, S. J.; Sdano, M. A.; McDonald, S. M.; Formosa, T.; Hill, C. P.

    2011-05-13

    The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the {approx} 900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.

  19. Crystallization and preliminary X-ray analysis of the complex of the first von Willebrand type C domain bound to bone morphogenetic protein 2

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Li-yan; Zhang, Jin-li [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Kotzsch, Alexander [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Sebald, Walter [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Mueller, Thomas D., E-mail: mueller@botanik.uni-wuerzburg.de [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany)

    2008-04-01

    Crystals of the complex of the first von Willebrand type C domain (VWC1) of crossveinless 2 (CV2) bound to bone morphogenetic protein 2 (BMP2) exist in two tetragonal crystal forms belonging to either space group P4{sub 1}2{sub 1}2 or I4{sub 1}, with one complete BMP2 dimer and two CV2 VWC1 domains per asymmetric unit, and diffract to 2.6 Å resolution. Crossveinless 2 (CV2) is a member of the chordin family, a protein superfamily that modulates the activity of bone morphogenetic proteins such as BMP2. The BMPs represent a large group of secreted proteins that control many steps during embryonal development and in tissue and organ homeostasis in the adult organism. The gene encoding the first von Willebrand type C domain (VWC1) of CV2 was cloned, expressed in Escherichia coli and purified to homogeneity. The binary complex of CV2 VWC1 and BMP2 was purified and subjected to crystallization. Crystals of SeMet-labelled proteins were obtained in two different forms belonging to the tetragonal space groups P4{sub 1}2{sub 1}2 and I4{sub 1}, with unit-cell parameters a = b = 86.7, c = 139.2 Å and a = b = 83.7, c = 139.6 Å, respectively. Initial analysis suggests that a complete binary complex consisting of one BMP2 dimer bound to two CV2 VWC1 domains is present in the asymmetric unit.

  20. Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point.

    Science.gov (United States)

    Hong, Eunmi; Doucleff, Michaeleen; Wemmer, David E

    2009-07-03

    Transcription initiation by bacterial sigma(54)-RNA polymerase requires a conformational change of the holopolymerase-DNA complex, driven by an enhancer-binding protein. Although structures of the core polymerase and the more common sigma(70) factor have been determined, little is known about the structure of the sigma(54) variant. We report here the structure of an Aquifex aeolicus sigma(54) domain (residues 69-198), which binds core RNA polymerase. The structure is composed of two distinct subdomains held together by a small, conserved hydrophobic interface that appears to act as a fracture point in the structure. The N-terminal, four-helical subdomain has a negative surface and conserved residues that likely contact the core polymerase, while the C-terminal, three-helical bundle has a strongly positive patch that could contact DNA. Sequence conservation indicates that these structural features are conserved and are important for the role of sigma(54) in the polymerase complex.

  1. Properties of Sub-Wavelength Spherical Antennas With Arbitrarily Lossy Magnetodielectric Cores Approaching the Chu Lower Bound

    DEFF Research Database (Denmark)

    Hansen, Troels Vejle; Kim, Oleksiy S.; Breinbjerg, Olav

    2014-01-01

    For a spherical antenna exciting any arbitrary spherical mode, we derive exact closed-form expressions for the dissipated power and stored energy inside (and outside) the lossy magneto-dielectric spherical core, as well as the radiated power, radiation efficiency, and thus the radiation quality f...

  2. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA

    DEFF Research Database (Denmark)

    Andersen, Christian Brix Folsted; Ballut, Lionel; Johansen, Jesper Sanderhoff;

    2006-01-01

    In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric e...

  3. A Structural Switch between Agonist and Antagonist Bound Conformations for a Ligand-Optimized Model of the Human Aryl Hydrocarbon Receptor Ligand Binding Domain

    Directory of Open Access Journals (Sweden)

    Arden Perkins

    2014-10-01

    Full Text Available The aryl hydrocarbon receptor (AHR is a ligand-activated transcription factor that regulates the expression of a diverse group of genes. Exogenous AHR ligands include the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, which is a potent agonist, and the synthetic AHR antagonist N-2-(1H-indol-3ylethyl-9-isopropyl-2- (5-methylpyridin-3-yl-9H-purin-6-amine (GNF351. As no experimentally determined structure of the ligand binding domain exists, homology models have been utilized for virtual ligand screening (VLS to search for novel ligands. Here, we have developed an “agonist-optimized” homology model of the human AHR ligand binding domain, and this model aided in the discovery of two human AHR agonists by VLS. In addition, we performed molecular dynamics simulations of an agonist TCDD-bound and antagonist GNF351-bound version of this model in order to gain insights into the mechanics of the AHR ligand-binding pocket. These simulations identified residues 307–329 as a flexible segment of the AHR ligand pocket that adopts discrete conformations upon agonist or antagonist binding. This flexible segment of the AHR may act as a structural switch that determines the agonist or antagonist activity of a given AHR ligand.

  4. Blocking the Interactions between Calcium-Bound S100A12 Protein and the V Domain of RAGE Using Tranilast

    Science.gov (United States)

    Chiou, Jian Wei; Fu, Brian

    2016-01-01

    The receptor for advanced glycation end products (RAGE), a transmembrane receptor in the immunoglobulin superfamily, is involved in several inflammatory processes. RAGE induces cellular signaling pathways upon binding with various ligands, such as advanced glycation end products (AGEs), β-amyloids, and S100 proteins. The solution structure of S100A12 and the V ligand-binding region of RAGE have been reported previously. Using heteronuclear NMR spectroscopy to conduct 1H–15N heteronuclear single quantum coherence (HSQC) titration experiments, we identified and mapped the binding interface between S100A12 and the V domain of RAGE. The NMR chemical shift data were used as the constraints for the High Ambiguity Driven biomolecular DOCKing (HADDOCK) calculation to generate a structural model of the S100A12–V domain complex. In addition, tranilast (an anti-allergic drug) showed strong interaction with S100A12 in the 1H–15N HSQC titration, fluorescence experiments, and WST-1 assay. The results also indicated that tranilast was located at the binding site between S100A12 and the V domain, blocking interaction between these two proteins. Our results provide the mechanistic details for a structural model and reveal a potential precursor for an inhibitor for pro-inflammatory diseases, which could be useful for the development of new drugs. PMID:27598566

  5. Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins.

    Science.gov (United States)

    Leen, Eoin N; Kwok, K Y Rex; Birtley, James R; Simpson, Peter J; Subba-Reddy, Chennareddy V; Chaudhry, Yasmin; Sosnovtsev, Stanislav V; Green, Kim Y; Prater, Sean N; Tong, Michael; Young, Joanna C; Chung, Liliane M W; Marchant, Jan; Roberts, Lisa O; Kao, C Cheng; Matthews, Stephen; Goodfellow, Ian G; Curry, Stephen

    2013-05-01

    We report the solution structures of the VPg proteins from feline calicivirus (FCV) and murine norovirus (MNV), which have been determined by nuclear magnetic resonance spectroscopy. In both cases, the core of the protein adopts a compact helical structure flanked by flexible N and C termini. Remarkably, while the core of FCV VPg contains a well-defined three-helix bundle, the MNV VPg core has just the first two of these secondary structure elements. In both cases, the VPg cores are stabilized by networks of hydrophobic and salt bridge interactions. The Tyr residue in VPg that is nucleotidylated by the viral NS7 polymerase (Y24 in FCV, Y26 in MNV) occurs in a conserved position within the first helix of the core. Intriguingly, given its structure, VPg would appear to be unable to bind to the viral polymerase so as to place this Tyr in the active site without a major conformation change to VPg or the polymerase. However, mutations that destabilized the VPg core either had no effect on or reduced both the ability of the protein to be nucleotidylated and virus infectivity and did not reveal a clear structure-activity relationship. The precise role of the calicivirus VPg core in virus replication remains to be determined, but knowledge of its structure will facilitate future investigations.

  6. A Structural Model for the Membrane-Bound Form of the Juxtamembrane Domain of the Epidermal Growth Factor Receptor.

    Energy Technology Data Exchange (ETDEWEB)

    Choowongkomon, Kiattawee; Carlin, Cathleen R.; Sonnichsen, Frank D.

    2005-06-24

    The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family involved in the regulation of cellular proliferation and differentiation. Its juxtamembrane domain (JX), the region located between the transmembrane and kinase domains, plays important roles in receptor trafficking. Two sorting signals, a PXXP motif and a 658LL659 motif, are responsible for basolateral sorting in polarized epithelial cells, and a 679LL680 motif targets the ligand-activated receptor for lysosomal degradation. To understand the regulation of these signals, we characterized the structural properties of recombinant JX domain in aqueous solution and in dodecylphosphocholine (DPC) detergent. JX is inherently unstructured in aqueous solution, albeit a nascent helix encompasses the lysosomal sorting signal. In DPC micelles, structures derived from NMR data showed three amphipathic, helical segments. A large, internally inconsistent group of long range nuclear Overhauser effects suggest a close proximity of the helices, and the presence of significant conformational averaging. Models were determined for the average JX conformation using restraints representing the translational restriction due to micelle-surface adsorption, and the helix orientations were determined from residual dipolar couplings. Two equivalent average structural models were obtained that differ only in the relative orientation between first and second helices. In these models, the 658LL659 and 679LL680 motifs are located in the first and second helices and face the micelle surface, whereas the PXXP motif is located in a flexible helix-connecting region. The data suggest that the activity of these signals may be regulated by their membrane association and restricted accessibility in the intact receptor.

  7. Performance Analysis of Fission and Surface Source Iteration Method for Domain Decomposed Monte Carlo Whole-Core Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Yu Gwon; Oh, Yoo Min; Park, Hyang Kyu; Park, Kang Soon; Cho, Nam Zin [KAIST, Daejeon (Korea, Republic of)

    2016-05-15

    In this paper, two issues in the FSS iteration method, i.e., the waiting time for surface source data and the variance biases in local tallies are investigated for the domain decomposed, 3-D continuous-energy whole-core calculation. The fission sources are provided as usual, while the surface sources are provided by banking MC particles crossing local domain boundaries. The surface sources serve as boundary conditions for nonoverlapping local problems, so that each local problem can be solved independently. In this paper, two issues in the FSS iteration are investigated. One is quantifying the waiting time of processors to receive surface source data. By using nonblocking communication, 'time penalty' to wait for the arrival of the surface source data is reduced. The other important issue is underestimation of the sample variance of the tally because of additional inter-iteration correlations in surface sources. From the numerical results on a 3-D whole-core test problem, it is observed that the time penalty is negligible in the FSS iteration method and that the real variances of both pin powers and assembly powers are estimated by the HB method. For those purposes, three cases; Case 1 (1 local domain), Case 2 (4 local domains), Case 3 (16 local domains) are tested. For both Cases 2 and 3, the time penalties for waiting are negligible compared to the source-tracking times. However, for finer divisions of local domains, the loss of parallel efficiency caused by the different number of sources for local domains in symmetric locations becomes larger due to the stochastic errors in source distributions. For all test cases, the HB method very well estimates the real variances of local tallies. However, it is also noted that the real variances of local tallies estimated by the HB method show slightly smaller than the real variances obtained from 30 independent batch runs and the deviations become larger for finer divisions of local domains. The batch size used

  8. Core Histone Tail Domains Mediate Oligonucleosome Folding and Nucleosomal DNA Organization through Distinct Molecular Mechanisms

    National Research Council Canada - National Science Library

    Terace M. Fletcher; Jeffrey C. Hansen

    1995-01-01

    .... wrapping of DNA around the histone octamer. Mg ions can substitute for the tail domains to yield a trypsinized oligonucleosome structure that is indistinguishable from that of an intact nucleosomal array in low salt...

  9. Hepatitis B Virus Core Protein Phosphorylation Sites Affect Capsid Stability and Transient Exposure of the C-terminal Domain.

    Science.gov (United States)

    Selzer, Lisa; Kant, Ravi; Wang, Joseph C-Y; Bothner, Brian; Zlotnick, Adam

    2015-11-20

    Hepatitis B virus core protein has 183 amino acids divided into an assembly domain and an arginine-rich C-terminal domain (CTD) that regulates essential functions including genome packaging, reverse transcription, and intracellular trafficking. Here, we investigated the CTD in empty hepatitis B virus (HBV) T=4 capsids. We examined wild-type core protein (Cp183-WT) and a mutant core protein (Cp183-EEE), in which three CTD serines are replaced with glutamate to mimic phosphorylated protein. We found that Cp183-WT capsids were less stable than Cp183-EEE capsids. When we tested CTD sensitivity to trypsin, we detected two different populations of CTDs differentiated by their rate of trypsin cleavage. Interestingly, CTDs from Cp183-EEE capsids exhibited a much slower rate of proteolytic cleavage when compared with CTDs of Cp183-WT capsids. Cryo-electron microscopy studies of trypsin-digested capsids show that CTDs at five-fold symmetry vertices are most protected. We hypothesize that electrostatic interactions between glutamates and arginines in Cp183-EEE, particularly at five-fold, increase capsid stability and reduce CTD exposure. Our studies show that quasi-equivalent CTDs exhibit different rates of exposure and thus might perform distinct functions during the hepatitis B virus lifecycle. Our results demonstrate a structural role for CTD phosphorylation and indicate crosstalk between CTDs within a capsid particle. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Crystal structures of apo and inhibitor-bound TGFβR2 kinase domain: insights into TGFβR isoform selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Tebben, Andrew J.; Ruzanov, Maxim; Gao, Mian; Xie, Dianlin; Kiefer, Susan E.; Yan, Chunhong; Newitt, John A.; Zhang, Liping; Kim, Kyoung; Lu, Hao; Kopcho, Lisa M.; Sheriff, Steven

    2016-04-26

    The cytokine TGF-β modulates a number of cellular activities and plays a critical role in development, hemostasis and physiology, as well as in diseases including cancer and fibrosis. TGF-β signals through two transmembrane serine/threonine kinase receptors: TGFβR1 and TGFβR2. Multiple structures of the TGFβR1 kinase domain are known, but the structure of TGFβR2 remains unreported. Wild-type TGFβR2 kinase domain was refractory to crystallization, leading to the design of two mutated constructs: firstly, a TGFβR1 chimeric protein with seven ATP-site residues mutated to their counterparts in TGFβR2, and secondly, a reduction of surface entropy through mutation of six charged residues on the surface of the TGFβR2 kinase domain to alanines. These yielded apo and inhibitor-bound crystals that diffracted to high resolution (<2 Å). Comparison of these structures with those of TGFβR1 reveal shared ligand contacts as well as differences in the ATP-binding sites, suggesting strategies for the design of pan and selective TGFβR inhibitors.

  11. Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states.

    Science.gov (United States)

    Girish, Tavarekere S; Gopal, Balasubramanian

    2010-09-17

    Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn(2+)-dependent dipeptidase. The crystal structure of this protein in the Mn(2+)-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys(155) and Cys(178), are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.

  12. Unusual Domain Structure and Filamentary Superfluidity for 2D Hard-Core Bosons in Insulating Charge-Ordered Phase

    Science.gov (United States)

    Panov, Yu. D.; Moskvin, A. S.; Rybakov, F. N.; Borisov, A. B.

    2016-12-01

    We made use of a special algorithm for compute unified device architecture for NVIDIA graphics cards, a nonlinear conjugate-gradient method to minimize energy functional, and Monte-Carlo technique to directly observe the forming of the ground state configuration for the 2D hard-core bosons by lowering the temperature and its evolution with deviation away from half-filling. The novel technique allowed us to examine earlier implications and uncover novel features of the phase transitions, in particular, look upon the nucleation of the odd domain structure, emergence of filamentary superfluidity nucleated at the antiphase domain walls of the charge-ordered phase, and nucleation and evolution of different topological structures.

  13. CORE

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Hundebøll, Martin

    2013-01-01

    different flows. Instead of maintaining these approaches separate, we propose a protocol (CORE) that brings together these coding mechanisms. Our protocol uses random linear network coding (RLNC) for intra- session coding but allows nodes in the network to setup inter- session coding regions where flows...... intersect. Routes for unicast sessions are agnostic to other sessions and setup beforehand, CORE will then discover and exploit intersecting routes. Our approach allows the inter-session regions to leverage RLNC to compensate for losses or failures in the overhearing or transmitting process. Thus, we...... increase the benefits of XORing by exploiting the underlying RLNC structure of individual flows. This goes beyond providing additional reliability to each individual session and beyond exploiting coding opportunistically. Our numerical results show that CORE outperforms both forwarding and COPE...

  14. CORE

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Hundebøll, Martin

    2013-01-01

    different flows. Instead of maintaining these approaches separate, we propose a protocol (CORE) that brings together these coding mechanisms. Our protocol uses random linear network coding (RLNC) for intra- session coding but allows nodes in the network to setup inter- session coding regions where flows...... intersect. Routes for unicast sessions are agnostic to other sessions and setup beforehand, CORE will then discover and exploit intersecting routes. Our approach allows the inter-session regions to leverage RLNC to compensate for losses or failures in the overhearing or transmitting process. Thus, we...... increase the benefits of XORing by exploiting the underlying RLNC structure of individual flows. This goes beyond providing additional reliability to each individual session and beyond exploiting coding opportunistically. Our numerical results show that CORE outperforms both forwarding and COPE...

  15. Factor Analysis of the DePaul Symptom Questionnaire: Identifying Core Domains.

    Science.gov (United States)

    Jason, Leonard A; Sunnquist, Madison; Brown, Abigail; Furst, Jacob; Cid, Marjoe; Farietta, Jillianna; Kot, Bobby; Bloomer, Craig; Nicholson, Laura; Williams, Yolonda; Jantke, Rachel; Newton, Julia L; Strand, Elin Bolle

    2015-09-01

    The present study attempted to identify critical symptom domains of individuals with Myalgic Encephalomyelitis (ME) and chronic fatigue syndrome (CFS). Using patient and control samples collected in the United States, Great Britain, and Norway, exploratory factor analysis (EFA) was used to establish the underlying factor structure of ME and CFS symptoms. The EFA suggested a four-factor solution: post-exertional malaise, cognitive dysfunction, sleep difficulties, and a combined factor consisting of neuroendocrine, autonomic, and immune dysfunction symptoms. The use of empirical methods could help better understand the fundamental symptom domains of this illness.

  16. Core outcome domains for clinical trials in non-specific low back pain

    NARCIS (Netherlands)

    A. Chiarotto (Alessandro); R.A. Deyo (Richard); C.B. Terwee (Caroline); M. Boers (Maarten); R. Buchbinder (Rachelle); T.P. Corbin (Terry P.); L.O.P. Costa (Leonardo); N.E. Foster (Nadine); M. Grotle (Margreth); B.W. Koes (Bart); F.M. Kovacs (Francisco M.); C.-W.C. Lin (Chung-Wei Christine); C. Maher (Chris); A.M. Pearson (Adam M.); W.C. Peul (Wilco); M.L. Schoene (Mark L.); D.C. Turk (Dennis C.); M.W. van Tulder (Maurits); R.W.J.G. Ostelo (Raymond)

    2015-01-01

    textabstractPurpose: Inconsistent reporting of outcomes in clinical trials of patients with non-specific low back pain (NSLBP) hinders comparison of findings and the reliability of systematic reviews. A core outcome set (COS) can address this issue as it defines a minimum set of outcomes that should

  17. A seismic and gravitationally bound double star observed by Kepler. Implication for the presence of a convective core

    Science.gov (United States)

    Appourchaux, T.; Antia, H. M.; Ball, W.; Creevey, O.; Lebreton, Y.; Verma, K.; Vorontsov, S.; Campante, T. L.; Davies, G. R.; Gaulme, P.; Régulo, C.; Horch, E.; Howell, S.; Everett, M.; Ciardi, D.; Fossati, L.; Miglio, A.; Montalbán, J.; Chaplin, W. J.; García, R. A.; Gizon, L.

    2015-10-01

    Context. Solar-like oscillations have been observed by Kepler and CoRoT in many solar-type stars, thereby providing a way to probe stars using asteroseismology. Aims: The derivation of stellar parameters has usually been done with single stars. The aim of the paper is to derive the stellar parameters of a double-star system (HIP 93511), for which an interferometric orbit has been observed along with asteroseismic measurements. Methods: We used a time series of nearly two years of data for the double star to detect the two oscillation-mode envelopes that appear in the power spectrum. Using a new scaling relation based on luminosity, we derived the radius and mass of each star. We derived the age of each star using two proxies: one based upon the large frequency separation and a new one based upon the small frequency separation. Using stellar modelling, the mode frequencies allowed us to derive the radius, the mass, and the age of each component. In addition, speckle interferometry performed since 2006 has enabled us to recover the orbit of the system and the total mass of the system. Results: From the determination of the orbit, the total mass of the system is 2.34-0.33+0.45 M⊙. The total seismic mass using scaling relations is 2.47 ± 0.07 M⊙. The seismic age derived using the new proxy based upon the small frequency separation is 3.5 ± 0.3 Gyr. Based on stellar modelling, the mean common age of the system is 2.7-3.9 Gyr. The mean total seismic mass of the system is 2.34-2.53 M⊙ consistent with what we determined independently with the orbit. The stellar models provide the mean radius, mass, and age of the stars as RA = 1.82-1.87R⊙, MA = 1.25-1.39 M⊙, AgeA = 2.6-3.5 Gyr; RB = 1.22-1.25 R⊙, MB = 1.08-1.14 M⊙, AgeB = 3.35-4.21 Gyr. The models provide two sets of values for Star A: [1.25-1.27] M⊙ and [1.34-1.39] M⊙. We detect a convective core in Star A, while Star B does not have any. For the metallicity of the binary system of Z ≈ 0.02, we set

  18. A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.

    Science.gov (United States)

    Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien-Jen; Foo, Hooi Ling; Ho, Kok Lian

    2016-08-09

    DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed.

  19. Factor Analysis of the DePaul Symptom Questionnaire: Identifying Core Domains

    OpenAIRE

    Jason, Leonard A.; Sunnquist, Madison; Brown, Abigail; Furst, Jacob; Cid, Marjoe; Farietta, Jillianna; Kot, Bobby; Bloomer, Craig; Nicholson, Laura; Williams, Yolonda; Jantke, Rachel; Newton, Julia L.; Strand, Elin Bolle

    2015-01-01

    The present study attempted to identify critical symptom domains of individuals with Myalgic Encephalomyelitis (ME) and chronic fatigue syndrome (CFS). Using patient and control samples collected in the United States, Great Britain, and Norway, exploratory factor analysis (EFA) was used to establish the underlying factor structure of ME and CFS symptoms. The EFA suggested a four-factor solution: post-exertional malaise, cognitive dysfunction, sleep difficulties, and a combined factor consisti...

  20. Short-time Asymptotics of the Heat Kernel on Bounded Domain with Piecewise Smooth Boundary Conditions and Its Applications to an Ideal Gas

    Institute of Scientific and Technical Information of China (English)

    E.M.E. ZAYED

    2004-01-01

    The asymptotic expansion of the heat kernel Θ(t)(∞∑=(i=0))exp (-λi) where({λi}∞i=1) Are the eigen-values of negative Laplacian( -△n=-n∑k=1(θ/θxk)2)in Rn(n=2 or 3) is studied for short-time t for a general bounded domainθΩwith a smooth boundary θΩ.In this paper, we consider the case of a finite number of the Dirichlet conditions φ=0 on Γi (i = J +1,….,J)and the Neumann conditions and (θφ/θ vi) = 0 on Γi (i = J+1,…,k) and the Robin condition (θφ/θ vi+γi) θ=(I=k+1,… m) where γi are piecewise smooth positive impedancem(θφ=mUi=1Γi. )We construct the required asymptotics in the form of a power series over t. The senior coe.cients inthis series are speci.ed as functionals of the geometric shape of the domain Ω.This result is applied to calculatethe one-particle partition function of a "special ideal gas", i.e., the set of non-interacting particles set up in abox with Dirichlet, Neumann and Robin boundary conditions for the appropriate wave function. Calculationof the thermodynamic quantities for the ideal gas such as the internal energy, pressure and speci.c heat revealsthat these quantities alone are incapable of distinguishing between two di.erent shapes of the domain. Thisconclusion seems to be intuitively clear because it is based on a limited information given by a one-particlepartition function; nevertheless, its formal theoretical motivation is of some interest.

  1. Two forms of the membrane-bound state of the first C2 domain (C2A) of synaptotagminⅠand calcium-triggered membrane insertion

    Institute of Scientific and Technical Information of China (English)

    HE Yuhong; LI Xianghui; WANG Fu; XUE Yi; SUI Senfang

    2003-01-01

    The synaptic vesicle protein synaptotagminⅠ (sytⅠ) is a vesicle trans membrane protein present in synaptic vesicles, which has been proposed as the Ca 2+ sensor that regulates secretion. The C2A domain is the membrane proximal part of its cytoplasmic domain. The interaction between C2A and lipid bilayer has be en considered to be essential for triggering neurotransmitter release. In the pr esent work, the measurements of membrane surface tension and surface concentrati on showed that the C2A domain of sytⅠexhibited two membrane-bound states: the s urface adsorption state and the membrane insertion state. The surface absorption state formed in a Ca2+-independent manner with lower affinity, while the membra ne insertion state formed with high affinity was only found in the presence of C a2+. Both the Ca2+-independent and Ca2+-dependent sytⅠ- membrane interactions r equired anionic phospholipids, such as phosphatidylserine (PS). When expressed i nto rat pheochromocytoma (PC12) cells and human embryonic kidney (HEK-293) cells , as demonstrated by immunofluorescence staining and subcellular fractionation, most of the C2A was found at the plasma membrane, even when the cells were deple ted of Ca2+ by incubation with EGTA. These results suggested a new molecular mec hanism of sytⅠas a Ca2+ sensor in membrane fusion. Ca2+-independent surface ads orption might attach sytⅠto the release site during the docking or priming step . When intracellular Ca2+ increased, sytⅠtriggered the neurotransmitter release following the Ca2+-dependent penetration into the target membrane.

  2. Societal and individual burden of illness among fibromyalgia patients in France: Association between disease severity and OMERACT core domains

    Directory of Open Access Journals (Sweden)

    Perrot Serge

    2012-02-01

    Full Text Available Abstract Background Patients with fibromyalgia (FM report widespread pain, fatigue, and other functional limitations. This study aimed to provide an assessment of the burden of illness associated with FM in France and its association with disease severity and core domains as defined by Outcome Measures in Rheumatology Clinical Trials (OMERACT for FM. Methods This cross-sectional, observational study recruited patients with a prior diagnosis of FM from 18 community-based physician offices in France. Patients completed questions about FM impact (Fibromyalgia-Impact Questionnaire [FIQ], core symptoms (defined by OMERACT, health-related quality of life (EQ-5D, current overall health status (rated on a scale from 0 to 100, productivity, treatment satisfaction, and out-of-pocket expenses related to FM. Site staff recorded patients' treatment and health resource use based on medical record review. Costs were extrapolated from 4-week patient-reported data and 3-month clinical case report form data and calculated in 2008 Euros using a societal perspective. Tests of significance used the Kruskal-Wallis test or Fisher's Exact test where P Results Eighty-eight patients (mean 55.2 y; female:male 74:14 were recruited. The majority of patients (84.1% were prescribed medications for FM. Patients mainly described medications as a little/not at all effective (40.0% or somewhat effective (52.9%. Current Overall Health rating was 52.9 (± 17.8 and FIQ total score was 54.8 (± 17.3. FIQ total score was used to define FM severity, and 17 patients scored 0- Conclusions In a sample of 88 patients with FM from France, we found that FM poses a substantial economic and human burden on patients and society. FM severity level was significantly associated with patients' health status and core symptom domains.

  3. Updating the Psoriatic Arthritis (PsA) Core Domain Set: A Report from the PsA Workshop at OMERACT 2016.

    Science.gov (United States)

    Orbai, Ana-Maria; de Wit, Maarten; Mease, Philip J; Callis Duffin, Kristina; Elmamoun, Musaab; Tillett, William; Campbell, Willemina; FitzGerald, Oliver; Gladman, Dafna D; Goel, Niti; Gossec, Laure; Hoejgaard, Pil; Leung, Ying Ying; Lindsay, Chris; Strand, Vibeke; van der Heijde, Désirée M; Shea, Bev; Christensen, Robin; Coates, Laura; Eder, Lihi; McHugh, Neil; Kalyoncu, Umut; Steinkoenig, Ingrid; Ogdie, Alexis

    2017-10-01

    To include the patient perspective in accordance with the Outcome Measures in Rheumatology (OMERACT) Filter 2.0 in the updated Psoriatic Arthritis (PsA) Core Domain Set for randomized controlled trials (RCT) and longitudinal observational studies (LOS). At OMERACT 2016, research conducted to update the PsA Core Domain Set was presented and discussed in breakout groups. The updated PsA Core Domain Set was voted on and endorsed by OMERACT participants. We conducted a systematic literature review of domains measured in PsA RCT and LOS, and identified 24 domains. We conducted 24 focus groups with 130 patients from 7 countries representing 5 continents to identify patient domains. We achieved consensus through 2 rounds of separate surveys with 50 patients and 75 physicians, and a nominal group technique meeting with 12 patients and 12 physicians. We conducted a workshop and breakout groups at OMERACT 2016 in which findings were presented and discussed. The updated PsA Core Domain Set endorsed with 90% agreement by OMERACT 2016 participants included musculoskeletal disease activity, skin disease activity, fatigue, pain, patient's global assessment, physical function, health-related quality of life, and systemic inflammation, which were recommended for all RCT and LOS. These were important, but not required in all RCT and LOS: economic cost, emotional well-being, participation, and structural damage. Independence, sleep, stiffness, and treatment burden were on the research agenda. The updated PsA Core Domain Set was endorsed at OMERACT 2016. Next steps for the PsA working group include evaluation of PsA outcome measures and development of a PsA Core Outcome Measurement Set.

  4. New experimental treatments of core social domain in Autism Spectrum Disorders

    Directory of Open Access Journals (Sweden)

    Roberto eCanitano

    2014-06-01

    Full Text Available Current therapeutics in Autism Spectrum Disorders (ASD only treat the associated symptoms, without addressing core social dysfunctions. A paradigm shift in research of the pathogenesis of ASD, its synaptic abnormalities and altered signaling in multiple dynamic systems, have led to new experimental treatments for treating the core social abnormalities of ASD. NMDA antagonists, especially memantine, have been introduced in clinical trials addressing glutamatergic transmission in children and adolescents with ASD. GABAergic signaling has been targeted in trials using the GABAB receptor agonist arbaclofen for ASD patients with promising results. Oxytocin has been recognized as implicated in social development and affiliative behaviours. Preliminary findings from clinical trials using oxytocin in children with ASD show encouraging improvements in social cognition, but larger studies are needed. In two of the single gene disorders associated with ASD, Insulin Growth Factor (IGF-1 is a new treatment that has been tested in Rett Syndrome and Phelan-McDermid Syndrome (Chromosome 22 deletion syndrome. IGF-1 has been demonstrated to reverse the reduction in the number of excitatory synapses and the density of neurons that characterize these conditions in animal studies and it is being introduced as an experimental treatment..As a novel approach to verify treatment efficacy,neural processing modifications were recently evaluated by fMRI after a Pivotal Response Training (PRT intervention. Another study of neural changes in response to treatment examined variations in EEG signaling in patientsafter an Early Start Denver Model (ESDM intervention.

  5. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element.

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R; Jauch, Ralf

    2014-10-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6-DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit.

  6. Protocol for the development of a core domain set for hidradenitis suppurativa trial outcomes

    DEFF Research Database (Denmark)

    Thorlacius, Linnea; Ingram, John R; Garg, Amit

    2017-01-01

    Delphi rounds are then planned together with 2 face-to-face consensus meetings (1 in Europe and 1 in the USA) to ensure global representation. ETHICS AND DISSEMINATION: The study will be performed according to the Helsinki declaration. All results from the study, including inconclusive or negative...... for dealing with these problems is to develop a core outcome set (COS). A COS is a list of outcomes that are meant as mandatory and should be measured and reported in all clinical trials. The aim of this study is to develop a COS for the management of HS. METHOD AND ANALYSIS: An international steering group...... of researchers, clinicians and a patient research partner will guide the COS development. 6 stakeholder groups are involved: patients, dermatologists, surgeons, nurses, industry representatives and drug regulatory authorities. A 1:1 ratio of patients:healthcare professionals is aimed for. The initial list...

  7. Re-directing CD4+ T cell responses with the flanking residues of MHC class II-bound peptides: the core is not enough

    Directory of Open Access Journals (Sweden)

    David Kenneth Cole

    2013-07-01

    Full Text Available Recombinant αβ T cell receptors (TCRs recognise short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8+ T cells that recognise mainly cytosol-derived peptides in the context of MHC class I (pMHC-I, and CD4+ T cells that recognise peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II. Unlike the more uniform peptide lengths (usually 8-13mers bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type but with variable peptide flanking residues (PFRs that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8+ and CD4+ T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the TCR including the functional importance of MHC-II peptide flanking residues. We consider how factors such as anatomical location, inflammatory milieu and particular types of APC might, in theory, contribute to the quantitative (i.e. pMHC ligand frequency as well as qualitative (i.e. variable PFR nature of peptide epitopes, and hence offer a means of control and influence of a CD4+ T cell response. Lastly, we review our recent findings showing how modifications to these flanking regions modify CD4+ T cell antigen recognition. These findings may have novel applications for the development of CD4+ T cell peptide vaccines and diagnostics.

  8. Re-Directing CD4(+) T Cell Responses with the Flanking Residues of MHC Class II-Bound Peptides: The Core is Not Enough.

    Science.gov (United States)

    Holland, Christopher J; Cole, David K; Godkin, Andrew

    2013-01-01

    Recombinant αβ T cell receptors, expressed on T cell membranes, recognize short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8(+) T cells that recognize mainly cytosol-derived peptides in the context of MHC class I (pMHC-I), and CD4(+) T cells that recognize peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II). Unlike the more uniform peptide lengths (usually 8-13mers) bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type) but with variable peptide flanking residues (PFRs) that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation) and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8(+) and CD4(+) T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the T cell receptor including the functional importance of MHC-II PFRs. We consider how factors such as anatomical location, inflammatory milieu, and particular types of antigen presenting cell might, in theory, contribute to the quantitative (i.e., pMHC ligand frequency) as well as qualitative (i.e., variable PFR) nature of peptide epitopes, and hence offer a means of control and influence of a CD4(+) T cell response. Lastly, we review our recent findings showing how modifications to MHC-II PFRs can modify CD4(+) T cell antigen recognition. These findings may have novel applications for the development of CD4(+) T cell peptide vaccines and diagnostics.

  9. Domain Decomposition Strategy for Pin-wise Full-Core Monte Carlo Depletion Calculation with the Reactor Monte Carlo Code

    Directory of Open Access Journals (Sweden)

    Jingang Liang

    2016-06-01

    Full Text Available Because of prohibitive data storage requirements in large-scale simulations, the memory problem is an obstacle for Monte Carlo (MC codes in accomplishing pin-wise three-dimensional (3D full-core calculations, particularly for whole-core depletion analyses. Various kinds of data are evaluated and quantificational total memory requirements are analyzed based on the Reactor Monte Carlo (RMC code, showing that tally data, material data, and isotope densities in depletion are three major parts of memory storage. The domain decomposition method is investigated as a means of saving memory, by dividing spatial geometry into domains that are simulated separately by parallel processors. For the validity of particle tracking during transport simulations, particles need to be communicated between domains. In consideration of efficiency, an asynchronous particle communication algorithm is designed and implemented. Furthermore, we couple the domain decomposition method with MC burnup process, under a strategy of utilizing consistent domain partition in both transport and depletion modules. A numerical test of 3D full-core burnup calculations is carried out, indicating that the RMC code, with the domain decomposition method, is capable of pin-wise full-core burnup calculations with millions of depletion regions.

  10. Homology modelling of the core domain of the endogenous lectin comitin: structural basis for its mannose-binding specificity.

    Science.gov (United States)

    Barre, A; Van Damme, E J; Peumans, W J; Rougé, P

    1999-03-01

    The N-terminal core domain of comitin from the slime mold Dictyostelium discoideum has been modelled from the X-ray coordinates of the monocot mannose-binding lectin from snowdrop (Galanthus nivalis). Docking experiments performed on the three-dimensional model showed that two of the three mannose-binding sites of the comitin monomer are functional. They are located at both ends of the comitin dimer whereas the actin-interacting region occurs in the central hinge region where both monomers are non covalently associated. This distribution is fully consistent with the bifunctional character of comitin which is believed to link the Golgi vesicles exhibiting mannosylated membrane glycans to the actin cytoskeleton in the cell.

  11. The repeat domain of the melanosome fibril protein Pmel17 forms the amyloid core promoting melanin synthesis.

    Science.gov (United States)

    McGlinchey, Ryan P; Shewmaker, Frank; McPhie, Peter; Monterroso, Begoña; Thurber, Kent; Wickner, Reed B

    2009-08-18

    Pmel17 is a melanocyte protein necessary for eumelanin deposition 1 in mammals and found in melanosomes in a filamentous form. The luminal part of human Pmel17 includes a region (RPT) with 10 copies of a partial repeat sequence, pt.e.gttp.qv., known to be essential in vivo for filament formation. We show that this RPT region readily forms amyloid in vitro, but only under the mildly acidic conditions typical of the lysosome-like melanosome lumen, and the filaments quickly become soluble at neutral pH. Under the same mildly acidic conditions, the Pmel filaments promote eumelanin formation. Electron diffraction, circular dichroism, and solid-state NMR studies of Pmel17 filaments show that the structure is rich in beta sheet. We suggest that RPT is the amyloid core domain of the Pmel17 filaments so critical for melanin formation.

  12. THE DARWIN MODEL IN 2-D BOUNDED MULTIPLY CONNECTED DOMAINS AND ITS NUMERICAL SOLUTION%二维有界多连通区域上的达尔文模型及其数值解

    Institute of Scientific and Technical Information of China (English)

    廖才秀

    2012-01-01

    In this paper, we study the Darwin model in 2-D bounded multiply connected domains and its numerical solution. The mixed variational formulations are established. We use P2 — Po finite element to approximate the variational problem, prove its well-posedness and finally provide the convergence analysis.

  13. Time Is Not Space: Core Computations and Domain-Specific Networks for Mental Travels.

    Science.gov (United States)

    Gauthier, Baptiste; van Wassenhove, Virginie

    2016-11-23

    Humans can consciously project themselves in the future and imagine themselves at different places. Do mental time travel and mental space navigation abilities share common cognitive and neural mechanisms? To test this, we recorded fMRI while participants mentally projected themselves in time or in space (e.g., 9 years ago, in Paris) and ordered historical events from their mental perspective. Behavioral patterns were comparable for mental time and space and shaped by self-projection and by the distance of historical events to the mental position of the self, suggesting the existence of egocentric mapping in both dimensions. Nonetheless, self-projection in space engaged the medial and lateral parietal cortices, whereas self-projection in time engaged a widespread parietofrontal network. Moreover, while a large distributed network was found for spatial distances, temporal distances specifically engaged the right inferior parietal cortex and the anterior insula. Across these networks, a robust overlap was only found in a small region of the inferior parietal lobe, adding evidence for its role in domain-general egocentric mapping. Our findings suggest that mental travel in time or space capitalizes on egocentric remapping and on distance computation, which are implemented in distinct dimension-specific cortical networks converging in inferior parietal lobe.

  14. Protocol for the development of a core domain set for hidradenitis suppurativa trial outcomes

    Science.gov (United States)

    Thorlacius, Linnea; Garg, Amit; Villumsen, Bente; Esmann, Solveig; Kirby, Joslyn S; Gottlieb, Alice B; Merola, Joseph F; Dellavalle, Robert; Jemec, Gregor B E

    2017-01-01

    Introduction Randomised controlled trials (RCTs) should have well-defined primary and secondary outcomes to answer questions generated by the main hypotheses. However, for the chronic, inflammatory skin disease hidradenitis suppurativa (HS), the reported outcome measures are numerous and diverse. A recent systematic review found a total of 30 outcome measure instruments in 12 RCTs. This use of a broad range of outcome measures can increase difficulties in interpretation and comparison of results and may potentially obstruct appropriate evidence synthesis by causing reporting bias. One strategy for dealing with these problems is to develop a core outcome set (COS). A COS is a list of outcomes that are meant as mandatory and should be measured and reported in all clinical trials. The aim of this study is to develop a COS for the management of HS. Method and analysis An international steering group of researchers, clinicians and a patient research partner will guide the COS development. 6 stakeholder groups are involved: patients, dermatologists, surgeons, nurses, industry representatives and drug regulatory authorities. A 1:1 ratio of patients:healthcare professionals is aimed for. The initial list of candidate items will be obtained by combining three data sets: (1) a systematic review of the literature, (2) US and Danish qualitative interview studies involving patients with HS and (3) an online healthcare professional (HCP) item generation survey. To reach consensus on the COS, 4 anonymous online Delphi rounds are then planned together with 2 face-to-face consensus meetings (1 in Europe and 1 in the USA) to ensure global representation. Ethics and dissemination The study will be performed according to the Helsinki declaration. All results from the study, including inconclusive or negative results, will be published in peer-reviewed indexed journals. The study will involve different stakeholder groups to ensure that the developed COS will be suitable and well

  15. Lactoperoxidase folding and catalysis relies on the stabilization of the alpha-helix rich core domain: a thermal unfolding study.

    Science.gov (United States)

    Boscolo, Barbara; Leal, Sónia S; Ghibaudi, Elena M; Gomes, Cláudio M

    2007-09-01

    Lactoperoxidase (LPO) belongs to the mammalian peroxidase family and catalyzes the oxidation of halides, pseudo-halides and a number of aromatic substrates at the expense of hydrogen peroxide. Despite the complex physiological role of LPO and its potential involvement in carcinogenic mechanisms, cystic fibrosis and inflammatory processes, little is known on the folding and structural stability of this protein. We have undertaken an investigation of the conformational dynamics and catalytic properties of LPO during thermal unfolding, using complementary biophysical techniques (differential scanning calorimetry, electron spin resonance, optical absorption, fluorescence and circular dichroism spectroscopies) together with biological activity assays. LPO is a particularly stable protein, capable of maintaining catalysis and structural integrity up to a high temperature, undergoing irreversible unfolding at 70 degrees C. We have observed that the first stages of the thermal denaturation involve a minor conformational change occurring at 40 degrees C, possibly at the level of the protein beta-sheets, which nevertheless does not result in an unfolding transition. Only at higher temperature, the protein hydrophobic core, which is rich in alpha-helices, unfolds with concomitant disruption of the catalytic heme pocket and activity loss. Evidences concerning the stabilizing role of the disulfide bridges and the covalently bound heme cofactor are shown and discussed in the context of understanding the structural stability determinants in a relatively large protein.

  16. Humanized-single domain antibodies (VH/VHH) that bound specifically to Naja kaouthia phospholipase A2 and neutralized the enzymatic activity.

    Science.gov (United States)

    Chavanayarn, Charnwit; Thanongsaksrikul, Jeeraphong; Thueng-In, Kanyarat; Bangphoomi, Kunan; Sookrung, Nitat; Chaicumpa, Wanpen

    2012-07-01

    Naja kaouthia (monocled cobra) venom contains many isoforms of secreted phospholipase A2 (sPLA(2)). The PLA(2) exerts several pharmacologic and toxic effects in the snake bitten subject, dependent or independent on the enzymatic activity. N. kaouthia venom appeared in two protein profiles, P3 and P5, after fractionating the venom by ion exchange column chromatography. In this study, phage clones displaying humanized-camel single domain antibodies (VH/V(H)H) that bound specifically to the P3 and P5 were selected from a humanized-camel VH/V(H)H phage display library. Two phagemid transfected E. coli clones (P3-1 and P3-3) produced humanized-V(H)H, while another clone (P3-7) produced humanized-VH. At the optimal venom:antibody ratio, the VH/V(H)H purified from the E. coli homogenates neutralized PLA(2) enzyme activity comparable to the horse immune serum against the N. kaouthia holo-venom. Homology modeling and molecular docking revealed that the VH/V(H)H covered the areas around the PLA(2) catalytic groove and inserted their Complementarity Determining Regions (CDRs) into the enzymatic cleft. It is envisaged that the VH/V(H)H would ameliorate/abrogate the principal toxicity of the venom PLA(2) (membrane phospholipid catabolism leading to cellular and subcellular membrane damage which consequently causes hemolysis, hemorrhage, and dermo-/myo-necrosis), if they were used for passive immunotherapy of the cobra bitten victim. The speculation needs further investigations.

  17. Potato lectin activates basophils and mast cells of atopic subjects by its interaction with core chitobiose of cell-bound non-specific immunoglobulin E.

    Science.gov (United States)

    Pramod, S N; Venkatesh, Y P; Mahesh, P A

    2007-06-01

    A major factor in non-allergic food hypersensitivity could be the interaction of dietary lectins with mast cells and basophils. Because immunoglobulin E (IgE) contains 10-12% carbohydrates, lectins can activate and degranulate these cells by cross-linking the glycans of cell-bound IgE. The present objective focuses on the effect of potato lectin (Solanum tuberosum agglutinin; STA) for its ability to release histamine from basophils in vitro and mast cells in vivo from non-atopic and atopic subjects. In this study, subjects were selected randomly based on case history and skin prick test responses with food, pollen and house dust mite extracts. Skin prick test (SPT) was performed with STA at 100 microg/ml concentration. Histamine release was performed using leucocytes from non-atopic and atopic subjects and rat peritoneal exudate cells. SPT on 110 atopic subjects using STA showed 39 subjects positive (35%); however, none showed STA-specific IgE; among 20 non-atopic subjects, none were positive by SPT. Maximal histamine release was found to be 65% in atopic subjects (n = 7) compared to 28% in non-atopic subjects (n = 5); the release was inhibited specifically by oligomers of N-acetylglucosamine and correlates well with serum total IgE levels (R(2) = 0.923). Binding of STA to N-linked glycoproteins (horseradish peroxidase, avidin and IgG) was positive by dot blot and binding assay. As potato lectin activates and degranulates both mast cells and basophils by interacting with the chitobiose core of IgE glycans, higher intake of potato may increase the clinical symptoms as a result of non-allergic food hypersensitivity in atopic subjects.

  18. Insight into the Unfolding Properties of Chd64, a Small, Single Domain Protein with a Globular Core and Disordered Tails.

    Directory of Open Access Journals (Sweden)

    Aneta Tarczewska

    Full Text Available Two major lipophilic hormones, 20-hydroxyecdysone (20E and juvenile hormone (JH, govern insect development and growth. While the mode of action of 20E is well understood, some understanding of JH-dependent signalling has been attained only in the past few years, and the crosstalk of the two hormonal pathways remains unknown. Two proteins, the calponin-like Chd64 and immunophilin FKBP39 proteins, have recently been found to play pivotal roles in the formation of dynamic, multiprotein complex that cross-links these two signalling pathways. However, the molecular mechanism of the interaction remains unexplored. The aim of this work was to determine structural elements of Chd64 to provide an understanding of molecular basis of multiple interactions. We analysed Chd64 in two unrelated insect species, Drosophila melanogaster (DmChd64 and Tribolium castaneum (TcChd64. Using hydrogen-deuterium exchange mass spectrometry (HDX-MS, we showed that both Chd64 proteins have disordered tails that outflank the globular core. The folds of the globular cores of both Chd64 resemble the calponin homology (CH domain previously resolved by crystallography. Monitoring the unfolding of DmChd64 and TcChd64 by far-ultraviolet (UV circular dichroism (CD spectroscopy, fluorescence spectroscopy and size-exclusion chromatography (SEC revealed a highly complex process. Chd64 unfolds and forms of a molten globule (MG-like intermediate state. Furthermore, our data indicate that in some conditions, Chd64 may exists in discrete structural forms, indicating that the protein is pliable and capable of easily acquiring different conformations. The plasticity of Chd64 and the existence of terminal intrinsically disordered regions (IDRs may be crucial for multiple interactions with many partners.

  19. Typing of core and backbone domains of mucin-type oligosaccharides from human ovarian-cyst glycoproteins by 500-MHz 1H-NMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Mutsaers, J.H.G.M.; Halbeek, H. van; Wu, A.M.; Kabat, E.A.

    1986-01-01

    Human blood-group A active glycoproteins from ovarian-cyst fluid were subjected to Smith degradation and subsequent beta-elimination. The resulting oligosaccharide-alditols represent the core and backbone domains of the O-linked carbohydrate chains. Nine of these, ranging in size from disaccharides

  20. Measurement of homonuclear three-bond J(HNH{alpha}) coupling constants in unlabeled peptides complexed with labeled proteins: Application to a decapeptide inhibitor bound to the proteinase domain of the NS3 protein of hepatitis C virus (HCV)

    Energy Technology Data Exchange (ETDEWEB)

    Cicero, Daniel O.; Barbato, Gaetano; Koch, Uwe; Ingallinella, Paolo; Bianchi, Elisabetta; Sambucini, Sonia; Neddermann, Petra; De Francesco, Raffaele; Pessi, Antonello; Bazzo, Renzo

    2001-05-15

    A new isotope-filtered experiment has been designed to measure homonuclear three-bond J(H{sup N}H{sup {alpha}}) coupling constants of unlabeled peptides complexed with labeled proteins. The new experiment is based on the 3D HNHA pulse scheme, and belongs to the 'quantitative J-correlation' type. It has been applied to a decapeptide inhibitor bound to the proteinase domain of the NS3 protein of human hepatitis C virus (HCV)

  1. Structural characterization of the glycoprotein GP2 core domain from the CAS virus, a novel arenavirus-like species.

    Science.gov (United States)

    Koellhoffer, Jayne F; Dai, Zhou; Malashkevich, Vladimir N; Stenglein, Mark D; Liu, Yanyun; Toro, Rafael; S Harrison, Joseph; Chandran, Kartik; DeRisi, Joseph L; Almo, Steven C; Lai, Jonathan R

    2014-04-03

    Fusion of the viral and host cell membranes is a necessary first step for infection by enveloped viruses and is mediated by the envelope glycoprotein. The transmembrane subunits from the structurally defined "class I" glycoproteins adopt an α-helical "trimer-of-hairpins" conformation during the fusion pathway. Here, we present our studies on the envelope glycoprotein transmembrane subunit, GP2, of the CAS virus (CASV). CASV was recently identified from annulated tree boas (Corallus annulatus) with inclusion body disease and is implicated in the disease etiology. We have generated and characterized two protein constructs consisting of the predicted CASV GP2 core domain. The crystal structure of the CASV GP2 post-fusion conformation indicates a trimeric α-helical bundle that is highly similar to those of Ebola virus and Marburg virus GP2 despite CASV genome homology to arenaviruses. Denaturation studies demonstrate that the stability of CASV GP2 is pH dependent with higher stability at lower pH; we propose that this behavior is due to a network of interactions among acidic residues that would destabilize the α-helical bundle under conditions where the side chains are deprotonated. The pH-dependent stability of the post-fusion structure has been observed in Ebola virus and Marburg virus GP2, as well as other viruses that enter via the endosome. Infection experiments with CASV and the related Golden Gate virus support a mechanism of entry that requires endosomal acidification. Our results suggest that, despite being primarily arenavirus like, the transmembrane subunit of CASV is extremely similar to the filoviruses.

  2. P- T- t constraints on the development of the Doi Inthanon metamorphic core complex domain and implications for the evolution of the western gneiss belt, northern Thailand

    Science.gov (United States)

    Macdonald, A. S.; Barr, S. M.; Miller, B. V.; Reynolds, P. H.; Rhodes, B. P.; Yokart, B.

    2010-01-01

    The western gneiss belt in northern Thailand is exposed within two overlapping Cenozoic structural domains: the extensional Doi Inthanon metamorphic core complex domain located west of the Chiang Mai basin, and the Mae Ping strike-slip fault domain located west of the Tak batholith. New P- T estimates and U-Pb and 40Ar/ 39Ar age determinations from the Doi Inthanon domain show that the gneiss there records a complex multi-stage history that can be represented by a clockwise P- T- t path. U-Pb zircon and titanite dating of mylonitic calc-silicate gneiss from the Mae Wang area of the complex indicates that the paragneissic sequence experienced high-grade, medium-pressure metamorphism (M1) in the Late Triassic - Early Jurassic (ca. 210 Ma), in good agreement with previously determined zircon ages from the underlying core orthogneiss exposed on Doi Inthanon. Late Cretaceous monazite ages of 84 and 72 Ma reported previously from the core orthogneiss are attributed to a thermal overprint (M2) to upper-amphibolite facies in the sillimanite field. U-Pb zircon and monazite dating of granitic mylonite from the Doi Suthep area of the complex provides an upper age limit of 40 Ma (Late Eocene) for the early stage(s) of development of the actual core complex, by initially ductile, low-angle extensional shearing under lower amphibolite-facies conditions (M3), accompanied by near-isothermal diapiric rise and decompression melting. 40Ar/ 39Ar laserprobe dating of muscovite from both Doi Suthep and Doi Inthanon provided Miocene ages of ca. 26-15 Ma, representing cooling through the ca. 350 °C isotherm and marking late-stage development of the core complex by detachment faulting of the cover rocks and isostatic uplift of the sheared core zone and mantling gneisses in the footwall. Similarities in the thermochronology of high-grade gneisses exposed in the core complex and shear zone domains in the western gneiss belt of northern Thailand (and also in northern Vietnam, Laos, Yunnan

  3. Bound entanglement and entanglement bounds

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, Simeon [Physikalisch-Astronomische Fakultaet, Friedrich-Schiller-Univesitaet Jena (Germany)]|[Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany); Melo, Fernando de; Mintert, Florian; Buchleitner, Andreas [Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany)]|[Max-Planck-Institut fuer Physik komplexer Systeme, Noethnitzer Str.38, D-01187 Dresden (Germany); Bae, Joonwoo [School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-012 (Korea); Hiesmayr, Beatrix [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria)

    2008-07-01

    We investigate the separability of Bell-diagonal states of two qutrits. By using lower bounds to algebraically estimate concurrence, we find convex regions of bound entangled states. Some of these regions exactly coincide with the obtained results when employing optimal entanglement witnesses, what shows that the lower bound can serve as a precise detector of entanglement. Some hitherto unknown regions of bound entangled states were discovered with this approach, and delimited efficiently.

  4. A mixed time-frequency domain method to describe the dynamic behaviour of a discrete medium bounded by a linear continuum

    NARCIS (Netherlands)

    Hoving, J.S.; Metrikine, A.

    2015-01-01

    To minimize the calculation time required by numerical models that de- scribe dynamic interactions involving nonlinear behaviour, it is useful to divide the model into two separate domains. One domain close to the interaction point, which consists of a sophisticated model capable of describing

  5. Quantitative determination of vortex core dimensions in head‑to‑head domain walls using off‑axis electron holography

    DEFF Research Database (Denmark)

    Junginger, F; Klaui, M; Backes, D

    2008-01-01

    In this paper, we present a complete three-dimensional characterization of vortex core spin structures, which is important for future magnetic data storage based on vortex cores in disks and in wires. Using electron holography to examine vortices in patterned Permalloy devices we have quantitativ......In this paper, we present a complete three-dimensional characterization of vortex core spin structures, which is important for future magnetic data storage based on vortex cores in disks and in wires. Using electron holography to examine vortices in patterned Permalloy devices we have...

  6. Identification of a novel antimicrobial peptide from human hepatitis B virus core protein arginine-rich domain (ARD.

    Directory of Open Access Journals (Sweden)

    Heng-Li Chen

    Full Text Available The rise of multidrug-resistant (MDR pathogens causes an increasing challenge to public health. Antimicrobial peptides are considered a possible solution to this problem. HBV core protein (HBc contains an arginine-rich domain (ARD at its C-terminus, which consists of 16 arginine residues separated into four clusters (ARD I to IV. In this study, we demonstrated that the peptide containing the full-length ARD I-IV (HBc147-183 has a broad-spectrum antimicrobial activity at micro-molar concentrations, including some MDR and colistin (polymyxin E-resistant Acinetobacter baumannii. Furthermore, confocal fluorescence microscopy and SYTOX Green uptake assay indicated that this peptide killed Gram-negative and Gram-positive bacteria by membrane permeabilization or DNA binding. In addition, peptide ARD II-IV (HBc153-176 and ARD I-III (HBc147-167 were found to be necessary and sufficient for the activity against P. aeruginosa and K. peumoniae. The antimicrobial activity of HBc ARD peptides can be attenuated by the addition of LPS. HBc ARD peptide was shown to be capable of direct binding to the Lipid A of lipopolysaccharide (LPS in several in vitro binding assays. Peptide ARD I-IV (HBc147-183 had no detectable cytotoxicity in various tissue culture systems and a mouse animal model. In the mouse model by intraperitoneal (i.p. inoculation with Staphylococcus aureus, timely treatment by i.p. injection with ARD peptide resulted in 100-fold reduction of bacteria load in blood, liver and spleen, as well as 100% protection of inoculated animals from death. If peptide was injected when bacterial load in the blood reached its peak, the protection rate dropped to 40%. Similar results were observed in K. peumoniae using an IVIS imaging system. The finding of anti-microbial HBc ARD is discussed in the context of commensal gut microbiota, development of intrahepatic anti-viral immunity and establishment of chronic infection with HBV. Our current results suggested that

  7. Identification of a novel antimicrobial peptide from human hepatitis B virus core protein arginine-rich domain (ARD).

    Science.gov (United States)

    Chen, Heng-Li; Su, Pei-Yi; Chang, Ya-Shu; Wu, Szu-Yao; Liao, You-Di; Yu, Hui-Ming; Lauderdale, Tsai-Ling; Chang, Kaichih; Shih, Chiaho

    2013-01-01

    The rise of multidrug-resistant (MDR) pathogens causes an increasing challenge to public health. Antimicrobial peptides are considered a possible solution to this problem. HBV core protein (HBc) contains an arginine-rich domain (ARD) at its C-terminus, which consists of 16 arginine residues separated into four clusters (ARD I to IV). In this study, we demonstrated that the peptide containing the full-length ARD I-IV (HBc147-183) has a broad-spectrum antimicrobial activity at micro-molar concentrations, including some MDR and colistin (polymyxin E)-resistant Acinetobacter baumannii. Furthermore, confocal fluorescence microscopy and SYTOX Green uptake assay indicated that this peptide killed Gram-negative and Gram-positive bacteria by membrane permeabilization or DNA binding. In addition, peptide ARD II-IV (HBc153-176) and ARD I-III (HBc147-167) were found to be necessary and sufficient for the activity against P. aeruginosa and K. peumoniae. The antimicrobial activity of HBc ARD peptides can be attenuated by the addition of LPS. HBc ARD peptide was shown to be capable of direct binding to the Lipid A of lipopolysaccharide (LPS) in several in vitro binding assays. Peptide ARD I-IV (HBc147-183) had no detectable cytotoxicity in various tissue culture systems and a mouse animal model. In the mouse model by intraperitoneal (i.p.) inoculation with Staphylococcus aureus, timely treatment by i.p. injection with ARD peptide resulted in 100-fold reduction of bacteria load in blood, liver and spleen, as well as 100% protection of inoculated animals from death. If peptide was injected when bacterial load in the blood reached its peak, the protection rate dropped to 40%. Similar results were observed in K. peumoniae using an IVIS imaging system. The finding of anti-microbial HBc ARD is discussed in the context of commensal gut microbiota, development of intrahepatic anti-viral immunity and establishment of chronic infection with HBV. Our current results suggested that HBc ARD

  8. Hepatitis B virus DNA-negative dane particles lack core protein but contain a 22-kDa precore protein without C-terminal arginine-rich domain.

    Science.gov (United States)

    Kimura, Tatsuji; Ohno, Nobuhiko; Terada, Nobuo; Rokuhara, Akinori; Matsumoto, Akihiro; Yagi, Shintaro; Tanaka, Eiji; Kiyosawa, Kendo; Ohno, Shinichi; Maki, Noboru

    2005-06-10

    DNA-negative Dane particles have been observed in hepatitis B virus (HBV)-infected sera. The capsids of the empty particles are thought to be composed of core protein but have not been studied in detail. In the present study, the protein composition of the particles was examined using new enzyme immunoassays for the HBV core antigen (HBcAg) and for the HBV precore/core proteins (core-related antigens, HBcrAg). HBcrAg were abundant in fractions slightly less dense than HBcAg and HBV DNA. Three times more Dane-like particles were observed in the HBcrAg-rich fraction than in the HBV DNA-rich fraction by electron microscopy. Western blots and mass spectrometry identified the HBcrAg as a 22-kDa precore protein (p22cr) containing the uncleaved signal peptide and lacking the arginine-rich domain that is involved in binding the RNA pregenome or the DNA genome. In sera from 30 HBV-infected patients, HBcAg represented only a median 10.5% of the precore/core proteins in enveloped particles. These data suggest that most of the Dane particles lack viral DNA and core capsid but contain p22cr. This study provides a model for the formation of the DNA-negative Dane particles. The precore proteins, which lack the arginine-rich nucleotide-binding domain, form viral RNA/DNA-negative capsid-like particles and are enveloped and released as empty particles.

  9. Identification, modeling, and characterization studies of Tetrahymena thermophila myosin FERM domains suggests a conserved core fold but functional differences.

    Science.gov (United States)

    Martin, Che L; Singh, Shaneen M

    2015-11-01

    Myosins (MYO) define a superfamily of motor proteins which facilitate movement along cytoskeletal actin filaments in an ATP-dependent manner. To date, over 30 classes of myosin have been defined that vary in their roles and distribution across different taxa. The multidomain tail of myosin is responsible for the observed functional differences in different myosin classes facilitating differential binding to different cargos. One domain found in this region, the FERM domain, is found in several diverse proteins and is involved in many biological functions ranging from cell adhesion and actin-driven cytoskeleton assembly to cell signaling. Recently, new classes of unconventional myosin have been identified in Tetrahymena thermophila. In this study, we have identified, modeled, and characterized eight FERM domains from the unconventional T. thermophila myosins as their complete functional MyTH4-FERM cassettes. Our results reveal notable sequence, structural, and electrostatic differences between T. thermophila and other characterized FERM domains. Specifically, T. thermophila FERM domains contain helical inserts or extensions, which contribute to significant differences in surface electrostatic profiles of T. thermophila myosin FERMs when compared to the conventional FERM domains. Analyses of the modeled domains reveal differences in key functional residues as well as phosphoinositide-binding signatures and affinities. The work presented here broadens the scope of our understanding of myosin classes and their inherent functions, and provides a platform for experimentalists to design rational experimental studies to test the functional roles for T. thermophila myosins.

  10. SAS solution structures of the apo and Mg2+/BeF3(-)-bound receiver domain of DctD from Sinorhizobium meliloti.

    Science.gov (United States)

    Nixon, B Tracy; Yennawar, Hemant P; Doucleff, Michaeleen; Pelton, Jeffrey G; Wemmer, David E; Krueger, Susan; Kondrashkina, Elena

    2005-10-25

    Two-component signal transduction is the predominant information processing mechanism in prokaryotes and is also present in single-cell eukaryotes and higher plants. A phosphorylation-based switch is commonly used to activate as many as 40 different types of output domains in more than 6000 two-component response regulators that can be identified in the sequence databases. Previous biochemical and crystallographic studies showed that phosphorylation of the two-component receiver domain of DctD causes a switch between alternative dimeric forms, but it was unclear from the crystal lattice of the activated protein precisely which of four possible dimeric configurations is the biologically relevant one [Park, S., et al. (2002) FASEB J. 16, 1964-1966]. Here we report solution structures of the apo and activated DctD receiver domain derived from small angle scattering data. The apo dimer closely resembles that seen in the crystal structure, and the solution data for the activated protein eliminate two of the possible four dimeric conformations seen in the crystal lattice and strongly implicate one as the biologically relevant structure. These results corroborate the previously proposed model for how receiver domains regulate their downstream AAA+ ATPase domains.

  11. Core domain and outcome measurement sets for shoulder pain trials are needed: Systematic review of physical therapy trials

    NARCIS (Netherlands)

    M.J. Page (Matthew J.); J.E. McKenzie (Joanne E.); S.E. Green (Sally E.); D.E. Beaton (Dorcas E.); N.B. Jain (Nitin B.); M. Lenza (Mario); A.P. Verhagen (Arianne P.); S. Surace (Stephen); J. Deitch (Jessica); R. Buchbinder (Rachelle)

    2015-01-01

    textabstractObjectives To explore the outcome domains and measurement instruments reported in published randomized controlled trials of physical therapy interventions for shoulder pain (rotator cuff disease, adhesive capsulitis, or nonspecific shoulder pain). Study Design and Setting We included tri

  12. Polyglutamine Amyloid Core Boundaries and Flanking Domain Dynamics in Huntingtin Fragment Fibrils Determined by Solid-State Nuclear Magnetic Resonance

    OpenAIRE

    Hoop, Cody L.; Lin, Hsiang-Kai; Kar, Karunakar; Hou, Zhipeng; Poirier, Michelle A.; Wetzel, Ronald; van der Wel, Patrick C.A.

    2014-01-01

    In Huntington’s disease, expansion of a polyglutamine (polyQ) domain in the huntingtin (htt) protein leads to misfolding and aggregation. There is much interest in the molecular features that distinguish monomeric, oligomeric, and fibrillar species that populate the aggregation pathway and likely differ in cytotoxicity. The mechanism and rate of aggregation are greatly affected by the domains flanking the polyQ segment within exon 1 of htt. A “protective” C-terminal proline-rich flanking doma...

  13. Establishing Core Outcome Domains in Hemodialysis: Report of the Standardized Outcomes in Nephrology-Hemodialysis (SONG-HD) Consensus Workshop.

    Science.gov (United States)

    Tong, Allison; Manns, Braden; Hemmelgarn, Brenda; Wheeler, David C; Evangelidis, Nicole; Tugwell, Peter; Crowe, Sally; Van Biesen, Wim; Winkelmayer, Wolfgang C; O'Donoghue, Donal; Tam-Tham, Helen; Shen, Jenny I; Pinter, Jule; Larkins, Nicholas; Youssouf, Sajeda; Mandayam, Sreedhar; Ju, Angela; Craig, Jonathan C

    2017-01-01

    Evidence-informed decision making in clinical care and policy in nephrology is undermined by trials that selectively report a large number of heterogeneous outcomes, many of which are not patient centered. The Standardized Outcomes in Nephrology-Hemodialysis (SONG-HD) Initiative convened an international consensus workshop on November 7, 2015, to discuss the identification and implementation of a potential core outcome set for all trials in hemodialysis. The purpose of this article is to report qualitative analyses of the workshop discussions, describing the key aspects to consider when establishing core outcomes in trials involving patients on hemodialysis therapy. Key stakeholders including 8 patients/caregivers and 47 health professionals (nephrologists, policymakers, industry, and researchers) attended the workshop. Attendees suggested that identifying core outcomes required equitable stakeholder engagement to ensure relevance across patient populations, flexibility to consider evolving priorities over time, deconstruction of language and meaning for conceptual consistency and clarity, understanding of potential overlap and associations between outcomes, and an assessment of applicability to the range of interventions in hemodialysis. For implementation, they proposed that core outcomes must have simple, inexpensive, and validated outcome measures that could be used in clinical care (quality indicators) and trials (including pragmatic trials) and endorsement by regulatory agencies. Integrating these recommendations may foster acceptance and optimize the uptake and translation of core outcomes in hemodialysis, leading to more informative research, for better treatment and improved patient outcomes.

  14. Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding

    Energy Technology Data Exchange (ETDEWEB)

    Sidote,D.; Barbieri, C.; Wu, T.; Stock, A.

    2008-01-01

    The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Angstroms resolution. The structure establishes a 10-stranded {beta} fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

  15. Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding

    Science.gov (United States)

    Sidote, David J.; Barbieri, Christopher M.; Wu, Ti; Stock, Ann M.

    2008-01-01

    SUMMARY The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Å resolution. The structure establishes a 10-stranded β fold for the LytTR domain and reveals a novel mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA-binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This novel mode of protein-DNA interacton provides a potential target for future antimicrobial drug design. PMID:18462677

  16. Structure of the Staphylococcus aureus AgrA LytTR domain bound to DNA reveals a beta fold with an unusual mode of binding.

    Science.gov (United States)

    Sidote, David J; Barbieri, Christopher M; Wu, Ti; Stock, Ann M

    2008-05-01

    The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 A resolution. The structure establishes a 10-stranded beta fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

  17. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

    DEFF Research Database (Denmark)

    Wu, R R; Couchman, J R

    1997-01-01

    Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now...... obtained cDNA clones encoding the entire bamacan core protein of Mr = 138 kD, which reveal a five domain, head-rod-tail configuration. The head and tail are potentially globular, while the central large rod probably forms coiled-coil structures, with one large central and several very short interruptions....... This molecular architecture is novel for an extracellular matrix molecule, but it resembles that of a group of intracellular proteins, including some proposed to stabilize the mitotic chromosome scaffold. We have previously proposed a similar stabilizing role for bamacan in the basement membrane matrix...

  18. Cyclin-dependent kinase 2 phosphorylates s/t-p sites in the hepadnavirus core protein C-terminal domain and is incorporated into viral capsids.

    Science.gov (United States)

    Ludgate, Laurie; Ning, Xiaojun; Nguyen, David H; Adams, Christina; Mentzer, Laura; Hu, Jianming

    2012-11-01

    Phosphorylation of the hepadnavirus core protein C-terminal domain (CTD) is important for viral RNA packaging, reverse transcription, and subcellular localization. Hepadnavirus capsids also package a cellular kinase. The identity of the host kinase that phosphorylates the core CTD or gets packaged remains to be resolved. In particular, both the human hepatitis B virus (HBV) and duck hepatitis B virus (DHBV) core CTDs harbor several conserved serine/threonine-proline (S/T-P) sites whose phosphorylation state is known to regulate CTD functions. We report here that the endogenous kinase in the HBV capsids was blocked by chemical inhibitors of the cyclin-dependent kinases (CDKs), in particular, CDK2 inhibitors. The kinase phosphorylated the HBV CTD at the serine-proline (S-P) sites. Furthermore, we were able to detect CDK2 in purified HBV capsids by immunoblotting. Purified CDK2 phosphorylated the S/T-P sites of the HBV and DHBV CTD in vitro. Inhibitors of CDKs, of CDK2 in particular, decreased both HBV and DHBV CTD phosphorylation in vivo. Moreover, CDK2 inhibitors blocked DHBV CTD phosphorylation, specifically at the S/T-P sites, in a mammalian cell lysate. These results indicate that cellular CDK2 phosphorylates the functionally critical S/T-P sites of the hepadnavirus core CTD and is incorporated into viral capsids.

  19. SWIFT: Using task-based parallelism, fully asynchronous communication, and graph partition-based domain decomposition for strong scaling on more than 100,000 cores

    CERN Document Server

    Schaller, Matthieu; Chalk, Aidan B G; Draper, Peter W

    2016-01-01

    We present a new open-source cosmological code, called SWIFT, designed to solve the equations of hydrodynamics using a particle-based approach (Smooth Particle Hydrodynamics) on hybrid shared/distributed-memory architectures. SWIFT was designed from the bottom up to provide excellent strong scaling on both commodity clusters (Tier-2 systems) and Top100-supercomputers (Tier-0 systems), without relying on architecture-specific features or specialized accelerator hardware. This performance is due to three main computational approaches: (1) Task-based parallelism for shared-memory parallelism, which provides fine-grained load balancing and thus strong scaling on large numbers of cores. (2) Graph-based domain decomposition, which uses the task graph to decompose the simulation domain such that the work, as opposed to just the data, as is the case with most partitioning schemes, is equally distributed across all nodes. (3) Fully dynamic and asynchronous communication, in which communication is modelled as just anot...

  20. Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication

    Directory of Open Access Journals (Sweden)

    Belhumeur Pierre

    2008-11-01

    Full Text Available Abstract Background HIV-1 integrase (IN is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s and/or motif(s required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of

  1. Development of a Provisional Core Domain Set for Polymyalgia Rheumatica : Report from the OMERACT 12 Polymyalgia Rheumatica Working Group

    NARCIS (Netherlands)

    Helliwell, Toby; Brouwer, Elisabeth; Pease, Colin T.; Hughes, Rodney; Hill, Catherine L.; Neill, Lorna M.; Halls, Serena; Simon, Lee S.; Mallen, Christian D.; Boers, Maarten; Kirwan, John R.; Mackie, Sarah L.

    2016-01-01

    Objective. The Outcome Measures in Rheumatology (OMERACT) polymyalgia rheumatica (PMR) working group aims to develop a core set of outcome measures to be used in clinical trials for PMR. Previous reports from OMERACT 11 included a qualitative study of the patient experience and a preliminary literat

  2. 球面区域上buckling特征值的万有估计%UNIVERSAL BOUNDS ON EIGENVALUES OF THE BUCKLING PROBLEM ON SPHERICAL DOMAINS

    Institute of Scientific and Technical Information of China (English)

    黄广月; 李兴校; 曹林芬

    2011-01-01

    We study the eigenvalues of buckling problem on domains in the unit sphere.By introducing a new parameter and using Cauchy inequality,we optimize the inequality obtained by Wang and Xia in[12].%本文研究了球面域上的buckling特征值问题.通过引入新的参数和使用Cauchy不等式,优化了Wang-Xia在文献[1 2]中的不等式.

  3. Dense SDM (12-core × 3-mode) transmission over 527 km with 33.2-ns mode-dispersion employing low-complexity parallel MIMO frequency-domain equalization

    DEFF Research Database (Denmark)

    Shibahara, K.; Mizuno, T.; Takara, H.;

    We demonstrate 12-core × 3-mode dense SDM transmission over 527 km graded-index multi-core few-mode fiber without mode-dispersion management. Employing low baud rate multi-carrier signal and frequency-domain equalization enables 33.2-ns DMD compensation with low computational complexity. © 2015 OSA...

  4. Bound simian virus 40 translocates to caveolin-enriched membrane domains, and its entry is inhibited by drugs that selectively disrupt caveolae.

    Science.gov (United States)

    Anderson, H A; Chen, Y; Norkin, L C

    1996-11-01

    Simian virus 40 (SV40) entry leading to infection occurred only after the virus was at the cell surface for 1.5 to 2 h. SV40 infectious entry was not sensitive to cytosol acidification, a treatment that blocks endocytosis via clathrin-coated vesicles. Instead, SV40 infectious entry was blocked by treating cells with the phorbol ester PMA or nystatin, which selectively disrupts caveolae. In control experiments, transferrin internalization was sensitive to cytosol acidification but was not sensitive to PMA or nystatin. Also, absorbed transferrin entered cells within minutes. Finally, bound SV40 translocated to caveolin-enriched membrane complexes isolated by a Triton X-100 insolubility protocol. Treatment with nystatin did not impair SV40 binding but did block the partitioning of virus into the caveolin-enriched complexes.

  5. Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine

    DEFF Research Database (Denmark)

    Frydenvang, Karla Andrea; Lash, L Leanne; Naur, Peter

    2009-01-01

    The prevailing structural model for ligand activation of ionotropic glutamate receptors posits that agonist efficacy arises from the stability and magnitude of induced domain closure in the ligand-binding core structure. Here we describe an exception to the correlation between ligand efficacy...... and domain closure. A weakly efficacious partial agonist of very low potency for homomeric iGluR5 kainate receptors, 8,9-dideoxy-neodysiherbaine (MSVIII-19), induced a fully closed iGluR5 ligand-binding core. The degree of relative domain closure, ~30 degrees , was similar to that we resolved...... to inter-domain hydrogen bonds residues Glu441 and Ser721 in the iGluR5-S1S2 structure. The weaker interactions of MSVIII-19 with iGluR5 compared to DH, together with altered stability of the inter-domain interaction, may be responsible for the apparent uncoupling of domain closure and channel opening...

  6. Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common beta-chain bound to an antagonist.

    Science.gov (United States)

    Rossjohn, J; McKinstry, W J; Woodcock, J M; McClure, B J; Hercus, T R; Parker, M W; Lopez, A F; Bagley, C J

    2000-04-15

    Heterodimeric cytokine receptors generally consist of a major cytokine-binding subunit and a signaling subunit. The latter can transduce signals by more than 1 cytokine, as exemplified by the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-2 (IL-2), and IL-6 receptor systems. However, often the signaling subunits in isolation are unable to bind cytokines, a fact that has made it more difficult to obtain structural definition of their ligand-binding sites. This report details the crystal structure of the ligand-binding domain of the GM-CSF/IL-3/IL-5 receptor beta-chain (beta(c)) signaling subunit in complex with the Fab fragment of the antagonistic monoclonal antibody, BION-1. This is the first single antagonist of all 3 known eosinophil-producing cytokines, and it is therefore capable of regulating eosinophil-related diseases such as asthma. The structure reveals a fibronectin type III domain, and the antagonist-binding site involves major contributions from the loop between the B and C strands and overlaps the cytokine-binding site. Furthermore, tyrosine(421) (Tyr(421)), a key residue involved in receptor activation, lies in the neighboring loop between the F and G strands, although it is not immediately adjacent to the cytokine-binding residues in the B-C loop. Interestingly, functional experiments using receptors mutated across these loops demonstrate that they are cooperatively involved in full receptor activation. The experiments, however, reveal subtle differences between the B-C loop and Tyr(421), which is suggestive of distinct functional roles. The elucidation of the structure of the ligand-binding domain of beta(c) also suggests how different cytokines recognize a single receptor subunit, which may have implications for homologous receptor systems. (Blood. 2000;95:2491-2498)

  7. Structure of the cytoplasmic domain of TcpE, the inner membrane core protein required for assembly of the Vibrio cholerae toxin-coregulated pilus.

    Science.gov (United States)

    Kolappan, Subramaniapillai; Craig, Lisa

    2013-04-01

    Type IV pili are long thin surface-displayed polymers of the pilin subunit that are present in a diverse group of bacteria. These multifunctional filaments are critical to virulence for pathogens such as Vibrio cholerae, which use them to form microcolonies and to secrete the colonization factor TcpF. The type IV pili are assembled from pilin subunits by a complex inner membrane machinery. The core component of the type IV pilus-assembly platform is an integral inner membrane protein belonging to the GspF superfamily of secretion proteins. These proteins somehow convert chemical energy from ATP hydrolysis by an assembly ATPase on the cytoplasmic side of the inner membrane to mechanical energy for extrusion of the growing pilus filament out of the inner membrane. Most GspF-family inner membrane core proteins are predicted to have N-terminal and central cytoplasmic domains, cyto1 and cyto2, and three transmembrane segments, TM1, TM2 and TM3. Cyto2 and TM3 represent an internal repeat of cyto1 and TM1. Here, the 1.88 Å resolution crystal structure of the cyto1 domain of V. cholerae TcpE, which is required for assembly of the toxin-coregulated pilus, is reported. This domain folds as a monomeric six-helix bundle with a positively charged membrane-interaction face at one end and a hydrophobic groove at the other end that may serve as a binding site for partner proteins in the pilus-assembly complex.

  8. The Acquisition of Bound and Free Anaphora.

    Science.gov (United States)

    Koster, Jan; Koster, Charlotte

    Most linguists assume that bound anaphors such as "himself" are connected with their antecedents in a different way from free anaphors such as "him." Bound anaphora resolution is deterministic, based on Principle A of Chomsky's binding theory. Free anaphors, pronominals, cannot be bound in the domain of reflexives (principle…

  9. Microbial starch-binding domains are superior to granule-bound starch synthase I for anchoring luciferase to potato starch granules

    Institute of Scientific and Technical Information of China (English)

    JI Qin; Jean-Paul VINCKEN; Luc C.J.M. SUURS; Richard G.F. VISSER

    2006-01-01

    Microbial starch-binding domains (SBD) and granule-hound starch synthase I (GBSSI) are proteins which are accumulated in potato starch granules. The efficiency of SBD and GBSSI for targeting active luciferase reporter proteins to granules during starch biosynthesis was compared. GBSSI or SBD sequences were fused to the N- or C-terminus of the luciferase (LUC) gene, via an artificial Pro-Thr encoding linker sequence. The genes were introduced into an amylose-free (am f) potato mutant. It appeared that SBD was superior to GBSSI as a targeting sequence, mainly because the luciferase retained higher activity in the SBD-containing fusion proteins than in the GBSSI-containing ones.

  10. Phosphorylation regulates fibrillation of an aggregation core peptide in the second repeat of microtubule-binding domain of human tau.

    Science.gov (United States)

    Inoue, Masafumi; Kaida, Shinji; Nakano, Shun; Annoni, Chiara; Nakata, Eiji; Konno, Takashi; Morii, Takashi

    2014-11-15

    Hyperphosphorylation of the microtubule-associated protein tau is believed to play a crucial role in the neurofibrillary tangles formation in Alzheimer’s disease brain. In this study, fibril formation of peptides containing the critical sequences for tau aggregation VQIINK and a plausible serine phosphorylation site of tau at its C-terminal was investigated. All the peptides formed fibrils with the typical cross-b structural core. However, stability of the fibrils was highly sensitive to the pH conditions for the phosphorylated VQIINK peptide, suggesting a regulatory role of phosphorylation for the amyloid-formation of tau.

  11. The pro region required for folding of carboxypeptidase Y is a partially folded domain with little regular structural core

    DEFF Research Database (Denmark)

    Sørensen, P; Winther, Jakob R.; Kaarsholm, N C

    1993-01-01

    The pro region of carboxypeptidase Y (CPY) from yeast is necessary for the correct folding of the enzyme [Winther, J. R., & Sørensen P. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 9330-9334]. Using fluorescence, circular dichroism, and heteronuclear NMR analyses, it is demonstrated that the isolated...... pro region is a partially folded protein domain under the conditions where it is functional. It is characterized by a relatively high content of secondary structural elements but a very low content of defined tertiary structure. Although these characteristics are reminiscent of the compact denatured...

  12. Cytotoxicity and DNA cleavage with core-shell nanocomposites functionalized by a KH domain DNA binding peptide

    Science.gov (United States)

    Bazak, Remon; Ressl, Jan; Raha, Sumita; Doty, Caroline; Liu, William; Wanzer, Beau; Salam, Seddik Abdel; Elwany, Samy; Paunesku, Tatjana; Woloschak, Gayle E.

    2013-11-01

    A nanoconjugate was composed of metal oxide nanoparticles decorated with peptides and fluorescent dye and tested for DNA cleavage following UV light activation. The peptide design was based on a DNA binding domain, the so called KH domain of the hnRNPK protein. This ``KH peptide'' enabled cellular uptake of nanoconjugates and their entry into cell nuclei. The control nanoconjugate carried no peptide; it consisted only of the metal oxide nanoparticle prepared as Fe3O4@TiO2 nanocomposite and the fluorescent dye alizarin red S. These components of either construct are responsible for nanoconjugate activation by UV light and the resultant production of reactive oxygen species (ROS). Production of ROS at different subcellular locations causes damage to different components of cells: only nanoconjugates inside cell nuclei can be expected to cause DNA cleavage. Degradation of cellular DNA with KH peptide decorated nanoconjugates exceeded the DNA damage obtained from control, no-peptide nanoconjugate counterparts. Moreover, caspase activation and cell death were more extensive in the same cells.A nanoconjugate was composed of metal oxide nanoparticles decorated with peptides and fluorescent dye and tested for DNA cleavage following UV light activation. The peptide design was based on a DNA binding domain, the so called KH domain of the hnRNPK protein. This ``KH peptide'' enabled cellular uptake of nanoconjugates and their entry into cell nuclei. The control nanoconjugate carried no peptide; it consisted only of the metal oxide nanoparticle prepared as Fe3O4@TiO2 nanocomposite and the fluorescent dye alizarin red S. These components of either construct are responsible for nanoconjugate activation by UV light and the resultant production of reactive oxygen species (ROS). Production of ROS at different subcellular locations causes damage to different components of cells: only nanoconjugates inside cell nuclei can be expected to cause DNA cleavage. Degradation of cellular DNA

  13. Hartree–Fock variational bounds for ground state energy of chargeless fermions with finite magnetic moment in the presence of a hard core potential: A stable ferromagnetic state

    Indian Academy of Sciences (India)

    Sudhanshu S Jha; S D Mahanti

    2007-05-01

    We use different determinantal Hartree–Fock (HF) wave functions to calculate true variational upper bounds for the ground state energy of spin-half fermions in volume 0, with mass , electric charge zero, and magnetic moment , interacting through magnetic dipole–dipole interaction. We find that at high densities when the average interparticle distance 0 becomes small compared to the magnetic length m ≡ 22/ħ2, a ferromagnetic state with spheroidal occupation function ↑ $(\\vec{k})$, involving quadrupolar deformation, gives a lower upper bound compared to the variational energy for the uniform paramagnetic state or for the state with dipolar deformation. This system is unstable towards infinite density collapse, but we show explicitly that a suitable short-range repulsive (hard core) interaction of strength 0 and range a can stop this collapse. The existence of a stable equilibrium high density ferromagnetic state with spheroidal occupation function is possible as long as the ratio of coupling constants cm ≡ (03/2) is not very smallcompared to 1.

  14. The Rho Termination Factor of Clostridium botulinum contains a Prion-Like Domain with a highly Amyloidogenic Core

    Directory of Open Access Journals (Sweden)

    Irantzu ePallares

    2016-01-01

    Full Text Available Prion-like proteins can switch between a soluble intrinsically disordered conformation and a highly ordered amyloid assembly. This conformational promiscuity is encoded in specific sequence regions, known as prion domains (PrDs. Prions are best known as the causative factors of neurological diseases in mammals. However, bioinformatics analyses reveal that proteins bearing PrDs are present in all kingdoms of life, including bacteria, thus supporting the idea that they serve conserved beneficial cellular functions. Despite the proportion of predicted prion-like proteins in bacterial proteomes is generally low, pathogenic species seem to have a higher prionic load, suggesting that these malleable proteins may favor pathogenic traits. In the present work, we performed a stringent computational analysis of the Clostridium botulinum pathogen proteome in the search for prion-like proteins. A total of 54 candidates were predicted for this anaerobic bacterium, including the transcription termination Rho factor. This RNA-binding protein has been shown to play a crucial role in bacterial adaptation to changing environments. We show here that the predicted disordered PrD domain of this RNA-binding protein contains an inner, highly polar, asparagine-rich short sequence able to spontaneously self-assemble into amyloid-like structures, bearing thus the potential to induce a Rho factor conformational switch that might rewire gene expression in response to environmental conditions.

  15. (1)H, (15)N and (13)C resonance assignments for free and IEEVD peptide-bound forms of the tetratricopeptide repeat domain from the human E3 ubiquitin ligase CHIP.

    Science.gov (United States)

    Zhang, Huaqun; McGlone, Cameron; Mannion, Matthew M; Page, Richard C

    2017-04-01

    The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the (1)H, (13)C, and (15)N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.

  16. Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

    Energy Technology Data Exchange (ETDEWEB)

    B Brown; T Wood; W Peti; R Page

    2011-12-31

    Bacterial cultures, especially biofilms, produce a small number of persister cells, a genetically identical subpopulation of wild type cells that are metabolically dormant, exhibit multidrug tolerance, and are highly enriched in bacterial toxins. The gene most highly up-regulated in Escherichia coli persisters is mqsR, a ribonuclease toxin that, along with mqsA, forms a novel toxin-antitoxin (TA) system. Like all known TA systems, both the MqsR-MqsA complex and MqsA alone regulate their own transcription. Despite the importance of TA systems in persistence and biofilms, very little is known about how TA modules, and antitoxins in particular, bind and recognize DNA at a molecular level. Here, we report the crystal structure of MqsA bound to a 26-bp fragment from the mqsRA promoter. We show that MqsA binds DNA predominantly via its C-terminal helix-turn-helix domain, with direct binding of recognition helix residues Asn{sup 97} and Arg{sup 010} to the DNA major groove. Unexpectedly, the structure also revealed that the MqsA N-terminal domain interacts with the DNA phosphate backbone. This results in a more than 105{sup o} rotation of the N-terminal domains between the free and complexed states, an unprecedented rearrangement for an antitoxin. The structure also shows that MqsA bends the DNA by more than 55{sup o} in order to achieve symmetrical binding. Finally, using a combination of biochemical and NMR studies, we show that the DNA sequence specificity of MqsA is mediated by direct readout.

  17. Solution structure of histone chaperone ANP32B: interaction with core histones H3-H4 through its acidic concave domain.

    Science.gov (United States)

    Tochio, Naoya; Umehara, Takashi; Munemasa, Yoshiko; Suzuki, Toru; Sato, Shin; Tsuda, Kengo; Koshiba, Seizo; Kigawa, Takanori; Nagai, Ryozo; Yokoyama, Shigeyuki

    2010-08-01

    Eukaryotic gene expression is regulated by histone deposition onto and eviction from nucleosomes, which are mediated by several chromatin-modulating factors. Among them, histone chaperones are key factors that facilitate nucleosome assembly. Acidic nuclear phosphoprotein 32B (ANP32B) belongs to the ANP32 family, which shares N-terminal leucine-rich repeats (LRRs) and a C-terminal variable anionic region. The C-terminal region functions as an inhibitor of histone acetylation, but the functional roles of the LRR domain in chromatin regulation have remained elusive. Here, we report that the LRR domain of ANP32B possesses histone chaperone activity and forms a curved structure with a parallel beta-sheet on the concave side and mostly helical elements on the convex side. Our analyses revealed that the interaction of ANP32B with the core histones H3-H4 occurs on its concave side, and both the acidic and hydrophobic residues that compose the concave surface are critical for histone binding. These results provide a structural framework for understanding the functional mechanisms of acidic histone chaperones.

  18. Connective tissue disease related interstitial lung diseases and idiopathic pulmonary fibrosis: provisional core sets of domains and instruments for use in clinical trials.

    Science.gov (United States)

    Saketkoo, Lesley Ann; Mittoo, Shikha; Huscher, Dörte; Khanna, Dinesh; Dellaripa, Paul F; Distler, Oliver; Flaherty, Kevin R; Frankel, Sid; Oddis, Chester V; Denton, Christopher P; Fischer, Aryeh; Kowal-Bielecka, Otylia M; LeSage, Daphne; Merkel, Peter A; Phillips, Kristine; Pittrow, David; Swigris, Jeffrey; Antoniou, Katerina; Baughman, Robert P; Castelino, Flavia V; Christmann, Romy B; Christopher-Stine, Lisa; Collard, Harold R; Cottin, Vincent; Danoff, Sonye; Highland, Kristin B; Hummers, Laura; Shah, Ami A; Kim, Dong Soon; Lynch, David A; Miller, Frederick W; Proudman, Susanna M; Richeldi, Luca; Ryu, Jay H; Sandorfi, Nora; Sarver, Catherine; Wells, Athol U; Strand, Vibeke; Matteson, Eric L; Brown, Kevin K; Seibold, James R

    2014-05-01

    Clinical trial design in interstitial lung diseases (ILDs) has been hampered by lack of consensus on appropriate outcome measures for reliably assessing treatment response. In the setting of connective tissue diseases (CTDs), some measures of ILD disease activity and severity may be confounded by non-pulmonary comorbidities. The Connective Tissue Disease associated Interstitial Lung Disease (CTD-ILD) working group of Outcome Measures in Rheumatology-a non-profit international organisation dedicated to consensus methodology in identification of outcome measures-conducted a series of investigations which included a Delphi process including >248 ILD medical experts as well as patient focus groups culminating in a nominal group panel of ILD experts and patients. The goal was to define and develop a consensus on the status of outcome measure candidates for use in randomised controlled trials in CTD-ILD and idiopathic pulmonary fibrosis (IPF). A core set comprising specific measures in the domains of lung physiology, lung imaging, survival, dyspnoea, cough and health-related quality of life is proposed as appropriate for consideration for use in a hypothetical 1-year multicentre clinical trial for either CTD-ILD or IPF. As many widely used instruments were found to lack full validation, an agenda for future research is proposed. Identification of consensus preliminary domains and instruments to measure them was attained and is a major advance anticipated to facilitate multicentre RCTs in the field.

  19. A truncated fragment of Ov-ASP-1 consisting of the core pathogenesis-related-1 (PR-1) domain maintains adjuvanticity as the full-length protein.

    Science.gov (United States)

    Guo, Jingjing; Yang, Yi; Xiao, Wenjun; Sun, Weilai; Yu, Hong; Du, Lanying; Lustigman, Sara; Jiang, Shibo; Kou, Zhihua; Zhou, Yusen

    2015-04-15

    The Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has good adjuvanticity for a variety of antigens and vaccines, probably due to its ability activate antigen-processing cells (APCs). However, the functional domain of Ov-ASP-1 as an adjuvant is not clearly defined. Based on the structural prediction of this protein family, we constructed a 16-kDa recombinant protein of Ov-ASP-1 that contains only the core pathogenesis-related-1 (PR-1) domain (residues 10-153), designated ASPPR. We found that ASPPR exhibits adjuvanticity similar to that of the full-length Ov-ASP-1 (residues 10-220) for various antigens, including ovalbumin (OVA), HBsAg protein antigen, and the HIV peptide 5 (Pep5) antigen, but it is more suitable for vaccine design in ASPPR-antigen fusion proteins, and more stable in PBS than Ov-ASP-1 stored at -70 °C. These results suggest that ASPPR might be the functional region of Ov-ASP-1 as an adjuvant, and therefore could be developed as an adjuvant for human use. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Cell-Free Hepatitis B Virus Capsid Assembly Dependent on the Core Protein C-Terminal Domain and Regulated by Phosphorylation

    Science.gov (United States)

    Ludgate, Laurie; Liu, Kuancheng; Luckenbaugh, Laurie; Streck, Nicholas; Eng, Stacey; Voitenleitner, Christian; Delaney, William E.

    2016-01-01

    ABSTRACT Multiple subunits of the hepatitis B virus (HBV) core protein (HBc) assemble into an icosahedral capsid that packages the viral pregenomic RNA (pgRNA). The N-terminal domain (NTD) of HBc is sufficient for capsid assembly, in the absence of pgRNA or any other viral or host factors, under conditions of high HBc and/or salt concentrations. The C-terminal domain (CTD) is deemed dispensable for capsid assembly although it is essential for pgRNA packaging. We report here that HBc expressed in a mammalian cell lysate, rabbit reticulocyte lysate (RRL), was able to assemble into capsids when (low-nanomolar) HBc concentrations mimicked those achieved under conditions of viral replication in vivo and were far below those used previously for capsid assembly in vitro. Furthermore, at physiologically low HBc concentrations in RRL, the NTD was insufficient for capsid assembly and the CTD was also required. The CTD likely facilitated assembly under these conditions via RNA binding and protein-protein interactions. Moreover, the CTD underwent phosphorylation and dephosphorylation events in RRL similar to those seen in vivo which regulated capsid assembly. Importantly, the NTD alone also failed to accumulate in mammalian cells, likely resulting from its failure to assemble efficiently. Coexpression of the full-length HBc rescued NTD assembly in RRL as well as NTD expression and assembly in mammalian cells, resulting in the formation of mosaic capsids containing both full-length HBc and the NTD. These results have important implications for HBV assembly during replication and provide a facile cell-free system to study capsid assembly under physiologically relevant conditions, including its modulation by host factors. IMPORTANCE Hepatitis B virus (HBV) is an important global human pathogen and the main cause of liver cancer worldwide. An essential component of HBV is the spherical capsid composed of multiple copies of a single protein, the core protein (HBc). We have

  1. Positive Root Bounds and Root Separation Bounds

    Science.gov (United States)

    Herman, Aaron Paul

    In this thesis, we study two classes of bounds on the roots of a polynomial (or polynomial system). A positive root bound of a polynomial is an upper bound on the largest positive root. A root separation bound of a polynomial is a lower bound on the distance between the roots. Both classes of bounds are fundamental tools in computer algebra and computational real algebraic geometry, with numerous applications. In the first part of the thesis, we study the quality of positive root bounds. Higher quality means that the relative over-estimation (the ratio of the bound and the largest positive root) is smaller. We find that all known positive root bounds can be arbitrarily bad. We then show that a particular positive root bound is tight for certain important classes of polynomials. In the remainder of the thesis, we turn to root separation bounds. We observe that known root separation bounds are usually very pessimistic. To our surprise, we also find that known root separation bounds are not compatible with the geometry of the roots (unlike positive root bounds). This motivates us to derive new root separation bounds. In the second part of this thesis, we derive a new root separation for univariate polynomials by transforming a known bound into a new improved bound. In the third part of this thesis, we use a similar strategy to derive a new improved root separation bound for polynomial systems.

  2. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

    Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.

    La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.

  3. A case study from the chemistry core of the Pittsburgh Molecular Library Screening Center: the Polo-like kinase polo-box domain (Plk1-PBD).

    Science.gov (United States)

    Wipf, Peter; Arnold, David; Carter, Karen; Dong, Shuzhi; Johnston, Paul A; Sharlow, Elizabeth; Lazo, John S; Huryn, Donna

    2009-01-01

    The Polo-like kinase (Plk) family comprises four cell cycle serine/threonine kinases, Plk1-4. Among these, Plk1 has been most thoroughly characterized; it contains a conserved kinase domain and a C-terminal docking site for S/T-phosphorylated proteins (polo-box domain, PBD). Polo-like kinases are deregulated in oncogenesis and therefore constitute a therapeutic target for cancer. A high throughput screening campaign was carried out by the Pittsburgh Molecular Library Screening Center (PMLSC), using a fluorescence polarization assay with recombinant Plk1-PBD to monitor the inhibition of binding of an optimal phosphopeptide substrate motif with recombinant Plk1-PBD. Screening of 97,090 small molecule library samples provided by the NIH Small Molecule Repository distributed by DPI Galapagos led to 11 confirmed hits. The Pittsburgh MLSCN Chemistry Core selected one of the structurally most tractable hits, SID 861574, for chemical hit-to-probe development. A broad chemistry program was initiated that developed new strategies for 6-amino- and 6-hydroxy uracil synthesis as well as acylanilides, and generated a total of 70 analogs. Out of 46 analogues tested, none, nor the resynthesized hit, showed affinity to Plk1-PBD in the follow up assays. In contrast, re-assays of the original screening materials displayed activities similar to the original HTS assay. We ultimately concluded that an impurity in the commercial material led to the positive screening artifact. This case study highlights our development of a synthesis of 6-position functionalized uracil analogs, but also illustrates the importance of careful quality and compound stability monitoring of screening collections.

  4. Pedestrian flows in bounded domains with obstacles

    CERN Document Server

    Piccoli, Benedetto

    2008-01-01

    In this paper we systematically apply the mathematical structures by time-evolving measures developed in a previous work to the macroscopic modeling of pedestrian flows. We propose a discrete-time Eulerian model, in which the space occupancy by pedestrians is described via a sequence of Radon positive measures generated by a push-forward recursive relation. We assume that two fundamental aspects of pedestrian behavior rule the dynamics of the system: On the one hand, the will to reach specific targets, which determines the main direction of motion of the walkers; on the other hand, the tendency to avoid crowding, which introduces interactions among the individuals. The resulting model is able to reproduce several experimental evidences of pedestrian flows pointed out in the specialized literature, being at the same time much easier to handle, from both the analytical and the numerical point of view, than other models relying on nonlinear hyperbolic conservation laws. This makes it suitable to address two-dime...

  5. Insights into the Inhibition of the p90 Ribosomal S6 Kinase (RSK) by the Flavonol Glycoside SL0101 from the 1.5 Å Crystal Structure of the N-Terminal Domain of RSK2 with Bound Inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Utepbergenov, Darkhan; Derewenda, Urszula; Olekhnovich, Natalya; Szukalska, Gabriela; Banerjee, Budhaditya; Hilinski, Michael K.; Lannigan, Deborah A.; Stukenberg, P. Todd; Derewenda, Zygmunt S. (Lodz - Poland); (UV)

    2012-09-11

    The p90 ribosomal S6 family of kinases (RSK) are potential drug targets, due to their involvement in cancer and other pathologies. There are currently only two known selective inhibitors of RSK, but the basis for selectivity is not known. One of these inhibitors is a naturally occurring kaempferol-a-l-diacetylrhamnoside, SL0101. Here, we report the crystal structure of the complex of the N-terminal kinase domain of the RSK2 isoform with SL0101 at 1.5 {angstrom} resolution. The refined atomic model reveals unprecedented structural reorganization of the protein moiety, as compared to the nucleotide-bound form. The entire N-lobe, the hinge region, and the aD-helix undergo dramatic conformational changes resulting in a rearrangement of the nucleotide binding site with concomitant formation of a highly hydrophobic pocket spatially suited to accommodate SL0101. These unexpected results will be invaluable in further optimization of the SL0101 scaffold as a promising lead for a novel class of kinase inhibitors.

  6. The 2.5 Å Crystal Structure of the SIRT1 Catalytic Domain Bound to Nicotinamide Adenine Dinucleotide (NAD + ) and an Indole (EX527 Analogue) Reveals a Novel Mechanism of Histone Deacetylase Inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xun; Allison, Dagart; Condon, Bradley; Zhang, Feiyu; Gheyi, Tarun; Zhang, Aiping; Ashok, Sheela; Russell, Marijane; MacEwan, Iain; Qian, Yuewei; Jamison, James A.; Luz, John Gately

    2013-02-14

    The sirtuin SIRT1 is a NAD+-dependent histone deacetylase, a Sir2 family member, and one of seven human sirtuins. Sirtuins are conserved from archaea to mammals and regulate transcription, genome stability, longevity, and metabolism. SIRT1 regulates transcription via deacetylation of transcription factors such as PPARγ, NFκB, and the tumor suppressor protein p53. EX527 (27) is a nanomolar SIRT1 inhibitor and a micromolar SIRT2 inhibitor. To elucidate the mechanism of SIRT inhibition by 27, we determined the 2.5 Å crystal structure of the SIRT1 catalytic domain (residues 241–516) bound to NAD+ and the 27 analogue compound 35. 35 binds deep in the catalytic cleft, displacing the NAD+ nicotinamide and forcing the cofactor into an extended conformation. The extended NAD+ conformation sterically prevents substrate binding. The SIRT1/NAD+/35 crystal structure defines a novel mechanism of histone deacetylase inhibition and provides a basis for understanding, and rationally improving, inhibition of this therapeutically important target by drug-like molecules.

  7. Enhancement of cytotoxic T lymphocyte activity by dendritic cells loaded with Tat-protein transduction domain-fused hepatitis B virus core antigen

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The protein transduction domain (PTD) of human immuno-deficiency virus-1-Tat protein has a unique potency to pen-etrate the cellular membranes. To synthesize the sequence of Tat-PTD and hepatitis B virus core antigen (HBcAg), we spliced these sequences and linked a fusion gene into the pMAL-c2x vector. The fusion proteins were purified by affin-ity chromatography and pulsed with bone marrow -derived den-dritic cells (DCs), and the transduction of recombinant pro-tein was detected by immunofluorescence antibody assay.Results showed that recombinant PTD-HBcAg could pen-etrate into DC cytoplasm while recombinant HBcAg was de-tected on the surface of cells. The percentage of DC surface molecules, such as CD80, CD86 and major histocompatibii-ity complex Ⅱ, and production of cytokine (IL-12pT0) induced by recombinant PTD-HBcAg were significantly higher than those induced by recombinant HBcAg or tumor necrosis fac-tor-α. DCs treated with PTD-HBcAg induced T cells to dif-ferentiate into specific cytotoxic T lymphocytes (CTLs) and enhanced the CTL killing response. In conclusion, the ex-pressed and purified PTD-HBcAg fusion protein could pen-etrate into cells through the plasma membrane, promote DC maturation, and enhance T cells response to generate HBcAg-specific CTLs efficiently.

  8. Core Transmembrane Domain 6 Plays a Pivotal Role in the Transport Cycle of the Sodium/Proline Symporter PutP.

    Science.gov (United States)

    Bracher, Susanne; Schmidt, Claudia C; Dittmer, Sophie I; Jung, Heinrich

    2016-12-09

    Crystal structures of transporters with a LeuT-type structural fold assign core transmembrane domain 6 (TM6') a central role in substrate binding and translocation. Here, the function of TM6' in the sodium/proline symporter PutP, a member of the solute/sodium symporter family, was investigated. A complete scan of TM6' identified eight amino acids as particularly important for PutP function. Of these residues, Tyr-248, His-253, and Arg-257 impact sodium binding, whereas Arg-257 and Ala-260 may participate in interactions leading to closure of the inner gate. Furthermore, the previous suggestion of an involvement of Trp-244, Tyr-248, and Pro-252 in proline binding is further supported. In addition, substitution of Gly-245, Gly-247, and Gly-250 affects the amount of PutP in the membrane. A Cys accessibility analysis suggests an involvement of the inner half of TM6' in the formation of a hydrophilic pathway that is open to the inside in the absence of ligands and closed in the presence of sodium and proline. In conclusion, the results demonstrate that TM6' plays a central role in substrate binding and release on the inner side of the membrane also in PutP and extend the knowledge on functionally relevant amino acids in transporters with a LeuT-type structural fold.

  9. The core domain of Aquifex aeolicus tRNA (m7G46) methyltransferase has the methyl-transfer activity to tRNA.

    Science.gov (United States)

    Tomikawa, Chie; Hori, Hiroyuki

    2006-01-01

    Transfer RNA (m(7)G46) methyltransferase [TrmB] catalyses the transfer of methyl groups from S-adenosyl-L-methionine to the N(7)-atom of guanine at position 46 in tRNA. TrmB proteins from thermophilic bacteria such as Aquifex aeolicus have a long C-terminal region as compared to those from mesophilic bacteria. Further, N-terminal region observed in TrmB proteins from mesophiles is missing in A. aeolicus TrmB. Therefore, we considered that this distinct C-terminal region in A. aeolicus TrmB might compensate the N-terminal region in mesophile TrmB and function as a part of tRNA binding site. To confirm this idea, we deleted the C-terminal region by introduction of the stop codon at position 202. To our surprise, methyl-transfer assay using yeast tRNA(Phe) transcript clearly showed that the resultant mutant protein (Glu202Stop) had an enzymatic activity. Thus, the core domain of the A. aeolicus TrmB has a methyl-transfer activity.

  10. A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly.

    Science.gov (United States)

    Ballandras, Allison; Moreau, Karen; Robert, Xavier; Confort, Marie-Pierre; Merceron, Romain; Haser, Richard; Ronfort, Corinne; Gouet, Patrice

    2011-01-01

    Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD) of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A) and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1). These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1) IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T). Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3). A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA.

  11. Computations of Bergman Kernels on Hua Domains

    Institute of Scientific and Technical Information of China (English)

    殷慰萍; 王安; 赵振刚; 赵晓霞; 管冰辛

    2001-01-01

    @@The Bergman kernel function plays an important ro1e in several complex variables.There exists the Bergman kernel function on any bounded domain in Cn. But we can get the Bergman kernel functions in explicit formulas for a few types of domains only,for example:the bounded homogeneous domains and the egg domain in some cases.

  12. Humanized-Single Domain Antibodies (VH/VHH that Bound Specifically to Naja kaouthia Phospholipase A2 and Neutralized the Enzymatic Activity

    Directory of Open Access Journals (Sweden)

    Wanpen Chaicumpa

    2012-07-01

    Full Text Available Naja kaouthia (monocled cobra venom contains many isoforms of secreted phospholipase A2 (sPLA2. The PLA2 exerts several pharmacologic and toxic effects in the snake bitten subject, dependent or independent on the enzymatic activity. N. kaouthia venom appeared in two protein profiles, P3 and P5, after fractionating the venom by ion exchange column chromatography. In this study, phage clones displaying humanized-camel single domain antibodies (VH/VHH that bound specifically to the P3 and P5 were selected from a humanized-camel VH/VHH phage display library. Two phagemid transfected E. coli clones (P3-1 and P3-3 produced humanized-VHH, while another clone (P3-7 produced humanized-VH. At the optimal venom:antibody ratio, the VH/VHH purified from the E. coli homogenates neutralized PLA2 enzyme activity comparable to the horse immune serum against the N. kaouthia holo-venom. Homology modeling and molecular docking revealed that the VH/VHH covered the areas around the PLA2 catalytic groove and inserted their Complementarity Determining Regions (CDRs into the enzymatic cleft. It is envisaged that the VH/VHH would ameliorate/abrogate the principal toxicity of the venom PLA2 (membrane phospholipid catabolism leading to cellular and subcellular membrane damage which consequently causes hemolysis, hemorrhage, and dermo-/myo-necrosis, if they were used for passive immunotherapy of the cobra bitten victim. The speculation needs further investigations.

  13. Cellulose hydrolysis and binding with Trichoderma reesei Cel5A and Cel7A and their core domains in ionic liquid solutions.

    Science.gov (United States)

    Wahlström, Ronny; Rahikainen, Jenni; Kruus, Kristiina; Suurnäkki, Anna

    2014-04-01

    Ionic liquids (ILs) dissolve lignocellulosic biomass and have a high potential as pretreatment prior to total enzymatic hydrolysis. ILs are, however, known to inactivate cellulases. In this article, enzymatic hydrolysis of microcrystalline cellulose (MCC) and enzyme binding onto the cellulosic substrate were studied in the presence of cellulose-dissolving ILs. Two different ILs, 1,3-dimethylimidazolium dimethylphosphate ([DMIM]DMP) and 1-ethyl-3-methylimidazolium acetate ([EMIM]AcO), and two monocomponent cellulases, Trichoderma reesei cellobiohydrolase Cel7A and endoglucanase Cel5A, were used in the study. The role and IL sensitivity of the carbohydrate-binding module (CBM) were studied by performing hydrolysis and binding experiments with both the intact cellulases, and their respective core domains (CDs). Based on hydrolysis yields and substrate binding experiments for the intact enzymes and their CDs in the presence of ILs, the function of the CBM appeared to be very IL sensitive. Binding data suggested that the CBM was more important for the substrate binding of endoglucanase Cel5A than for the binding of cellobiohydrolase Cel7A. The CD of Cel7A was able to bind well to cellulose even without a CBM, whereas Cel5A CD had very low binding affinity. Hydrolysis also occurred with Cel5A CD even if this protein had very low binding affinity in all the studied matrices. Binding and hydrolysis were less affected by the studied ILs for Cel7A than for Cel5A. To our knowledge, this is the first systematic study of IL effects on cellulase substrate binding. © 2013 Wiley Periodicals, Inc.

  14. Single domain SmCo5@Co exchange-coupled magnets prepared from core/shell Sm[Co(CN)6]·4H2O@GO particles: a novel chemical approach.

    Science.gov (United States)

    Yang, Ce; Jia, Lihui; Wang, Shouguo; Gao, Chen; Shi, Dawei; Hou, Yanglong; Gao, Song

    2013-12-20

    SmCo5 based magnets with smaller size and larger maximum energy product have been long desired in various fields such as renewable energy technology, electronic industry and aerospace science. However, conventional relatively rough synthetic strategies will lead to either diminished magnetic properties or irregular morphology, which hindered their wide applications. In this article, we present a facile chemical approach to prepare 200 nm single domain SmCo5@Co core/shell magnets with coercivity of 20.7 kOe and saturation magnetization of 82 emu/g. We found that the incorporation of GO sheets is responsible for the generation of the unique structure. The single domain SmCo5 core contributes to the large coercivity of the magnets and the exchange-coupled Co shell enhances the magnetization. This method can be further utilized in the synthesis other Sm-Co based exchange-coupled magnets.

  15. Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase.

    Science.gov (United States)

    Romanyuk, Nataliya D; Rigden, Daniel J; Vatamaniuk, Olena K; Lang, Albert; Cahoon, Rebecca E; Jez, Joseph M; Rea, Philip A

    2006-07-01

    Phytochelatin (PC) synthases are gamma-glutamylcysteine (gamma-Glu-Cys) dipeptidyl transpeptidases that catalyze the synthesis of heavy metal-binding PCs, (gamma-Glu-Cys)nGly polymers, from glutathione (GSH) and/or shorter chain PCs. Here it is shown through investigations of the enzyme from Arabidopsis (Arabidopsis thaliana; AtPCS1) that, although the N-terminal half of the protein, alone, is sufficient for core catalysis through the formation of a single-site enzyme acyl intermediate, it is not sufficient for acylation at a second site and augmentative stimulation by free Cd2+. A purified N-terminally hexahistidinyl-tagged AtPCS1 truncate containing only the first 221 N-terminal amino acid residues of the enzyme (HIS-AtPCS1_221tr) is competent in the synthesis of PCs from GSH in media containing Cd2+ or the synthesis of S-methyl-PCs from S-methylglutathione in media devoid of heavy metal ions. However, whereas its full-length hexahistidinyl-tagged equivalent, HIS-AtPCS1, undergoes gamma-Glu-Cys acylation at two sites during the Cd2+-dependent synthesis of PCs from GSH and is stimulated by free Cd2+ when synthesizing S-methyl-PCs from S-methylglutathione, HIS-AtPCS1_221tr undergoes gamma-Glu-Cys acylation at only one site when GSH is the substrate and is not directly stimulated, but instead inhibited, by free Cd2+ when S-methylglutathione is the substrate. Through the application of sequence search algorithms capable of detecting distant homologies, work we reported briefly before but not in its entirety, it has been determined that the N-terminal half of AtPCS1 and its equivalents from other sources have the hallmarks of a papain-like, Clan CA Cys protease. Whereas the fold assignment deduced from these analyses, which substantiates and is substantiated by the recent determination of the crystal structure of a distant prokaryotic PC synthase homolog from the cyanobacterium Nostoc, is capable of explaining the strict requirement for a conserved Cys residue, Cys-56

  16. Lower Bounds on Paraclique Density.

    Science.gov (United States)

    Hagan, Ronald D; Langston, Michael A; Wang, Kai

    2016-05-11

    The scientific literature teems with clique-centric clustering strategies. In this paper we analyze one such method, the paraclique algorithm. Paraclique has found practical utility in a variety of application domains, and has been successfully employed to reduce the effects of noise. Nevertheless, its formal analysis and worst-case guarantees have remained elusive. We address this issue by deriving a series of lower bounds on paraclique densities.

  17. Image Fusion Method Based on Bound-Constrained Optimal Projection Gradient for NMF in TINST Domain%基于边界约束最优投影梯度NMF的TINST域图像融合方法

    Institute of Scientific and Technical Information of China (English)

    才华; 陈广秋; 刘广文; 耿朕野; 杨勇

    2016-01-01

    Aiming at the problem of multi-modality images fusion,we proposed an image fusion method based on bound-constrained optimal projection gradient for non-negative matrix factorization (NMF)in translation invariance nonseparable shearlet transform (TINST)domain.The problem of low fusion accuracy in some existing typical fusion methods was solved effectively.Images were decomposed to some subbands by translation invariance nonseparable shearlet transform. The low-frequency subband coefficients were regarded as original observed data,and the low-frequency subband coefficients were obtained by bound-constrained optimal projection gradient for NMF algorithm.High-frequency directional suband coefficients were used as external input excitation and edge intensity was served as linking strength of each neuron in pulse coupled neural networks (PCNN) and after the fire processing and compare-selection computing, fused high-frequency directional suband coefficients were obtained.Finally,all the fused subbands were reconstructed to an image by translation invariance nonseparable shearlet inverse transform.In order to verify the efficiency of the proposed method,some compared fusion experiments were implemented on several sets of different modality images.Subjective and objective evaluation on fused image indicates that the proposed method is better than a few existing typical fusion techniques based on multi-scale decomposition (MSD).%针对多模态图像的融合问题,提出一种平移不变不可分离剪切波结合边界约束最优投影梯度非负矩阵分解的图像融合方法,解决了已有融合方法中融合精度较低的问题。该方法利用平移不变不可分离剪切波对源图像进行分解;将低频子带系数视为原始观测数据,采用边界约束最优投影梯度非负矩阵分解算法得到包含特征基的融合低频子带系数,将高频方向子带系数作为脉冲耦合神经网络的外部输入激励,边缘强度作

  18. Elucidation of the molecular basis of selective recognition uncovers the interaction site for the core domain of scorpion alpha-toxins on sodium channels.

    Science.gov (United States)

    Gur, Maya; Kahn, Roy; Karbat, Izhar; Regev, Noa; Wang, Jinti; Catterall, William A; Gordon, Dalia; Gurevitz, Michael

    2011-10-07

    Neurotoxin receptor site-3 at voltage-gated Na(+) channels is recognized by various peptide toxin inhibitors of channel inactivation. Despite extensive studies of the effects of these toxins, their mode of interaction with the channel remained to be described at the molecular level. To identify channel constituents that interact with the toxins, we exploited the opposing preferences of LqhαIT and Lqh2 scorpion α-toxins for insect and mammalian brain Na(+) channels. Construction of the DIV/S1-S2, DIV/S3-S4, DI/S5-SS1, and DI/SS2-S6 external loops of the rat brain rNa(v)1.2a channel (highly sensitive to Lqh2) in the background of the Drosophila DmNa(v)1 channel (highly sensitive to LqhαIT), and examination of toxin activity on the channel chimera expressed in Xenopus oocytes revealed a substantial decrease in LqhαIT effect, whereas Lqh2 was as effective as at rNa(v)1.2a. Further substitutions of individual loops and specific residues followed by examination of gain or loss in Lqh2 and LqhαIT activities highlighted the importance of DI/S5-S6 (pore module) and the C-terminal region of DIV/S3 (gating module) of rNa(v)1.2a for Lqh2 action and selectivity. In contrast, a single substitution of Glu-1613 to Asp at DIV/S3-S4 converted rNa(v)1.2a to high sensitivity toward LqhαIT. Comparison of depolarization-driven dissociation of Lqh2 and mutant derivatives off their binding site at rNa(v)1.2a mutant channels has suggested that the toxin core domain interacts with the gating module of DIV. These results constitute the first step in better understanding of the way scorpion α-toxins interact with voltage-gated Na(+)-channels at the molecular level.

  19. Functional interactions of the AF-2 activation domain core region of the human androgen receptor with the amino-terminal domain and with the transcriptional coactivator TIF2 (transcriptional intermediary factor2)

    NARCIS (Netherlands)

    C.A. Berrevoets (Cor); P. Doesburg (Paul); K. Steketee (Karine); J. Trapman (Jan); A.O. Brinkmann (Albert)

    1998-01-01

    textabstractPrevious studies in yeast and mammalian cells showed a functional interaction between the amino-terminal domain and the carboxy-terminal, ligand-binding domain (LBD) of the human androgen receptor (AR). In the present study, the AR subdomains involved in thi

  20. A terahertz time-domain study on the estimation of opto-mechanical properties of pharmaceutical tablets using the Hashin-Shtrikman bounds for refractive index: a case study of microcrystalline cellulose and starch acetate compacts

    Science.gov (United States)

    Bawuah, Prince; Peiponen, Kai-Erik

    2016-06-01

    This work highlights the use of Hashin-Shtrikman (H-S) bounds in the prediction and verification of the effective refractive index, the height and the Young's modulus of given training sets of pharmaceutical compacts using the measured time delay of a THz pulse traversing the compacts. Set A consisted of 13 microcrystalline cellulose (MCC) compacts whereas set B was made up of 5 starch acetate (SA) compacts. MCC is a typical ingredient of many pharmaceutical tablets. In the case of the MCC compacts, tight and closely matched bounds were obtained between the experimental, the calculated upper, lower bound values for the effective refractive index, and the height values. This promising outcome has shown the high possibility of utilizing H-S bounds in the verification and prediction of the decision level of useful parameters, which can serve as a quality check for pharmaceutical tablets. For the SA compacts, although less tight bounds were observed, the experimental values for the effective refractive index and the Young's modulus were closely matched with the upper and the lower bounds, respectively. We therefore speculate based on the above observations that the MCC tablets contain an almost evenly distributed spherically shaped air voids whereas in the SA compacts, this assumption might not necessary be true.

  1. Amino acid regions 572-579 and 657-666 of the spacer domain of ADAMTS13 provide a common antigenic core required for binding of antibodies in patients with acquired TTP.

    Science.gov (United States)

    Luken, Brenda M; Turenhout, Ellen A M; Kaijen, Paul H P; Greuter, Mascha J; Pos, Wouter; van Mourik, Jan A; Fijnheer, Rob; Voorberg, Jan

    2006-09-01

    Antibodies directed against ADAMTS13 have been detected in the majority of patients with acquired thrombotic thrombocytopenic purpura (TTP). We have previously localized a major antigenic determinant within the spacer domain of ADAMTS13. To identify the amino acid residues of the spacer domain that are involved in binding of anti-ADAMTS13 antibodies, we constructed a series of fifteen hybrids (designated A-O) in which 5-10 amino acids of the spacer domain were exchanged for the corresponding region of ADAMTS1. Plasma from six patients with antibodies directed against the spacer domain was analyzed for reactivity with the ADAMTS13/ADAMTS1 chimeras. Exchange of amino acid residues 572-579 (hybrid C) and 657-666 (hybrid M) completely abolished the binding of antibodies from all six patients analyzed. Regions 580-587 (D), 602-620 (G, H), 629-638 (J), and 667-767 (N) contributed to binding of antibodies from patients 2, 4, and 5 (epitope present within regions CDGHJMN). Antibodies derived from patient 1 required region 602-620 (G, H) for binding (CGHM-epitope). For antibodies of patient 3, residues 564-571 (B), 580-587 (D), and 629-638 (J) were required (BCDJM-epitope), whereas replacement of residues 602-610 (G) and 629-638 (J) greatly diminished binding of antibodies from patient 6 (CGJM-epitope). Despite the presumably polyclonal origin of the antibodies present in plasma of patients, our results suggest that residues 572-579 (C) and 657-666 (M) comprise a common antigenic core region that is crucial for binding of anti-ADAMTS13 antibodies. Other regions that spatially surround this antigenic core further modulate binding of antibodies to the spacer domain.

  2. Viscosity bound versus the universal relaxation bound

    Science.gov (United States)

    Hod, Shahar

    2017-10-01

    For gauge theories with an Einstein gravity dual, the AdS/CFT correspondence predicts a universal value for the ratio of the shear viscosity to the entropy density, η / s = 1 / 4 π. The holographic calculations have motivated the formulation of the celebrated KSS conjecture, according to which all fluids conform to the lower bound η / s ≥ 1 / 4 π. The bound on η / s may be regarded as a lower bound on the relaxation properties of perturbed fluids and it has been the focus of much recent attention. In particular, it was argued that for a class of field theories with Gauss-Bonnet gravity dual, the shear viscosity to entropy density ratio, η / s, could violate the conjectured KSS bound. In the present paper we argue that the proposed violations of the KSS bound are strongly constrained by Bekenstein's generalized second law (GSL) of thermodynamics. In particular, it is shown that physical consistency of the Gauss-Bonnet theory with the GSL requires its coupling constant to be bounded by λGB ≲ 0 . 063. We further argue that the genuine physical bound on the relaxation properties of physically consistent fluids is ℑω(k > 2 πT) > πT, where ω and k are respectively the proper frequency and the wavenumber of a perturbation mode in the fluid.

  3. Modeling agreement on bounded scales.

    Science.gov (United States)

    Vanbelle, Sophie; Lesaffre, Emmanuel

    2017-01-01

    Agreement is an important concept in medical and behavioral sciences, in particular in clinical decision making where disagreements possibly imply a different patient management. The concordance correlation coefficient is an appropriate measure to quantify agreement between two scorers on a quantitative scale. However, this measure is based on the first two moments, which could poorly summarize the shape of the score distribution on bounded scales. Bounded outcome scores are common in medical and behavioral sciences. Typical examples are scores obtained on visual analog scales and scores derived as the number of positive items on a questionnaire. These kinds of scores often show a non-standard distribution, like a J- or U-shape, questioning the usefulness of the concordance correlation coefficient as agreement measure. The logit-normal distribution has shown to be successful in modeling bounded outcome scores of two types: (1) when the bounded score is a coarsened version of a latent score with a logit-normal distribution on the [0,1] interval and (2) when the bounded score is a proportion with the true probability having a logit-normal distribution. In the present work, a model-based approach, based on a bivariate generalization of the logit-normal distribution, is developed in a Bayesian framework to assess the agreement on bounded scales. This method permits to directly study the impact of predictors on the concordance correlation coefficient and can be simply implemented in standard Bayesian softwares, like JAGS and WinBUGS. The performances of the new method are compared to the classical approach using simulations. Finally, the methodology is used in two different medical domains: cardiology and rheumatology.

  4. Functions of bounded variation

    OpenAIRE

    Lind, Martin

    2006-01-01

    The paper begins with a short survey of monotone functions. The functions of bounded variation are introduced and some basic properties of these functions are given. Finally the jump function of a function of bounded variation is defined.

  5. Upward Bound alum honored

    OpenAIRE

    Felker, Susan B.

    2005-01-01

    Robert Cobb Jr., of Greensboro, N.C., a 1986-89 participant in the Virginia Tech Upward Bound program, was recently named Virginia's TRIO Achiever for 2004. Federal TRIO programs include Upward Bound and Educational Talent Search.

  6. Molecular determinants of interactions between the N-terminal domain and the transmembrane core that modulate hERG K+ channel gating.

    Directory of Open Access Journals (Sweden)

    Jorge Fernández-Trillo

    Full Text Available A conserved eag domain in the cytoplasmic amino terminus of the human ether-a-go-go-related gene (hERG potassium channel is critical for its slow deactivation gating. Introduction of gene fragments encoding the eag domain are able to restore normal deactivation properties of channels from which most of the amino terminus has been deleted, and also those lacking exclusively the eag domain or carrying a single point mutation in the initial residues of the N-terminus. Deactivation slowing in the presence of the recombinant domain is not observed with channels carrying a specific Y542C point mutation in the S4-S5 linker. On the other hand, mutations in some initial positions of the recombinant fragment also impair its ability to restore normal deactivation. Fluorescence resonance energy transfer (FRET analysis of fluorophore-tagged proteins under total internal reflection fluorescence (TIRF conditions revealed a substantial level of FRET between the introduced N-terminal eag fragments and the eag domain-deleted channels expressed at the membrane, but not between the recombinant eag domain and full-length channels with an intact amino terminus. The FRET signals were also minimized when the recombinant eag fragments carried single point mutations in the initial portion of their amino end, and when Y542C mutated channels were used. These data suggest that the restoration of normal deactivation gating by the N-terminal recombinant eag fragment is an intrinsic effect of this domain directed by the interaction of its N-terminal segment with the gating machinery, likely at the level of the S4-S5 linker.

  7. Bidirectional lipid droplet velocities are controlled by differential binding strengths of HCV core DII protein.

    Science.gov (United States)

    Lyn, Rodney K; Hope, Graham; Sherratt, Allison R; McLauchlan, John; Pezacki, John Paul

    2013-01-01

    Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein's lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV.

  8. Bidirectional Lipid Droplet Velocities Are Controlled by Differential Binding Strengths of HCV Core DII Protein

    Science.gov (United States)

    Lyn, Rodney K.; Hope, Graham; Sherratt, Allison R.; McLauchlan, John; Pezacki, John Paul

    2013-01-01

    Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein’s lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV. PMID:24223760

  9. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-19

    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  10. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    The domain concept, originally suggested by Schmidt-Rohr in the 1930’s (as credited in Fishman’s writings in the 1970s), was an attempt to sort out different areas of language use in multilingual societies, which are relevant for language choice. In Fishman’s version, domains were considered...... not described in terms of domains, and recent research e.g. about the multilingual communities in the Danish-German border area seems to confirm this....

  11. Recommended patient-reported core set of symptoms and quality-of-life domains to measure in ovarian cancer treatment trials.

    Science.gov (United States)

    Donovan, Kristine A; Donovan, Heidi S; Cella, David; Gaines, Martha E; Penson, Richard T; Plaxe, Steven C; von Gruenigen, Vivian E; Bruner, Deborah Watkins; Reeve, Bryce B; Wenzel, Lari

    2014-07-01

    There is no consensus as to what symptoms or quality-of-life (QOL) domains should be measured as patient-reported outcomes (PROs) in ovarian cancer clinical trials. A panel of experts convened by the National Cancer Institute reviewed studies published between January 2000 and August 2011. The results were included in and combined with an expert consensus-building process to identify the most salient PROs for ovarian cancer clinical trials. We identified a set of PROs specific to ovarian cancer: abdominal pain, bloating, cramping, fear of recurrence/disease progression, indigestion, sexual dysfunction, vomiting, weight gain, and weight loss. Additional PROs identified in parallel with a group charged with identifying the most important PROs across cancer types were anorexia, cognitive problems, constipation, diarrhea, dyspnea, fatigue, nausea, neuropathy, pain, and insomnia. Physical and emotional domains were considered to be the most salient domains of QOL. Findings of the review and consensus process provide good support for use of these ovarian cancer-specific PROs in ovarian cancer clinical trials.

  12. On the Applicability of Lower Bounds for Solving Rectilinear

    DEFF Research Database (Denmark)

    Clausen, Jens; Karisch, Stefan E.; Perregaard, M.;

    1998-01-01

    The quadratic assignment problem (QAP) belongs to the hard core of NP-hard optimization problems. After almost forty years of research only relatively small instances can be solved to optimality. The reason is that the quality of the lower bounds available for exact methods is not sufficient....... Recently, lower bounds based on decomposition were proposed for the so called rectilinear QAP that proved to be the strongest for a large class of problem instances. We investigate the strength of these bounds when applied not only at the root node of a search tree but as the bound function used...... in a Branch-and-Bound code solving large scale QAPs....

  13. Presence of a polyadenylated RNA fragment encoding the membrane domain for immunoglobulin alpha chain indicates that mRNAs for both secreted and membrane-bound alpha chains can be produced from the same RNA transcript.

    OpenAIRE

    Stavnezer, J.

    1986-01-01

    RNA blotting was employed to examine polyadenylated immunoglobulin alpha chain RNAs in a B lymphoma synthesizing membrane-bound and secretory IgA and in a hybridoma which synthesizes predominantly secretory IgA. Both cell lines were derived from the I.29 lymphoma and expressed the identical heavy chain variable region gene. In addition to the predicted mRNA precursors, four novel species of polyadenylated alpha RNAs were detected. The presence of a RNA species which was too large to have the ...

  14. Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

    NARCIS (Netherlands)

    Breukers, J.A.P.J.; Hoekstra, R.J.

    2004-01-01

    For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

  15. Graviton Mass Bounds

    CERN Document Server

    de Rham, Claudia; Tolley, Andrew J; Zhou, Shuang-Yong

    2016-01-01

    Recently, aLIGO has announced the first direct detections of gravitational waves, a direct manifestation of the propagating degrees of freedom of gravity. The detected signals GW150914 and GW151226 have been used to examine the basic properties of these gravitational degrees of freedom, particularly setting an upper bound on their mass. It is timely to review what the mass of these gravitational degrees of freedom means from the theoretical point of view, particularly taking into account the recent developments in constructing consistent massive gravity theories. Apart from the GW150914 mass bound, a few other observational bounds have been established from the effects of the Yukawa potential, modified dispersion relation and fifth force that are all induced when the fundamental gravitational degrees of freedom are massive. We review these different mass bounds and examine how they stand in the wake of recent theoretical developments and how they compare to the bound from GW150914.

  16. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  17. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  18. A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants.

    Science.gov (United States)

    Hofberger, Johannes A; Zhou, Beifei; Tang, Haibao; Jones, Jonathan D G; Schranz, M Eric

    2014-11-08

    Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes. By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

  19. Multicolor Bound Soliton Molecule

    CERN Document Server

    Luo, Rui; Lin, Qiang

    2015-01-01

    We show a new class of bound soliton molecule that exists in a parametrically driven nonlinear optical cavity with appropriate dispersion characteristics. The composed solitons exhibit distinctive colors but coincide in time and share a common phase, bound together via strong inter-soliton four-wave mixing and Cherenkov radiation. The multicolor bound soliton molecule shows intriguing spectral locking characteristics and remarkable capability of spectrum management to tailor soliton frequencies, which may open up a great avenue towards versatile generation and manipulation of multi-octave spanning phase-locked Kerr frequency combs, with great potential for applications in frequency metrology, optical frequency synthesis, and spectroscopy.

  20. Core Outcome Domains for early phase clinical trials of sound-, psychology-, and pharmacology-based interventions to manage chronic subjective tinnitus in adults: the COMIT'ID study protocol for using a Delphi process and face-to-face meetings to establish consensus.

    Science.gov (United States)

    Fackrell, Kathryn; Smith, Harriet; Colley, Veronica; Thacker, Brian; Horobin, Adele; Haider, Haúla F; Londero, Alain; Mazurek, Birgit; Hall, Deborah A

    2017-08-23

    The reporting of outcomes in clinical trials of subjective tinnitus indicates that many different tinnitus-related complaints are of interest to investigators, from perceptual attributes of the sound (e.g. loudness) to psychosocial impacts (e.g. quality of life). Even when considering one type of intervention strategy for subjective tinnitus, there is no agreement about what is critically important for deciding whether a treatment is effective. The main purpose of this observational study is, therefore to, develop Core Outcome Domain Sets for the three different intervention strategies (sound, psychological, and pharmacological) for adults with chronic subjective tinnitus that should be measured and reported in every clinical trial of these interventions. Secondary objectives are to identify the strengths and limitations of our study design for recruiting and reducing attrition of participants, and to explore uptake of the core outcomes. The 'Core Outcome Measures in Tinnitus: International Delphi' (COMIT'ID) study will use a mixed-methods approach that incorporates input from health care users at the pre-Delphi stage, a modified three-round Delphi survey and final consensus meetings (one for each intervention). The meetings will generate recommendations by stakeholder representatives on agreed Core Outcome Domain Sets specific to each intervention. A subsequent step will establish a common cross-cutting Core Outcome Domain Set by identifying the common outcome domains included in all three intervention-specific Core Outcome Domain Sets. To address the secondary objectives, we will gather feedback from participants about their experience of taking part in the Delphi process. We aspire to conduct an observational cohort study to evaluate uptake of the core outcomes in published studies at 7 years following Core Outcome Set publication. The COMIT'ID study aims to develop a Core Outcome Domain Set that is agreed as critically important for deciding whether a

  1. Lower bounds for the minimum distance of algebraic geometry codes

    DEFF Research Database (Denmark)

    Beelen, Peter

    , such as the Goppa bound, the Feng-Rao bound and the Kirfel-Pellikaan bound. I will finish my talk by giving several examples. Especially for two-point codes, the generalized order bound is fairly easy to compute. As an illustration, I will indicate how a lower bound can be obtained for the minimum distance of some......A one-point AG-code is an algebraic geometry code based on a divisor whose support consists of one point. Since the discovery of the Feng-Rao lower bound for the minimum distance, there has been a renewed interest in such codes. This lower bound is also called the order bound. An alternative...... description of these codes in terms of order domains has been found. In my talk I will indicate how one can use the ideas behind the order bound to obtain a lower bound for the minimum distance of any AG-code. After this I will compare this generalized order bound with other known lower bounds...

  2. A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5.

    Science.gov (United States)

    Tilton, John C; Wilen, Craig B; Didigu, Chukwuka A; Sinha, Rohini; Harrison, Jessamina E; Agrawal-Gamse, Caroline; Henning, Elizabeth A; Bushman, Frederick D; Martin, Jeffrey N; Deeks, Steven G; Doms, Robert W

    2010-10-01

    CCR5 antagonists inhibit HIV entry by binding to a coreceptor and inducing changes in the extracellular loops (ECLs) of CCR5. In this study, we analyzed viruses from 11 treatment-experienced patients who experienced virologic failure on treatment regimens containing the CCR5 antagonist maraviroc (MVC). Viruses from one patient developed high-level resistance to MVC during the course of treatment. Although resistance to one CCR5 antagonist is often associated with broad cross-resistance to other agents, these viruses remained sensitive to most other CCR5 antagonists, including vicriviroc and aplaviroc. MVC resistance was dependent upon mutations within the V3 loop of the viral envelope (Env) protein and was modulated by additional mutations in the V4 loop. Deep sequencing of pretreatment plasma viral RNA indicated that resistance appears to have occurred by evolution of drug-bound CCR5 use, despite the presence of viral sequences predictive of CXCR4 use. Envs obtained from this patient before and during MVC treatment were able to infect cells expressing very low CCR5 levels, indicating highly efficient use of a coreceptor. In contrast to previous reports in which CCR5 antagonist-resistant viruses interact predominantly with the N terminus of CCR5, these MVC-resistant Envs were also dependent upon the drug-modified ECLs of CCR5 for entry. Our results suggest a model of CCR5 cross-resistance whereby viruses that predominantly utilize the N terminus are broadly cross-resistant to multiple CCR5 antagonists, whereas viruses that require both the N terminus and antagonist-specific ECL changes demonstrate a narrow cross-resistance profile.

  3. Persistence of noncompact normally hyperbolic invariant manifolds in bounded geometry

    CERN Document Server

    Eldering, J

    2012-01-01

    We prove a persistence result for noncompact normally hyperbolic invariant manifolds in the setting of Riemannian manifolds of bounded geometry. Bounded geometry of the ambient manifold is a crucial assumption required to control the uniformity of all estimates throughout the proof. The $C^{k,\\alpha}$-smoothness result is optimal with respect to the spectral gap condition involved. The core of the persistence proof is based on the Perron method. In the process we derive new results on noncompact submanifolds in bounded geometry: a uniform tubular neighborhood theorem and uniform smooth approximation of a submanifold. The submanifolds considered are assumed to be uniformly $C^k$ bounded in an appropriate sense.

  4. Lectures on Bound states

    CERN Document Server

    Hoyer, Paul

    2016-01-01

    Even a first approximation of bound states requires contributions of all powers in the coupling. This means that the concept of "lowest order bound state" needs to be defined. In these lectures I discuss the "Born" (no loop, lowest order in $\\hbar$) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. As a check of the method, Positronium states of any momentum are determined as eigenstates of the QED Hamiltonian, quantized at equal time. Analogously, states bound by a strong external field $A^\\mu(\\xv)$ are found as eigenstates of the Dirac Hamiltonian. Their Fock states have dynamically created $e^+e^-$ pairs, whose distribution is determined by the Dirac wave function. The linear potential of $D=1+1$ dimensions confines electrons but repels positrons. As a result, the mass spectrum is continuous and the wave functions have features of both bound states and plane waves. The classical solutions of Gauss' law are explored for hadrons in QCD. A non-vanishing bo...

  5. Bounding species distribution models

    Institute of Scientific and Technical Information of China (English)

    Thomas J. STOHLGREN; Catherine S. JARNEVICH; Wayne E. ESAIAS; Jeffrey T. MORISETTE

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern.Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development,yet there is no recommended best practice for “clamping” model extrapolations.We relied on two commonly used modeling approaches:classification and regression tree (CART) and maximum entropy (Maxent) models,and we tested a simple alteration of the model extrapolations,bounding extrapolations to the maximum and minimum values of primary environmental predictors,to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States.Findings suggest that multiple models of bounding,and the most conservative bounding of species distribution models,like those presented here,should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5):642-647,2011].

  6. Shedding of cell membrane-bound proteoglycans.

    Science.gov (United States)

    Nam, Eon Jeong; Park, Pyong Woo

    2012-01-01

    Membrane-bound proteoglycans function primarily as coreceptors for many glycosaminoglycan (GAG)-binding ligands at the cell surface. The majority of membrane-bound proteoglycans can also function as soluble autocrine or paracrine effectors as their extracellular domains, replete with all GAG chains, are enzymatically cleaved and released from the cell surface by ectodomain shedding. In particular, the ectodomain shedding of syndecans, a major family of cell surface heparan sulfate proteoglycans, is an important posttranslational mechanism that modulates diverse pathophysiological processes. Syndecan shedding is a tightly controlled process that regulates the onset, progression, and resolution of various infectious and noninfectious inflammatory diseases. This review describes methods to induce and measure the shedding of cell membrane-bound proteoglycans, focusing on syndecan shedding as a prototypic example.

  7. Information, Utility & Bounded Rationality

    CERN Document Server

    Ortega, Pedro A

    2011-01-01

    Perfectly rational decision-makers maximize expected utility, but crucially ignore the resource costs incurred when determining optimal actions. Here we employ an axiomatic framework for bounded rational decision-making based on a thermodynamic interpretation of resource costs as information costs. This leads to a variational "free utility" principle akin to thermodynamical free energy that trades off utility and information costs. We show that bounded optimal control solutions can be derived from this variational principle, which leads in general to stochastic policies. Furthermore, we show that risk-sensitive and robust (minimax) control schemes fall out naturally from this framework if the environment is considered as a bounded rational and perfectly rational opponent, respectively. When resource costs are ignored, the maximum expected utility principle is recovered.

  8. Bounded Computational Capacity Equilibrium

    CERN Document Server

    Hernandez, Penelope

    2010-01-01

    We study repeated games played by players with bounded computational power, where, in contrast to Abreu and Rubisntein (1988), the memory is costly. We prove a folk theorem: the limit set of equilibrium payoffs in mixed strategies, as the cost of memory goes to 0, includes the set of feasible and individually rational payoffs. This result stands in sharp contrast to Abreu and Rubisntein (1988), who proved that when memory is free, the set of equilibrium payoffs in repeated games played by players with bounded computational power is a strict subset of the set of feasible and individually rational payoffs. Our result emphasizes the role of memory cost and of mixing when players have bounded computational power.

  9. On Bounded Weight Codes

    CERN Document Server

    Bachoc, Christine; Cohen, Gerard; Sole, Patrick; Tchamkerten, Aslan

    2010-01-01

    The maximum size of a binary code is studied as a function of its length N, minimum distance D, and minimum codeword weight W. This function B(N,D,W) is first characterized in terms of its exponential growth rate in the limit as N tends to infinity for fixed d=D/N and w=W/N. The exponential growth rate of B(N,D,W) is shown to be equal to the exponential growth rate of A(N,D) for w <= 1/2, and equal to the exponential growth rate of A(N,D,W) for 1/2< w <= 1. Second, analytic and numerical upper bounds on B(N,D,W) are derived using the semidefinite programming (SDP) method. These bounds yield a non-asymptotic improvement of the second Johnson bound and are tight for certain values of the parameters.

  10. Bounding Noncommutative QCD

    CERN Document Server

    Carlson, C E; Lebed, R F; Carlson, Carl E.; Carone, Christopher D.; Lebed, Richard F.

    2001-01-01

    Jurco, Moller, Schraml, Schupp, and Wess have shown how to construct noncommutative SU(N) gauge theories from a consistency relation. Within this framework, we present the Feynman rules for noncommutative QCD and compute explicitly the most dangerous Lorentz-violating operator generated through radiative corrections. We find that interesting effects appear at the one-loop level, in contrast to conventional noncommutative U(N) gauge theories, leading to a stringent bound. Our results are consistent with others appearing recently in the literature that suggest collider limits are not competitive with low-energy tests of Lorentz violation for bounding the scale of spacetime noncommutativity.

  11. The Hausdorff core problem on simple polygons

    Directory of Open Access Journals (Sweden)

    Reza Dorrigiv

    2014-02-01

    Full Text Available A polygon \\(Q\\ is a \\(k\\-bounded Hausdorff Core of a polygon \\(P\\ if \\(P\\ contains \\(Q\\, \\(Q\\ is convex, and the Hausdorff distance between \\(P\\ and \\(Q\\ is at most \\(k\\. A Hausdorff Core of \\(P\\ is a \\(k\\-bounded Hausdorff Core of \\(P\\ with the minimum possible value of \\(k\\, which we denote \\(k_{\\min}\\. Given any \\(k\\ and any \\(\\varepsilon\\gt 0\\, we describe an algorithm for computing a \\(k'\\-bounded Hausdorff Core (if one exists in \\(O(n^3+n^2\\varepsilon^{-4}(\\log n+ \\varepsilon^{-2}\\ time, where \\(k'\\lt k+d_{\\text{rad}}\\cdot\\varepsilon\\ and \\(d_{\\text{rad}}\\ is the radius of the smallest disc that encloses \\(P\\ and whose center is in \\(P\\. We use this solution to provide an approximation algorithm for the optimization Hausdorff Core problem which results in a solution of size \\(k_{\\min}+d_{\\text{rad}}\\cdot\\varepsilon\\ in \\(O(\\log(\\varepsilon^{-1}(n^3+n^2\\varepsilon^{-4}(\\log n+ \\varepsilon^{-2}\\ time. Finally, we describe an approximation scheme for the \\(k\\-bounded Hausdorff Core problem which, given a polygon \\(P\\, a distance \\(k\\, and any \\(\\varepsilon\\gt 0\\, answers true if there is a \\(((1+\\varepsilonk\\-bounded Hausdorff Core and false if there is no \\(k\\-bounded Hausdorff Core. The running time of the approximation scheme is in \\(O(n^3+n^2\\varepsilon^{-4}(\\log n+ \\varepsilon^{-2}\\.

  12. 3.5A cryoEM structure of hepatitis B virus core assembled from full-length core protein.

    Directory of Open Access Journals (Sweden)

    Xuekui Yu

    Full Text Available The capsid shell of infectious hepatitis B virus (HBV is composed of 240 copies of a single protein called HBV core antigen (HBc. An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149. Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90° from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment.

  13. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

  14. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  15. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  16. The DMM Bound

    DEFF Research Database (Denmark)

    Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias

    2010-01-01

    of variables. One application is to the bitsize of the eigenvalues and eigenvectors of an integer matrix, which also yields a new proof that the problem is polynomial. We also compare against recent lower bounds on the absolute value of the root coordinates by Brownawell and Yap [5], obtained under...

  17. Transmission of stability information through the N-domain of tropomyosin is interrupted by a stabilizing mutation (A109L) in the hydrophobic core of the stability control region (residues 97-118).

    Science.gov (United States)

    Kirwan, J Paul; Hodges, Robert S

    2014-02-14

    Tropomyosin (Tm) is an actin-binding, thin filament, two-stranded α-helical coiled-coil critical for muscle contraction and cytoskeletal function. We made the first identification of a stability control region (SCR), residues 97-118, in the Tm sequence that controls overall protein stability but is not required for folding. We also showed that the individual α-helical strands of the coiled-coil are stabilized by Leu-110, whereas the hydrophobic core is destabilized in the SCR by Ala residues at three consecutive d positions. Our hypothesis is that the stabilization of the individual α-helices provides an optimum stability and allows functionally beneficial dynamic motion between the α-helices that is critical for the transmission of stabilizing information along the coiled-coil from the SCR. We prepared three recombinant (rat) Tm(1-131) proteins, including the wild type sequence, a destabilizing mutation L110A, and a stabilizing mutation A109L. These proteins were evaluated by circular dichroism (CD) and differential scanning calorimetry. The single mutation L110A destabilizes the entire Tm(1-131) molecule, showing that the effect of this mutation is transmitted 165 Å along the coiled-coil in the N-terminal direction. The single mutation A109L prevents the SCR from transmitting stabilizing information and separates the coiled-coil into two domains, one that is ∼9 °C more stable than wild type and one that is ∼16 °C less stable. We know of no other example of the substitution of a stabilizing Leu residue in a coiled-coil hydrophobic core position d that causes this dramatic effect. We demonstrate the importance of the SCR in controlling and transmitting the stability signal along this rodlike molecule.

  18. Transmission of Stability Information through the N-domain of Tropomyosin Is Interrupted by a Stabilizing Mutation (A109L) in the Hydrophobic Core of the Stability Control Region (Residues 97–118)

    Science.gov (United States)

    Kirwan, J. Paul; Hodges, Robert S.

    2014-01-01

    Tropomyosin (Tm) is an actin-binding, thin filament, two-stranded α-helical coiled-coil critical for muscle contraction and cytoskeletal function. We made the first identification of a stability control region (SCR), residues 97–118, in the Tm sequence that controls overall protein stability but is not required for folding. We also showed that the individual α-helical strands of the coiled-coil are stabilized by Leu-110, whereas the hydrophobic core is destabilized in the SCR by Ala residues at three consecutive d positions. Our hypothesis is that the stabilization of the individual α-helices provides an optimum stability and allows functionally beneficial dynamic motion between the α-helices that is critical for the transmission of stabilizing information along the coiled-coil from the SCR. We prepared three recombinant (rat) Tm(1–131) proteins, including the wild type sequence, a destabilizing mutation L110A, and a stabilizing mutation A109L. These proteins were evaluated by circular dichroism (CD) and differential scanning calorimetry. The single mutation L110A destabilizes the entire Tm(1–131) molecule, showing that the effect of this mutation is transmitted 165 Å along the coiled-coil in the N-terminal direction. The single mutation A109L prevents the SCR from transmitting stabilizing information and separates the coiled-coil into two domains, one that is ∼9 °C more stable than wild type and one that is ∼16 °C less stable. We know of no other example of the substitution of a stabilizing Leu residue in a coiled-coil hydrophobic core position d that causes this dramatic effect. We demonstrate the importance of the SCR in controlling and transmitting the stability signal along this rodlike molecule. PMID:24362038

  19. The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens

    Energy Technology Data Exchange (ETDEWEB)

    Geisbrecht, B V; Hamaoka, B Y; Perman, B; Zemla, A; Leahy, D J

    2005-10-14

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  20. Conformational phases of membrane bound cytoskeletal filaments

    Science.gov (United States)

    Quint, David A.; Grason, Gregory; Gopinathan, Ajay

    2013-03-01

    Membrane bound cytoskeletal filaments found in living cells are employed to carry out many types of activities including cellular division, rigidity and transport. When these biopolymers are bound to a membrane surface they may take on highly non-trivial conformations as compared to when they are not bound. This leads to the natural question; What are the important interactions which drive these polymers to particular conformations when they are bound to a surface? Assuming that there are binding domains along the polymer which follow a periodic helical structure set by the natural monomeric handedness, these bound conformations must arise from the interplay of the intrinsic monomeric helicity and membrane binding. To probe this question, we study a continuous model of an elastic filament with intrinsic helicity and map out the conformational phases of this filament for various mechanical and structural parameters in our model, such as elastic stiffness and intrinsic twist of the filament. Our model allows us to gain insight into the possible mechanisms which drive real biopolymers such as actin and tubulin in eukaryotes and their prokaryotic cousins MreB and FtsZ to take on their functional conformations within living cells.

  1. On Entropy Bounds and Holography

    CERN Document Server

    Halyo, Edi

    2009-01-01

    We show that the holographic entropy bound for gravitational systems and the Bekenstein entropy bound for nongravitational systems are holographically related. Using the AdS/CFT correspondence, we find that the Bekenstein bound on the boundary is obtained from the holographic bound in the bulk by minimizing the boundary energy with respect the AdS radius or the cosmological constant. This relation may also ameliorate some problems associated with the Bekenstein bound.

  2. Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif.

    Science.gov (United States)

    Samatanga, Brighton; Andreou, Alexandra Z; Klostermeier, Dagmar

    2017-01-23

    DEAD-box proteins share a structurally similar core of two RecA-like domains (RecA_N and RecA_C) that contain the conserved motifs for ATP-dependent RNA unwinding. In many DEAD-box proteins the helicase core is flanked by ancillary domains. To understand the regulation of the DEAD-box helicase YxiN by its C-terminal RNA recognition motif (RRM), we investigated the effect of RNA binding to the RRM on its position relative to the core, and on core activities. RRM/RNA complex formation substantially shifts the RRM from a position close to the RecA_C to the proximity of RecA_N, independent of RNA contacts with the core. RNA binding to the RRM is communicated to the core, and stimulates ATP hydrolysis and RNA unwinding. The conformational space of the core depends on the identity of the RRM-bound RNA. Allosteric regulation of core activities by RNA-induced movement of ancillary domains may constitute a general regulatory mechanism of DEAD-box protein activity.

  3. Crystal structure of YwpF from Staphylococcus aureus reveals its architecture comprised of a β-barrel core domain resembling type VI secretion system proteins and a two-helix pair.

    Science.gov (United States)

    Lee, Sang Jae; Lee, Kyu-Yeon; Lee, Ki-Young; Kim, Dong-Gyun; Kim, Soon-Jong; Lee, Bong-Jin

    2015-04-01

    The ywpF gene (SAV2097) of the Staphylococcus aureus strain Mu50 encodes the YwpF protein, which may play a role in antibiotic resistance. Here, we report the first crystal structure of the YwpF superfamily from S. aureus at 2.5-Å resolution. The YwpF structure consists of two regions: an N-terminal core β-barrel domain that shows structural similarity to type VI secretion system (T6SS) proteins (e.g., Hcp1, Hcp3, and EvpC) and a C-terminal two-helix pair. Although the monomer structure of S. aureus YwpF resembles those of T6SS proteins, the dimer/tetramer model of S. aureus YwpF is distinct from the functionally important hexameric ring of T6SS proteins. We therefore suggest that the S. aureus YwpF may have a different function compared to T6SS proteins. © 2015 Wiley Periodicals, Inc.

  4. 基于TDR多芯信号电缆故障测试装置的研制%MULTI-CORE CABLE TEST DEVICE BASED ON TIME DOMAIN REFLECTOMETRY (TDR)

    Institute of Scientific and Technical Information of China (English)

    吕瀚; 吴雄伟; 关伟智; 吴林斌

    2011-01-01

    This paper presents a multi-core cable test device based on the time domain reflectometry(TDR). A microcontroller of C8051F005 is used for controling CPLD to send pulse signal to the cable. With this design and dual joint measurement mode, the faults of cable shorted, mixed and the position of borken wires can be quickly detected and the presion of fault fixed-point position can be within 5 m. Because of the low cost and convenient operation ,the design will have good application prospects.%介绍一种基于时域脉冲反射(TDR)的多芯电缆故障测试装置.使用C8051F005单片机为处理核心,控制CPLD向电缆注入脉冲信号,通过双机联测的方式在电缆两端点同时进行测量,可快速判断电缆短接,混接以及芯线断线等故障以及故障点的位置,故障位置定点可精确到5 m以内,该装置设计成本低廉,操作方便,具有良好的应用前景.

  5. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studie....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  6. Bounded Satisfiability for PCTL

    CERN Document Server

    Bertrand, Nathalie; Schewe, Sven

    2012-01-01

    While model checking PCTL for Markov chains is decidable in polynomial-time, the decidability of PCTL satisfiability, as well as its finite model property, are long standing open problems. While general satisfiability is an intriguing challenge from a purely theoretical point of view, we argue that general solutions would not be of interest to practitioners: such solutions could be too big to be implementable or even infinite. Inspired by bounded synthesis techniques, we turn to the more applied problem of seeking models of a bounded size: we restrict our search to implementable -- and therefore reasonably simple -- models. We propose a procedure to decide whether or not a given PCTL formula has an implementable model by reducing it to an SMT problem. We have implemented our techniques and found that they can be applied to the practical problem of sanity checking -- a procedure that allows a system designer to check whether their formula has an unexpectedly small model.

  7. Reaching Fleming's dicrimination bound

    CERN Document Server

    Gruebl, Gebhard

    2012-01-01

    Any rule for identifying a quantum system's state within a set of two non-orthogonal pure states by a single measurement is flawed. It has a non-zero probability of either yielding the wrong result or leaving the query undecided. This also holds if the measurement of an observable $A$ is repeated on a finite sample of $n$ state copies. We formulate a state identification rule for such a sample. This rule's probability of giving the wrong result turns out to be bounded from above by $1/n\\delta_{A}^{2}$ with $\\delta_{A}=|_{1}-_{2}|/(\\Delta_{1}A+\\Delta_{2}A).$ A larger $\\delta_{A}$ results in a smaller upper bound. Yet, according to Fleming, $\\delta_{A}$ cannot exceed $\\tan\\theta$ with $\\theta\\in(0,\\pi/2) $ being the angle between the pure states under consideration. We demonstrate that there exist observables $A$ which reach the bound $\\tan\\theta$ and we determine all of them.

  8. Stellar cooling bounds on new light particles: including plasma effects

    CERN Document Server

    Hardy, Edward

    2016-01-01

    Strong constraints on the coupling of new light particles to the Standard Model (SM) arise from their production in the hot cores of stars, and the effects of this on stellar cooling. The large electron density in stellar cores significantly modifies the in-medium propagation of SM states. For new light particles which have an effective in-medium mixing with the photon, such plasma effects can result in parametrically different production rates to those obtained from a naive calculation. Taking these previously-neglected contributions into account, we make updated estimates for the stellar cooling bounds on a number of light new particle candidates. In particular, we improve the bounds on light (m < keV) scalars coupling to electrons or nucleons by up to 3 orders of magnitude in the coupling squared, significantly revise the supernova cooling bounds on dark photon couplings, and qualitatively change the mass dependence of stellar bounds on new vectors.

  9. BOUNDING PYRAMIDS AND BOUNDING CONES FOR TRIANGULAR BEZIER SURFACES

    Institute of Scientific and Technical Information of China (English)

    Jian-song Deng; Fa-lai Chen; Li-li Wang

    2000-01-01

    This paper describes practical approaches on how to construct bounding pyramids and bounding cones for triangular Bézier surfaces. Examples are provided to illustrate the process of construction and comparison is made between various surface bounding volumes. Furthermore, as a starting point for the construction,we provide a way to compute hodographs of triangular Bézier surfaces and improve the algorithm for computing the bounding cone of a set of vectors.

  10. A bound on chaos

    Energy Technology Data Exchange (ETDEWEB)

    Maldacena, Juan [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States); Shenker, Stephen H. [Stanford Institute for Theoretical Physics and Department of Physics, Stanford University,382 Via Pueblo Mall, Stanford, CA (United States); Stanford, Douglas [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States)

    2016-08-17

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent λ{sub L}≤2πk{sub B}T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  11. Regularity of Bound States

    DEFF Research Database (Denmark)

    Faupin, Jeremy; Møller, Jacob Schach; Skibsted, Erik

    2011-01-01

    We study regularity of bound states pertaining to embedded eigenvalues of a self-adjoint operator H, with respect to an auxiliary operator A that is conjugate to H in the sense of Mourre. We work within the framework of singular Mourre theory which enables us to deal with confined massless Pauli–......–Fierz models, our primary example, and many-body AC-Stark Hamiltonians. In the simpler context of regular Mourre theory, our results boil down to an improvement of results obtained recently in [8, 9]....

  12. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent $\\lambda_L \\le 2 \\pi k_B T/\\hbar$. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  13. The Explicit Computations of the Bergman Kernels on Generalized Hua Domains

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@The Bergman kernel function plays an important role in several complex variables. There exists the Bergman kernel function on any bounded domain in Cn. But we can get the Bergman kernel functions in explicit formulas for a few types of domains only, for instance, the bounded homogeneous domains and the egg domains in some cases.

  14. Delay Bounds for Multiclass FIFO

    OpenAIRE

    Jiang, Yuming; Misra, Vishal

    2016-01-01

    FIFO is perhaps the simplest scheduling discipline. For single-class FIFO, its delay guarantee performance has been extensively studied: The well-known results include a stochastic delay bound for $GI/GI/1$ by Kingman and a deterministic delay bound for $D/D/1$ by Cruz. However, for multiclass FIFO, few such results are available. To fill the gap, we prove delay bounds for multiclass FIFO in this work, considering both deterministic and stochastic cases. Specifically, delay bounds are present...

  15. Bounded Fixed-Point Iteration

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1992-01-01

    they obtain a quadratic bound. These bounds are shown to be tight. Specializing the case of strict and additive functions to functionals of a form that would correspond to iterative programs they show that a linear bound is tight. This is related to several analyses studied in the literature (including...

  16. Error bounds for set inclusions

    Institute of Scientific and Technical Information of China (English)

    ZHENG; Xiyin(郑喜印)

    2003-01-01

    A variant of Robinson-Ursescu Theorem is given in normed spaces. Several error bound theorems for convex inclusions are proved and in particular a positive answer to Li and Singer's conjecture is given under weaker assumption than the assumption required in their conjecture. Perturbation error bounds are also studied. As applications, we study error bounds for convex inequality systems.

  17. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    2014-01-01

    Ice cores from Antarctica, from Greenland, and from a number of smaller glaciers around the world yield a wealth of information on past climates and environments. Ice cores offer unique records on past temperatures, atmospheric composition (including greenhouse gases), volcanism, solar activity......, dustiness, and biomass burning, among others. In Antarctica, ice cores extend back more than 800,000 years before present (Jouzel et al. 2007), whereas. Greenland ice cores cover the last 130,000 years...

  18. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    2014-01-01

    Ice cores from Antarctica, from Greenland, and from a number of smaller glaciers around the world yield a wealth of information on past climates and environments. Ice cores offer unique records on past temperatures, atmospheric composition (including greenhouse gases), volcanism, solar activity......, dustiness, and biomass burning, among others. In Antarctica, ice cores extend back more than 800,000 years before present (Jouzel et al. 2007), whereas. Greenland ice cores cover the last 130,000 years...

  19. Multifunctions of bounded variation

    Science.gov (United States)

    Vinter, R. B.

    2016-02-01

    Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.

  20. Bounded Densities and Their Derivatives: Extension to Other Domains

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, Victor

    2009-01-01

    . This paper presents a short introductory discussion on the general area of impecision in statistical theory and practice, and briefly introduces the further papers in this collection, demonstrating the importance of the adequate modelling of imprecision in different aeras of application....

  1. Bounded Densities and Their Derivatives: Extension to Other Domains

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, Victor

    2009-01-01

    . This paper presents a short introductory discussion on the general area of impecision in statistical theory and practice, and briefly introduces the further papers in this collection, demonstrating the importance of the adequate modelling of imprecision in different aeras of application....

  2. Network partition via a bound of the spectral radius

    CERN Document Server

    Mondragon, R J

    2015-01-01

    Based on the density of connections between the nodes of high degree, we introduce two bounds of the spectral radius. We use these bounds to split a network into two sets, one of these sets contains the high degree nodes, we refer to this set as the spectral--core. The degree of the nodes of the subnetwork formed by the spectral--core gives an approximation to the top entries of the leading eigenvector of the whole network. We also present some numerical examples showing the dependancy of the spectral--core with the assortativity coefficient, its evaluation in several real networks and how the properties of the spectral--core can be used to reduce the spectral radius.

  3. A structural role for the PHP domain in E. coli DNA polymerase III.

    Science.gov (United States)

    Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; Lamers, Meindert H

    2013-05-14

    In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

  4. Nuclear dynamics of K¯ bound states

    Science.gov (United States)

    Mareš, J.; Friedman, E.; Gal, A.

    2006-07-01

    K¯ nuclear bound states were generated dynamically within a relativistic mean field (RMF) model. Substantial polarization of the core nucleus was found for light nuclei. The behavior of the dynamically calculated width ΓK¯ as function of the K¯ binding energy was studied. A lower limit of ΓK¯ ˜ 35 - 45 MeV for 1s K¯ nuclear states in light nuclei such as 12C was placed on the width expected for deep binding in the range B K¯ ˜ 100 - 200 MeV.

  5. Schedule refinement for homogeneous multi-core processors in the presence of manufacturing-caused heterogeneity

    Institute of Scientific and Technical Information of China (English)

    Zhi-xiang CHEN; Zhao-lin LI; Shan CAO; Fang WANG; Jie ZHOU

    2015-01-01

    Multi-core homogeneous processors have been widely used to deal with computation-intensive embed-ded applications. However, with the continuous down scaling of CMOS technology, within-die variations in the manufacturing process lead to a significant spread in the operating speeds of cores within homogeneous multi-core processors. Task scheduling approaches, which do not consider such heterogeneity caused by within-die variations, can lead to an overly pessimistic result in terms of performance. To realize an optimal performance according to the actual maximum clock frequencies at which cores can run, we present a heterogeneity-aware schedule refining (HASR) scheme by fully exploiting the heterogeneities of homogeneous multi-core processors in embedded domains. We analyze and show how the actual maximum frequencies of cores are used to guide the scheduling. In the scheme, representative chip operating points are selected and the corresponding optimal schedules are generated as candidate schedules. During the booting of each chip, according to the actual maximum clock frequencies of cores, one of the candidate schedules is bound to the chip to maximize the performance. A set of applications are designed to evaluate the proposed scheme. Experimental results show that the proposed scheme can improve the performance by an average value of 22.2%, compared with the baseline schedule based on the worst case timing analysis. Compared with the conventional task scheduling approach based on the actual maximum clock frequencies, the proposed scheme also improves the performance by up to 12%.

  6. Formation of "bound

    Science.gov (United States)

    Nowak, K.; Kästner, M.; Miltner, A.

    2009-04-01

    During degradation of organic pollutants in soil, metabolites, microbial biomass, CO2and "bound" residues ("non-extractable" residues in soil organic matter) are formed. Enhanced transformation of these contaminants into "bound" residues has been proposed as an alternative remediation method for polluted soils. However, this kind of residues may pose a potential risk for the environment due to their chemical structure and possible remobilization under different conditions. Therefore particular attention is given actually to "bound" residues. Part of these non-extractable residues may be "biogenic," because microorganisms use the carbon from the pollutant to form their biomass components (fatty acids, amino acids, amino sugars), which subsequently may be incorporated into soil organic matter. Furthermore, the CO2 originating from mineralization of xenobiotics, can be re-assimilated by microorganisms and also incorporated into "biogenic residue". The hazard posed by "bound" residues may be overestimated because they are "biogenic" (contain microbial fatty acids and amino acids). The knowledge about the pathways of "biogenic residue" formation is necessary for a proper assessment of the fate of tested pollutants and their turnover in the soil environment. Moreover, these data are needed to establish the realistic degradation rates of the contaminants in soil. The main objectives of this study are: to quantify the extent of "biogenic residue" (fatty acids, amino acids, amino sugars) formation during the degradation of a model pollutant (2,4-dichlorophenoxyacetic acid = 2,4-D) and during CO2 assimilation by microorganisms and to evaluate which components are mainly incorporated into "bound" residues. To investigate the extent of "biogenic residue" formation in soil during the degradation of 2,4-D, experiments with either 14C-U-ring and 13C6-2,4-D or carboxyl-14C 2,4-D were performed. The incubation experiments were performed according to OECD test guideline 307, in the

  7. Efficient Proof Engines for Bounded Model Checking of Hybrid Systems

    DEFF Research Database (Denmark)

    Fränzle, Martin; Herde, Christian

    2005-01-01

    In this paper we present HySat, a new bounded model checker for linear hybrid systems, incorporating a tight integration of a DPLL-based pseudo-Boolean SAT solver and a linear programming routine as core engine. In contrast to related tools like MathSAT, ICS, or CVC, our tool exploits all...

  8. Evaluation Codes from Order Domain Theory

    DEFF Research Database (Denmark)

    Andersen, Henning Ejnar; Geil, Hans Olav

    2008-01-01

    bound is easily extended to deal with any generalized Hamming weights. We interpret our methods into the setting of order domain theory. In this way we fill in an obvious gap in the theory of order domains. [28] T. Shibuya and K. Sakaniwa, A Dual of Well-Behaving Type Designed Minimum Distance, IEICE...

  9. Bounding approaches to system identification

    CERN Document Server

    Norton, John; Piet-Lahanier, Hélène; Walter, Éric

    1996-01-01

    In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.

  10. On functions of bounded variation

    OpenAIRE

    Aistleitner, Christoph; Pausinger, Florian; Svane, Anne Marie; Tichy, Robert F.

    2015-01-01

    The recently introduced concept of $\\mathcal{D}$-variation unifies previous concepts of variation of multivariate functions. In this paper, we give an affirmative answer to the open question from Pausinger \\& Svane (J. Complexity, 2014) whether every function of bounded Hardy--Krause variation is Borel measurable and has bounded $\\mathcal{D}$-variation. Moreover, we show that the space of functions of bounded $\\mathcal{D}$-variation can be turned into a commutative Banach algebra.

  11. Upper bounds for centerlines

    CERN Document Server

    Bukh, Boris

    2011-01-01

    In 2008, Bukh, Matousek, and Nivasch conjectured that for every n-point set S in R^d and every k, 0 <= k <= d-1, there exists a k-flat f in R^d (a "centerflat") that lies at "depth" (k+1) n / (k+d+1) - O(1) in S, in the sense that every halfspace that contains f contains at least that many points of S. This claim is true and tight for k=0 (this is Rado's centerpoint theorem), as well as for k = d-1 (trivial). Bukh et al. showed the existence of a (d-2)-flat at depth (d-1) n / (2d-1) - O(1) (the case k = d-2). In this paper we concentrate on the case k=1 (the case of "centerlines"), in which the conjectured value for the leading constant is 2/(d+2). We prove that 2/(d+2) is an *upper bound* for the leading constant. Specifically, we show that for every fixed d and every n there exists an n-point set in R^d for which no line in R^d lies at depth larger than 2n/(d+2) + o(n). This point set is the "stretched grid"---a set which has been previously used by Bukh et al. for other related purposes.

  12. ABC transporter architecture and regulatory roles of accessory domains

    NARCIS (Netherlands)

    Biemans-Oldehinkel, E; Doeven, MK; Poolman, B

    2006-01-01

    We present an overview of the architecture of ATP-binding cassette (ABC) transporters and dissect the systems in core and accessory domains. The ABC transporter core is formed by the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) that constitute the actual translocator. The a

  13. Clinical grades: upward bound.

    Science.gov (United States)

    Walsh, Catherine M; Seldomridge, Lisa A

    2005-04-01

    This study examined the relationship of grades earned in paired theory and clinical courses. Data collected during academic years 1997 to 2002 confirmed that grade inflation exists in clinical nursing courses. Problems involved in awarding grades for clinical performance are discussed (e.g., standards of clinical performance, methods used in evaluation of clinical performance, the impossibility of faculty omnipresence, the influence of student effort in grading, the effect of recency, the challenges of keeping good anecdotal records). Solutions to grading problems are proposed, including dividing up performance into agreed-on elements, measurement of these elements on a grading scale that allows for more differentiation of quality in evaluating clinical performance, assigning grades from the beginning of a clinical course, emphasizing all three domains of clinical practice, and evaluating student performance in both laboratory and, clinical settings.

  14. The interior transmission problem and bounds on transmission eigenvalues

    CERN Document Server

    Hitrik, Michael; Ola, Petri; Päivärinta, Lassi

    2010-01-01

    We study the interior transmission eigenvalue problem for sign-definite multiplicative perturbations of the Laplacian in a bounded domain. We show that all but finitely many complex transmission eigenvalues are confined to a parabolic neighborhood of the positive real axis.

  15. Dense SDM (12-Core × 3-Mode) Transmission Over 527 km With 33.2-ns Mode-Dispersion Employing Low-Complexity Parallel MIMO Frequency-Domain Equalization

    DEFF Research Database (Denmark)

    Shibahara, Kohki; Lee, Doohwan; Kobayashi, Takayuki;

    2016-01-01

    as intercore crosstalk. Mode dependent loss/gain effect was also mitigated by employing both a ring-core FM erbium-doped fiber amplifier and a free-space optics type gain equalizer. By combining these advanced techniques together, we finally demonstrate 12-core × 3-mode dense SDM transmission over 527-km GI MC...

  16. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2010-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  17. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2008-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  18. New classes of domains with explicit Bergman kernel

    Institute of Scientific and Technical Information of China (English)

    YIN Weiping; LU Keping; Roos GUY

    2004-01-01

    We introduce two classes of egg type domains, built on general boundedsymmetric domains, for which we obtain the Bergman kernel inexplicit formulas. As an auxiliary tool, we compute the integralof complex powers of the generic norm on a bounded symmetricdomains using the well-known integral of Selberg. Thisgeneralizes matrix integrals of Hua and leads to a specialpolynomial with integer or half-integer coefficients attached toeach irreducible bounded symmetric domain.

  19. Kodiak: An Implementation Framework for Branch and Bound Algorithms

    Science.gov (United States)

    Smith, Andrew P.; Munoz, Cesar A.; Narkawicz, Anthony J.; Markevicius, Mantas

    2015-01-01

    Recursive branch and bound algorithms are often used to refine and isolate solutions to several classes of global optimization problems. A rigorous computation framework for the solution of systems of equations and inequalities involving nonlinear real arithmetic over hyper-rectangular variable and parameter domains is presented. It is derived from a generic branch and bound algorithm that has been formally verified, and utilizes self-validating enclosure methods, namely interval arithmetic and, for polynomials and rational functions, Bernstein expansion. Since bounds computed by these enclosure methods are sound, this approach may be used reliably in software verification tools. Advantage is taken of the partial derivatives of the constraint functions involved in the system, firstly to reduce the branching factor by the use of bisection heuristics and secondly to permit the computation of bifurcation sets for systems of ordinary differential equations. The associated software development, Kodiak, is presented, along with examples of three different branch and bound problem types it implements.

  20. A Lower Bound on Concurrence

    Institute of Scientific and Technical Information of China (English)

    LIU Li-Guo; TIAN Cheng-Lin; CHEN Ping-Xing; YUAN Nai-Chang

    2009-01-01

    We derive an analytical lower bound on the concurrence for bipartite quantum systems with an improved computable cross norm or realignment criterion and an improved positive partial transpose criterion respectively.Furthermore we demonstrate that our bound is better than that obtained from the local uncertainty relations criterion with optimal local orthogonal observables which is known as one of the best estimations of concurrence.

  1. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

    In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.

  2. Anaphoric Pronouns and Bound Variables

    Science.gov (United States)

    Wasow, Thomas

    1975-01-01

    Deals with certain problems inherent in deriving anaphoric pronouns from bound variables. Syntactic rules applied to determine anaphora relations cannot be applied if anaphoric pronouns and their antecedents have identical underlying forms. An approach to anaphora which preserves some advantages of the bound-variable theory without the problems is…

  3. Hepatitis C Virus E2 Envelope Glycoprotein Core Structure

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Leopold; Giang, Erick; Nieusma, Travis; Kadam, Rameshwar U.; Cogburn, Kristin E.; Hua, Yuanzi; Dai, Xiaoping; Stanfield, Robyn L.; Burton, Dennis R.; Ward, Andrew B.; Wilson, Ian A.; Law, Mansun

    2014-08-26

    Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.

  4. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...

  5. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    2010-01-01

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...

  6. Asynchronous Bounded Expected Delay Networks

    CERN Document Server

    Bakhshi, Rena; Fokkink, Wan; Pang, Jun

    2010-01-01

    The commonly used asynchronous bounded delay (ABD) network models assume a fixed bound on message delay. We propose a probabilistic network model, called asynchronous bounded expected delay (ABE) model. Instead of a strict bound, the ABE model requires only a bound on the expected message delay. While the conditions of ABD networks restrict the set of possible executions, in ABE networks all asynchronous executions are possible, but executions with extremely long delays are less probable. In contrast to ABD networks, ABE networks cannot be synchronised efficiently. At the example of an election algorithm, we show that the minimal assumptions of ABE networks are sufficient for the development of efficient algorithms. For anonymous, unidirectional ABE rings of known size N we devise a probabilistic leader election algorithm having average message and time complexity O(N).

  7. Post-translational regulation of expression and conformation of an immunoglobulin domain in yeast surface display.

    Science.gov (United States)

    Parthasarathy, Ranganath; Subramanian, Shyamsundar; Boder, Eric T; Discher, Dennis E

    2006-01-01

    Display of heterologous proteins on the surface of Saccharomyces cerevisiae is increasingly being exploited for directed evolution because of straightforward cell screens. However, yeast post-translationally modifies proteins in ways that must be factored into library engineering and refinement. Here, we express the extracellular immunoglobulin domain of an ubiquitous mammalian membrane protein, CD47, which is implicated in cancer, immunocompatibility, and motility. CD47 has multiple sites of glycosylation and a core disulfide bond. We assess the effects of both of these post-translational modifications on expression and antibody binding. CD47's extracellular domain is fused to the yeast mating protein Aga2p on the cell wall, and the resulting fusion protein binds several key antibodies, including a conformation-sensitive antibody. Site-by-site mutagenesis of CD47's five N-linked glycosylation sites progressively decreases expression levels on yeast, but folding appears stable. Cysteine mutations disrupt the expected core disulfide, and also decrease protein expression levels, though not to the extent seen with complete deglycosylation. However, with the core disulfide mutants, antibody binding proves to be lower than expected from expression levels and glycosylation is clearly reduced compared to wild-type. The results indicate that glycosylation regulates heterologous display on yeast more than core disulfides do and thus suggest bounds on directed evolution by post-translational processing.

  8. Peaks, plateaus, canyons, and craters: The complex geometry of simple mid-domain effect models

    DEFF Research Database (Denmark)

    Colwell, Robert K.; Gotelli, Nicholas J.; Rahbek, Carsten

    2009-01-01

    Background: Geographic ranges, randomly located within a bounded geographical domain, Geographic ranges, randomly located within a bounded geographical domain, produce a central hump of species richness (the mid-domain effect, MDE). The hump arises from geometric constraints on the location of ra...... of a uniform size generate more complex patterns, including peaks, plateaus, canyons, and craters of species richness....

  9. Solution NMR Structure of the Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site

    Energy Technology Data Exchange (ETDEWEB)

    Ramelot, Theresa A.; Cort, John R.; Goldsmith-Fischman, Sharon; Kornhaber, Greg J.; Xiao, Rong; Shastry, Ritu; Acton, Thomas; Honig, Barry; Montelione, Gaetano; Kennedy, Michael A.

    2004-11-19

    IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an {alpha}-{beta} sandwich architecture with a three-stranded antiparallel {beta}-sheet and four {alpha}-helices. A nascent helix is located N-terminal to the core structure. The zinc is ligated by three cysteines and one histidine that are located in and near conformationally dynamic loops at one end of the IscU structure. Removal of the zinc metal by chelation results in widespread loss of structure in the apo form. The zinc-bound IscU may be a good model for iron-loaded IscU and may demonstrate structural features found in the iron-sulfur cluster bound form. Structural and functional similarities, genomic context in operons containing other homologous genes, and distributions of conserved surface residues support the hypothesis that IscU protein domains are homologous (i.e. derived from a common ancestor) with the SufE/YgdK family of iron sulfur cluster assembly proteins.

  10. Ice Cores

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature, precipitation, atmospheric trace gases, and other aspects of climate and environment derived from ice cores drilled on glaciers and ice...

  11. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    extensions. Combined with the fact that the language definition does not provide a formal semantics, it is an arduous task to work formally with the language (e.g. to give an implementation). In this paper we identify a core subset of the language, called Core BPEL, which has fewer and simpler constructs......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...... formally with WS-BPEL, as one, without loss of generality, need only consider the much simpler Core BPEL. This report may also be viewed as an addendum to the WS-BPEL standard specification, which clarifies the WS-BPEL syntax and presents the essential elements of the language in a more concise way...

  12. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    extensions. Combined with the fact that the language definition does not provide a formal semantics, it is an arduous task to work formally with the language (e.g. to give an implementation). In this paper we identify a core subset of the language, called Core BPEL, which has fewer and simpler constructs......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...... formally with WS-BPEL, as one, without loss of generality, need only consider the much simpler Core BPEL. This report may also be viewed as an addendum to the WS-BPEL standard specification, which clarifies the WS-BPEL syntax and presents the essential elements of the language in a more concise way...

  13. Core benefits

    National Research Council Canada - National Science Library

    Keith, Brian W

    2010-01-01

    This SPEC Kit explores the core employment benefits of retirement, and life, health, and other insurance -benefits that are typically decided by the parent institution and often have significant governmental regulation...

  14. The Out-bound and In-bound Travelling Market

    Institute of Scientific and Technical Information of China (English)

    Emily Yu

    2009-01-01

    @@ As the Spring Festival of China with a long vocation of seven days nationally is approaching,more and more attention is paid to the out-bound and inn-bound trayeling market.Will people hold their pockets firmly in the"cold winter"of world-wide financial crisis,or will they grab the great discount of traveling and take a good relax?

  15. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  16. Bounds for Certain Character Sums

    Institute of Scientific and Technical Information of China (English)

    杨锦; 郑志勇

    2003-01-01

    This paper shows a connection between exponential sums and character sums. In particular, we introduce a character sum that is an analog of the classical Kloosterman sums and establish the analogous Weil-Estermann's upper bound for it. The paper also analyzes a generalized Hardy-Littlewood example for character sums, which shows that the upper bounds given here are the best possible. The analysis makes use of local bounds for the exponential sums and character sums. The basic theorems have been previously established.

  17. Bounded Model Checking of CTL

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Tao; Cong-Hua Zhou; Zhong Chen; Li-Fu Wang

    2007-01-01

    Bounded Model Checking has been recently introduced as an efficient verification method for reactive systems.This technique reduces model checking of linear temporal logic to propositional satisfiability.In this paper we first present how quantified Boolean decision procedures can replace BDDs.We introduce a bounded model checking procedure for temporal logic CTL* which reduces model checking to the satisfiability of quantified Boolean formulas.Our new technique avoids the space blow up of BDDs, and extends the concept of bounded model checking.

  18. Bounded fractional diffusion in geological media: Definition and Lagrangian approximation

    Science.gov (United States)

    Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang

    2016-11-01

    Spatiotemporal fractional-derivative models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and nonzero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing nonzero-value spatial-nonlocal boundary conditions with directional superdiffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eulerian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the nonlocal and nonsymmetric fractional diffusion. For a nonzero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite domains to those with any size and boundary conditions.

  19. Structure of a human rhinovirus-bivalently bound antibody complex: implications for viral neutralization and antibody flexibility.

    OpenAIRE

    1993-01-01

    The structure of a neutralizing immunoglobulin (monoclonal antibody mAb17-IA), bound to human rhinovirus 14 (HRV14), has been determined by cryo-electron microscopy and image reconstruction. The antibody bound bivalently across icosahedral twofold axes of the virus, and there were no detectable conformational changes in the capsid. Thus, bivalently bound IgGs do not appear to cause gross deformations in the capsid. Differences between the electron density of the constant domains of the bound ...

  20. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    Energy Technology Data Exchange (ETDEWEB)

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. [MSKCC

    2014-08-20

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  1. Computing Constrained Cramer Rao Bounds

    CERN Document Server

    Tune, Paul

    2012-01-01

    We revisit the problem of computing submatrices of the Cram\\'er-Rao bound (CRB), which lower bounds the variance of any unbiased estimator of a vector parameter $\\vth$. We explore iterative methods that avoid direct inversion of the Fisher information matrix, which can be computationally expensive when the dimension of $\\vth$ is large. The computation of the bound is related to the quadratic matrix program, where there are highly efficient methods for solving it. We present several methods, and show that algorithms in prior work are special instances of existing optimization algorithms. Some of these methods converge to the bound monotonically, but in particular, algorithms converging non-monotonically are much faster. We then extend the work to encompass the computation of the CRB when the Fisher information matrix is singular and when the parameter $\\vth$ is subject to constraints. As an application, we consider the design of a data streaming algorithm for network measurement.

  2. An Inequality for Bounded Functions

    CERN Document Server

    Kouba, Omran

    2012-01-01

    In this note we prove optimal inequalities for bounded functions in terms of their deviation from their mean. These results extend and generalize some known inequalities due to Thong (2011) and Perfetti (2011)

  3. Bound states in string nets

    Science.gov (United States)

    Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien

    2016-11-01

    We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

  4. Bound states in string nets

    CERN Document Server

    Schulz, M D; Vidal, J

    2016-01-01

    We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

  5. Some bounds for quantum copying

    CERN Document Server

    Rastegin, A E

    2001-01-01

    We derive lower bounds on the absolute error and the relative error of an abstract copying of two-state set. We do not specify a copying transformation and a dimension of state space. Only the unitarity of quantum mechanical transformations is used. Our approach is based on the notion of angle between two states. We first prove several useful statements, simply expressed in terms of angles. We then examine a lower bound on the absolute error, that was first considered by Hillery and Buzek. Our reasonings supplement and reinforce the results, obtained by them. So, we derive more strong bounds on the absolute error, and we also consider a tradeoff between size of error and corresponding probability distributions. After that we examine a lower bound on the relative error.

  6. Local conformational stability of HIV-1 gp120 in unliganded and CD4-bound states as defined by amide hydrogen/deuterium exchange.

    Science.gov (United States)

    Kong, Leopold; Huang, Chih-Chin; Coales, Stephen J; Molnar, Kathleen S; Skinner, Jeff; Hamuro, Yoshitomo; Kwong, Peter D

    2010-10-01

    The binding reaction of the HIV-1 gp120 envelope glycoprotein to the CD4 receptor involves exceptional changes in enthalpy and entropy. Crystal structures of gp120 in unliganded and various ligand-bound states, meanwhile, reveal an inner domain able to fold into diverse conformations, a structurally invariant outer domain, and, in the CD4-bound state, a bridging sheet minidomain. These studies, however, provide only hints as to the flexibility of each state. Here we use amide hydrogen/deuterium exchange coupled to mass spectrometry to provide quantifications of local conformational stability for HIV-1 gp120 in unliganded and CD4-bound states. On average, unliganded core gp120 displayed >10,000-fold slower exchange of backbone-amide hydrogens than a theoretically unstructured protein of the same composition, with binding by CD4 reducing the rate of gp120 amide exchange a further 10-fold. For the structurally constant CD4, alterations in exchange correlated well with alterations in binding surface (P value = 0.0004). For the structurally variable gp120, however, reductions in flexibility extended outside the binding surface, and regions of expected high structural diversity (inner domain/bridging sheet) displayed roughly 20-fold more rapid exchange in the unliganded state than regions of low diversity (outer domain). Thus, despite an extraordinary reduction in entropy, neither unliganded gp120 nor free CD4 was substantially unstructured, suggesting that most of the diverse conformations that make up the gp120 unliganded state are reasonably ordered. The results provide a framework for understanding how local conformational stability influences entropic change, conformational diversity, and structural rearrangements in the gp120-CD4 binding reaction.

  7. P2-16: Dual-Bound Model and the Role of Time Bound in Perceptual Decision Making

    Directory of Open Access Journals (Sweden)

    Daeseob Lim

    2012-10-01

    Full Text Available The diffusion model (DM encapsulates the dynamics of perceptual decision within a ‘diffusion field’ that is defined by a basis with sensory-evidence (SE and time vectors. At the core of the DM, it assumes that a decision is not made until an evidence particle drifts in the diffusion field and eventually hits one of the two pre-fixed bounds defined in the SE axis. This assumption dictates when and which choice is made by referring to when and which bound will be hit by the evidence particle. What if urgency pressures the decision system to make a choice even when the evidence particle has yet hit the SE bound? Previous modeling attempts at coping with time pressure, despite differences in detail, all manipulated the coordinate of SE bounds. Here, we offer a novel solution by adopting another bound on the time axis. This ‘dual-bound’ model (DBM posits that decisions can also be made when the evidence particle hits a time bound, which is determined on a trial-by-trial basis by a ‘perceived time interval’ – how long the system can stay in the ‘diffusion’ field. The classic single-bound model (SBM exhibited systematic errors in predicting both the reaction time distributions and the time-varying bias in choice. Those errors were not corrected by previously proposed variants of the SBM until the time bound was introduced. The validity of the DBM was further supported by the strong across-individual correlation between observed precision of interval timing and the predicted trial-by-trial variability of the time bound.

  8. Closeness to spheres of hypersurfaces with normal curvature bounded below

    Energy Technology Data Exchange (ETDEWEB)

    Borisenko, A A [Sumy State University, Sumy (Ukraine); Drach, K D [V. N. Karazin Kharkiv National University, Faculty of Mathematics and Mechanics, Kharkiv (Ukraine)

    2013-11-30

    For a Riemannian manifold M{sup n+1} and a compact domain Ω⊂ M{sup n+1} bounded by a hypersurface ∂Ω with normal curvature bounded below, estimates are obtained in terms of the distance from O to ∂Ω for the angle between the geodesic line joining a fixed interior point O in Ω to a point on ∂Ω and the outward normal to the surface. Estimates for the width of a spherical shell containing such a hypersurface are also presented. Bibliography: 9 titles.

  9. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    that enables secure end-to-end communication with home automation devices, and it supports device revocations as well as a structure of intersecting sets of nodes for scalability. Devices in the Trusted Domain are registered in a list that is distributed using a robust epidemic protocol optimized...

  10. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy

    2012-01-01

    In CSCW, how much do we need to know about another domain/culture before we observe, intersect and intervene with designs. What optimally would that other culture need to know about us? Is this a “how long is a piece of string” question, or an inquiry where we can consider a variety of contexts a...

  11. Mutual information challenges entropy bounds

    CERN Document Server

    Casini, H

    2006-01-01

    We consider some formulations of the entropy bounds at the semiclassical level. The entropy S(V) localized in a region V is divergent in quantum field theory (QFT). Instead of it we focus on the mutual information I(V,W)=S(V)+S(W)-S(V U W) between two different non-intersecting sets V and W. This is a low energy quantity, independent of the regularization scheme. In addition, the mutual information is bounded above by twice the entropy corresponding to the sets involved. Calculations of I(V,W) in QFT show that the entropy in empty space cannot be renormalized to zero, and must be actually very large. We find that this entropy due to the vacuum fluctuations violates the FMW bound in Minkowski space. The mutual information also gives a precise, cutoff independent meaning to the statement that the number of degrees of freedom increases with the volume in QFT. If the holographic bound holds, this points to the essential non locality of the physical cutoff. Violations of the Bousso bound would require conformal th...

  12. Exact, approximate solutions and error bounds for coupled implicit systems of partial differential equations

    Directory of Open Access Journals (Sweden)

    Lucas Jódar

    1992-01-01

    Full Text Available In this paper coupled implicit initial-boundary value systems of second order partial differential equations are considered. Given a finite domain and an admissible error ϵ an analytic approximate solution whose error is upper bounded by ϵ in the given domain is constructed in terms of the data.

  13. Bootstrap bound for conformal multi-flavor QCD on lattice

    CERN Document Server

    Nakayama, Yu

    2016-01-01

    The recent work by Iha et al shows an upper bound on mass anomalous dimension $\\gamma_m$ of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in $SU(N_F)_V$ symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in $SU(N_f)_L \\times SU(N_f)_R$ symmetric conformal field theories. For $N_f=8$, our bound implies $\\gamma_m < 1.31$ to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

  14. Bootstrap bound for conformal multi-flavor QCD on lattice

    Energy Technology Data Exchange (ETDEWEB)

    Nakayama, Yu [Department of Physics, Rikkyo University,Toshima, Tokyo 171-8501 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo,5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8583 (Japan)

    2016-07-08

    The recent work by Iha et al. shows an upper bound on mass anomalous dimension γ{sub m} of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in SU(N{sub F}){sub V} symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in SU(N{sub f}){sub L}×SU(N{sub f}){sub R} symmetric conformal field theories. For N{sub f}=8, our bound implies γ{sub m}<1.31 to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

  15. Eta nuclear bound states revisited

    CERN Document Server

    Friedman, E; Mareš, J

    2013-01-01

    The strong energy dependence of the s-wave eta-N scattering amplitude at and below threshold, as evident in coupled-channels K-matrix fits and chiral models that incorporate the S11 N*(1535) resonance, is included self consistently in eta-nuclear bound state calculations. This approach, applied recently in calculations of kaonic atoms and Kbar-nuclear bound states, is found to impose stronger constraints than ever on the onset of eta-nuclear binding, with a minimum value of Re a_{eta N} approximately 0.9 fm required to accommodate an eta-4He bound state. Binding energies and widths of eta-nuclear states are calculated within several underlying eta-N models for nuclei across the periodic table, including eta-25Mg for which some evidence was proposed in a recent COSY experiment.

  16. Improved Range Searching Lower Bounds

    DEFF Research Database (Denmark)

    Larsen, Kasper Green; Nguyen, Huy L.

    2012-01-01

    Table of Contents -------------------------------------------------------------------------------- In this paper we present a number of improved lower bounds for range searching in the pointer machine and the group model. In the pointer machine, we prove lower bounds for the approximate simplex...... range reporting problem. In approximate simplex range reporting, points that lie within a distance of ε ⋅ Diam(s) from the border of a query simplex s, are free to be included or excluded from the output, where ε ≥ 0 is an input parameter to the range searching problem. We prove our lower bounds...... by constructing a hard input set and query set, and then invoking Chazelle and Rosenberg's [CGTA'96] general theorem on the complexity of navigation in the pointer machine. For the group model, we show that input sets and query sets that are hard for range reporting in the pointer machine (i.e. by Chazelle...

  17. Experimental activation of bound entanglement.

    Science.gov (United States)

    Kaneda, Fumihiro; Shimizu, Ryosuke; Ishizaka, Satoshi; Mitsumori, Yasuyoshi; Kosaka, Hideo; Edamatsu, Keiichi

    2012-07-27

    Entanglement is one of the essential resources in quantum information and communication technology (QICT). The entanglement thus far explored and applied to QICT has been pure and distillable entanglement. Yet, there is another type of entanglement, called "bound entanglement," which is not distillable by local operations and classical communication. We demonstrate the experimental "activation" of the bound entanglement held in the four-qubit Smolin state, unleashing its immanent entanglement in distillable form, with the help of auxiliary two-qubit entanglement and local operations and classical communication. We anticipate that it opens the way to a new class of QICT applications that utilize more general classes of entanglement than ever, including bound entanglement.

  18. Distributed k-Core Decomposition

    CERN Document Server

    Montresor, Alberto; Miorandi, Daniele

    2011-01-01

    Among the novel metrics used to study the relative importance of nodes in complex networks, k-core decomposition has found a number of applications in areas as diverse as sociology, proteinomics, graph visualization, and distributed system analysis and design. This paper proposes new distributed algorithms for the computation of the k-core decomposition of a network, with the purpose of (i) enabling the run-time computation of k-cores in "live" distributed systems and (ii) allowing the decomposition, over a set of connected machines, of very large graphs, that cannot be hosted in a single machine. Lower bounds on the algorithms complexity are given, and an exhaustive experimental analysis on real-world graphs is provided.

  19. Inner Core Rotation from Geomagnetic Westward Drift and a Stationary Spherical Vortex in Earth's Core

    Science.gov (United States)

    Voorhies, C. V.

    1999-01-01

    The idea that geomagnetic westward drift indicates convective leveling of the planetary momentum gradient within Earth's core is pursued in search of a differentially rotating mean state, upon which various oscillations and secular effects might be superimposed. The desired state conforms to roughly spherical boundary conditions, minimizes dissipative interference with convective cooling in the bulk of the core, yet may aide core cooling by depositing heat in the uppermost core and lower mantle. The variational calculus of stationary dissipation applied to a spherical vortex within the core yields an interesting differential rotation profile akin to spherical Couette flow bounded by thin Hartmann layers. Four boundary conditions are required. To concentrate shear induced dissipation near the core-mantle boundary, these are taken to be: (i) no-slip at the core-mantle interface; (ii) geomagnetically estimated bulk westward flow at the base of the core-mantle boundary layer; (iii) no-slip at the inner-outer core interface; and, to describe magnetic locking of the inner core to the deep outer core, (iv) hydrodynamically stress-free at the inner-outer core boundary. By boldly assuming the axial core angular momentum anomaly to be zero, the super-rotation of the inner core is calculated to be at most 1.5 degrees per year.

  20. Lower Bounds for Sparse Recovery

    CERN Document Server

    Ba, Khanh Do; Price, Eric; Woodruff, David P

    2011-01-01

    We consider the following k-sparse recovery problem: design an m x n matrix A, such that for any signal x, given Ax we can efficiently recover x' satisfying ||x-x'||_1 <= C min_{k-sparse} x"} ||x-x"||_1. It is known that there exist matrices A with this property that have only O(k log (n/k)) rows. In this paper we show that this bound is tight. Our bound holds even for the more general /randomized/ version of the problem, where A is a random variable and the recovery algorithm is required to work for any fixed x with constant probability (over A).

  1. Variables Bounding Based Retiming Algorithm

    Institute of Scientific and Technical Information of China (English)

    宫宗伟; 林争辉; 陈后鹏

    2002-01-01

    Retiming is a technique for optimizing sequential circuits. In this paper, wediscuss this problem and propose an improved retiming algorithm based on variables bounding.Through the computation of the lower and upper bounds on variables, the algorithm can signi-ficantly reduce the number of constraints and speed up the execution of retiming. Furthermore,the elements of matrixes D and W are computed in a demand-driven way, which can reducethe capacity of memory. It is shown through the experimental results on ISCAS89 benchmarksthat our algorithm is very effective for large-scale sequential circuits.

  2. Bounds for Completely Decomposable Jacobians

    CERN Document Server

    Duursma, Iwan

    2010-01-01

    A curve over the field of two elements with completely decomposable Jacobian is shown to have at most six rational points and genus at most 26. The bounds are sharp. The previous upper bound for the genus was 145. We also show that a curve over the field of $q$ elements with more than $q^{m/2}+1$ rational points has at least one Frobenius angle in the open interval $(\\pi/m,3\\pi/m)$. The proofs make use of the explicit formula method.

  3. Core Java

    CERN Document Server

    Horstmann, Cay S

    2013-01-01

    Fully updated to reflect Java SE 7 language changes, Core Java™, Volume I—Fundamentals, Ninth Edition, is the definitive guide to the Java platform. Designed for serious programmers, this reliable, unbiased, no-nonsense tutorial illuminates key Java language and library features with thoroughly tested code examples. As in previous editions, all code is easy to understand, reflects modern best practices, and is specifically designed to help jumpstart your projects. Volume I quickly brings you up-to-speed on Java SE 7 core language enhancements, including the diamond operator, improved resource handling, and catching of multiple exceptions. All of the code examples have been updated to reflect these enhancements, and complete descriptions of new SE 7 features are integrated with insightful explanations of fundamental Java concepts.

  4. Transmembrane and secreted MUC1 probes show trafficking-dependent changes in O-glycan core profiles.

    Science.gov (United States)

    Engelmann, Katja; Kinlough, Carol L; Müller, Stefan; Razawi, Hani; Baldus, Stephan E; Hughey, Rebecca P; Hanisch, Franz-Georg

    2005-11-01

    The human mucin MUC1 is expressed both as a transmembrane heterodimeric protein complex that recycles via the trans-Golgi network (TGN) and as a secreted isoform. To determine whether differences in cellular trafficking might influence the O-glycosylation profiles on these isoforms, we developed a model system consisting of membrane-bound and secretory-recombinant glycosylation probes. Secretory MUC1-S contains only a truncated repeat domain, whereas in MUC1-M constructs this domain is attached to the native transmembrane and cytoplasmic domains of MUC1 either directly (M0) or via an intermitting nonfunctional (M1) or functional sperm protein-enterokinase-agrin (SEA) module (M2); the SEA module contains a putative proteolytic cleavage site and is associated with proteins receiving extensive O-glycosylation. We showed that MUC1-M2 simulates endogenous MUC1 by recycling from the cell surface of Chinese hamster ovary (CHO) mutant ldlD14 cells through intracellular compartments where its glycosylation continues. The profiles of O-linked glycans on MUC1-S secreted by epithelial EBNA-293 and MCF-7 breast cancer cells revealed patterns dominated by core 2-based oligosaccharides. In contrast, the respective membrane-shed probes expressed in the same cells showed a complete shift to patterns dominated by sialyl core 1. In conclusion, glycan core profiles reflected the subcellular trafficking pathways of the secretory or membranous probes and the modifying activities of the resident glycosyltransferases.

  5. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    2010-01-01

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  6. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  7. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...

  8. Wronskian Method for Bound States

    Science.gov (United States)

    Fernandez, Francisco M.

    2011-01-01

    We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider…

  9. Variational Bounds for Creeping Composites

    Science.gov (United States)

    Procházka, Petr

    2010-05-01

    In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.

  10. Pieter Paul Rubens, "Prometheus Bound."

    Science.gov (United States)

    Shoemaker, Marla K.

    1986-01-01

    Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)

  11. CD(4) has bounded width

    CERN Document Server

    Carvalho, Catarina; Marković, Petar; Maróti, Miklós

    2007-01-01

    We prove that the constraint languages invariant under a short sequence of J\\'onsson terms (containing at most three non-trivial ternary terms) are tractable by showing that they have bounded width. This improves the previous result by Kiss and Valeriote and presents some evidence that the Larose-Zadori conjecture holds in the congruence-distributive case.

  12. Pieter Paul Rubens, "Prometheus Bound."

    Science.gov (United States)

    Shoemaker, Marla K.

    1986-01-01

    Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)

  13. Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide.

    Science.gov (United States)

    Macias, M J; Hyvönen, M; Baraldi, E; Schultz, J; Sudol, M; Saraste, M; Oschkinat, H

    1996-08-15

    The WW domain is a new protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro. It is present in a number of signalling and regulatory proteins, often in several copies. Here we investigate the solution structure of the WW domain of human YAP65 (for Yes kinase-associated protein) in complex with proline-rich peptides containing the core motif PPxY. The structure of the domain with the bound peptide GTPPPPYTVG is a slightly curved, three-stranded, antiparallel beta-sheet. Two prolines pack against the first tryptophan, forming a hydrophobic buckle on the convex side of the sheet. The concave side has three exposed hydrophobic residues (tyrosine, tryptophan and leucine) which form the binding site for the ligand. A non-conserved isoleucine in the amino-terminal flanking region covers a hydrophobic patch and stabilizes the WW domain of human YAP65 in vitro. The structure of the WW domain differs from that of the SH3 domain and reveals a new design for a protein module that uses stacked aromatic surface residues to arrange a binding site for proline-rich peptides.

  14. A Functional Calculus for Quotient Bounded Operators

    Directory of Open Access Journals (Sweden)

    Sorin Mirel Stoian

    2006-12-01

    Full Text Available If (X, P is a sequentially locally convex space, then a quotient bounded operator T beloging to QP is regular (in the sense of Waelbroeck if and only if it is a bounded element (in the sense of Allan of algebra QP. The classic functional calculus for bounded operators on Banach space is generalized for bounded elements of algebra QP.

  15. Domain Walls in SU(5)

    CERN Document Server

    Poghosian, L E; Pogosian, Levon; Vachaspati, Tanmay

    2000-01-01

    We consider the Grand Unified SU(5) model with a small or vanishing cubic term in the adjoint scalar field in the potential. This gives the model an approximate or exact Z$_2$ symmetry whose breaking leads to domain walls. The simplest domain wall has the structure of a kink across which the Higgs field changes sign ($\\Phi \\to -\\Phi$) and inside which the full SU(5) is restored. The kink is shown to be perturbatively unstable for all parameters. We then construct a domain wall solution that is lighter than the kink and show it to be perturbatively stable for a range of parameters. The symmetry in the core of this domain wall is smaller than that outside. The interactions of the domain wall with magnetic monopole is discussed and it is shown that magnetic monopoles with certain internal space orientations relative to the wall pass through the domain wall. Magnetic monopoles in other relative internal space orientations are likely to be swept away on collision with the domain walls, suggesting a scenario where ...

  16. Bimodal intramolecular excitation energy transfer in a multichromophore photosynthetic model system: hybrid fusion proteins comprising natural phycobilin- and artificial chlorophyll-binding domains.

    Science.gov (United States)

    Zeng, Xiao-Li; Tang, Kun; Zhou, Nan; Zhou, Ming; Hou, Harvey J M; Scheer, Hugo; Zhao, Kai-Hong; Noy, Dror

    2013-09-11

    The phycobilisomes of cyanobacteria and red-algae are highly efficient peripheral light-harvesting complexes that capture and transfer light energy in a cascade of excitation energy transfer steps through multiple phycobilin chromophores to the chlorophylls of core photosystems. In this work, we focus on the last step of this process by constructing simple functional analogs of natural phycobilisome-photosystem complexes that are based on bichromophoric protein complexes comprising a phycobilin- and a chlorophyll- or porphyrin-binding domain. The former is based on ApcE(1-240), the N-terminal chromophore-binding domain of the phycobilisome's L(CM) core-membrane linker, and the latter on HP7, a de novo designed four-helix bundle protein that was originally planned as a high-affinity heme-binding protein, analogous to b-type cytochromes. We fused a modified HP7 protein sequence to ApcEΔ, a water-soluble fragment of ApcE(1-240) obtained by excising a putative hydrophobic loop sequence of residues 77-153. HP7 was fused either to the N- or the C-terminus of ApcEΔ or inserted between residues 76 and 78, thereby replacing the native hydrophobic loop domain. We describe the assembly, spectral characteristics, and intramolecular excitation energy transfer of two unique systems: in the first, the short-wavelength absorbing zinc-mesoporphyrin is bound to the HP7 domain and serves as an excitation-energy donor to the long-wavelength absorbing phycocyanobilin bound to the ApcE domain; in the second, the short-wavelength absorbing phycoerythrobilin is bound to the ApcE domain and serves as an excitation energy donor to the long-wavelength absorbing zinc-bacteriochlorophyllide bound to the HP7 domain. All the systems that were constructed and tested exhibited significant intramolecular fluorescence resonance energy transfer with yields ranging from 21% to 50%. This confirms that our modular, covalent approach for studying EET between the cyclic and open chain tetrapyrroles is

  17. Papain digestion of crude Trichoderma reesei cellulase: Purification and properties of cellobiohydrolase I and II core proteins

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Brown, J.P.; Evans, B.R.; Affholter, K.A.

    1992-01-01

    Papain digestion of a crude Trichoderma reesei cellulose preparation followed by gel filtration on a Superdex column resulted in the separation of cellobiohydrolase (CBH) I and II core proteins (cp). They were further purified to apparent homogeneity by chromatofocusing. N-terminal protein sequencing of the CBH II cp preparation confirmed its identity. A comparison of the catalytic activity and cellulose-binding ability of these core proteins was made. The major differences between them were the findings that CBH II cp possessed a sixfold higher specific activity toward p-nitrophenylcellobioside than the native CBH II preparation and still bound to microcrystalline cellulose, unlike CBH I cp. Neither CBH I cp nor CBH II cp had activity toward carboxymethylcellulose, but both were able to hydrolyze barley b-glucan. These data suggest that removal of the cellulose-binding domain and hinge region from CBH I and II have different effects on their properties.

  18. Papain digestion of crude Trichoderma reesei cellulase: Purification and properties of cellobiohydrolase I and II core proteins

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J.; Brown, J.P.; Evans, B.R.; Affholter, K.A.

    1992-12-01

    Papain digestion of a crude Trichoderma reesei cellulose preparation followed by gel filtration on a Superdex column resulted in the separation of cellobiohydrolase (CBH) I and II core proteins (cp). They were further purified to apparent homogeneity by chromatofocusing. N-terminal protein sequencing of the CBH II cp preparation confirmed its identity. A comparison of the catalytic activity and cellulose-binding ability of these core proteins was made. The major differences between them were the findings that CBH II cp possessed a sixfold higher specific activity toward p-nitrophenylcellobioside than the native CBH II preparation and still bound to microcrystalline cellulose, unlike CBH I cp. Neither CBH I cp nor CBH II cp had activity toward carboxymethylcellulose, but both were able to hydrolyze barley b-glucan. These data suggest that removal of the cellulose-binding domain and hinge region from CBH I and II have different effects on their properties.

  19. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    Chhanda Samanta

    2001-08-01

    The essential aspect of contemporary physics is to understand properties of nucleonic matter that constitutes the world around us. Over the years research in nuclear physics has provided strong guidance in understanding the basic principles of nuclear interactions. But, the scenario of nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare nuclei are posing new challenges to both theory and experiments. Fortunately, nature has provided a few loosely bound stable nuclei that have been studied thoroughly for decades. Attempts are being made to find a consistent picture for the unstable nuclei starting from their stable counterparts. Some significant differences in the structure and reaction mechanisms are found.

  20. Space-bounded communication complexity

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.

    2013-01-01

    In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory....... When a player receives a bit of communication, he "compresses" his state. This compression may be an arbitrary function of his current memory contents, his input, and the bit of communication just received; the only restriction is that the compression must return at most s(n) bits. We obtain memory...

  1. Characterizing Class I WW domains defines key specificity determinants and generates mutant domains with novel specificities.

    Science.gov (United States)

    Kasanov, J; Pirozzi, G; Uveges, A J; Kay, B K

    2001-03-01

    WW domains are small protein interaction modules found in a wide range of eukaryotic signaling and structural proteins. Five classes of WW domains have been annotated to date, where each class is largely defined by the type of peptide ligand selected, rather than by similarities within WW domains. Class I WW domains bind Pro-Pro-Xxx-Tyr containing ligands, and it would be of interest to determine residues within the domains that determine this specificity. Fourteen WW domains selected Leu/Pro-Pro-Xxx-Tyr containing peptides ligands via phage display and were thus designated as Class 1 WW domains. These domains include those present in human YAP (hYAP) and WWP3, as well as those found in ubiquitin protein ligases of the Nedd4 family, including mouse Nedd4 (mNedd4), WWP1, WWP2 and Rsp5. Comparing the primary structures of these WW domains highlighted a set of highly conserved residues, in addition to those originally noted to occur within WW domains. Substitutions at two of these conserved positions completely inhibited ligand binding, whereas substitution at a non-conserved position did not. Moreover, mutant WW domains containing substitutions at conserved positions bound novel peptide ligands. Class I WW domains contain a highly conserved set of residues that are important in selecting Pro-Xxx-Tyr containing peptide ligands. The presence of these residues within an uncharacterized WW domain can be used to predict its ability to bind Pro-Xxx-Tyr containing peptide ligands.

  2. Wronskian method for bound states

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, Francisco M, E-mail: fernande@quimica.unlp.edu.ar [INIFTA (UNLP, CONICET), Division Quimica Teorica, Boulevard 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2011-05-15

    We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider an exactly solvable model, the Gaussian potential well, and a two-well potential proposed earlier for the interpretation of the infrared spectrum of ammonia.

  3. Bound Modes in Dielectric Microcavities

    CERN Document Server

    Visser, P M; Lenstra, D

    2002-01-01

    We demonstrate how exactly bound cavity modes can be realized in dielectric structures other than 3d photonic crystals. For a microcavity consisting of crossed anisotropic layers, we derive the cavity resonance frequencies, and spontaneous emission rates. For a dielectric structure with dissipative loss and central layer with gain, the beta factor of direct spontaneous emission into a cavity mode and the laser threshold is calculated.

  4. Entropy Bounds in Spherical Space

    CERN Document Server

    Brevik, I; Odintsov, S D; Brevik, Iver; Milton, Kimball A.; Odintsov, Sergei D.

    2002-01-01

    Exact calculations are given for the Casimir energy for various fields in $R\\times S^3$ geometry. The Green's function method naturally gives a result in a form convenient in the high-temperature limit, while the statistical mechanical approach gives a form appropriate for low temperatures. The equivalence of these two representations is demonstrated. Some discrepancies with previous work are noted. In no case, even for ${\\cal N}=4$ SUSY, is the ratio of entropy to energy found to be bounded.

  5. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math...

    Science.gov (United States)

    2013-03-26

    ... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... Upward Bound Math Science Annual Performance Report. OMB Control Number: 1840-NEW. Type of Review: New... under the regular Upward Bound (UB) and Upward Bound Math and Science (UBMS) Programs. The Department is...

  6. On the structure of Fatou domains

    Institute of Scientific and Technical Information of China (English)

    CUI GuiZhen; PENG Wen Juan

    2008-01-01

    Let U be a multiply-connected fixed attracting Fatou domain of a rational map f. We prove that there exist a rational map g and a completely invariant Fatou domain Ⅴ of g such that (f, U)and (g, V) are holomorphically conjugate, and each non-trivial Julia component of g is a quasi-circle which bounds an eventually superattracting Fatou domain of g containing at most one postcritical point of g. Moreover, g is unique up to a holomorphic conjugation.

  7. On the structure of Fatou domains

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Let U be a multiply-connected fixed attracting Fatou domain of a rational map f.We prove that there exist a rational map g and a completely invariant Fatou domain V of g such that(f,U) and(g,V) are holomorphically conjugate,and each non-trivial Julia component of g is a quasi-circle which bounds an eventually superattracting Fatou domain of g containing at most one postcritical point of g.Moreover,g is unique up to a holomorphic conjugation.

  8. The Cost of Bounded Curvature

    CERN Document Server

    Kim, Hyo-Sil

    2011-01-01

    We study the motion-planning problem for a car-like robot whose turning radius is bounded from below by one and which is allowed to move in the forward direction only (Dubins car). For two robot configurations $\\sigma, \\sigma'$, let $\\ell(\\sigma, \\sigma')$ be the shortest bounded-curvature path from $\\sigma$ to $\\sigma'$. For $d \\geq 0$, let $\\ell(d)$ be the supremum of $\\ell(\\sigma, \\sigma')$, over all pairs $(\\sigma, \\sigma')$ that are at Euclidean distance $d$. We study the function $\\dub(d) = \\ell(d) - d$, which expresses the difference between the bounded-curvature path length and the Euclidean distance of its endpoints. We show that $\\dub(d)$ decreases monotonically from $\\dub(0) = 7\\pi/3$ to $\\dub(\\ds) = 2\\pi$, and is constant for $d \\geq \\ds$. Here $\\ds \\approx 1.5874$. We describe pairs of configurations that exhibit the worst-case of $\\dub(d)$ for every distance $d$.

  9. Bounds on Black Hole Spins

    CERN Document Server

    Daly, Ruth A

    2009-01-01

    Beam powers and black hole masses of 48 extended radio sources are combined to obtain lower bounds on the spins and magnetic field strengths of supermassive black holes. This is done in the context of the models of Blandford & Znajek (1977) (the 'BZ' model) and Meier (1999); a parameterization for bounds in the context of other models is suggested. The bounds obtained for very powerful classical double radio sources in the BZ model are consistent with black hole spins of order unity for sources at high redshift. The black hole spins are largest for the highest redshift sources and decrease for sources at lower redshift; the sources studied have redshifts between zero and two. Lower power radio sources associated with central dominant galaxies may have black hole spins that are significantly less than one. Combining this analysis with other results suggests that the maximum values of black hole spin associated with powerful radio galaxies decline from values of order unity at a redshift of 2 to values of o...

  10. Bounds on Generalized Huffman Codes

    CERN Document Server

    Baer, Michael B

    2007-01-01

    New lower and upper bounds are obtained for the compression of optimal binary prefix codes according to various nonlinear codeword length objectives. Like the coding bounds for Huffman coding - which concern the traditional linear code objective of minimizing average codeword length -- these are in terms of a form of entropy and the probability of the most probable input symbol. As in Huffman coding, some upper bounds can be found using sufficient conditions for the codeword corresponding to the most probable symbol being one bit long. Whereas having probability no less than 0.4 is a tight sufficient condition for this to be the case in Huffman coding, other penalties differ, some having a tighter condition, some a looser condition, and others having no such sufficient condition. The objectives explored here are ones for which optimal codes can be found using a generalized form of Huffman coding. These objectives include one related to queueing (an increasing exponential average), one related to single-shot c...

  11. [beta subsccript 2]-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Cong; Sawaya, Michael R.; Eisenberg, David (UCLA)

    2011-08-09

    {beta}{sub 2}-microglobulin ({beta}{sub 2}-m) is the light chain of the type I major histocompatibility complex. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. Despite the devastating effects of dialysis-related amyloidosis, full understanding of how fibrils form from soluble {beta}{sub 2}-m remains elusive. Here we show that {beta}{sub 2}-m can oligomerize and fibrillize via three-dimensional domain swapping. Isolating a covalently bound, domain-swapped dimer from {beta}{sub 2}-m oligomers on the pathway to fibrils, we were able to determine its crystal structure. The hinge loop that connects the swapped domain to the core domain includes the fibrillizing segment LSFSKD, whose atomic structure we also determined. The LSFSKD structure reveals a class 5 steric zipper, akin to other amyloid spines. The structures of the dimer and the zipper spine fit well into an atomic model for this fibrillar form of {beta}{sub 2}-m, which assembles slowly under physiological conditions.

  12. On interpretations of bounded arithmetic and bounded set theory

    CERN Document Server

    Pettigrew, Richard

    2008-01-01

    In a recent paper, Kaye and Wong proved the following result, which they considered to belong to the folklore of mathematical logic. THEOREM: The first-order theories of Peano arithmetic and ZF with the axiom of infinity negated are mutually interpretable with interpretations that are inverse to each other. In this note, I describe a theory of sets that stands in the same relation to the bounded arithmetic IDelta0 + exp. Because of the weakness of this theory of sets, I cannot straightforwardly adapt Kaye and Wong's interpretation of the arithmetic in the set theory. Instead, I am forced to produce a different interpretation.

  13. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter

    2004-01-01

    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function....... The bounds apply to moregeneral problems than existing bounding methods do. For instance, since strict concavityis not required, linear models and piecewise linear approximations can bedealt with. Despite the generality, the bounds perform well in comparison with existingmethods even when applied...... to approximations of a standard (strictly concave)growth model.KEYWORDS: Numerical approximation errors, Bellman contractions, Error bounds...

  14. Verifying the error bound of numerical computation implemented in computer systems

    Science.gov (United States)

    Sawada, Jun

    2013-03-12

    A verification tool receives a finite precision definition for an approximation of an infinite precision numerical function implemented in a processor in the form of a polynomial of bounded functions. The verification tool receives a domain for verifying outputs of segments associated with the infinite precision numerical function. The verification tool splits the domain into at least two segments, wherein each segment is non-overlapping with any other segment and converts, for each segment, a polynomial of bounded functions for the segment to a simplified formula comprising a polynomial, an inequality, and a constant for a selected segment. The verification tool calculates upper bounds of the polynomial for the at least two segments, beginning with the selected segment and reports the segments that violate a bounding condition.

  15. .Gov Domains API

    Data.gov (United States)

    General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

  16. The Upper Bounds of Arbitrary Eigenvalues for Uniformly Elliptic Operators with Higher Orders

    Institute of Scientific and Technical Information of China (English)

    Gao Jia; Xiao-ping Yang

    2006-01-01

    Let Ω(∪)Rm (m≥2) be a bounded domain with piecewise smooth and Lipschitz boundary (e)Ω. Let t and r be two nonnegative integers with t ≥ r + 1. In this paper, we consider the variable-coefficient eigenvalue problems with uniformly elliptic differential operators on the left-hand side and (-△)r on the right-hand side.Some upper bounds of the arbitrary eigenvalue are obtained, and several known results are generalized.

  17. Bound Polaron Pair Formation in Poly (phenylenevinylenes)

    Science.gov (United States)

    Rothberg, Lewis

    The following sections are included: * INTRODUCTION * PHOTOGENERATED YIELD OF SINGLET EXCITONS * AGGREGRATION EFFECTS ON EXCITED STATE PHOTO-GENERATION * ASSIGNMENT TO BOUND POLARON PAIRS AND DISCUSSION * PROBLEMS WITH THE BOUND POLARON PAIR PICTURE AND CONCLUSION * REFERENCES

  18. An Exponential Bound for Cox Regression☆

    Science.gov (United States)

    Kosorok, M. R.

    2012-01-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold. PMID:23565013

  19. An Exponential Bound for Cox Regression.

    Science.gov (United States)

    Goldberg, Y; Kosorok, M R

    2012-07-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold.

  20. New bounds for multi-dimensional packing

    OpenAIRE

    Seiden, S.; Stee, van, Rob

    2001-01-01

    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d=2, are as follows: A new upper bound of 2.66013 for online box packing, a new $14/9 + varepsilon$ polynomial time offline approximation algorithm for square packing, a new upper bound ...

  1. Computational rationality: linking mechanism and behavior through bounded utility maximization.

    Science.gov (United States)

    Lewis, Richard L; Howes, Andrew; Singh, Satinder

    2014-04-01

    We propose a framework for including information-processing bounds in rational analyses. It is an application of bounded optimality (Russell & Subramanian, 1995) to the challenges of developing theories of mechanism and behavior. The framework is based on the idea that behaviors are generated by cognitive mechanisms that are adapted to the structure of not only the environment but also the mind and brain itself. We call the framework computational rationality to emphasize the incorporation of computational mechanism into the definition of rational action. Theories are specified as optimal program problems, defined by an adaptation environment, a bounded machine, and a utility function. Such theories yield different classes of explanation, depending on the extent to which they emphasize adaptation to bounds, and adaptation to some ecology that differs from the immediate local environment. We illustrate this variation with examples from three domains: visual attention in a linguistic task, manual response ordering, and reasoning. We explore the relation of this framework to existing "levels" approaches to explanation, and to other optimality-based modeling approaches.

  2. The helical domain of a G protein alpha subunit is a regulator of its effector.

    Science.gov (United States)

    Liu, W; Northup, J K

    1998-10-27

    The alpha subunit (Galpha) of heterotrimeric G proteins is a major determinant of signaling selectivity. The Galpha structure essentially comprises a GTPase "Ras-like" domain (RasD) and a unique alpha-helical domain (HD). We used the vertebrate phototransduction model to test for potential functions of HD and found that the HD of the retinal transducin Galpha (Galphat) and the closely related gustducin (Galphag), but not Galphai1, Galphas, or Galphaq synergistically enhance guanosine 5'-gamma[-thio]triphosphate bound Galphat (GalphatGTPgammaS) activation of bovine rod cGMP phosphodiesterase (PDE). In addition, both HDt and HDg, but not HDi1, HDs, or HDq attenuate the trypsin-activated PDE. GalphatGDP and HDt attenuation of trypsin-activated PDE saturate with similar affinities and to an identical 38% of initial activity. These data suggest that interaction of intact Galphat with the PDE catalytic core may be caused by the HD moiety, and they indicate an independent site(s) for the HD moiety of Galphat within the PDE catalytic core in addition to the sites for the inhibitory Pgamma subunits. The HD moiety of GalphatGDP is an attenuator of the activated catalytic core, whereas in the presence of activated GalphatGTPgammaS the independently expressed HDt is a potent synergist. Rhodopsin catalysis of Galphat activation enhances the PDE activation produced by subsaturating levels of Galphat, suggesting a HD-moiety synergism from a transient conformation of Galphat. These results establish HD-selective regulations of vertebrate retinal PDE, and they provide evidence demonstrating that the HD is a modulatory domain. We suggest that the HD works in concert with the RasD, enhancing the efficiency of G protein signaling.

  3. Probability bounds analysis for nonlinear population ecology models.

    Science.gov (United States)

    Enszer, Joshua A; Andrei Măceș, D; Stadtherr, Mark A

    2015-09-01

    Mathematical models in population ecology often involve parameters that are empirically determined and inherently uncertain, with probability distributions for the uncertainties not known precisely. Propagating such imprecise uncertainties rigorously through a model to determine their effect on model outputs can be a challenging problem. We illustrate here a method for the direct propagation of uncertainties represented by probability bounds though nonlinear, continuous-time, dynamic models in population ecology. This makes it possible to determine rigorous bounds on the probability that some specified outcome for a population is achieved, which can be a core problem in ecosystem modeling for risk assessment and management. Results can be obtained at a computational cost that is considerably less than that required by statistical sampling methods such as Monte Carlo analysis. The method is demonstrated using three example systems, with focus on a model of an experimental aquatic food web subject to the effects of contamination by ionic liquids, a new class of potentially important industrial chemicals.

  4. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    D. Massaro

    2012-01-01

    This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of

  5. Bound entangled states invariant under Ux

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Wang Zhi-Xi

    2008-01-01

    This paper obtains an entangled condition for isotropic-like states by using an atomic map. It constructs a class of bound entangled states from the entangled condition and shows that the partial transposition of the state from the constructed bound entangled class is an edge bound entangled state by using range criterion.

  6. Tight adversary bounds for composite functions

    NARCIS (Netherlands)

    Hoyer, P.; Spalek, R.

    2005-01-01

    The quantum adversary method is a very versatile method for proving lower bounds on quantum algorithms. It has many equivalent formulations, yields tight bounds for many computational problems, and has natural connections to classical lower bounds. One of its formulations is in terms of the spectral

  7. Determining Normal-Distribution Tolerance Bounds Graphically

    Science.gov (United States)

    Mezzacappa, M. A.

    1983-01-01

    Graphical method requires calculations and table lookup. Distribution established from only three points: mean upper and lower confidence bounds and lower confidence bound of standard deviation. Method requires only few calculations with simple equations. Graphical procedure establishes best-fit line for measured data and bounds for selected confidence level and any distribution percentile.

  8. Computing the bounds on the loss rates

    OpenAIRE

    Fourneau J.-M.; Mokdad L.; Pekergin N.

    2002-01-01

    We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.

  9. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil

    2014-01-01

    graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...

  10. Counting Young Tableaux of Bounded Height

    Science.gov (United States)

    Bergeron, Francois; Gascon, Francis

    2000-03-01

    We show that formulas of Gessel, for the generating functions for Young standard tableaux of height bounded by k (see [2]), satisfy linear differential equations, with polynomial coefficients, equivalent to P-recurrences conjectured by Favreau, Krob and the first author (see [1]) for the number of bounded height tableaux and pairs of bounded height tableaux.

  11. Boosting equal time bound states

    CERN Document Server

    Dietrich, Dennis D; Jarvinen, Matti

    2012-01-01

    We present an explicit and exact boost of a relativistic bound state defined at equal time of the constituents in the Born approximation (lowest order in hbar). To this end, we construct the Poincar\\'e generators of QED and QCD in D=1+1 dimensions, using Gauss' law to express A^0 in terms of the fermion fields in A^1=0 gauge. We determine the fermion-antifermion bound states in the Born approximation as eigenstates of the time and space translation generators P^0 and P^1. The boost operator is combined with a gauge transformation so as to maintain the gauge condition A^1=0 in the new frame. We verify that the boosted state remains an eigenstate of P^0 and P^1 with appropriately transformed eigenvalues and determine the transformation law of the equal-time, relativistic wave function. The shape of the wave function is independent of the CM momentum when expressed in terms of a variable, which is quadratically related to the distance x between the fermions. As a consequence, the Lorentz contraction of the wave ...

  12. Asymmetric dark matter bound state

    Science.gov (United States)

    Bi, Xiao-Jun; Kang, Zhaofeng; Ko, P.; Li, Jinmian; Li, Tianjun

    2017-02-01

    We propose an interesting framework for asymmetric scalar dark matter (ADM), which has novel collider phenomenology in terms of an unstable ADM bound state (ADMonium) produced via Higgs portals. ADMonium is a natural consequence of the basic features of ADM: the (complex scalar) ADM is charged under a dark local U (1 )d symmetry which is broken at a low scale and provides a light gauge boson X . The dark gauge coupling is strong and then ADM can annihilate away into X -pair effectively. Therefore, the ADM can form a bound state due to its large self-interaction via X mediation. To explore the collider signature of ADMonium, we propose that ADM has a two-Higgs doublet portal. The ADMonium can have a sizable mixing with the heavier Higgs boson, which admits a large cross section of ADMonium production associated with b b ¯. The resulting signature at the LHC depends on the decays of X . In this paper we consider a case of particular interest: p p →b b ¯ +ADMonium followed by ADMonium→2 X →2 e+e- where the electrons are identified as (un)converted photons. It may provide a competitive explanation to heavy di-photon resonance searches at the LHC.

  13. Endurance bounds of aerial systems

    Science.gov (United States)

    Harrington, Aaron M.; Kroninger, Christopher M.

    2014-06-01

    Within the past few years micro aerial vehicles (MAVs) have received much more attention and are starting to proliferate into military as well as civilian roles. However, one of the major drawbacks for this technology currently, has been their poor endurance, usually below 10 minutes. This is a direct result of the inefficiencies inherent in their design. Often times, designers do not consider the various components in the vehicle design and match their performance to the desired mission for the vehicle. These vehicles lack a prescribed set of design guidelines or empirically derived design equations which often limits their design to selection of commercial off-the-shelf components without proper consideration of their affect on vehicle performance. In the current study, the design space for different vehicle configurations has been examined including insect flapping, avian flapping, rotary wing, and fixed wing, and their performance bounds are established. The propulsion system typical of a rotary wing vehicle is analyzed to establish current baselines for efficiency of vehicles at this scale. The power draw from communications is analyzed to determine its impact on vehicle performance. Finally, a representative fixed wing MAV is examined and the effects of adaptive structures as a means for increasing vehicle endurance and range are examined. This paper seeks to establish the performance bounds for micro air vehicles and establish a path forward for future designs so that efficiency may be maximized.

  14. Subdivision, Sampling, and Initialization Strategies for Simplical Branch and Bound in Global Optimization

    DEFF Research Database (Denmark)

    Clausen, Jens; Zilinskas, A,

    2002-01-01

    two schemes for sampling points of the function: midpoint sampling and vertex sampling. The convergence of the algorithm is proved, and numerical results are presented for the two dimensional case, for which also a special initial covering is presented. (C) 2002 Elsevier Science Ltd. All rights......We consider the problem of optimizing a Lipshitzian function. The branch and bound technique is a well-known solution method, and the key components for this are the subdivision scheme, the bound calculation scheme, and the initialization. For Lipschitzian optimization, the bound calculations...... are based on the sampling of function values. We propose a branch and bound algorithm based on regular simplexes. Initially, the domain in question is covered with regular simplexes, and our subdivision scheme maintains this property. The bound calculation becomes both simple and efficient, and we describe...

  15. Dielectric relaxation time and structure of bound water in biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Mashimo, S.; Kuwabara, S.; Yagihara, S.; Higasi, K.

    1987-12-03

    The dielectric behavior of living tissues and a number of biological materials was examined by new equipment of the time domain reflectometry method in a wide frequency range of 10/sup 7/-10/sup 10/ Hz. The authors found two peaks of Debye absorption around 100 MHz and 20 GHz for all the materials. The low-frequency absorption is probably due to bound water while the high-frequency absorption to free water. From the observed relaxation times of bound water a hypothesis is ventured on the structure of bound water and its relaxation mechanism.

  16. Probing Andreev bound states in one-atom superconducting contacts

    Energy Technology Data Exchange (ETDEWEB)

    Pothier, Hugues; Janvier, Camille; Tosi, Leandro; Girit, Caglar; Goffman, Marcelo; Esteve, Daniel; Urbina, Cristian [Quantronics Group, SPEC, CEA-Saclay (France)

    2015-07-01

    Superconductors are characterized by a dissipationless current. Since the work of Josephson 50 years ago, it is known that a supercurrent can even flow through tunnel junctions between superconductors. This Josephson effect also occurs through any type of ''weak links'' between superconductors: non-superconducting materials, constrictions,.. A unified understanding of the Josephson effect has emerged from a mesoscopic description of weak links. It relies on the existence of doublets of localized states that have energies below the superconducting gap: the Andreev bound states. I will present experiments performed on the simplest conductor possible, a single-atom contact between superconductors, that illustrate these concepts. The most recent work demonstrates time-domain manipulation of quantum superpositions of Andreev bound states.

  17. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4

    Institute of Scientific and Technical Information of China (English)

    Nianshuang Wang; Xuanling Shi; Liwei Jiang; Senyan Zhang; Dongli Wang; Pei Tong; Dongxing Guo

    2013-01-01

    The spike glycoprotein (S) of recently identified Middle East respiratory syndrome coronavirus (MERS-CoV) targets the cellular receptor,dipeptidyl peptidase 4 (DPP4).Sequence comparison and modeling analysis have revealed a putative receptor-binding domain (RBD) on the viral spike,which mediates this interaction.We report the 3.0 (A)resolution crystal structure of MERS-CoV RBD bound to the extracellular domain of human DPP4.Our results show that MERS-CoV RBD consists of a core and a receptor-binding subdomain.The receptor-binding subdomain interacts with DPP4 p-propeller but not its intrinsic hydrolase domain.MERS-CoV RBD and related SARS-CoV RBD share a high degree of structural similarity in their core subdomains,but are notably divergent in the receptorbinding subdomain.Mutagenesis studies have identified several key residues in the receptor-binding subdomain that are critical for viral binding to DPP4 and entry into the target cell.The atomic details at the interface between MERS-CoV RBD and DPP4 provide structural understanding of the virus and receptor interaction,which can guide development of therapeutics and vaccines against MERS-CoV infection.

  18. Decoherence in time evolution of bound entanglement

    CERN Document Server

    Sun, Z; Sun, C P; Wang, X; Sun, Zhe; Wang, Xiaoguang

    2007-01-01

    We study a dynamic process of disentanglement by considering the time evolution of bound entanglement for a quantum open system, two qutrits coupling to a common environment. Here, the initial quantum correlations of the two qutrits are characterized by the bound entanglement. In order to show the universality of the role of environment on bound entanglement, both bosonic and spin environments are considered. We found that the bound entanglement displays collapses and revivals, and it can be stable against small temperature and time change. The thermal fluctuation effects on bound entanglement are also considered.

  19. Bounded fractional diffusion in geological media: Definition and Lagrangian approximation

    Science.gov (United States)

    Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang

    2016-01-01

    Spatiotemporal Fractional-Derivative Models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and non-zero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing non-zero-value spatial-nonlocal boundary conditions with directional super-diffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eularian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the non-local and non-symmetric fractional diffusion. For a non-zero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite do mains to those with any size and boundary conditions.

  20. Lower bounds on volumes of hyperbolic Haken 3-manifolds

    Science.gov (United States)

    Agol, Ian; Storm, Peter A.; Thurston, William P.

    2007-10-01

    We prove a volume inequality for 3-manifolds having C^{0} metrics ``bent'' along a surface and satisfying certain curvature conditions. The result makes use of Perelman's work on the Ricci flow and geometrization of closed 3-manifolds. Corollaries include a new proof of a conjecture of Bonahon about volumes of convex cores of Kleinian groups, improved volume estimates for certain Haken hyperbolic 3-manifolds, and a lower bound on the minimal volume of orientable hyperbolic 3-manifolds. An appendix compares estimates of volumes of hyperbolic 3-manifolds drilled along a closed embedded geodesic with experimental data.

  1. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  2. Exact entanglement bases and general bound entanglement

    CERN Document Server

    Zhong, Z Z

    2004-01-01

    In this paper, we give the more general bound entangled states associated with the unextendible product bases (UPB), i.e. by using of the exact entanglement bases (EEB) and the complete basis with unextendible product bases (CBUPB), we prove that the arbitrary convex sums of the uniform mixtures (bound entangled states) associated with UPBs are still bound entangled states. Further, we discuss the equivalent transformation group and classification of the CBUPBs, and by using this classification, we prove that in the meaning of indistinguishability, the set of the above all possible bound entangled states can be reduced to the set of all possible mixtures of some fixed basic bound entangled states. At last, we prove that every operating of the partial transposition (PT) map acting upon a density matrix under any bipartite partitioning induces a mapping from the above reduced set of bound entangled states to oneself, which corresponds to a non-identical permutation of the basic bound entangled states.

  3. Thermodynamic law from the entanglement entropy bound

    CERN Document Server

    Park, Chanyong

    2015-01-01

    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamics-like law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we also find that a global quench unlike the excitation does not preserve the entanglement entropy bound.

  4. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  5. Bound states in the continuum

    Science.gov (United States)

    Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin

    2016-09-01

    Bound states in the continuum (BICs) are waves that remain localized even though they coexist with a continuous spectrum of radiating waves that can carry energy away. Their very existence defies conventional wisdom. Although BICs were first proposed in quantum mechanics, they are a general wave phenomenon and have since been identified in electromagnetic waves, acoustic waves in air, water waves and elastic waves in solids. These states have been studied in a wide range of material systems, such as piezoelectric materials, dielectric photonic crystals, optical waveguides and fibres, quantum dots, graphene and topological insulators. In this Review, we describe recent developments in this field with an emphasis on the physical mechanisms that lead to BICs across seemingly very different materials and types of waves. We also discuss experimental realizations, existing applications and directions for future work.

  6. Towards Bounded Infeasible Code Detection

    CERN Document Server

    Christ, Jürgen; Schäf, Martin

    2012-01-01

    A first step towards more reliable software is to execute each statement and each control-flow path in a method once. In this paper, we present a formal method to automatically compute test cases for this purpose based on the idea of a bounded infeasible code detection. The method first unwinds all loops in a program finitely often and then encodes all feasible executions of the loop-free programs in a logical formula. Helper variables are introduced such that a theorem prover can reconstruct the control-flow path of a feasible execution from a satisfying valuation of this formula. Based on this formula, we present one algorithm that computes a feasible path cover and one algorithm that computes a feasible statement cover. We show that the algorithms are complete for loop-free programs and that they can be implemented efficiently. We further provide a sound algorithm to compute procedure summaries which makes the method scalable to larger programs.

  7. Topology optimization of bounded acoustic problems using the hybrid finite element-wave based method

    DEFF Research Database (Denmark)

    Goo, Seongyeol; Wang, Semyung; Kook, Junghwan

    2017-01-01

    This paper presents an alternative topology optimization method for bounded acoustic problems that uses the hybrid finite element-wave based method (FE-WBM). The conventional method for the topology optimization of bounded acoustic problems is based on the finite element method (FEM), which...... is limited to low frequency applications due to considerable computational efforts. To this end, we propose a gradient-based topology optimization method that uses the hybrid FE-WBM whereby the entire domain of a problem is partitioned into design and non-design domains. In this respect, the FEM is used...... as a design domain of topology optimization, and the WBM is used as a non-design domain to increase computational efficiency. The adjoint variable method based on the hybrid FE-WBM is also proposed as a means of computing design sensitivities. Numerical examples are presented to demonstrate the effectiveness...

  8. Dual-core antiresonant hollow core fibers.

    Science.gov (United States)

    Liu, Xuesong; Fan, Zhongwei; Shi, Zhaohui; Ma, Yunfeng; Yu, Jin; Zhang, Jing

    2016-07-25

    In this work, dual-core antiresonant hollow core fibers (AR-HCFs) are numerically demonstrated, based on our knowledge, for the first time. Two fiber structures are proposed. One is a composite of two single-core nested nodeless AR-HCFs, exhibiting low confinement loss and a circular mode profile in each core. The other has a relatively simple structure, with a whole elliptical outer jacket, presenting a uniform and wide transmission band. The modal couplings of the dual-core AR-HCFs rely on a unique mechanism that transfers power through the air. The core separation and the gap between the two cores influence the modal coupling strength. With proper designs, both of the dual-core fibers can have low phase birefringence and short modal coupling lengths of several centimeters.

  9. Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

    Science.gov (United States)

    D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

    2015-03-01

    Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

  10. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.

    1996-07-01

    Assessment of the variability in population values plays an important role in the analysis of scientific data. Analysis of scientific data often involves developing a bound on a proportion of a population. Sometimes simple probability bounds are obtained using formulas involving known mean and variance parameters and replacing the parameters by sample estimates. The resulting bounds are only approximate and fail to account for the variability in the estimated parameters. Tolerance bounds provide bounds on population proportions which account for the variation resulting from the estimated mean and variance parameters. A beta content, gamma confidence tolerance interval is constructed so that a proportion beta of the population lies within the region bounded by the interval with confidence gamma. An application involving corrosion measurements is used to illustrate the use of tolerance bounds for different situations. Extensions of standard tolerance intervals are applied to generate regression tolerance bounds, tolerance bounds for more general models of measurements collected over time, and tolerance intervals for varying precision data. Tolerance bounds also provide useful information for designing the collection of future data.

  11. Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

    Energy Technology Data Exchange (ETDEWEB)

    Pathuri, P.; Nguyen, E.T.; Svard, S.G.; Luecke, H.; /UC, Irvine /Uppsala U. /Karolinska Inst.

    2007-07-12

    Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutive over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower

  12. The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Vincenzo A.; Shepherd, Sharon M.; English, Grant; Coulthurst, Sarah J.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

    2011-12-01

    The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.

  13. Animal MRI Core

    Data.gov (United States)

    Federal Laboratory Consortium — The Animal Magnetic Resonance Imaging (MRI) Core develops and optimizes MRI methods for cardiovascular imaging of mice and rats. The Core provides imaging expertise,...

  14. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H

    2007-03-20

    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  15. Nonadditivity of Rains' bound for distillable entanglement

    Science.gov (United States)

    Wang, Xin; Duan, Runyao

    2017-06-01

    Rains' bound is arguably the best known upper bound of the distillable entanglement by operations completely preserving positivity of partial transpose (PPT) and was conjectured to be additive and coincide with the asymptotic relative entropy of entanglement. We disprove both conjectures by explicitly constructing a special class of mixed two-qubit states. We then introduce an additive semidefinite programming lower bound (EM) for the asymptotic Rains' bound, and it immediately becomes a computable lower bound for entanglement cost of bipartite states. Furthermore, EM is also proved to be the best known upper bound of the PPT-assisted deterministic distillable entanglement and gives the asymptotic rates for all pure states and some class of genuinely mixed states.

  16. Process expression of bounded Petri nets

    Institute of Scientific and Technical Information of China (English)

    吴哲辉

    1996-01-01

    The concept of process expression of bounded Petri nets is presented.Moreover,an algorithm to find the process expression for a bounded Petri net is given.A process expression of a bounded Petri net is a regular expression whose every alphabet symbol represents a basic subprocess of the net.The regular set expressed by the regular expression is the set of all surjective processes of a bounded Petri net.A surjective process of a bounded Petri net is a process of this net in which every s-cut corresponds to a reachable marking of the net.Therefore,all surjective processes of a bounded Petri net can be obtained as long as its process expression and the basic subprocess represented by the alphabet symbols of the process expression are given.

  17. Thermodynamic law from the entanglement entropy bound

    Science.gov (United States)

    Park, Chanyong

    2016-04-01

    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamicslike law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we show that the deformed modular Hamiltonian under a global quench also satisfies the generalized entanglement entropy boundary after introducing a new quantity called the entanglement chemical potential.

  18. Bounds on double-diffusive convection

    Science.gov (United States)

    Balmforth, Neil J.; Ghadge, Shilpa A.; Kettapun, Atichart; Mandre, Shreyas D.

    2006-12-01

    We consider double-diffusive convection between two parallel plates and compute bounds on the flux of the unstably stratified species using the background method. The bound on the heat flux for Rayleigh Bénard convection also serves as a bound on the double-diffusive problem (with the thermal Rayleigh number equal to that of the unstably stratified component). In order to incorporate a dependence of the bound on the stably stratified component, an additional constraint must be included, like that used by Joseph (Stability of Fluid Motion, 1976, Springer) to improve the energy stability analysis of this system. Our bound extends Joseph's result beyond his energy stability boundary. At large Rayleigh number, the bound is found to behave like R_T(1/2) for fixed ratio R_S/R_T, where R_T and R_S are the Rayleigh numbers of the unstably and stably stratified components, respectively.

  19. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics

    2013-06-15

    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  20. Conditionally bounding analytic ranks of elliptic curves

    CERN Document Server

    Bober, Jonathan W

    2011-01-01

    We describe a method for bounding the rank of an elliptic curve under the assumptions of the Birch and Swinnerton-Dyer conjecture and the generalized Riemann hypothesis. As an example, we compute, under these conjectures, exact upper bounds for curves which are known to have rank at least as large as 20, 21, 22, 23, and 24. For the known curve of rank at least 28, we get a bound of 30.

  1. Computing the bounds on the loss rates

    Directory of Open Access Journals (Sweden)

    Fourneau J.-M.

    2002-01-01

    Full Text Available We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.

  2. Scalable Capacity Bounding Models for Wireless Networks

    OpenAIRE

    Du, Jinfeng; Medard, Muriel; Xiao, Ming; Skoglund, Mikael

    2014-01-01

    The framework of network equivalence theory developed by Koetter et al. introduces a notion of channel emulation to construct noiseless networks as upper (resp. lower) bounding models, which can be used to calculate the outer (resp. inner) bounds for the capacity region of the original noisy network. Based on the network equivalence framework, this paper presents scalable upper and lower bounding models for wireless networks with potentially many nodes. A channel decoupling method is proposed...

  3. A disappearing heritage: the clinical core of schizophrenia

    DEFF Research Database (Denmark)

    Parnas, Josef

    2011-01-01

    ("schizoidia" and "latent schizophrenia"). The fundamental features are manifest across all domains of consciousness: subjective experience, expression, cognition, affectivity, behavior, and willing. Yet, the specificity of the core was only graspable at a more comprehensive Gestalt-level, variously designated...

  4. Alteration of helical vortex core without change in flow topology

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2011-01-01

    The abrupt expansion of the slender vortex core with changes in flow topology is commonly known as vortex breakdown. We present new experimental observations of an alteration of the helical vortex core in wall bounded turbulent flow with abrupt growth in core size, but without change in flow...... topology. The helical symmetry as such is preserved, although the characteristic parameters of helical symmetry of the vortex core transfer from a smooth linear variation to a different trend under the influence of a non-uniform pressure gradient, causing an increase in helical pitch without changing its...

  5. Purification and Structural Analysis of LEM-Domain Proteins.

    Science.gov (United States)

    Herrada, Isaline; Bourgeois, Benjamin; Samson, Camille; Buendia, Brigitte; Worman, Howard J; Zinn-Justin, Sophie

    2016-01-01

    LAP2-emerin-MAN1 (LEM)-domain proteins are modular proteins characterized by the presence of a conserved motif of about 50 residues. Most LEM-domain proteins localize at the inner nuclear membrane, but some are also found in the endoplasmic reticulum or nuclear interior. Their architecture has been analyzed by predicting the limits of their globular domains, determining the 3D structure of these domains and in a few cases calculating the 3D structure of specific domains bound to biological targets. The LEM domain adopts an α-helical fold also found in SAP and HeH domains of prokaryotes and unicellular eukaryotes. The LEM domain binds to BAF (barrier-to-autointegration factor; BANF1), which interacts with DNA and tethers chromatin to the nuclear envelope. LAP2 isoforms also share an N-terminal LEM-like domain, which binds DNA. The structure and function of other globular domains that distinguish LEM-domain proteins from each other have been characterized, including the C-terminal dimerization domain of LAP2α and C-terminal WH and UHM domains of MAN1. LEM-domain proteins also have large intrinsically disordered regions that are involved in intra- and intermolecular interactions and are highly regulated by posttranslational modifications in vivo.

  6. Risk Bounds for Infinitely Divisible Distribution

    CERN Document Server

    Zhang, Chao

    2012-01-01

    In this paper, we study the risk bounds for samples independently drawn from an infinitely divisible (ID) distribution. In particular, based on a martingale method, we develop two deviation inequalities for a sequence of random variables of an ID distribution with zero Gaussian component. By applying the deviation inequalities, we obtain the risk bounds based on the covering number for the ID distribution. Finally, we analyze the asymptotic convergence of the risk bound derived from one of the two deviation inequalities and show that the convergence rate of the bound is faster than the result for the generic i.i.d. empirical process (Mendelson, 2003).

  7. Some Improved Nonperturbative Bounds for Fermionic Expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)

    2016-06-15

    We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

  8. Bounds in the location-allocation problem

    DEFF Research Database (Denmark)

    Juel, Henrik

    1981-01-01

    Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources.......Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources....

  9. Conductivity bounds in probe brane models

    CERN Document Server

    Ikeda, Tatsuhiko N; Nakai, Yuichiro

    2016-01-01

    We discuss upper and lower bounds on the electrical conductivity of finite temperature strongly coupled quantum field theories, holographically dual to probe brane models, within linear response. In a probe limit where disorder is introduced entirely through an inhomogeneous background charge density, we find simple lower and upper bounds on the electrical conductivity in arbitrary dimensions. In field theories in two spatial dimensions, we show that both bounds persist even when disorder is included in the bulk metric. We discuss the challenges with finding sharp lower bounds on conductivity in three or more spatial dimensions when the metric is inhomogeneous.

  10. A violation of the covariant entropy bound?

    CERN Document Server

    Masoumi, Ali

    2014-01-01

    Several arguments suggest that the entropy density at high energy density $\\rho$ should be given by the expression $s=K\\sqrt{\\rho/G}$, where $K$ is a constant of order unity. On the other hand the covariant entropy bound requires that the entropy on a light sheet be bounded by $A/4G$, where $A$ is the area of the boundary of the sheet. We find that in a suitably chosen cosmological geometry, the above expression for $s$ violates the covariant entropy bound. We consider different possible explanations for this fact; in particular the possibility that entropy bounds should be defined in terms of volumes of regions rather than areas of surfaces.

  11. Experience in forming and core mixtures by Alphaset technology

    OpenAIRE

    I. Vasková; Smolková, M.; J. Malik; Š. Eperješi

    2008-01-01

    Chemically bound mixtures have had the evolution effect upon the economical and quality aspects of the foundry operations since they presentation at the market. The higher output and significantly increased production efficiency of moulds and cores has lead to the material increase in the quality and profit of the foundries. It can be seen that in last several years the knowledge of bounds based on the organic resins has made enormous advances. The higher strength, improved properties under e...

  12. Experience in forming and core mixtures by Alphaset technology

    OpenAIRE

    I. Vasková; M. Smolková; J. Malik; Eperješi Š.

    2008-01-01

    Chemically bound mixtures have had the evolution effect upon the economical and quality aspects of the foundry operations since they presentation at the market. The higher output and significantly increased production efficiency of moulds and cores has lead to the material increase in the quality and profit of the foundries. It can be seen that in last several years the knowledge of bounds based on the organic resins has made enormous advances. The higher strength, improved properties under e...

  13. On the energy of bound states for magnetic Schrödinger operators

    DEFF Research Database (Denmark)

    Fournais, Søren; Kachmar, Ayman

    2009-01-01

    We provide a leading order semiclassical asymptotics of the energy of bound states for magnetic Neumann Schrödinger operators in two-dimensional (exterior) domains with smooth boundaries. The asymptotics is valid all the way up to the bottom of the essential spectrum. When the spectral parameter...

  14. A Stronger LP Bound for Formula Size Lower Bounds via Clique Constraints

    CERN Document Server

    Ueno, Kenya

    2009-01-01

    We introduce a new technique proving formula size lower bounds based on the linear programming bound originally introduced by Karchmer, Kushilevitz and Nisan [11] and the theory of stable set polytope. We apply it to majority functions and prove their formula size lower bounds improved from the classical result of Khrapchenko [13]. Moreover, we introduce a notion of unbalanced recursive ternary majority functions motivated by a decomposition theory of monotone self-dual functions and give integrally matching upper and lower bounds of their formula size. We also show monotone formula size lower bounds of balanced recursive ternary majority functions improved from the quantum adversary bound of Laplante, Lee and Szegedy [15].

  15. Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1

    Science.gov (United States)

    Schwartz, T.; Lowenhaupt, K.; Kim, Y. G.; Li, L.; Brown, B. A. 2nd; Herbert, A.; Rich, A.

    1999-01-01

    Zalpha is a peptide motif that binds to Z-DNA with high affinity. This motif binds to alternating dC-dG sequences stabilized in the Z-conformation by means of bromination or supercoiling, but not to B-DNA. Zalpha is part of the N-terminal region of double-stranded RNA adenosine deaminase (ADAR1), a candidate enzyme for nuclear pre-mRNA editing in mammals. Zalpha is conserved in ADAR1 from many species; in each case, there is a second similar motif, Zbeta, separated from Zalpha by a more divergent linker. To investigate the structure-function relationship of Zalpha, its domain structure was studied by limited proteolysis. Proteolytic profiles indicated that Zalpha is part of a domain, Zab, of 229 amino acids (residues 133-361 in human ADAR1). This domain contains both Zalpha and Zbeta as well as a tandem repeat of a 49-amino acid linker module. Prolonged proteolysis revealed a minimal core domain of 77 amino acids (positions 133-209), containing only Zalpha, which is sufficient to bind left-handed Z-DNA; however, the substrate binding is strikingly different from that of Zab. The second motif, Zbeta, retains its structural integrity only in the context of Zab and does not bind Z-DNA as a separate entity. These results suggest that Zalpha and Zbeta act as a single bipartite domain. In the presence of substrate DNA, Zab becomes more resistant to proteases, suggesting that it adopts a more rigid structure when bound to its substrate, possibly with conformational changes in parts of the protein.

  16. An outer bound for 2-receiver discrete memoryless broadcast channels

    OpenAIRE

    Nair, Chandra

    2008-01-01

    An outer bound to the two-receiver discrete memoryless broadcast channel is presented. We compare it to the known outer bounds and show that the outer bound presented is at least as tight as the existing bounds.

  17. Cores in Dwarf Galaxies from Fermi Repulsion

    CERN Document Server

    Randall, Lisa; Unwin, James

    2016-01-01

    We show that Fermi repulsion can lead to cored density profiles in dwarf galaxies for sub-keV fermionic dark matter. We treat the dark matter as a quasi-degenerate self-gravitating Fermi gas and calculate its density profile assuming hydrostatic equilibrium. We find that suitable dwarf galaxy cores of larger than 130 pc can be achieved for fermion dark matter with mass in the range 70 eV - 400 eV. While in conventional dark matter scenarios, such sub-keV thermal dark matter would be excluded by free streaming bounds, the constraints are ameliorated in models with dark matter at lower temperature than conventional thermal scenarios, such as the Flooded Dark Matter model that we have previously considered. Modifying the arguments of Tremaine and Gunn we derive a conservative lower bound on the mass of fermionic dark matter of 70 eV and a stronger lower bound from Lyman-$\\alpha$ clouds of about 470 eV, leading to slightly smaller cores than have been observed. We comment on this result and how the tension is rel...

  18. Conflict Resolution (CORE) for Software Quality Factors

    Science.gov (United States)

    1993-05-01

    theory. Evaluate recent algorithm and concept developments for possible use in CORE. IH-34 SECTION IV REFERENCES [1] Jeffrey A. Lasky and Alan R...February, 1985. [5] Ruben Prieto -Diaz and Guillermo Arango (eds.), Domain Analysis and Software Systems Modeling, IEEE Computer Society Press, 1991. [6

  19. Towards a Certified Lightweight Array Bound Checker for Java Bytecode

    Science.gov (United States)

    Pichardie, David

    2009-01-01

    Dynamic array bound checks are crucial elements for the security of a Java Virtual Machines. These dynamic checks are however expensive and several static analysis techniques have been proposed to eliminate explicit bounds checks. Such analyses require advanced numerical and symbolic manipulations that 1) penalize bytecode loading or dynamic compilation, 2) complexify the trusted computing base. Following the Foundational Proof Carrying Code methodology, our goal is to provide a lightweight bytecode verifier for eliminating array bound checks that is both efficient and trustable. In this work, we define a generic relational program analysis for an imperative, stackoriented byte code language with procedures, arrays and global variables and instantiate it with a relational abstract domain as polyhedra. The analysis has automatic inference of loop invariants and method pre-/post-conditions, and efficient checking of analysis results by a simple checker. Invariants, which can be large, can be specialized for proving a safety policy using an automatic pruning technique which reduces their size. The result of the analysis can be checked efficiently by annotating the program with parts of the invariant together with certificates of polyhedral inclusions. The resulting checker is sufficiently simple to be entirely certified within the Coq proof assistant for a simple fragment of the Java bytecode language. During the talk, we will also report on our ongoing effort to scale this approach for the full sequential JVM.

  20. Nanopore sensing of individual transcription factors bound to DNA

    Science.gov (United States)

    Squires, Allison; Atas, Evrim; Meller, Amit

    2015-06-01

    Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.

  1. Estimation of Bounded and Unbounded Trajectories in Diffusion MRI.

    Science.gov (United States)

    Ning, Lipeng; Westin, Carl-Fredrik; Rathi, Yogesh

    2016-01-01

    Disentangling the tissue microstructural information from the diffusion magnetic resonance imaging (dMRI) measurements is quite important for extracting brain tissue specific measures. The autocorrelation function of diffusing spins is key for understanding the relation between dMRI signals and the acquisition gradient sequences. In this paper, we demonstrate that the autocorrelation of diffusion in restricted or bounded spaces can be well approximated by exponential functions. To this end, we propose to use the multivariate Ornstein-Uhlenbeck (OU) process to model the matrix-valued exponential autocorrelation function of three-dimensional diffusion processes with bounded trajectories. We present detailed analysis on the relation between the model parameters and the time-dependent apparent axon radius and provide a general model for dMRI signals from the frequency domain perspective. For our experimental setup, we model the diffusion signal as a mixture of two compartments that correspond to diffusing spins with bounded and unbounded trajectories, and analyze the corpus-callosum in an ex-vivo data set of a monkey brain.

  2. Estimation of bounded and unbounded trajectories in diffusion MRI

    Directory of Open Access Journals (Sweden)

    Lipeng eNing

    2016-03-01

    Full Text Available Disentangling the tissue microstructural information from the diffusion magnetic resonance imaging (dMRI measurements is quite important for extracting brain tissue specific measures. The autocorrelation function of diffusing spins is key for understanding the relation between dMRI signals and the acquisition gradient sequences. In this paper, we demonstrate that the autocorrelation of diffusion in restricted or bounded spaces can be well approximated by exponential functions. To this end, we propose to use the multivariate Ornstein-Uhlenbeck (OU process to model the matrix-valued exponential autocorrelation function of three-dimensional diffusion processes with bounded trajectories. We present detailed analysis on the relation between the model parameters and the time-dependent apparent axon radius and provide a general model for dMRI signals from the frequency domain perspective. For our experimental setup, we model the diffusion signal as a mixture of two compartments that correspond to diffusing spins with bounded and unbounded trajectories, and analyze the corpus-callosum in an ex-vivo data set of a monkey brain.

  3. Life sciences domain analysis model.

    Science.gov (United States)

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H; Klemm, Juli D

    2012-01-01

    Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science.

  4. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  5. Error estimates for a numerical method for the compressible Navier-Stokes system on sufficiently smooth domains

    OpenAIRE

    Feireisl, Eduard; Hošek, Radim; Maltese, David; Novotný, Antonín

    2015-01-01

    We derive an a priori error estimate for the numerical solution obtained by time and space discretization by the finite volume/finite element method of the barotropic Navier--Stokes equations. The numerical solution on a convenient polyhedral domain approximating a sufficiently smooth bounded domain is compared with an exact solution of the barotropic Navier--Stokes equations with a bounded density. The result is unconditional in the sense that there are no assumed bounds on the numerical sol...

  6. Domain wall stability in ferroelectrics with space charges

    Energy Technology Data Exchange (ETDEWEB)

    Zuo, Yinan, E-mail: zuo@mfm.tu-darmstadt.de; Genenko, Yuri A.; Klein, Andreas; Stein, Peter; Xu, Baixiang [Institute of Materials Science, Technische Universität Darmstadt, D-64287 Darmstadt (Germany)

    2014-02-28

    Significant effect of semiconductor properties on domain configurations in ferroelectrics is demonstrated, especially in the case of doped materials. Phase field simulations are performed for ferroelectrics with space charges due to donors and electronic charge carriers. The free charges introduced thereby can act as a source for charge compensation at domain walls with uncompensated polarization bound charges. Results indicate that the equilibrium position of a domain wall with respect to its rotation in a head-to-head or a tail-to-tail domain configuration depends on the charge defect concentration and the Fermi level position.

  7. Hamilton-Jacobi method for curved domain walls and cosmologies

    Science.gov (United States)

    Skenderis, Kostas; Townsend, Paul K.

    2006-12-01

    We use Hamiltonian methods to study curved domain walls and cosmologies. This leads naturally to first-order equations for all domain walls and cosmologies foliated by slices of maximal symmetry. For Minkowski and AdS-sliced domain walls (flat and closed FLRW cosmologies) we recover a recent result concerning their (pseudo)supersymmetry. We show how domain-wall stability is consistent with the instability of AdS vacua that violate the Breitenlohner-Freedman bound. We also explore the relationship to Hamilton-Jacobi theory and compute the wave-function of a 3-dimensional closed universe evolving towards de Sitter spacetime.

  8. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

    Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of domains determines the function of the protein, its subcellular localization and the interacti

  9. Estimating Lower Bound and Upper Bound of a Markov chain over a noisy communication channel with Poisson distribution

    Directory of Open Access Journals (Sweden)

    Vinay Mahajan

    2012-06-01

    Full Text Available Under the assumption that the encoders’ observations are conditionally independent Markov chains given an unobserved time-invariant random variable, results on the structure of optimal real-time encoding and decoding functions are obtained. The problem with noiseless channels and perfect memory at the receiver is then considered. A new methodology to find the structure of optimal real-time encoders is employed. A sufficient statistic with a time-invariant domain is found for this problem. This methodology exploits the presence of common information between the encoders and the receiver when communication is over noiseless channels. In this paper we estimate the lower bond, upper bond and define the encoder. In the previous design approach they follow Markov Chain approach to estimating the upper bound and define the encoder. In this dissertation we follow poison distribution to finding the lower bound and upper bound. Poisson can be viewed as an approximation to the binomial distribution. The approximation is good enough to be useful even when the sample size (N is only moderately large (say N > 50 and the probability (p is only relatively small (p < .2 The advantage of the Poisson distribution, of course, is that if N is large you need only know p to determine the approximate distribution of events. With the binomial distribution you also need to know N.

  10. K¯ nuclear bound states in a dynamical model

    Science.gov (United States)

    Mareš, J.; Friedman, E.; Gal, A.

    2006-05-01

    A comprehensive data base of K-atom level shifts and widths is re-analyzed in order to study the density dependence of the K¯-nuclear optical potential. Significant departure from a tρ form is found only for ρ(r)/ρ ≲ 0.2 and extrapolation to nuclear-matter density ρ yields an attractive potential, about 170 MeV deep. Partial restoration of chiral symmetry compatible with pionic atoms and low-energy pion-nuclear data plays no role at the relevant low-density regime, but this effect is not ruled out at densities of order ρ and beyond. K¯-nuclear bound states are generated across the periodic table self consistently, using a relativistic mean-field model Lagrangian which couples the K¯ to the scalar and vector meson fields mediating the nuclear interactions. The reduced phase space available for K¯ absorption from these bound states is taken into account by adding an energy-dependent imaginary term which underlies the corresponding K¯-nuclear level widths, with a strength required by fits to the atomic data. Substantial polarization of the core nucleus is found for light nuclei, and the binding energies and widths calculated in this dynamical model differ appreciably from those calculated for a static nucleus. A wide range of binding energies is spanned by varying the K¯ couplings to the meson fields. Our calculations provide a lower limit of Γ=50±10 MeV on the width of nuclear bound states for K¯-binding energy in the range B˜100-200 MeV. Comments are made on the interpretation of the FINUDA experiment at DAΦNE which claimed evidence for deeply bound Kpp states in light nuclei.

  11. Application of supersymmetric quantum mechanics to study bound state properties of exotic hypernuclei

    CERN Document Server

    Khan, Md Abdul

    2015-01-01

    Bound state properties of few single and double-$\\Lambda$ hypernuclei is critically examined in the framework of core-$\\Lambda$ and core+$\\Lambda+\\Lambda$ few-body model applying hyperspherical harmonics expansion method (HHEM). The $\\Lambda\\Lambda$ potential is chosen phenomenologically while the core-$\\Lambda$ potential is obtained by folding a phenomenological $\\Lambda N$ interaction into the density distribution of the core. The depth of the effective $\\Lambda N$ potential is adjusted to reproduce the experimental data for the core-$\\Lambda$ subsystem. The three-body Schr\\"odinger equation is solved by hyperspherical adiabatic approximation (HAA) to get the ground state energy and wave function. The ground state wavefunction is used to construct the supersymmetric partner potential following prescription of supersymmetric quantum mechanics (SSQM) algebra. The newly constructed supersymmetric partner potential is used to solve the three-body Schr\\"odinger equation to get the energy and wavefunction for the...

  12. No-arbitrage bounds for financial scenarios

    DEFF Research Database (Denmark)

    Geyer, Alois; Hanke, Michael; Weissensteiner, Alex

    2014-01-01

    We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...

  13. Optimal online bounded space multidimensional packing

    NARCIS (Netherlands)

    L. Epstein (Lea); R. van Stee (Rob)

    2003-01-01

    textabstractWe solve an open problem in the literature by providing an online algorithm for multidimensional bin packing that uses only bounded space. We show that it is optimal among bounded space algorithms for any dimension $d>1$. Its asymptotic performance ratio is $(Pi_{infty})^d$, where

  14. New bounds for multi-dimensional packing

    NARCIS (Netherlands)

    S. Seiden; R. van Stee (Rob)

    2001-01-01

    textabstractNew upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The

  15. Lower Bounds of Concurrence for Multipartite States

    CERN Document Server

    Zhu, Xue-Na; Fei, Shao-Ming

    2012-01-01

    We study the entanglement of multipartite quantum states. Some lower bounds of the multipartite concurrence are reviewed. We further present more effective lower bounds for detecting and qualifying entanglement, by establishing functional relations between the concurrence and the generalized partial transpositions of the multipartite systems.

  16. A Note on Geodesically Bounded -Trees

    Directory of Open Access Journals (Sweden)

    Kirk WA

    2010-01-01

    Full Text Available It is proved that a complete geodesically bounded -tree is the closed convex hull of the set of its extreme points. It is also noted that if is a closed convex geodesically bounded subset of a complete -tree and if a nonexpansive mapping satisfies then has a fixed point. The latter result fails if is only continuous.

  17. New bounds for multi-dimensional packing

    NARCIS (Netherlands)

    Seiden, S.; Stee, R. van

    2001-01-01

    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results,

  18. Threshold Circuit Lower Bounds on Cryptographic Functions

    NARCIS (Netherlands)

    Kiltz, E.; Simon, H.U.

    2005-01-01

    In this work, we are interested in non-trivial upper bounds on the spectral norm of binary matrices $M$ from {-1, 1} $^{N × N}$. It is known that the distributed Boolean function represented by $M$ is hard to compute in various restricted models of computation if the spectral norm is bounded from ab

  19. Experimental evidence of bounds of quantum correlations

    CERN Document Server

    Bovino, F A; Castelletto, S; Degiovanni, I P; Rastello, M L; Berchera, I R

    2003-01-01

    We implemented the experiment proposed by Cabello [arXiv:quant-ph/0309172] to test the bounds of quantum correlation. As expected from the theory we found that, for certain choices of local observables, Cirel'son's bound of the Clauser-Horne-Shimony-Holt inequality ($2\\sqrt{2}$) is not reached by any quantum states.

  20. Spatial coagulation with bounded coagulation rate

    OpenAIRE

    Bailleul, Ismael

    2010-01-01

    We prove that the spatial coagulation equation with bounded coagulation rate is well-posed for all times in a given class of kernels if the convection term of the underlying particle dynamics has divergence bounded below by a positive constant. Multiple coagulations, fragmentation and scattering are also considered.