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Sample records for locally constant functions

  1. Cosmological constant and local gravity

    SciTech Connect

    Bernabeu, Jose; Espinoza, Catalina; Mavromatos, Nick E.

    2010-04-15

    We discuss the linearization of Einstein equations in the presence of a cosmological constant, by expanding the solution for the metric around a flat Minkowski space-time. We demonstrate that one can find consistent solutions to the linearized set of equations for the metric perturbations, in the Lorentz gauge, which are not spherically symmetric, but they rather exhibit a cylindrical symmetry. We find that the components of the gravitational field satisfying the appropriate Poisson equations have the property of ensuring that a scalar potential can be constructed, in which both contributions, from ordinary matter and {Lambda}>0, are attractive. In addition, there is a novel tensor potential, induced by the pressure density, in which the effect of the cosmological constant is repulsive. We also linearize the Schwarzschild-de Sitter exact solution of Einstein's equations (due to a generalization of Birkhoff's theorem) in the domain between the two horizons. We manage to transform it first to a gauge in which the 3-space metric is conformally flat and, then, make an additional coordinate transformation leading to the Lorentz gauge conditions. We compare our non-spherically symmetric solution with the linearized Schwarzschild-de Sitter metric, when the latter is transformed to the Lorentz gauge, and we find agreement. The resulting metric, however, does not acquire a proper Newtonian form in terms of the unique scalar potential that solves the corresponding Poisson equation. Nevertheless, our solution is stable, in the sense that the physical energy density is positive.

  2. Local constants of motion imply information propagation

    NASA Astrophysics Data System (ADS)

    Friesdorf, M.; Werner, A. H.; Goihl, M.; Eisert, J.; Brown, W.

    2015-11-01

    Interacting quantum many-body systems are expected to thermalize, in the sense that the evolution of local expectation values approaches a stationary value resembling a thermal ensemble. This intuition is notably contradicted in systems exhibiting many-body localisation (MBL). In stark contrast to the non-interacting case of Anderson localisation, the entanglement of states grows without limit over time, albeit slowly. In this work, we establish a novel link between quantum information theory and notions of condensed matter physics, capturing this phenomenon in the Heisenberg picture. We show that the mere existence of local constants of motion, often taken as the defining property of MBL, together with a generic spectrum of the Hamiltonian, is already sufficient to rigorously prove information propagation: these systems can be used to send a classical bit over arbitrary distances, in that the impact of a local perturbation can be detected arbitrarily far away. This counterintuitive result is compatible with and further corroborates the intuition of a slow entanglement growth following global quenches in MBL systems. We perform a detailed perturbation analysis of quasi-local constants of motion and also show that they indeed can be used to construct efficient spectral tensor networks, as recently suggested. Our results provide a detailed and at the same time model-independent picture of information propagation in MBL systems.

  3. Local Pain Dynamics during Constant Exhaustive Exercise

    PubMed Central

    Hristovski, Robert; Tenenbaum, Gershon

    2015-01-01

    The purpose of this study was to delineate the topological dynamics of pain and discomfort during constant exercise performed until volitional exhaustion. Eleven physical education students were tested while cycling and running at a “hard” intensity level (e.g., corresponding to Borg’s RPE (6–20) = 15). During the tests, participants reported their discomfort and pain on a body map every 15s. “Time on task” for each participant was divided into five equal non-overlapping temporal windows within which their ratings were considered for analysis. The analyses revealed that the number of body locations with perceived pain and discomfort increased throughout the five temporal windows until reaching the mean (± SE) values of 4.2 ± 0.7 and 4.1 ± 0.6 in cycling and running, respectively. The dominant locations included the quadriceps and hamstrings during cycling and quadriceps and chest during running. In conclusion, pain seemed to spread throughout the body during constant cycling and running performed up to volitional exhaustion with differences between cycling and running in the upper body but not in the lower body dynamics. PMID:26421436

  4. Local Pain Dynamics during Constant Exhaustive Exercise.

    PubMed

    Slapsinskaite, Agne; Razon, Selen; Balagué Serre, Natàlia; Hristovski, Robert; Tenenbaum, Gershon

    2015-01-01

    The purpose of this study was to delineate the topological dynamics of pain and discomfort during constant exercise performed until volitional exhaustion. Eleven physical education students were tested while cycling and running at a "hard" intensity level (e.g., corresponding to Borg's RPE (6-20) = 15). During the tests, participants reported their discomfort and pain on a body map every 15s. "Time on task" for each participant was divided into five equal non-overlapping temporal windows within which their ratings were considered for analysis. The analyses revealed that the number of body locations with perceived pain and discomfort increased throughout the five temporal windows until reaching the mean (± SE) values of 4.2 ± 0.7 and 4.1 ± 0.6 in cycling and running, respectively. The dominant locations included the quadriceps and hamstrings during cycling and quadriceps and chest during running. In conclusion, pain seemed to spread throughout the body during constant cycling and running performed up to volitional exhaustion with differences between cycling and running in the upper body but not in the lower body dynamics.

  5. Local elastic constants in thin films of an fcc crystal.

    PubMed

    van Workum, Kevin; de Pablo, Juan J

    2003-03-01

    In this work we present a formalism for the calculation of the local elastic constants in inhomogeneous systems based on a method of planes. Unlike previous work, this formalism does not require the partitioning of the system into a set of finite volumes over which average elastic constants are calculated. Results for the calculation of the local elastic constants of a nearest-neighbor Lennard-Jones fcc crystal in the bulk and in a thin film are presented. The local constants are calculated at exact planes of the (001) face of the crystal. The average elastic constants of the bulk system are also computed and are consistent with the local constants. Additionally we present the local stress profiles in the thin film when a small uniaxial strain is applied. The resulting stress profile compares favorably with the stress profile predicted via the local elastic constants. The surface melting of a model for argon for which experimental and simulation data are available is also studied within the framework of this formalism.

  6. Methodology for extracting local constants from petroleum cracking flows

    DOEpatents

    Chang, Shen-Lin; Lottes, Steven A.; Zhou, Chenn Q.

    2000-01-01

    A methodology provides for the extraction of local chemical kinetic model constants for use in a reacting flow computational fluid dynamics (CFD) computer code with chemical kinetic computations to optimize the operating conditions or design of the system, including retrofit design improvements to existing systems. The coupled CFD and kinetic computer code are used in combination with data obtained from a matrix of experimental tests to extract the kinetic constants. Local fluid dynamic effects are implicitly included in the extracted local kinetic constants for each particular application system to which the methodology is applied. The extracted local kinetic model constants work well over a fairly broad range of operating conditions for specific and complex reaction sets in specific and complex reactor systems. While disclosed in terms of use in a Fluid Catalytic Cracking (FCC) riser, the inventive methodology has application in virtually any reaction set to extract constants for any particular application and reaction set formulation. The methodology includes the step of: (1) selecting the test data sets for various conditions; (2) establishing the general trend of the parametric effect on the measured product yields; (3) calculating product yields for the selected test conditions using coupled computational fluid dynamics and chemical kinetics; (4) adjusting the local kinetic constants to match calculated product yields with experimental data; and (5) validating the determined set of local kinetic constants by comparing the calculated results with experimental data from additional test runs at different operating conditions.

  7. Tuning sum rules with window functions for optical constant evaluation

    NASA Astrophysics Data System (ADS)

    Rodríguez-de Marcos, Luis V.; Méndez, José A.; Larruquert, Juan I.

    2016-07-01

    Sum rules are a useful tool to evaluate the global consistency of a set of optical constants. We present a procedure to spectrally tune sum rules to evaluate the local consistency of optical constants. It enables enhancing the weight of a desired spectral range within the sum-rule integral. The procedure consists in multiplying the complex refractive index with an adapted function, which is named window function. Window functions are constructed through integration of Lorentz oscillators. The asymptotic decay of these window functions enables the derivation of a multiplicity of sum rules akin to the inertial sum rule, along with one modified version of f-sum rule. This multiplicity of sum rules combined with the free selection of the photon energy range provides a double way to tune the spectral contribution within the sum rule. Window functions were applied to reported data of SrF2 and of Al films in order to check data consistency over the spectrum. The use of window functions shows that the optical constants of SrF2 are consistent in a broad spectrum. Regarding Al, some spectral ranges are seen to present a lower consistency, even though the standard sum rules with no window function did not detect inconsistencies. Hence window functions are expected to be a helpful tool to evaluate the local consistency of optical constants.

  8. Positive cosmological constant, non-local gravity and horizon entropy

    NASA Astrophysics Data System (ADS)

    Solodukhin, Sergey N.

    2012-08-01

    We discuss a class of (local and non-local) theories of gravity that share same properties: (i) they admit the Einstein spacetime with arbitrary cosmological constant as a solution; (ii) the on-shell action of such a theory vanishes and (iii) any (cosmological or black hole) horizon in the Einstein spacetime with a positive cosmological constant does not have a non-trivial entropy. The main focus is made on a recently proposed non-local model. This model has two phases: with a positive cosmological constant Λ>0 and with zero Λ. The effective gravitational coupling differs essentially in these two phases. Generalizing the previous result of Barvinsky we show that the non-local theory in question is free of ghosts on the background of any Einstein spacetime and that it propagates a standard spin-2 particle. Contrary to the phase with a positive Λ, where the entropy vanishes for any type of horizon, in an Einstein spacetime with zero cosmological constant the horizons have the ordinary entropy proportional to the area. We conclude that, somewhat surprisingly, the presence of any, even extremely tiny, positive cosmological constant should be important for the proper resolution of the entropy problem and, possibly, the information puzzle.

  9. Measurement of Local Peltier Constant at a Microcontact

    NASA Astrophysics Data System (ADS)

    Koyano, Mikio; Akashi, Naoya

    2009-07-01

    Our novel apparatus measures the local Peltier constant at a thermoelectric material microregion. A narrow metal needle probe contacts a sample mounted into a small adiabatic vacuum chamber with a pressure of about 10-4 Pa. A␣stepping-motor-type nano-actuator controls the probe’s contact pressure. We measured DC and AC I- V characteristics at the microcontact to determine thermoelectric properties. We measured I- V characteristics between the probe and a commercial (Bi,Sb)2Te3 surface. Measured values of local Peltier constants are of the same order as the bulk Peltier constant π: ca. 55 mV. They increase with increased contact resistance, suggesting that contact size affects thermoelectricity.

  10. Grothendieck's constant and local models for noisy entangled quantum states

    SciTech Connect

    Acin, Antonio; Gisin, Nicolas; Toner, Benjamin

    2006-06-15

    We relate the nonlocal properties of noisy entangled states to Grothendieck's constant, a mathematical constant appearing in Banach space theory. For two-qubit Werner states {rho}{sub p}{sup W}=p|{psi}{sup -}><{psi}{sup -}|+(1-p)1/4, we show that there is a local model for projective measurements if and only if p{<=}1/K{sub G}(3), where K{sub G}(3) is Grothendieck's constant of order 3. Known bounds on K{sub G}(3) prove the existence of this model at least for p < or approx. 0.66, quite close to the current region of Bell violation, p{approx}0.71. We generalize this result to arbitrary quantum states.

  11. On the local variation of the Hubble constant

    SciTech Connect

    Odderskov, Io; Hannestad, Steen; Haugbølle, Troels E-mail: sth@phys.au.dk

    2014-10-01

    We have carefully studied how local measurements of the Hubble constant, H{sub 0}, can be influenced by a variety of different parameters related to survey depth, size, and fraction of the sky observed, as well as observer position in space. Our study is based on N-body simulations of structure in the standard ΛCDM model and our conclusion is that the expected variance in measurements of H{sub 0} is far too small to explain the current discrepancy between the low value of H{sub 0} inferred from measurements of the cosmic microwave background (CMB) by the Planck collaboration and the value measured directly in the local universe by use of Type Ia supernovae. This conclusion is very robust and does not change with different assumptions about effective sky coverage and depth of the survey or observer position in space.

  12. The local Hurwitz constant and Diophantine approximation on Hecke groups

    NASA Astrophysics Data System (ADS)

    Lehner, J.

    1990-10-01

    Define the Hecke group by {G_q} = < {( {begin{array}{*{20}{c}} 1 & {{⪉mb... ...{array}{*{20}{c}} 0 & { - 1} 1 & 0 } )} rangle , {λ _q} = 2cos π /q , q = 3,4, ldots . We call {G_q}(∞ ) the {G_q} -rationals, and R - {G_q}(∞ ) the {G_q} -irrationals. The problem we treat here is the approximation of {G_q} -irrationals by {G_q} -rationals. Let M(α ) be the upper bound of numbers c for which \\vertα - k/m\\vert < 1/c{m^2} for all {G_q} -irrationals and infinitely many k/m in {G_q}(∞ ) . Set h_q'= {inf _α }M(α ) . We call h_q' the Hurwitz constant for {G_q} . It is known that h_q'= 2 , q even; h_q'= 2{(1 + {(1 - {λ _q}/2)^2})^{1/2}} , q odd. In this paper we prove this result by using {λ _q} -continued fractions, as developed previously by D. Rosen. Write α - frac{{{P_{n - 1}}}}{{{Q_{n - 1}}}} = frac{{{{( - 1)}^{... ...}{\\varepsilon _2} \\cdots {\\varepsilon _n}}}{{{m_{n - 1}}(α )Q_{n - 1}^2}}, where {\\varepsilon _i} = ± 1 and {P_i}/{Q_i} are the convergents of the {λ _q} -continued fraction for α . Then M(α ) = {overline {lim } _n}{m_n}(α ) . We call {m_n}(α ) the local Hurwitz constant. In the final section we prove some results on the local Hurwitz constant. For example (Theorem 4), it is shown that if q is odd and {\\varepsilon _{n + 1}} = {\\varepsilon _{n + 2}} = + 1 , then {m_i} ≥ {(λ _q^2 + 4)^{1/2}} > h_q' for at least one of i = n - 1,n,n + 1 .

  13. Assessment of DFT functionals with fluorine-fluorine coupling constants

    NASA Astrophysics Data System (ADS)

    García de la Vega, J. M.; San Fabián, J.

    2015-07-01

    Density functional theory (DFT) calculations of nuclear magnetic resonance (NMR) spin-spin coupling constants (SSCCs) provide an important contribution for understanding experimentally observed values. It is known that calculated SSCCs using DFT methods correlate well with those experimentally measured. Unlike most of SSCCs, in fluorine compounds, fluorine-fluorine SSCC JFF shows that the Fermi contact (FC) term is not dominant, particularly for JFF in polyfluorinated organic molecules. In order to devise a DFT approach that would correctly reproduce the variation of SSCCs within a series of fluorine compounds, we test several DFT-based approaches, using different exchange and correlation functionals. Isotropic contributions to NMR fluorine-fluorine coupling constants (FC, spin-dipolar, SD, paramagnetic spin-orbit, PSO, and diamagnetic spin-orbit, DSO) have been calculated. Results show that DFT methods give appropriate values for nJFF (n = 4 to 7), while for geminal and vicinal JFF present large deviations from experimental values. For the latter SSCCs (2JFF and 3JFF), the four contributions (FC, SD, PSO and DSO) are analysed as a function of the local and nonlocal exchange in 1,1- and 1,2-difluoroethylene. Although FC term is not dominant for these SSCCs, the variation of this contribution with exchange is remarkable. On the other hand, SD and PSO contributions can be suitably computed without and with exact exchange, respectively. This article is dedicated to the memory of Prof. N. C. Handy, whose contributions to the development of Theoretical Chemistry have been widely recognized.

  14. Behavior near constant solutions of functional differential equations

    NASA Technical Reports Server (NTRS)

    Hale, J. K.

    1974-01-01

    Techniques have been developed to determine in a systematic way the local behavior near constant solutions. Local integral manifolds play a very important role in this development, as they have also for ordinary differential equations. An attempt is made to indicate a few more applications of these methods to some problems in bifurcation in the spirit of Sotomayor (to appear) and to a growth model of Cooke and Yorke (to appear). It is also shown how to prove a theorem on stability under constantly acting disturbances using these methods.

  15. The Not so Constant Gravitational "Constant" G as a Function of Quantum Vacuum

    NASA Astrophysics Data System (ADS)

    Maxmilian Caligiuri, Luigi

    Gravitation is still the less understood among the fundamental forces of Nature. The ultimate physical origin of its ruling constant G could give key insights in this understanding. According to the Einstein's Theory of General Relativity, a massive body determines a gravitational potential that alters the speed of light, the clock's rate and the particle size as a function of the distance from its own center. On the other hand, it has been shown that the presence of mass determines a modification of Zero-Point Field (ZPF) energy density within its volume and in the space surrounding it. All these considerations strongly suggest that also the constant G could be expressed as a function of quantum vacuum energy density somehow depending on the distance from the mass whose presence modifies the ZPF energy structure. In this paper, starting from a constitutive medium-based picture of space, it has been formulated a model of gravitational constant G as a function of Planck's time and Quantum Vacuum energy density in turn depending on the radial distance from center of the mass originating the gravitational field, supposed as spherically symmetric. According to this model, in which gravity arises from the unbalanced physical vacuum pressure, gravitational "constant" G is not truly unchanging but slightly varying as a function of the distance from the mass source of gravitational potential itself. An approximate analytical form of such dependence has been discussed. The proposed model, apart from potentially having deep theoretical consequences on the commonly accepted picture of physical reality (from cosmology to matter stability), could also give the theoretical basis for unthinkable applications related, for example, to the field of gravity control and space propulsion.

  16. Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Gates, T. S.

    2007-01-01

    A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

  17. Localization of dilatancy in Ohshima granite under constant uniaxial stress

    NASA Astrophysics Data System (ADS)

    Yanagidani, Takashi; Ehara, Shoji; Nishizawa, Osamu; Kusunose, Kinichiro; Terada, Makoto

    1985-07-01

    The localization of dilatancy during creep of Ohshima granite under uniaxial compression was observed. Hypocenters of 3933 acoustic emission (AE) events were accurately located. It was found that the mechanical behavior of Ohshima granite was controlled by the localization of microcracks. During the stage of loading up to the creep stress, which is 83% of the average short-term fracture strength, the hypocenters of AE events were randomly distributed throughout the specimen. As soon as the primary creep began, abrupt migration and clustering of AE hypocenters into several near-surface zones were observed. AE events formed volumetric concentrations. This migration and clustering strongly suggested the rapid localized development of dilatancy at the very beginning of the primary creep stage. The distribution of AE hypocenters observed in this stage was unchanged until final faulting. By the end of the primary creep stage, AE events began to concentrate into one of these clusters, while the activities of other clusters gradually decayed. This change spread broadly and continuously in time during the creep. In the most active cluster, clustering of AE events by itself gave rise to more AE events. The shape of this cluster was spheroidal with the long axis parallel to the loading axis. No evidence directly related to planar focusing of dilatancy was found. Surface strains were mapped. The axial strain distributions in the loading interval showed that the state of stress within the sample was homogeneous. A large change in both axial and circumferential strain fields occurred during the early stage of the primary creep. After this drastic change, the pattern of strain distribution remained unchanged in the subsequent stage of the creep. The accelerated increase in one of the circumferential strain gauges during the tertiary creep stage showed strongly localized deformation preceding faulting. The development of localized dilatancy identified by hypocenter locations was

  18. Improved ground-state electronic structure and optical dielectric constants with a semilocal exchange functional

    NASA Astrophysics Data System (ADS)

    Vlček, Vojtěch; Steinle-Neumann, Gerd; Leppert, Linn; Armiento, Rickard; Kümmel, Stephan

    2015-01-01

    A recently published generalized gradient approximation functional within density functional theory (DFT) has shown, in a few paradigm tests, an improved KS orbital description over standard (semi)local approximations. The characteristic feature of this functional is an enhancement factor that diverges like s ln(s ) for large reduced density gradients s which leads to unusual properties. We explore the improved orbital description of this functional more thoroughly by computing the electronic band structure, band gaps, and the optical dielectric constants in semiconductors, Mott insulators, and ionic crystals. Compared to standard semilocal functionals, we observe improvement in both the band gaps and the optical dielectric constants. In particular, the results are similar to those obtained with orbital functionals or by perturbation theory methods in that it opens band gaps in systems described as metallic by standard (semi)local density functionals, e.g., Ge, α -Sn, and CdO.

  19. Radius Constants for Analytic Functions with Fixed Second Coefficient

    PubMed Central

    Nargesi, Mahnaz M.; Ali, Rosihan M.; Ravichandran, V.

    2014-01-01

    Let f(z) = z + ∑n=2∞anzn be analytic in the unit disk with the second coefficient a2 satisfying |a2 | = 2b, 0 ≤ b ≤ 1. Sharp radius of Janowski starlikeness is obtained for functions f whose nth coefficient satisfies |an | ≤ cn + d  (c, d ≥ 0) or |an | ≤ c/n  (c > 0  and  n ≥ 3). Other radius constants are also obtained for these functions, and connections with earlier results are made. PMID:25101327

  20. Ig Constant Region Effects on Variable Region Structure and Function

    PubMed Central

    Janda, Alena; Bowen, Anthony; Greenspan, Neil S.; Casadevall, Arturo

    2016-01-01

    The adaptive humoral immune response is responsible for the generation of antimicrobial proteins known as immunoglobulin molecules or antibodies. Immunoglobulins provide a defense system against pathogenic microbes and toxins by targeting them for removal and/or destruction. Historically, antibodies have been thought to be composed of distinct structural domains known as the variable and constant regions that are responsible for antigen binding and mediating effector functions such as opsonization and complement activation, respectively. These domains were thought to be structurally and functionally independent. Recent work has revealed however, that in some families of antibodies, the two regions can influence each other. We will discuss the body of work that led to these observations, as well as the mechanisms that have been proposed to explain how these two different antibody regions may interact in the function of antigen binding. PMID:26870003

  1. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    SciTech Connect

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.

  2. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGES

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

  3. Calculation of trajectories using constant and slowly varying functions

    NASA Technical Reports Server (NTRS)

    Culpepper, B. K.

    1971-01-01

    A method is presented for calculating trajectories for the restricted problem of three bodies which utilizes conic propagation of the state vector with frequency correction of position and velocity by means of a constant or slowly varying function. This method of calculating trajectories was applied to the planar circular restricted three body problem, the planar elliptic restricted problem, and the ephemeral restricted problem. Two methods (the refined method and the straight forward method) of determining the direction of the position correction are presented for the circular restricted problem and the elliptic restricted problem of three bodies. Only the straight forward method was used with the ephemeral restricted problem. The earth, the moon, and a space vehicle comprise the restricted three body model that is used.

  4. Local field distribution near corrugated interfaces: Green's function formulation

    NASA Astrophysics Data System (ADS)

    Yu, K. W.; Wan, Jones T. K.

    2001-12-01

    We have developed a Green's function formalism to compute the local field distribution near an interface separating two media of different dielectric constants. The Maxwell's equations are converted into a surface integral equation; thus it greatly simplifies the solutions and yields accurate results for interfaces of arbitrary shape. The integral equation is solved and the local field distribution is obtained for a periodic interface.

  5. Corrections to the apparent value of the cosmological constant due to local inhomogeneities

    SciTech Connect

    Romano, Antonio Enea; Chen, Pisin E-mail: pisinchen@phys.ntu.edu.tw

    2011-10-01

    Supernovae observations strongly support the presence of a cosmological constant, but its value, which we will call apparent, is normally determined assuming that the Universe can be accurately described by a homogeneous model. Even in the presence of a cosmological constant we cannot exclude nevertheless the presence of a small local inhomogeneity which could affect the apparent value of the cosmological constant. Neglecting the presence of the inhomogeneity can in fact introduce a systematic misinterpretation of cosmological data, leading to the distinction between an apparent and true value of the cosmological constant. We establish the theoretical framework to calculate the corrections to the apparent value of the cosmological constant by modeling the local inhomogeneity with a ΛLTB solution. Our assumption to be at the center of a spherically symmetric inhomogeneous matter distribution correspond to effectively calculate the monopole contribution of the large scale inhomogeneities surrounding us, which we expect to be the dominant one, because of other observations supporting a high level of isotropy of the Universe around us. By performing a local Taylor expansion we analyze the number of independent degrees of freedom which determine the local shape of the inhomogeneity, and consider the issue of central smoothness, showing how the same correction can correspond to different inhomogeneity profiles. Contrary to previous attempts to fit data using large void models our approach is quite general. The correction to the apparent value of the cosmological constant is in fact present for local inhomogeneities of any size, and should always be taken appropriately into account both theoretically and observationally.

  6. De Sitter brane-world, localization of gravity, and the cosmological constant

    SciTech Connect

    Neupane, Ishwaree P.

    2011-04-15

    Cosmological models with a de Sitter 3-brane embedded in a 5-dimensional de Sitter spacetime (dS{sub 5}) give rise to a finite 4D Planck mass similar to that in Randall-Sundrum (RS) brane-world models in anti-de Sitter 5-dimensional spacetime(AdS{sub 5}). Yet, there arise a few important differences as compared to the results with a flat 3-brane or 4D Minkowski spacetime. For example, the mass reduction formula (MRF) M{sub Pl}{sup 2}=M{sub (5)}{sup 3}l{sub AdS} as well as the relationship M{sub Pl}{sup 2}=M{sub Pl(4+n)}{sup n+2}L{sup n} (with L being the average size or the radius of the n extra dimensions) expected in models of product-space (or Kaluza-Klein) compactifications get modified in cosmological backgrounds. In an expanding universe, a physically relevant MRF encodes information upon the 4-dimensional Hubble expansion parameter, in addition to the length and mass parameters L, M{sub Pl}, and M{sub Pl(4+n)}. If a bulk cosmological constant is present in the solution, then the reduction formula is further modified. With these new insights, we show that the localization of a massless 4D graviton as well as the mass hierarchy between M{sub Pl} and M{sub Pl(4+n)} can be explained in cosmological brane-world models. A notable advantage of having a 5D de Sitter bulk is that in this case the zero-mass wave function is normalizable, which is not necessarily the case if the bulk spacetime is anti-de Sitter. In spacetime dimensions D{>=}7, however, the bulk cosmological constant {Lambda}{sub b} can take either sign ({Lambda}{sub b}<0, =0, or >0). The D=6 case is rather inconclusive, in which case {Lambda}{sub b} may be introduced together with 2-form gauge field (or flux). We obtain some interesting classical gravity solutions that compactify higher-dimensional spacetime to produce a Robertson-Walker universe with de Sitter-type expansion plus one extra noncompact direction. We also show that such models can admit both an effective 4-dimensional Newton constant

  7. Empirical Estimation of Local Dielectric Constants: Toward Atomistic Design of Collagen Mimetic Peptides

    PubMed Central

    Pike, Douglas H.; Nanda, Vikas

    2017-01-01

    One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides. PMID:25784456

  8. Constant covariance in local vertical coordinates for near-circular orbits

    NASA Technical Reports Server (NTRS)

    Shepperd, Stanley W.

    1991-01-01

    A method is presented for devising a covariance matrix that either remains constant or grows in keeping with the presence of a period error in a rotating local-vertical coordinate system. The solution presented may prove useful in the initialization of simulation covariance matrices for near-circular-orbit problems. Use is made of the Clohessy-Wiltshire equations and the travelling-ellipse formulation.

  9. The effect of interacting dark energy on local measurements of the Hubble constant

    NASA Astrophysics Data System (ADS)

    Odderskov, Io; Baldi, Marco; Amendola, Luca

    2016-05-01

    In the current state of cosmology, where cosmological parameters are being measured to percent accuracy, it is essential to understand all sources of error to high precision. In this paper we present the results of a study of the local variations in the Hubble constant measured at the distance scale of the Coma Cluster, and test the validity of correcting for the peculiar velocities predicted by gravitational instability theory. The study is based on N-body simulations, and includes models featuring a coupling between dark energy and dark matter, as well as two ΛCDM simulations with different values of σ8. It is found that the variance in the local flows is significantly larger in the coupled models, which increases the uncertainty in the local measurements of the Hubble constant in these scenarios. By comparing the results from the different simulations, it is found that most of the effect is caused by the higher value of σ8 in the coupled cosmologies, though this cannot account for all of the additional variance. Given the discrepancy between different estimates of the Hubble constant in the universe today, cosmological models causing a greater cosmic variance is something that we should be aware of.

  10. Explicit infiltration function for boreholes under constant head conditions

    NASA Astrophysics Data System (ADS)

    Hinnell, A. C.; Lazarovitch, N.; Warrick, A. W.

    2009-10-01

    Infiltration per unit area of the source region from discs, strips and furrows has previously been shown to be the sum of the one-dimensional infiltration and an edge effect term. Here we apply the same approach to examine infiltration under a constant head from boreholes (both lined and unlined). A critical empirical parameter (γ) in the edge effect term is related to the radius of the borehole, soil hydraulic properties, boundary and initial conditions. For lined boreholes, γ has a narrow range and for the examples investigated, a constant value of 1.06 introduces less than 5% error compared to using the case-specific γ value. For unlined boreholes, γ is larger, ranging between 1.02 and 3.16 for the examples investigated, and should be estimated for specific conditions.

  11. Local unit invariance, back-reacting tractors and the cosmological constant problem

    NASA Astrophysics Data System (ADS)

    Bonezzi, R.; Corradini, O.; Waldron, A.

    2012-02-01

    When physics is expressed in a way that is independent of local choices of unit systems, Riemannian geometry is replaced by conformal geometry. Moreover masses become geometric, appearing as Weyl weights of tractors (conformal multiplets of fields necessary to keep local unit invariance manifest). The relationship between these weights and masses is through the scalar curvature. As a consequence mass terms are spacetime dependent for off-shell gravitational backgrounds, but happily constant for physical, Einstein manifolds. Unfortunately this introduces a naturalness problem because the scalar curvature is proportional to the cosmological constant. By writing down tractor stress tensors (multiplets built from the standard stress tensor and its first and second derivatives), we show how back-reaction solves this naturalness problem. We also show that classical back-reaction generates an interesting potential for scalar fields. We speculate that a proper description of how physical systems couple to scale, could improve our understanding of naturalness problems caused by the disparity between the particle physics and observed, cosmological constants. We further give some ideas how an ambient description of tractor calculus could lead to a Ricci-flat/CFT correspondence which generalizes the AdS side of Maldacena's duality to a Ricci-flat space of one higher dimension.

  12. The bond force constants of graphene and benzene calculated by density functional theory

    NASA Astrophysics Data System (ADS)

    Medina, J.; Avilés, F.; Tapia, A.

    2015-06-01

    Stretching (kr) and bending (kθ) bond force constants appropriate to describe the bond stiffness of graphene and benzene are calculated using density functional theory. The effect of employing different exchange-correlation functionals for the calculation of kr and kθ is discussed using the generalised gradient approximation (GGA) and the local density approximation (LDA). For benzene, kr = 7.93 mdyn Å-1 and kθ = 0.859 mdyn Å rad-2 using LDA, while kr = 7.67 mdyn Å-1 and kθ = 0.875 mdyn Å rad-2 using GGA. For graphene, kr = 7.40 mdyn Å-1 and kθ = 0.769 mdyn Å rad-2 using LDA, while kr = 6.88 mdyn Å-1 and kθ = 0.776 mdyn Å rad-2 using GGA. This means the difference between the bond force constants for benzene and graphene can be as large as ∼12%. The comparison between these two systems allows for elucidation of the effect of periodicity and substitution of carbon atoms by hydrogen in the stiffness of C-C bonds. This effect can be explained by a different redistribution of the charge density when the systems are subjected to strain. The parameters kr and kθ computed here can serve as an input to molecular mechanics or finite element codes of larger carbon molecules, which in the past had frequently assumed the same bond force constants for graphene, benzene or carbon nanotubes.

  13. Cancer stem cells: constantly evolving and functionally heterogeneous therapeutic targets.

    PubMed

    Yang, Tao; Rycaj, Kiera; Liu, Zhong-Min; Tang, Dean G

    2014-06-01

    Elucidating the origin of and dynamic interrelationship between intratumoral cell subpopulations has clear clinical significance in helping to understand the cellular basis of treatment response, therapeutic resistance, and tumor relapse. Cancer stem cells (CSC), together with clonal evolution driven by genetic alterations, generate cancer cell heterogeneity commonly observed in clinical samples. The 2013 Shanghai International Symposium on Cancer Stem Cells brought together leaders in the field to highlight the most recent progress in phenotyping, characterizing, and targeting CSCs and in elucidating the relationship between the cell-of-origin of cancer and CSCs. Discussions from the symposium emphasize the urgent need in developing novel therapeutics to target the constantly evolving CSCs.

  14. Functional Localization of Genetic Network Programming

    NASA Astrophysics Data System (ADS)

    Eto, Shinji; Hirasawa, Kotaro; Hu, Jinglu

    According to the knowledge of brain science, it is suggested that there exists cerebral functional localization, which means that a specific part of the cerebrum is activated depending on various kinds of information human receives. The aim of this paper is to build an artificial model to realize functional localization based on Genetic Network Programming (GNP), a new evolutionary computation method recently developed. GNP has a directed graph structure suitable for realizing functional localization. We studied the basic characteristics of the proposed system by making GNP work in a functionally localized way.

  15. Enzyme function is regulated by its localization.

    PubMed

    Gifford, Stacey M; Meyer, Pablo

    2015-12-01

    To better understand how enzyme localization affects enzyme activity we studied the cellular localization of the glycosyltransferase MurG, an enzyme necessary for cell wall synthesis at the spore during sporulation in the bacterium Bacillus subtilis. During sporulation MurG was gradually enriched to the membrane at the forespore and point mutations in a MurG helical domain disrupting its localization to the membrane caused severe sporulation defects, but did not affect localization nor caused detectable defects during exponential growth. We found that this localization is dependent on the phospholipid cardiolipin, as in strains where the cardiolipin-synthesizing genes were deleted, MurG levels were diminished at the forespore. Furthermore, in this cardiolipin-less strain, MurG localization during sporulation was rescued by external addition of purified cardiolipin. These results support localization as a critical factor in the regulation of proper enzyme function and catalysis.

  16. Vector meson masses from a hidden local symmetry in a constant magnetic field

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Mamiya; Matsuzaki, Shinya

    2016-06-01

    We discuss the magnetic responses of vector meson masses based on the hidden local symmetry (HLS) model in a constant magnetic field, described by the lightest two-flavor system including the pion, rho and omega mesons in the spectrum. The effective masses influenced under the magnetic field are evaluated according to the derivative or chiral expansion established in the HLS model. At the leading order O (p2), the g factor of the charged rho meson is fixed to be 2, implying that the rho meson at this order is treated just like a pointlike spin-1 particle. Beyond the leading order, one finds anomalous magnetic interactions of the charged rho meson, involving the anomalous magnetic moment, which give corrections to the effective mass. It is then suggested that up to O (p4) the charged rho meson tends to become massless. Of interest is that nontrivial magnetic dependence of neutral mesons emerges to give rise to the significant mixing among neutral mesons. Consequently, it leads to the dramatic enhancement of the omega meson mass, which is testable in future lattice simulations. Corrections from terms beyond O (p4) are also addressed.

  17. A 2.4% Determination of the Local Value of the Hubble Constant

    NASA Astrophysics Data System (ADS)

    Riess, Adam G.; Macri, Lucas M.; Hoffmann, Samantha L.; Scolnic, Dan; Casertano, Stefano; Filippenko, Alexei V.; Tucker, Brad E.; Reid, Mark J.; Jones, David O.; Silverman, Jeffrey M.; Chornock, Ryan; Challis, Peter; Yuan, Wenlong; Brown, Peter J.; Foley, Ryan J.

    2016-07-01

    We use the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST) to reduce the uncertainty in the local value of the Hubble constant from 3.3% to 2.4%. The bulk of this improvement comes from new near-infrared (NIR) observations of Cepheid variables in 11 host galaxies of recent type Ia supernovae (SNe Ia), more than doubling the sample of reliable SNe Ia having a Cepheid-calibrated distance to a total of 19; these in turn leverage the magnitude-redshift relation based on ˜300 SNe Ia at z < 0.15. All 19 hosts as well as the megamaser system NGC 4258 have been observed with WFC3 in the optical and NIR, thus nullifying cross-instrument zeropoint errors in the relative distance estimates from Cepheids. Other noteworthy improvements include a 33% reduction in the systematic uncertainty in the maser distance to NGC 4258, a larger sample of Cepheids in the Large Magellanic Cloud (LMC), a more robust distance to the LMC based on late-type detached eclipsing binaries (DEBs), HST observations of Cepheids in M31, and new HST-based trigonometric parallaxes for Milky Way (MW) Cepheids. We consider four geometric distance calibrations of Cepheids: (i) megamasers in NGC 4258, (ii) 8 DEBs in the LMC, (iii) 15 MW Cepheids with parallaxes measured with HST/FGS, HST/WFC3 spatial scanning and/or Hipparcos, and (iv) 2 DEBs in M31. The Hubble constant from each is 72.25 ± 2.51, 72.04 ± 2.67, 76.18 ± 2.37, and 74.50 ± 3.27 km s-1 Mpc-1, respectively. Our best estimate of H 0 = 73.24 ± 1.74 km s-1 Mpc-1 combines the anchors NGC 4258, MW, and LMC, yielding a 2.4% determination (all quoted uncertainties include fully propagated statistical and systematic components). This value is 3.4σ higher than 66.93 ± 0.62 km s-1 Mpc-1 predicted by ΛCDM with 3 neutrino flavors having a mass of 0.06 eV and the new Planck data, but the discrepancy reduces to 2.1σ relative to the prediction of 69.3 ± 0.7 km s-1 Mpc-1 based on the comparably precise combination of WMAP

  18. Constant illumination reduces circulating melatonin and impairs immune function in the cricket Teleogryllus commodus.

    PubMed

    Durrant, Joanna; Michaelides, Ellie B; Rupasinghe, Thusitha; Tull, Dedreia; Green, Mark P; Jones, Therésa M

    2015-01-01

    Exposure to constant light has a range of negative effects on behaviour and physiology, including reduced immune function in both vertebrates and invertebrates. It is proposed that the associated suppression of melatonin (a ubiquitous hormone and powerful antioxidant) in response to the presence of light at night could be an underlying mechanistic link driving the changes to immune function. Here, we investigated the relationship between constant illumination, melatonin and immune function, using a model invertebrate species, the Australian black field cricket, Teleogryllus commodus. Crickets were reared under either a 12 h light: 12 h dark regimen or a constant 24 h light regimen. Circulating melatonin concentration and immune function (haemocyte concentration, lytic activity and phenoloxidase (PO) activity) were assessed in individual adult crickets through the analysis of haemolymph. Constant illumination reduced melatonin and had a negative impact on haemocyte concentrations and lytic activity, but its effect on PO activity was less apparent. Our data provide the first evidence, to our knowledge, of a link between exposure to constant illumination and variation in haemocyte concentration in an invertebrate model, while also highlighting the potential complexity of the immune response following exposure to constant illumination. This study provides insight into the possible negative effect of artificial night-time lighting on the physiology of invertebrates, but whether lower and potentially more ecologically relevant levels of light at night produce comparable results, as has been reported in several vertebrate taxa, remains to be tested.

  19. Constant illumination reduces circulating melatonin and impairs immune function in the cricket Teleogryllus commodus

    PubMed Central

    Michaelides, Ellie B.; Rupasinghe, Thusitha; Tull, Dedreia; Green, Mark P.; Jones, Therésa M.

    2015-01-01

    Exposure to constant light has a range of negative effects on behaviour and physiology, including reduced immune function in both vertebrates and invertebrates. It is proposed that the associated suppression of melatonin (a ubiquitous hormone and powerful antioxidant) in response to the presence of light at night could be an underlying mechanistic link driving the changes to immune function. Here, we investigated the relationship between constant illumination, melatonin and immune function, using a model invertebrate species, the Australian black field cricket, Teleogryllus commodus. Crickets were reared under either a 12 h light: 12 h dark regimen or a constant 24 h light regimen. Circulating melatonin concentration and immune function (haemocyte concentration, lytic activity and phenoloxidase (PO) activity) were assessed in individual adult crickets through the analysis of haemolymph. Constant illumination reduced melatonin and had a negative impact on haemocyte concentrations and lytic activity, but its effect on PO activity was less apparent. Our data provide the first evidence, to our knowledge, of a link between exposure to constant illumination and variation in haemocyte concentration in an invertebrate model, while also highlighting the potential complexity of the immune response following exposure to constant illumination. This study provides insight into the possible negative effect of artificial night-time lighting on the physiology of invertebrates, but whether lower and potentially more ecologically relevant levels of light at night produce comparable results, as has been reported in several vertebrate taxa, remains to be tested. PMID:26339535

  20. Breathers and localized solitons for the Hirota–Maxwell–Bloch system on constant backgrounds in erbium doped fibers

    SciTech Connect

    Guo, Rui Hao, Hui-Qin

    2014-05-15

    In nonlinear erbium doped fibers, the Hirota–Maxwell–Bloch system with higher order effects usually governs the propagation of ultrashort pulses. New soliton solutions for this system are constructed on the constant backgrounds including one and two breathers and first and higher order localized soliton solutions. Considering the influence of higher order effects, propagation properties of those soliton solutions are discussed. -- Highlights: •The AB and Ma-breathers are derived on the constant backgrounds. •Dynamic features of two-breathers are discussed. •Localized solutions are generated from two different ways.

  1. Complex dielectric constant of various biomolecules as a function of wavelength using surface plasmon resonance

    NASA Astrophysics Data System (ADS)

    Paliwal, Ayushi; Tomar, Monika; Gupta, Vinay

    2014-07-01

    Present study focuses on determination of complex dielectric constant of biomolecules as function of frequency by means of surface plasmon resonance (SPR) technique without losing their biofunctionality. Surface plasmon modes have been excited in Kretschmann configuration at interface of ZnO-Au thin films. Various biomolecules (glucose oxidase, cholesterol oxidase, urease, and uricase) have been immobilized successfully on surface of ZnO thin film by electrostatic interaction. SPR reflectance curves for all biomolecules were recorded separately at different wavelengths (407-635 nm). Complex dielectric constant was determined by fitting the experimental SPR data with Fresnel's equations. Dielectric constant of all biomolecules shows frequency dispersion and attributed to ionic polarization.

  2. Time constants and feedback transfer functions of EBR-II (Experimental Breeder Reactor) subassembly types

    SciTech Connect

    Grimm, K.N.; Meneghetti, D.

    1986-09-01

    Time constants, feedback reactivity transfer functions and power coefficients are calculated for stereotypical subassemblies in the EBR-II reactor. These quantities are calculated from nodal reactivities obtained from a reactor kinetic code analysis for a step change in power. Due to the multiplicity of eigenvalues, there are several time constants for each nodal position in a subassembly. Compared with these calculated values are analytically derived values for the initial node of a given channel.

  3. On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

    NASA Astrophysics Data System (ADS)

    Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

    Locally dense basis sets (function. Employing these type of LDBSs we can reduce the number of necessary basis functions by about 30% without losing more than about 1 Hz in accuracy. The analysis of the four contributions to the vicinal fluorine-fluorine coupling constants shows that the non-contact orbital paramagnetic term is the most important contribution followed by the also non-contact spin-dipolar term. The Fermi contact term is the largest contribution only in the synperiplanar conformations of 1,2-difluoroethane and -propane.

  4. Challenges and implications of global modeling approaches that are alternatives to using constant plant functional types

    NASA Astrophysics Data System (ADS)

    Bodegom, P. V.

    2015-12-01

    In recent years a number of approaches have been developed to provide alternatives to the use of plant functional types (PFTs) with constant vegetation characteristics for simulating vegetation responses to climate changes. In this presentation, an overview of those approaches and their challenges is given. Some new approaches aim at removing PFTs altogether by determining the combination of vegetation characteristics that would fit local conditions best. Others describe the variation in traits within PFTs as a function of environmental drivers, based on community assembly principles. In the first approach, after an equilibrium has been established, vegetation composition and its functional attributes can change by allowing the emergence of a new type that is more fit. In the latter case, changes in vegetation attributes in space and time as assumed to be the result intraspecific variation, genetic adaptation and species turnover, without quantifying their respective importance. Hence, it is assumed that -by whatever mechanism- the community as a whole responds without major time lags to changes in environmental drivers. Recently, we showed that intraspecific variation is highly species- and trait-specific and that none of the current hypotheses on drivers of this variation seems to hold. Also genetic adaptation varies considerably among species and it is uncertain whether it will be fast enough to cope with climate change. Species turnover within a community is especially fast in herbaceous communities, but much slower in forest communities. Hence, it seems that assumptions made may not hold for forested ecosystems, but solutions to deal with this do not yet exist. Even despite the fact that responsiveness of vegetation to environmental change may be overestimated, we showed that -upon implementation of trait-environment relationships- major changes in global vegetation distribution are projected, to similar extents as to those without such responsiveness.

  5. H0, q0 and the local velocity field. [Hubble and deceleration constants in Big Bang expansion

    NASA Technical Reports Server (NTRS)

    Sandage, A.; Tammann, G. A.

    1982-01-01

    An attempt is made to find a systematic deviation from linearity for distances that are under the control of the Virgo cluster, and to determine the value of the mean random motion about the systematic flow, in order to improve the measurement of the Hubble and the deceleration constants. The velocity-distance relation for large and intermediate distances is studied, and type I supernovae are calibrated relatively as distance indicators and absolutely to obtain a new value for the Hubble constant. Methods of determining the deceleration constant are assessed, including determination from direct measurement, mean luminosity density, virgocentric motion, and the time scale test. The very local velocity field is investigated, and a solution is preferred with a random peculiar radial velocity of very nearby field galaxies of 90-100 km/s, and a Virgocentric motion of the local group of 220 km/s, leading to an underlying expansion rate of 55, in satisfactory agreement with the global value.

  6. Maximally localized Wannier functions: Theory and applications

    NASA Astrophysics Data System (ADS)

    Marzari, Nicola; Mostofi, Arash A.; Yates, Jonathan R.; Souza, Ivo; Vanderbilt, David

    2012-10-01

    The electronic ground state of a periodic system is usually described in terms of extended Bloch orbitals, but an alternative representation in terms of localized “Wannier functions” was introduced by Gregory Wannier in 1937. The connection between the Bloch and Wannier representations is realized by families of transformations in a continuous space of unitary matrices, carrying a large degree of arbitrariness. Since 1997, methods have been developed that allow one to iteratively transform the extended Bloch orbitals of a first-principles calculation into a unique set of maximally localized Wannier functions, accomplishing the solid-state equivalent of constructing localized molecular orbitals, or “Boys orbitals” as previously known from the chemistry literature. These developments are reviewed here, and a survey of the applications of these methods is presented. This latter includes a description of their use in analyzing the nature of chemical bonding, or as a local probe of phenomena related to electric polarization and orbital magnetization. Wannier interpolation schemes are also reviewed, by which quantities computed on a coarse reciprocal-space mesh can be used to interpolate onto much finer meshes at low cost, and applications in which Wannier functions are used as efficient basis functions are discussed. Finally the construction and use of Wannier functions outside the context of electronic-structure theory is presented, for cases that include phonon excitations, photonic crystals, and cold-atom optical lattices.

  7. Multidimensional stochastic approximation using locally contractive functions

    NASA Technical Reports Server (NTRS)

    Lawton, W. M.

    1975-01-01

    A Robbins-Monro type multidimensional stochastic approximation algorithm which converges in mean square and with probability one to the fixed point of a locally contractive regression function is developed. The algorithm is applied to obtain maximum likelihood estimates of the parameters for a mixture of multivariate normal distributions.

  8. The demise of constant price impact functions and single-time step models of speculation

    NASA Astrophysics Data System (ADS)

    Challet, Damien

    2007-08-01

    Constant and symmetric price impact functions, most commonly used in agent-based market modelling, are shown to give rise to paradoxical and inconsistent outcomes in the simplest case of arbitrage exploitation when open-hold-close actions are considered. The solution of the paradox lies in the non-constant nature of real-life price impact functions. A simple model that includes explicit position opening, holding, and closing is briefly introduced and its information ecology discussed, shedding new light on the relevance of the Minority Game to the study of financial markets.

  9. Local and Global Comparison of Continuous Functions

    SciTech Connect

    Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V

    2004-12-16

    We introduce local and global comparison measures for a collection of k {<=} d real-valued smooth functions on a common d-dimensional Riemannian manifold. For k = d = 2 we relate the measures to the set of critical points of one function restricted to the level sets of the other. The definition of the measures extends to piecewise linear functions for which they are easy to compute. The computation of the measures forms the centerpiece of a software tool which we use to study scientific datasets.

  10. Robust determination of maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Cancès, Éric; Levitt, Antoine; Panati, Gianluca; Stoltz, Gabriel

    2017-02-01

    We propose an algorithm to determine maximally localized Wannier functions (MLWFs). This algorithm, based on recent theoretical developments, does not require any physical input such as initial guesses for the Wannier functions, unlike popular schemes based on the projection method. We discuss how the projection method can fail on fine grids when the initial guesses are too far from MLWFs. We demonstrate that our algorithm is able to find localized Wannier functions through tests on two-dimensional systems, simplified models of semiconductors, and realistic DFT systems by interfacing with the wannier90 code. We also test our algorithm on the Haldane and Kane-Mele models to examine how it fails in the presence of topological obstructions.

  11. Analysis of agonist dissociation constants as assessed by functional antagonism in guinea pig left atria

    SciTech Connect

    Molenaar, P.; Malta, E.

    1986-04-01

    In electrically driven guinea pig left atria, positive inotropic responses to (-)-isoprenaline and the selective beta 1-adrenoceptor agonist RO363 were obtained in the absence and in the presence of the functional antagonists adenosine, carbachol, gallopamil, nifedipine, and Ro 03-7894. Each of the functional antagonists reduced the maximum response to both agonists and produced nonparallel rightward shifts in the cumulative concentration effect curves. For both agonists, dissociation constants (KA) were calculated using the equation described by Furchgott (1966) for irreversible antagonism. For RO363, which is a partial agonist with high agonist activity, the equations outlined for functional interaction by Mackay (1981) were also employed to calculate KA values. The KA values obtained by each method were compared with the dissociation constants (KD) for the two agonists determined from their ability to displace the radioligand (-)-(/sup 125/I)iodocyanopindolol from beta 1-adrenoceptors in guinea pig left atrial membrane preparations. The estimates of KA varied substantially from KD values. The KD values were taken as more accurate estimates of the true values for the dissociation constants because a high degree of correlation exists between pKD and pD2 values for a number of other beta-adrenoceptor agonists that behave as partial agonists and between pKD and pKB values for a number of beta-adrenoceptor antagonists. Thus, it appears that there are serious limitations in the current theory for using functional antagonism as a means of obtaining agonist dissociation constants.

  12. The elastic constants of rubrene determined by Brillouin scattering and density functional theory

    NASA Astrophysics Data System (ADS)

    Zhang, Yaqi; Manke, David R.; Sharifzadeh, Sahar; Briseno, Alejandro L.; Ramasubramaniam, Ashwin; Koski, Kristie J.

    2017-02-01

    The linear elastic stiffness tensor of the crystalline organic semiconductor, rubrene, is measured using Brillouin light scattering spectroscopy and computed from first-principles van der Waals density functional theory calculations. Results are compared with recent measurements of in-plane reduced elastic constants c¯ 22, c¯ 33 , and c¯ 23 determined through anisotropic buckling experiments.

  13. The Local [CII] Emission Line Luminosity Function

    NASA Astrophysics Data System (ADS)

    Hemmati, Shoubaneh

    2017-01-01

    I present, for the first time, the local [CII]158 $\\mu$m emission line luminosity function measured using a sample of more than 500 galaxies from the RBGS. [CII] luminosities are measured from the Herschel PACS observations of the LIRGs in the GOALS survey and estimated for the rest of the sample based on the far-IR luminosity and color. The sample covers 91.3% of the sky and is complete at $S_{60\\mu m} > 5.24 Jy$. We calculated the completeness as a function of [CII] line luminosity and distance, based on the far-IR color and flux densities. The [CII] luminosity function is constrained in the range $\\sim 10^{7-9} \\ L_{\\odot}$ from both the 1/Vmax and the STY maximum likelihood methods. The shape of our derived [CII] emission line luminosity function agrees well with the IR luminosity function. For the CO(1-0) and [CII] luminosity functions to agree, we propose a varying ratio of [CII]/CO(1-0) as a function of CO luminosity, with larger ratios for fainter CO luminosities. Limited [CII] high redshift observations as well as estimates based on the IR and UV luminosity functions, are suggestive of an evolution in the [CII] luminosity function similar to the evolution trend of the cosmic star formation rate density. ALMA with full capability will be able to confirm this prediction.

  14. THE ONSET OF ELECTRICAL BREAKDOWN IN DUST LAYERS: II. EFFECTIVE DIELECTRIC CONSTANT AND LOCAL FIELD ENHANCEMENT

    EPA Science Inventory

    Part 1 of the work has shown that electrical breakdown in dust layers obeys Paschen's Law, but occurs at applied field values which appear too small to initiate the breakdown. In this paper the authors show how an effective dielectric constant characterizing the dust layer can be...

  15. Ultrasonic imaging of highly scattering media from local measurements of the diffusion constant: Separation of coherent and incoherent intensities

    NASA Astrophysics Data System (ADS)

    Aubry, Alexandre; Derode, Arnaud

    2007-02-01

    As classical imaging fails with diffusive media, one way to image a multiple-scattering medium is to achieve local measurements of the dynamic transport properties of a wave undergoing diffusion. This paper presents a method to obtain local measurements of the diffusion constant D in a multiple-scattering medium. The experimental setup consists in an array of programmable transducers placed in front of the multiple-scattering medium to be imaged. By achieving Gaussian beamforming both at emission and reception, an array of virtual sources and receivers located in the near field is constructed. The time evolution of the incoherent component of the intensity backscattered on this virtual array is shown to represent directly the growth of the diffusive halo as Dt . A matrix treatment is proposed to separate the incoherent intensity from the coherent backscattering peak. Once the incoherent contribution is isolated, a local measurement of the diffusion constant is possible. The technique is applied to image the long-scale variations of D in a random-scattering sample made of two parts with a different concentration of cylindrical scatterers. This experimental result is obtained with ultrasonic waves around 3MHz . It illustrates the possibility of imaging diffusive media from local measurements of the diffusion constant, based on coherent Gaussian beamforming and a matrix “antisymmetrization,” which creates a virtual antireciprocity.

  16. Variational solutions by the use of stepwise constant functions. I - Linear case.

    NASA Technical Reports Server (NTRS)

    Yoshikawa, K. K.

    1972-01-01

    Demonstration that accurate solutions to the integral equation or to the extremal function can be easily obtained by the variational method in many cases when a stepwise constant function is used for the trial function. The evaluation procedure is simple and straightforward; integrals of the kernel function can be evaluated analytically; the method provides, when the solution involves singularities, the best mean value across the singularity; the results are accurate in both the detailed physical quantities and their averages; the resultant solution can be further integrated analytically over the parameters associated with the problem; and the method can be readily applied to nonlinear integral equations.

  17. Running coupling constant of ten-flavor QCD with the Schroedinger functional method

    SciTech Connect

    Hayakawa, M.; Uno, S.; Ishikawa, K.-I.; Osaki, Y.; Takeda, S.; Yamada, N.

    2011-04-01

    The walking technicolor theory attempts to realize electroweak symmetry breaking as the spontaneous chiral symmetry breakdown caused by the gauge dynamics with slowly varying gauge coupling constant and large mass anomalous dimension. Many-flavor QCD theories are candidates owning these features. We focus on the SU(3) gauge theory with ten flavors of massless fermions in the fundamental representation, and compute the gauge coupling constant in the Schroedinger functional scheme. Numerical simulation is performed with O(a)-unimproved lattice action, and the continuum limit is taken in linear in lattice spacing. We observe evidence that this theory possesses an infrared fixed point.

  18. Spatially resolved dielectric constant of confined water and its connection to the non-local nature of bulk water

    NASA Astrophysics Data System (ADS)

    Schaaf, Christian; Gekle, Stephan

    2016-08-01

    We use molecular dynamics simulations to compute the spatially resolved static dielectric constant of water in cylindrical and spherical nanopores as occurring, e.g., in protein water pockets or carbon nanotubes. For this, we derive a linear-response formalism which correctly takes into account the dielectric boundary conditions in the considered geometries. We find that in cylindrical confinement, the axial component behaves similar as the local density akin to what is known near planar interfaces. The radial dielectric constant shows some oscillatory features when approaching the surface if their radius is larger than about 2 nm. Most importantly, however, the radial component exhibits pronounced oscillations at the center of the cavity. These surprising features are traced back quantitatively to the non-local dielectric nature of bulk water.

  19. Time constants and transfer functions for a homogeneous 900 MWt metallic fueled LMR

    SciTech Connect

    Grimm, K.N.; Meneghetti, D.

    1988-01-01

    Nodal transfer functions are calculated for a 900 MWt U10Zr-fueled sodium cooled reactor. From the transfer functions the time constants, feedback reactivity transfer function coefficients, and power coefficients can be determined. These quantities are calculated for core fuel, upper and lower axial reflector steel, radial blanket fuel, radial reflector steel, and B/sub 4/C rod shaft expansion effect. The quantities are compared to the analogous quantities of a 60 MWt metallic-fueled sodium cooled Experimental Breeder Reactor II configuration. 8 refs., 2 figs., 6 tabs.

  20. Robust reconstruction of the rate constant distribution using the phase function method.

    PubMed

    Zhou, Yajun; Zhuang, Xiaowei

    2006-12-01

    Many biological processes exhibit complex kinetic behavior that involves a nontrivial distribution of rate constants. Characterization of the rate constant distribution is often critical for mechanistic understandings of these processes. However, it is difficult to extract a rate constant distribution from data measured in the time domain. This is due to the numerical instability of the inverse Laplace transform, a long-standing mathematical challenge that has hampered data analysis in many disciplines. Here, we present a method that allows us to reconstruct the probability distribution of rate constants from decay data in the time domain, without fitting to specific trial functions or requiring any prior knowledge of the rate distribution. The robustness (numerical stability) of this reconstruction method is numerically illustrated by analyzing data with realistic noise and theoretically proved by the continuity of the transformations connecting the relevant function spaces. This development enhances our ability to characterize kinetics and dynamics of biological processes. We expect this method to be useful in a broad range of disciplines considering the prevalence of complex exponential decays in many experimental systems.

  1. Global network influences on local functional connectivity

    PubMed Central

    Snyder, Adam C.; Morais, Michael J.; Willis, Cory M.; Smith, Matthew A.

    2015-01-01

    A central neuroscientific pursuit is understanding neuronal interactions that support computations underlying cognition and behavior. Although neurons interact across disparate scales – from cortical columns to whole-brain networks – research has been restricted to one scale at a time. We measured local interactions through multi-neuronal recordings while accessing global networks using scalp EEG in rhesus macaques. We measured spike count correlation, an index of functional connectivity with computational relevance, and EEG oscillations, which have been linked to various cognitive functions. We found a surprising non-monotonic relationship between EEG oscillation amplitude and spike count correlation, contrary to the intuitive expectation of a direct relationship. With a widely-used network model we replicated these findings by incorporating a private signal targeting inhibitory neurons, a common mechanism proposed for gain modulation. Finally, we report that spike count correlation explains nonlinearities in the relationship between EEG oscillations and response time in a spatial selective attention task. PMID:25799040

  2. The relation of local measures of Hubble's constant to its global value

    NASA Technical Reports Server (NTRS)

    Turner, Edwin L.; Cen, Renyue; Ostriker, Jeremiah P.

    1992-01-01

    The distributions of fractional deviations of local values form global H0 that observers with perfect distance data would find if they surveyed specified volumes of the universe are examined here using new very large scale calculations of cold dark matter (CDM) and primordial isocurvature baryonic (PIB) scenarios for the origin of structure. It is found that the expected deviations due to large-scale motions are larger than quoted observational errors unless very large volumes are surveyed. Even perfect sampling and distances of all galaxies within a sphere extending out to the distances of the Virgo and Coma clusters would leave 45 percent and 3 percent rms uncertainties, respectively, in the global value of H0 in the CDM model. It is shown that the local versus global error in an H0 determination can be roughly estimated by the angular variance seen over the sky in the expansion rate, and that a very rough correction from the local to the global H0 value can be derived.

  3. Performance of wave function and density functional methods for water hydrogen bond spin-spin coupling constants.

    PubMed

    García de la Vega, J M; Omar, S; San Fabián, J

    2017-04-01

    Spin-spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob's ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict (1) J O H , (2) J H H and (2h) J O O couplings, while (1h) J O H is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for (1) J O H and (2) J H H have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods. Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

  4. Electromechanical and electro-optical functions of plasticized PVC with colossal dielectric constant

    NASA Astrophysics Data System (ADS)

    Sato, Hiromu; Hirai, Toshihiro

    2013-04-01

    A soft dielectric polymer, plasticized poly(vinyl chloride) (PVC gel), has been known as a characteristic actuator with electrotactic creep deformation. The deformation can be applied for bending and contraction. The mechanism of the deformation has been attributed to the colossal dielectric constant of the gel induced by dc field. The dielectric constant at 1 Hz, jumps from less than10 to thousand times larger value. The huge dielectric constant suggests the gel can have electro-optic function. In this paper, we introduce the gel can bend light direction by applying a dc electric field. The PVC gel can bend light direction depending on the electric field. Detailed feature of the light bending will be introduced and discussed. Bending angle can be controlled by dielectric plasticizer and electric field. The components of the gel, PVC and plasticizer themselves, did not show any effect of electro-optical function like the PVC gel. The same feature can be observed in other polymer, like poly(vinyl alcohol)-dimethyl sulphoxide gel, too.

  5. Response of the Worldwide Side Impact Dummy (WorldSID) to Localized Constant-Speed Impacts.

    PubMed

    Sunnevång, Cecilia; Subit, Damien; Kindig, Matthew; Lessley, David; Lamp, John; Boström, Ola; Kent, Richard

    2011-01-01

    The objective of this study was to evaluate WorldSID constant-speed shoulder and thorax impact responses in terms of impact force, external and internal deflection (1D and 2D IR-Tracc response) for two velocities (1 m/s and 3 m/s), at three impact levels (shoulder, upper thorax and mid thorax) in three impact directions (lateral, +15° posterolateral, -15° anteraolateral). In addition, the impact force and external deflection were compared to previously published cadaver data. Each impact condition was repeated twice. A total of 42 tests were performed. The WorldSID's lowest peak impact force and external deflection were found for impact at shoulder level regardless of impact direction. Maximum force and deflection were found for impact at mid thorax. Comparison between WorldSID and PMHS showed similar external chest deflections for impacts at 3 m/s. The peak impact force response with respect to impact level was found to be reversed for the WorldSID compared to the PMHS, for which shoulder impact resulted in the highest peak force. External time history responses for the WorldSID compared to the one PMHS impacted at 1 m/s in lateral impact direction showed a significant difference in both timing and magnitude. External deflections at upper and mid thorax were approximately twice as high as the internal 1D deflection measured by the IR-Tracc. However, taking into account the rotation of the rib, the calculated 2D deflection response at the posterior impact direction was closer to the external deflection, and thus also to the PMHS deflection response at 3 m/s. These findings emphasize the need of 2D deflection measurement.

  6. Systematic Study of Locally Dense Basis Sets for NMR Shielding Constants.

    PubMed

    Reid, David M; Kobayashi, Rika; Collins, Michael A

    2014-01-14

    This paper presents a systematic study of partitioning schemes for locally dense basis sets in the context of NMR shielding calculations. The partitionings explored were based exclusively on connectivity and utilized the basis sets from the pcS-n series. Deviations from pcS-4 shieldings were calculated for a set of 28 organic molecules at the HF, B3LYP, and KT3 levels of theory, with the primary goal being the determination of an efficient scheme that achieves maximal deviations of 0.1 ppm for (1)H and 1 ppm for (13)C. Both atom based and group based divisions of basis sets were examined, with the latter providing the most promising results. It is demonstrated that for the systems studied, at least pcS-1 is required for all parts of the molecule. This, coupled with pcS-3 on the group of interest and pcS-2 on the adjacent groups, is sufficient to achieve the desired level of accuracy at a minimal computational expense. In addition, the suitability of the pcS-n basis sets for post-SCF methods was confirmed through a comparison with other standard basis sets at the MP2 level.

  7. Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

    SciTech Connect

    Hrycyna, Orest; Szydłowski, Marek E-mail: marek.szydlowski@uj.edu.pl

    2015-11-01

    Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory.

  8. Role of Möbius constants and scattering functions in Cachazo-He-Yuan scalar amplitudes

    NASA Astrophysics Data System (ADS)

    Lam, C. S.; Yao, York-Peng

    2016-05-01

    The integration over the Möbius variables leading to the Cachazo-He-Yuan double-color n -point massless scalar amplitude are carried out one integral at a time. Möbius invariance dictates the final amplitude to be independent of the three Möbius constants σr,σs,σt, but their choice affects integrations and the intermediate results. The effect of the Möbius constants, which will be held finite but otherwise arbitrary, the two sets of colors, and the scattering functions on each integration is investigated. A general systematic way to carry out the n -3 integrations is explained, each exposing one of the n -3 propagators of a single Feynman diagram. Two detailed examples are shown to illustrate the procedure, one a five-point amplitude, and the other a nine-point amplitude. Our procedure does not generate intermediate spurious poles, in contrast to what is common by choosing Möbius constants at 0, 1, and ∞ .

  9. Precision atomic spectroscopy for improved limits on variation of the fine structure constant and local position invariance.

    PubMed

    Fortier, T M; Ashby, N; Bergquist, J C; Delaney, M J; Diddams, S A; Heavner, T P; Hollberg, L; Itano, W M; Jefferts, S R; Kim, K; Levi, F; Lorini, L; Oskay, W H; Parker, T E; Shirley, J; Stalnaker, J E

    2007-02-16

    We report tests of local position invariance and the variation of fundamental constants from measurements of the frequency ratio of the 282-nm 199Hg+ optical clock transition to the ground state hyperfine splitting in 133Cs. Analysis of the frequency ratio of the two clocks, extending over 6 yr at NIST, is used to place a limit on its fractional variation of <5.8x10(-6) per change in normalized solar gravitational potential. The same frequency ratio is also used to obtain 20-fold improvement over previous limits on the fractional variation of the fine structure constant of |alpha/alpha|<1.3x10(-16) yr-1, assuming invariance of other fundamental constants. Comparisons of our results with those previously reported for the absolute optical frequency measurements in H and 171Yb+ vs other 133Cs standards yield a coupled constraint of -1.5x10(-15)

  10. Acid Dissociation Constants of Melamine Derivatives from Density Functional Theory Calculations

    NASA Astrophysics Data System (ADS)

    Jang, Yun Hee; Hwang, Sungu; Chang, Seo Bong; Ku, Jamin; Chung, Doo Soo

    2009-10-01

    Melamine and its hydrolysis products (ammeline, ammelide, and cyanuric acid) recently attracted great attention as major food contaminants. Developing analytical tools to quantify them requires exact knowledge of their acid dissociation constants (pKa values). Herein, we calculated the pKa values of these melamine derivatives in water, using a density functional theory quantum mechanical method [B3LYP/6-311++G(d,p)] in combination with the Poisson-Boltzmann continuum solvation model. The excellent agreement of the calculated values with the experimental ones shows that our method can be used to predict such properties of other food contaminants.

  11. The Effect of Local Orientation Change on the Detection of Contours Defined by Constant Curvature: Psychophysics and Image Statistics

    PubMed Central

    Khuu, Sieu K.; Cham, Joey; Hayes, Anthony

    2017-01-01

    In the present study, we investigated the detection of contours defined by constant curvature and the statistics of curved contours in natural scenes. In Experiment 1, we examined the degree to which human sensitivity to contours is affected by changing the curvature angle and disrupting contour curvature continuity by varying the orientation of end elements. We find that (1) changing the angle of contour curvature decreased detection performance, while (2) end elements oriented in the direction (i.e., clockwise) of curvature facilitated contour detection regardless of the curvature angle of the contour. In Experiment 2 we further established that the relative effect of end—element orientation on contour detection was not only dependent on their orientation (collinear or cocircular), but also their spatial separation from the contour, and whether the contour shape was curved or not (i.e., C-shaped or S-shaped). Increasing the spatial separation of end-elements reduced contour detection performance regardless of their orientation or the contour shape. However, at small separations, cocircular end-elements facilitated the detection of C-shaped contours, but not S-shaped contours. The opposite result was observed for collinear end-elements, which improved the detection of S- shaped, but not C-shaped contours. These dissociative results confirmed that the visual system specifically codes contour curvature, but the association of contour elements occurs locally. Finally, we undertook an analysis of natural images that mapped contours with a constant angular change and determined the frequency of occurrence of end elements with different orientations. Analogous to our behavioral data, this image analysis revealed that the mapped end elements of constantly curved contours are likely to be oriented clockwise to the angle of curvature. Our findings indicate that the visual system is selectively sensitive to contours defined by constant curvature and that this might

  12. The Effect of Local Orientation Change on the Detection of Contours Defined by Constant Curvature: Psychophysics and Image Statistics.

    PubMed

    Khuu, Sieu K; Cham, Joey; Hayes, Anthony

    2016-01-01

    In the present study, we investigated the detection of contours defined by constant curvature and the statistics of curved contours in natural scenes. In Experiment 1, we examined the degree to which human sensitivity to contours is affected by changing the curvature angle and disrupting contour curvature continuity by varying the orientation of end elements. We find that (1) changing the angle of contour curvature decreased detection performance, while (2) end elements oriented in the direction (i.e., clockwise) of curvature facilitated contour detection regardless of the curvature angle of the contour. In Experiment 2 we further established that the relative effect of end-element orientation on contour detection was not only dependent on their orientation (collinear or cocircular), but also their spatial separation from the contour, and whether the contour shape was curved or not (i.e., C-shaped or S-shaped). Increasing the spatial separation of end-elements reduced contour detection performance regardless of their orientation or the contour shape. However, at small separations, cocircular end-elements facilitated the detection of C-shaped contours, but not S-shaped contours. The opposite result was observed for collinear end-elements, which improved the detection of S- shaped, but not C-shaped contours. These dissociative results confirmed that the visual system specifically codes contour curvature, but the association of contour elements occurs locally. Finally, we undertook an analysis of natural images that mapped contours with a constant angular change and determined the frequency of occurrence of end elements with different orientations. Analogous to our behavioral data, this image analysis revealed that the mapped end elements of constantly curved contours are likely to be oriented clockwise to the angle of curvature. Our findings indicate that the visual system is selectively sensitive to contours defined by constant curvature and that this might reflect

  13. The star formation rate distribution function of the local Universe

    NASA Astrophysics Data System (ADS)

    Bothwell, M. S.; Kennicutt, R. C.; Johnson, B. D.; Wu, Y.; Lee, J. C.; Dale, D.; Engelbracht, C.; Calzetti, D.; Skillman, E.

    2011-08-01

    We present total infrared (IR) and ultraviolet (UV) luminosity functions derived from large representative samples of galaxies at z˜ 0, selected at IR and UV wavelengths from the Imperial IRAS Faint Source Catalogue redshift data base (IIFSCz) catalogue, and the GALEX All-Sky Imaging Survey (AIS), respectively. We augment these with deep Spitzer and GALEX imaging of galaxies in the 11 Mpc Local Volume Legacy (LVL) Survey, allowing us to extend these luminosity functions to lower luminosities (˜106 L⊙), and providing good constraints on the slope of the luminosity function at the extreme faint end for the first time. Using conventional star formation prescriptions, we generate from our data the star formation rate (SFR) distribution function for the local Universe. We find that it has a Schechter form, the faint-end slope has a constant value (to the limits of our data) of α=-1.51 ± 0.08 and the ‘characteristic’ SFR ψ* is 9.2 M⊙ yr-1. We also show the distribution function of the SFR volume density; we then use this to calculate a value for the total SFR volume density at z˜ 0 of 0.025 ± 0.0016 M⊙ yr-1 Mpc-3, of which ˜20 per cent is occurring in starbursts. Decomposing the total star formation by infrared luminosity, it can be seen that 9 ± 1 per cent is due to LIRGs, and 0.7 ± 0.2 per cent is occurring in ULIRGs. By comparing UV and IR emission for galaxies in our sample, we also calculate the fraction of star formation occurring in dust-obscured environments, and examine the distribution of dusty star formation: we find a very shallow slope at the highly extincted end, which may be attributable to line-of-sight orientation effects as well as conventional internal extinction.

  14. Carboxylic acid functional group analysis using constant neutral loss scanning-mass spectrometry.

    PubMed

    Dron, Julien; Eyglunent, Gregory; Temime-Roussel, Brice; Marchand, Nicolas; Wortham, Henri

    2007-12-12

    The present study describes the development of a new analytical technique for the functional group determination of the carboxylic moiety using atmospheric pressure chemical ionization-mass spectrometry (APCI-MS/MS) operated in the constant neutral loss scanning (CNLS) mode. Carboxylic groups were first derivatized into their corresponding methyl esters by reacting with BF3/methanol mix and the reaction mixture was then directly injected into the APCI chamber. The loss of methanol (m/z = 32 amu) resulting from the fragmentation of the protonated methyl esters was then monitored. Applying this method together with a statistical approach to reference mixtures containing 31 different carboxylic acids at randomly calculated concentrations demonstrated its suitability for quantitative functional group measurements with relative standard deviations below 15% and a detection limit of 0.005 mmol L(-1). Its applicability to environmental matrices was also shown through the determination of carboxylic acid concentrations inside atmospheric aerosol samples. To the best of our knowledge, it is the first time that the tandem mass spectrometry was successfully applied to functional group analysis, offering great perspectives in the characterization of complex mixtures which are prevailing in the field of environmental analysis as well as in the understanding of the chemical processes occurring in these matrices.

  15. Simultaneous determination of optical constants, local thickness and roughness of ZnSe thin films by imaging spectroscopic reflectometry

    NASA Astrophysics Data System (ADS)

    Nečas, D.; Ohlídal, I.; Franta, D.; Ohlídal, M.; Vodák, J.

    2016-01-01

    A rough non-uniform ZnSe thin film on a GaAs substrate is optically characterised using imaging spectroscopic reflectometry (ISR) in the visible, UV and near IR region, applied as a standalone technique. A global-local data processing algorithm is used to fit spectra from all pixels together and simultaneously determine maps of the local film thickness, roughness and overlayer thickness as well as spectral dependencies of film optical constants determined for the sample as a whole. The roughness of the film upper boundary is modelled using scalar diffraction theory (SDT), for which an improved calculation method is developed to process the large quantities of experimental data produced by ISR efficiently. This method avoids expensive operations by expressing the series obtained from SDT using a double recurrence relation and it is shown that it essentially eliminates the necessity for any speed-precision trade-offs in the SDT calculations. Comparison of characterisation results with the literature and other techniques shows the ability of multi-pixel processing to improve the stability and reliability of least-squares data fitting and demonstrates that standalone ISR, coupled with suitable data processing methods, is viable as a characterisation technique, even for thin films that are relatively far from ideal and require complex modelling.

  16. Pseudo-local Theories: A Functional Class Proposal

    NASA Astrophysics Data System (ADS)

    Taronna, Massimo

    In this article, using the language of jet space, we propose a functional class space for pseudo-local functionals. We test this functional class proposal in a number of examples ranging from string-field-theory to AdS/CFT dualities. Implications of the locality proposal at the quartic order are also discussed.

  17. Remote Control of Gene Function by Local Translation

    PubMed Central

    Jung, Hosung; Gkogkas, Christos G.; Sonenberg, Nahum; Holt, Christine E.

    2014-01-01

    The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function. PMID:24679524

  18. Benchmarking density-functional theory calculations of NMR shielding constants and spin-rotation constants using accurate coupled-cluster calculations.

    PubMed

    Teale, Andrew M; Lutnæs, Ola B; Helgaker, Trygve; Tozer, David J; Gauss, Jürgen

    2013-01-14

    Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.

  19. Local representation of the electronic dielectric response function

    DOE PAGES

    Lu, Deyu; Ge, Xiaochuan

    2015-12-11

    We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized,more » which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.« less

  20. Local representation of the electronic dielectric response function

    SciTech Connect

    Lu, Deyu; Ge, Xiaochuan

    2015-12-11

    We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized, which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.

  1. Non-Friedmann cosmology for the Local Universe, significance of the universal Hubble constant, and short-distance indicators of dark energy

    NASA Astrophysics Data System (ADS)

    Chernin, A. D.; Teerikorpi, P.; Baryshev, Yu. V.

    2006-09-01

    Based on the increasing evidence of the cosmological relevance of the local Hubble flow, we consider a simple analytical cosmological model for the Local Universe. This is a non-Friedmann model with a non-uniform static space-time. The major dynamical factor controlling the local expansion is the antigravity produced by the omnipresent and permanent dark energy of the cosmic vacuum (or the cosmological constant). The antigravity dominates at larger distances than 1-2 Mpc from the center of the Local group. The model gives a natural explanation of the two key quantitative characteristics of the local expansion flow, which are the local Hubble constant and the velocity dispersion of the flow. The observed kinematical similarity of the local and global flows of expansion is clarified by the model. We analytically demonstrate the efficiency of the vacuum cooling mechanism that allows one to see the Hubble law this close to the Local group. The "universal Hubble constant" HV (≈60 km s-1 Mpc-1), depending only on the vacuum density, has special significance locally and globally. The model makes a number of verifiable predictions. It also unexpectedly shows that the dwarf galaxies of the local flow with the shortest distances and lowest redshifts may be the most sensitive indicators of dark energy in our neighborhood.

  2. Local-basis-function approach to computed tomography

    NASA Astrophysics Data System (ADS)

    Hanson, K. M.; Wecksung, G. W.

    1985-12-01

    In the local basis-function approach, a reconstruction is represented as a linear expansion of basis functions, which are arranged on a rectangular grid and possess a local region of support. The basis functions considered here are positive and may overlap. It is found that basis functions based on cubic B-splines offer significant improvements in the calculational accuracy that can be achieved with iterative tomographic reconstruction algorithms. By employing repetitive basis functions, the computational effort involved in these algorithms can be minimized through the use of tabulated values for the line or strip integrals over a single-basis function. The local nature of the basis functions reduces the difficulties associated with applying local constraints on reconstruction values, such as upper and lower limits. Since a reconstruction is specified everywhere by a set of coefficients, display of a coarsely represented image does not require an arbitrary choice of an interpolation function.

  3. 'Syncing' Up with the Quinn-Rand-Strogatz Constant: Hurwitz-ZetaFunctions in Non-Linear physics

    SciTech Connect

    Durgin, Natalie J.; Garcia, Sofia M.; Flournoy, Tamara; Bailey,David H.

    2007-12-01

    This work extends the analytical and computationalinvestigation of the Quinn-Rand-Strogatz (QRS) constants from non-linearphysics. The QRS constants (c1, c2, ..., cN) are found in a Winfreeoscillator mean-field system used to examine the transition of coupledoscillators as they lose synchronization. The constants are part of anasymptotic expansion of a function related to the oscillatorsynchronization. Previous work used high-precision software packages toevaluate c1 to 42 decimal-digits, which made it possible to recognize andprove that c1 was the root of a certain Hurwitz-zeta function. Thisallowed a value of c2 to beconjectured in terms of c1. Therefore thereis interest in determining the exact values of these constants to highprecision in the hope that general relationships can be establishedbetween the constants and the zeta functions. Here, we compute the valuesof the higher order constants (c3, c4) to more than 42-digit precision byextending an algorithm developed by D.H. Bailey, J.M. Borwein and R.E.Crandall. Several methods for speeding up the computation are exploredand an alternate proof that c1 is the root of a Hurwitz-zeta function isattempted.

  4. Local hybrid functionals: an assessment for thermochemical kinetics.

    PubMed

    Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V

    2007-11-21

    Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b(tau(W)(r)tau(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.

  5. Local hybrid functionals: An assessment for thermochemical kinetics

    SciTech Connect

    Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V.

    2007-11-21

    Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b({tau}{sub W}(r)/{tau}(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.

  6. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory

    NASA Astrophysics Data System (ADS)

    Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M.

    2015-09-01

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H12C-12CH-DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

  7. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory.

    PubMed

    Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M

    2015-09-14

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H(12)C-(12)CH-DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

  8. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory

    SciTech Connect

    Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M.

    2015-09-14

    The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H{sup 12}C–{sup 12}CH–DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

  9. Functional localization of the supplementary motor area.

    PubMed

    Hiroshima, Satoru; Anei, Ryogo; Murakami, Noboru; Kamada, Kyousuke

    2014-01-01

    The supplementary motor area (SMA) is a key structure involved in behavioral planning and execution. Although many reports have indicated that SMA is organized somatotopically, its exact organization remains still unclear. This study aimed to functionally map SMA using functional magnetic resonance imaging (fMRI) and validate the fMRI-SMA by electrocortical stimulation (ECS) and postsurgical symptoms. Total 32 healthy volunteers and 24 patients participated in this study. Motor tasks were right and left finger tapping and language tasks included simple reading, lexical decision for presented words, and verb generating tasks. SPM8 was used to conduct individual and group analyses. In all subjects, the lexical decision task induced the greatest number of active fMRI pixels in SMA. fMRI during the language tasks showed anterior part of SMA compared to finger tapping tasks. We found an overlap spot with all different tasks in posterior part of SMA, which we termed SMA core. Six patients underwent awake craniotomy for ECS mapping for primary regions and SMA. During awake craniotomy, ECS to posterior part of SMA, which might involve the possible SMA core consistently, evoked both speech arrest and flaccid hemiparesis. The SMA mapping suggested posterior part of SMA might play more important roles in any executions, which might involve the SMA core.

  10. Semiconductor band gap localization via Gaussian function

    NASA Astrophysics Data System (ADS)

    Ullrich, B.; Brown, G. J.; Xi, H.

    2012-10-01

    To determine the band gap of bulk semiconductors with transmission spectroscopy alone is considered as an extremely difficult task because in the higher energy range, approaching and exceeding the band gap energy, the material is opaque yielding no useful data to be recorded. In this paper, by investigating the transmission of industrial GaSb wafers with a thickness of 500 µm, we demonstrate how these obstacles of transmission spectroscopy can be overcome. The key is the transmission spectrums’ derivative, which coincides with the Gaussian function. This understanding can be used to transfer Beers’ law in an integral form opening the pathway of band gap determinations based on mathematical parameters only. The work also emphasizes the correlation between the thermal band gap variation and Debye temperature.

  11. Local-hybrid functional based on the correlation length

    SciTech Connect

    Johnson, Erin R.

    2014-09-28

    Local-hybrid functionals involve position-dependent mixing of Hartree-Fock and density-functional exchange, which should allow improved performance relative to conventional hybrids by reducing the inherent delocalization error and improving the long-range behaviour. Herein, the same-spin correlation length, obtained from the Fermi-hole radius, is used as the mixing parameter. The performance of the resulting local-hybrid functional is assessed for standard thermochemical and kinetics benchmarks. The local hybrid is shown to perform significantly better than the corresponding global hybrid in almost all cases.

  12. POSSIBLE EXPERIMENTS ON WAVE FUNCTION LOCALIZATION DUE TO COMPTON SCATTERING

    SciTech Connect

    Aleksandrov, Alexander V; Danilov, Viatcheslav V; Gorlov, Timofey V; Liu, Yun; Shishlo, Andrei P; Nagaitsev,

    2013-01-01

    The reduction of a particle s wave function in the process of radiation or light scattering is a longstanding problem. Its solution will give a clue on processes that form, for example, wave functions of electrons constantly emitting synchrotron radiation quanta in storage rings. On a more global scale, it may shed light on wave function collapse due to the process of measurement. In this paper we consider various experimental options using Fermilab electron beams and a possible electron beam from the SNS linac and lasers to detect electron wave function change due to Compton scattering.

  13. The bond force constant and bulk modulus of small fullerenes using density functional theory and finite element analysis.

    PubMed

    Tapia, A; Villanueva, C; Peón-Escalante, R; Quintal, R; Medina, J; Peñuñuri, F; Avilés, F

    2015-06-01

    Dedicated bond force constant and bulk modulus of C n fullerenes (n = 20, 28, 36, 50, 60) are computed using density functional theory (DFT). DFT predicts bond force constants of 611, 648, 675, 686, and 691 N/m, for C20, C28, C36, C50, and C60, respectively, indicating that the bond force constant increases for larger fullerenes. The bulk modulus predicted by DFT increases with decreased fullerene diameter, from 0.874 TPa for C60 to 1.830 TPa for C20. The bond force constants predicted by DFT are then used as an input for finite element analysis (FEA) of the fullerenes, considered as spatial frames in structural models where the bond stiffness is represented by the DFT-computed bond force constant. In agreement with DFT, FEA predicts that smaller fullerenes are stiffer, and underestimates the bulk modulus with respect to DFT. The difference between the FEA and DFT predictions of the bulk modulus decreases as the size of the fullerene increases, from 20.9% difference for C20 to only 4% difference for C60. Thus, it is concluded that knowing the appropriate bond force constant, FEA can be used as a plausible approximation to model the elastic behavior of small fullerenes.

  14. fMRI alignment based on local functional connectivity patterns

    NASA Astrophysics Data System (ADS)

    Jiang, Di; Du, Yuhui; Cheng, Hewei; Jiang, Tianzi; Fan, Yong

    2012-02-01

    In functional neuroimaging studies, the inter-subject alignment of functional magnetic resonance imaging (fMRI) data is a necessary precursor to improve functional consistency across subjects. Traditional structural MRI based registration methods cannot achieve accurate inter-subject functional consistency in that functional units are not necessarily consistently located relative to anatomical structures due to functional variability across subjects. Although spatial smoothing commonly used in fMRI data preprocessing can reduce the inter-subject functional variability, it may blur the functional signals and thus lose the fine-grained information. In this paper we propose a novel functional signal based fMRI image registration method which aligns local functional connectivity patterns of different subjects to improve the inter-subject functional consistency. Particularly, the functional connectivity is measured using Pearson correlation. For each voxel of an fMRI image, its functional connectivity to every voxel in its local spatial neighborhood, referred to as its local functional connectivity pattern, is characterized by a rotation and shift invariant representation. Based on this representation, the spatial registration of two fMRI images is achieved by minimizing the difference between their corresponding voxels' local functional connectivity patterns using a deformable image registration model. Experiment results based on simulated fMRI data have demonstrated that the proposed method is more robust and reliable than the existing fMRI image registration methods, including maximizing functional correlations and minimizing difference of global connectivity matrices across different subjects. Experiment results based on real resting-state fMRI data have further demonstrated that the proposed fMRI registration method can statistically significantly improve functional consistency across subjects.

  15. Local Function Conservation in Sequence and Structure Space

    PubMed Central

    Weinhold, Nils; Sander, Oliver; Domingues, Francisco S.; Lengauer, Thomas; Sommer, Ingolf

    2008-01-01

    We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de). PMID:18604264

  16. Local function conservation in sequence and structure space.

    PubMed

    Weinhold, Nils; Sander, Oliver; Domingues, Francisco S; Lengauer, Thomas; Sommer, Ingolf

    2008-07-04

    We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de).

  17. Calculation of the Riesz constants and orthogonalization for incomplete systems of coherent states by means of theta functions

    NASA Astrophysics Data System (ADS)

    Kiselev, E. A.; Minin, L. A.; Novikov, I. Ya

    2016-08-01

    For systems of coherent states that are multiply rarefied with respect to von Neumann's complete system, we use Jacobi theta functions to obtain exact analytic expressions for the Riesz constants, investigate their behaviour as functions of the ratio of steps in the spatial and frequency domains, construct biorthogonal systems, and realize an orthogonalization procedure that preserves the structure of the windowed Fourier transform. Bibliography: 19 titles.

  18. How do electron localization functions describe π-electron delocalization?

    PubMed

    Steinmann, Stephan N; Mo, Yirong; Corminboeuf, Clemence

    2011-12-14

    Scalar fields provide an intuitive picture of chemical bonding. In particular, the electron localization function (ELF) has proven to be highly valuable in interpreting a broad range of bonding patterns. The discrimination between enhanced or reduced electron (de)localization within cyclic π-conjugated systems remains, however, challenging for ELF. In order to clearly distinguish between the local properties of ten highly and weakly π-(de)localized prototype systems, we compare the ELFs of both the canonical wave functions and electron-localized states (diabatic) with those of two closely related scalar fields: the electron localizability indicator (ELI-D) and the localized orbital locator (LOL). The simplest LOL function distinguishes enhanced from weak π-(de)localization in an insightful and reliable manner. LOL offers the finest contrast between annulenes with 4n/4n + 2 π electrons and their inorganic analogues as well as between hyperconjugated cyclopentadiene derivatives. LOL(π) also gives an appealing and intuitive picture of the π-bond. In contrast, the most popular ELF fails to capture subtle contrasting local electronic properties and suffers from the arbitrariness of the σ/π dissection. The orbital separation of the most recent ELI-D is clear-cut but the interpretations sometime less straightforward in the present context.

  19. Stability Constants of Technetium (IV) Oxalate Complexes as a Function of Ionic Strength

    SciTech Connect

    Xia, Yuanxian; Hess, Nancy J.; Felmy, Andrew R.

    2006-03-01

    Solvent extraction methods were used to determine the stability constants of Tc(IV) with oxalate anions in NaCl solutions ranging in concentration from 0.5 M to 2.0 M. All experiments were conducted in an atmosphere-controlled chamber under Ar atmosphere (< 1.0ppm O2). A reducing agent (hydrazine) was used during extractions to maintain technetium in the tetravalent oxidation state. Independent tests confirmed that the oxidation state of technetium did not change during extractions. The distribution ratio of Tc(IV) between the organic and aqueous phases was found to decrease as the concentration of oxalic acid increased. At the oxalic acid concentrations used in these experiments, the complexes TcO(Ox) and TcO(Ox)22- were found to be the dominant aqueous species. Based on these data, the thermodynamic stability constants of Tc(IV) with oxalate complexes were calculated by the Specific Ion Interaction Theory (SIT).

  20. Elastic constants of KMnF3 as functions of temperature and pressure

    NASA Astrophysics Data System (ADS)

    Cao, Wenwu; Barsch, Gerhard R.

    1988-10-01

    We have measured the single-crystal elastic constants of KMnF3 and their first pressure derivatives from 200 to 430 K at a frequency of 20 MHz by means of the ultrasonic-pulse-superposition method. Both sets of data show cusplike anomalies above the improper Oh-D4h ferroelastic transition at 186 K that extend up to 350 K. Above 350 K the temperature dependence is linear, making it possible to determine the bare harmonic and anharmonic constants by means of linear extrapolation to T=0. At room temperature the second pressure derivatives of the elastic constants were also measured. Analysis of the data on the basis of a model with Coulomb and short-range central force interactions indicates anomalously large fourth derivatives of the Mn-F and F-F pair potentials. A calculation of the temperature dependence of the elastic Grüneisen parameter is consistent with models for the acoustic anomaly according to which coupling between strains and order-parameter fluctuations is limited to frequencies less than the relaxation rate of the soft R25 mode.

  1. A Local and Global Function Model of the Liver

    PubMed Central

    Wang, Hesheng; Feng, Mary; Jackson, Andrew; Ten Haken, Randall K.; Lawrence, Theodore S.; Cao, Yue

    2015-01-01

    Purposes To develop a local and global function model in the liver based upon regional and organ function measurements to support individualized adaptive radiation therapy (RT). Methods and Materials A local and global model for liver function was developed to include both functional volume and the effect of functional variation of subunits. Adopting the assumption of parallel architecture in the liver, the global function was composed of a sum of local function probabilities of subunits, varying between 0 and 1. The model was fit to 59 datasets of liver regional and organ function measures from 23 patients obtained prior to, during and 1 month after RT. The local function probabilities of subunits were modeled by a sigmoid function in relating to MRI-derived portal venous perfusion values. The global function was fitted to a logarithm of an indocyanine green retention rate at 15 min (an overall liver function measure). Cross-validation was performed by leave-m-out tests. The model was further evaluated by fitting to the data divided based upon whether the patients had hepatocellular carcinoma (HCC) or not. Results The liver function model showed that 1) a perfusion value of 68.6 ml/(100g·min) yielded a local function probability of 0.5; 2) the probability reached 0.9 at a perfusion value of 98 ml/(100g·min), and 3) at a probability of 0.03 (corresponding perfusion of 38 ml/(100g·min)) or lower, the contribution to global function was lost. Cross-validations showed that the model parameters were stable. The model fitted to the data from the patients with HCC indicated that the same amount of portal venous perfusion was translated into less local function probability than the patients with non-HCC tumors. Conclusions The developed liver function model could provide a means to better assess individual and regional dose responses of hepatic functions, and provide guidance for individualized treatment planning of RT. PMID:26700712

  2. On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

    NASA Astrophysics Data System (ADS)

    Zarycz, M. Natalia C.; Provasi, Patricio F.; Sauer, Stephan P. A.

    2015-12-01

    It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

  3. On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

    SciTech Connect

    Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.

    2015-12-28

    It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH{sub 4}, NH{sub 3}, H{sub 2}O, SiH{sub 4}, PH{sub 3}, SH{sub 2}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and C{sub 2}H{sub 6}. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

  4. On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants.

    PubMed

    Zarycz, M Natalia C; Provasi, Patricio F; Sauer, Stephan P A

    2015-12-28

    It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

  5. Characterizing dynamic local functional connectivity in the human brain

    PubMed Central

    Deng, Lifu; Sun, Junfeng; Cheng, Lin; Tong, Shanbao

    2016-01-01

    Functional connectivity (FC), obtained from functional magnetic resonance imaging (fMRI), brings insights into the functional organization of the brain. Recently, rich and complex behaviour of brain has been revealed by the dynamic fluctuation of FC, which had previously been regarded as confounding ‘noise’. While the dynamics of long-distance, inter-regional FC has been extensively studied, the dynamics of local FC within a few millimetres in space remains largely unexplored. In this study, the local FC was depicted by regional homogeneity (ReHo), and the dynamics of local FC was obtained using sliding windows method. We observed a robust positive correlation between ReHo and its temporal variability, which was shown to be an intrinsic feature of the brain rather than a pure stochastic effect. Furthermore, fluctuation of ReHo was associated with global functional organization: (i) brain regions with higher centrality of inter-regional FC tended to possess higher ReHo variability; (ii) coherence of ReHo fluctuation was higher within brain’s functional modules. Finally, we observed alteration of ReHo variability during a motor task compared with resting-state. Our findings associated the temporal fluctuation of ReHo with brain function, opening up the possibility of dynamic local FC study in the future. PMID:27231194

  6. Spectral emissivities and optical constants of electromagnetically levitated liquid metals as functions of temperature and wavelength

    NASA Technical Reports Server (NTRS)

    Krishnan, S.; Hauge, R. H.; Margrave, J. L.

    1989-01-01

    The development of a noncontact temperature measurement device utilizing rotating analyzer ellipsometry is described. The technique circumvents the necessity of spectral emissivity estimation by direct measurement concomittant with radiance brightness. Using this approach, the optical properties of electromagnetically levitated liquid metals Cu, Ag, Au, Ni, Pd, Pt, and Zr were measured in situ at four wavelengths and up to 600 K superheat in the liquid. The data suggest an increase in the emissivity of the liquid compared with the incandescent solid. The data also show moderate temperature dependence of the spectral emissivity. A few measurements of the optical properties of undercooled liquid metals were also conducted. The data for both solids and liquids show excellent agreement with available values in the literature for the spectral emissivities as well as the optical constants.

  7. Symmetry-adapted Wannier functions in the maximal localization procedure

    NASA Astrophysics Data System (ADS)

    Sakuma, R.

    2013-06-01

    A procedure to construct symmetry-adapted Wannier functions in the framework of the maximally localized Wannier function approach [Marzari and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.56.12847 56, 12847 (1997); Souza, Marzari, and Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.65.035109 65, 035109 (2001)] is presented. In this scheme, the minimization of the spread functional of the Wannier functions is performed with constraints that are derived from symmetry properties of the specified set of the Wannier functions and the Bloch functions used to construct them, therefore one can obtain a solution that does not necessarily yield the global minimum of the spread functional. As a test of this approach, results of atom-centered Wannier functions for GaAs and Cu are presented.

  8. Steroidogenesis in the skin: implications for local immune functions

    PubMed Central

    Slominski, Andrzej; Zbytek, Bazej; Nikolakis, Georgios; Manna, Pulak R.; Skobowiat, Cezary; Zmijewski, Michal; Li, Wei; Janjetovic, Zorica; Postlethwaite, Arnold; Zouboulis, Christos C.; Tuckey, Robert C.

    2013-01-01

    The skin has developed a hierarchy of systems that encompasses the skin immune and local steroidogenic activities in order to protect the body against the external environment and biological factors and to maintain local homeostasis. Most recently it has been established that skin cells contain the entire biochemical apparatus necessary for production of glucocorticoids, androgens and estrogens either from precursors of systemic origin or, alternatively, through the conversion of cholesterol to pregnenolone and its subsequent transformation to biologically active steroids. Examples of these products are corticosterone, cortisol, testosterone, dihydrotesterone and estradiol. Their local production can be regulated by locally produced corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH) or cytokines. Furthermore the production of glucocorticoids is affected by ultraviolet B radiation. The level of production and nature of the final steroid products are dependent on the cell type or cutaneous compartment, e.g., epidermis, dermis, adnexal structures or adipose tissue. Locally produced glucocorticoids, androgens and estrogens affect functions of the epidermis and adnexal structures as well as local immune activity. Malfunction of these steroidogenic activities can lead to inflammatory disorders or autoimmune diseases. The cutaneous steroidogenic system can also have systemic effects, which are emphasized by significant skin contribution to circulating androgens and/or estrogens. Furthermore, local activity of CYP11A1 can produce novel 7 -steroids and secosteroids that are biologically active. Therefore, modulation of local steroidogenic activity may serve as a new therapeutic approach for treatment of inflammatory disorders, autoimmune processes or other skin disorders. In conclusion, the skin can be defined as an independent steroidogenic organ, whose activity can affect its functions and the development of local or systemic inflammatory or

  9. Steroidogenesis in the skin: implications for local immune functions.

    PubMed

    Slominski, Andrzej; Zbytek, Blazej; Nikolakis, Georgios; Manna, Pulak R; Skobowiat, Cezary; Zmijewski, Michal; Li, Wei; Janjetovic, Zorica; Postlethwaite, Arnold; Zouboulis, Christos C; Tuckey, Robert C

    2013-09-01

    The skin has developed a hierarchy of systems that encompasses the skin immune and local steroidogenic activities in order to protect the body against the external environment and biological factors and to maintain local homeostasis. Most recently it has been established that skin cells contain the entire biochemical apparatus necessary for production of glucocorticoids, androgens and estrogens either from precursors of systemic origin or, alternatively, through the conversion of cholesterol to pregnenolone and its subsequent transformation to biologically active steroids. Examples of these products are corticosterone, cortisol, testosterone, dihydrotesterone and estradiol. Their local production can be regulated by locally produced corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH) or cytokines. Furthermore the production of glucocorticoids is affected by ultraviolet B radiation. The level of production and nature of the final steroid products are dependent on the cell type or cutaneous compartment, e.g., epidermis, dermis, adnexal structures or adipose tissue. Locally produced glucocorticoids, androgens and estrogens affect functions of the epidermis and adnexal structures as well as local immune activity. Malfunction of these steroidogenic activities can lead to inflammatory disorders or autoimmune diseases. The cutaneous steroidogenic system can also have systemic effects, which are emphasized by significant skin contribution to circulating androgens and/or estrogens. Furthermore, local activity of CYP11A1 can produce novel 7Δ-steroids and secosteroids that are biologically active. Therefore, modulation of local steroidogenic activity may serve as a new therapeutic approach for treatment of inflammatory disorders, autoimmune processes or other skin disorders. In conclusion, the skin can be defined as an independent steroidogenic organ, whose activity can affect its functions and the development of local or systemic inflammatory or

  10. [Effect of a constant high intensity magnetic field on reproductive functions in male rats].

    PubMed

    Kokoreva, L V; Chuvpilo, T A; Pustynnikova, A M

    1990-01-01

    In two experiments male rats were exposed to a constant magnetic field (CMF) of 0.4 T either once for 3 hours or 56 times for the same time (throughout the entire spermatogenetic cycle). During the first week after exposure they were mated with untreated females. Some of the females were sacrificed on their 21st day of gestation. The following parameters were measured: percentage of implantations and resorptions, total fetal lethality, number and weight of alive fetuses, weight of placentas and ovaries, hydration of placentas and fetuses. At birth the duration of gestation, the amount of alive and dead newborns, their weight and distribution in the litter were determined. These parameters were used to evaluate the genetic quality of spermatozoa that were involved in fertilization. The pups were observed during the first month of life. The results obtained suggest that mature spermatozoa are resistant to a single CMF exposure and that this exposure causes no mutations in the gametes which may reduce fetal viability. However, chronic exposure to CMF leads to a small and significant increase of preimplantation lethality of fetuses which may indicate a higher frequency of lethal mutations in the gametes.

  11. Density functional theory study of indirect nuclear spin-spin coupling constants with spin-orbit corrections

    NASA Astrophysics Data System (ADS)

    Oprea, Corneliu I.; Rinkevicius, Zilvinas; Vahtras, Olav; Ågren, Hans; Ruud, Kenneth

    2005-07-01

    This work outlines the calculation of indirect nuclear spin-spin coupling constants with spin-orbit corrections using density functional response theory. The nonrelativistic indirect nuclear spin-spin couplings are evaluated using the linear response method, whereas the relativistic spin-orbit corrections are computed using quadratic response theory. The formalism is applied to the homologous systems H2X (X=O,S,Se,Te) and XH4 (X =C,Si,Ge,Sn,Pb) to calculate the indirect nuclear spin-spin coupling constants between the protons. The results confirm that spin-orbit corrections are important for compounds of the H2X series, for which the electronic structure allows for an efficient coupling between the nuclei mediated by the spin-orbit interaction, whereas in the case of the XH4 series the opposite situation is encountered and the spin-orbit corrections are negligible for all compounds of this series. In addition we analyze the performance of the density functional theory in the calculations of nonrelativistic indirect nuclear spin-spin coupling constants.

  12. Enhancing the accuracy of the Fowler method for monitoring non-constant work functions

    NASA Astrophysics Data System (ADS)

    Friedl, R.

    2016-04-01

    The Fowler method is a prominent non-invasive technique to determine the absolute work function of a surface based on the photoelectric effect. The evaluation procedure relies on the correlation of the photocurrent with the incident photon energy hν which is mainly dependent on the surface work function χ. Applying Fowler's theory of the photocurrent, the measurements can be fitted by the theoretical curve near the threshold hν⪆χ yielding the work function χ and a parameter A. The straightforward experimental implementation of the Fowler method is to use several particular photon energies, e.g. via interference filters. However, with a realization like that the restriction hν ≈ χ can easily be violated, especially when the work function of the material is decreasing during the measurements as, for instance, with coating or adsorption processes. This can lead to an overestimation of the evaluated work function value of typically some 0.1 eV, reaching up to more than 0.5 eV in an unfavorable case. A detailed analysis of the Fowler theory now reveals the background of that effect and shows that the fit-parameter A can be used to assess the accuracy of the determined value of χ conveniently during the measurements. Moreover, a scheme is introduced to quantify a potential overestimation and to perform a correction to χ to a certain extent. The issues are demonstrated exemplarily at the monitoring of the work function reduction of a stainless steel sample surface due to caesiation.

  13. Charge regulation and local dielectric function in planar polyelectrolyte brushes.

    PubMed

    Kumar, Rajeev; Sumpter, Bobby G; Kilbey, S Michael

    2012-06-21

    Understanding the effect of inhomogeneity on the charge regulation and dielectric properties, and how it depends on the conformational characteristics of the macromolecules is a long-standing problem. In order to address this problem, we have developed a field-theory to study charge regulation and local dielectric function in planar polyelectrolyte brushes. The theory is used to study a polyacid brush, which is comprised of chains end-grafted at the solid-fluid interface, in equilibrium with a bulk solution containing monovalent salt ions, solvent molecules, and pH controlling acid. In particular, we focus on the effects of the concentration of added salt and pH of the bulk in determining the local charge and dielectric function. Our theoretical investigations reveal that the dipole moment of the ion-pairs formed as a result of counterion adsorption on the chain backbones play a key role in affecting the local dielectric function. For polyelectrolytes made of monomers having dipole moments lower than the solvent molecules, dielectric decrement is predicted inside the brush region. However, the formation of ion-pairs (due to adsorption of counterions coming from the dissociation of added salt) more polar than the solvent molecules is shown to increase the magnitude of the dielectric function with respect to its bulk value. Furthermore, an increase in the bulk salt concentration is shown to increase the local charge inside the brush region.

  14. Using the electron localization function to correct for confinement physics in semi-local density functional theory

    SciTech Connect

    Hao, Feng Mattsson, Ann E.; Armiento, Rickard

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  15. Using the electron localization function to correct for confinement physics in semi-local density functional theory.

    PubMed

    Hao, Feng; Armiento, Rickard; Mattsson, Ann E

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu-O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  16. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

    Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  17. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    NASA Astrophysics Data System (ADS)

    Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  18. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane.

    PubMed

    Zarycz, M Natalia C; Sauer, Stephan P A; Provasi, Patricio F

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes--SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  19. Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Schwenke, David W.; Chaban, Galina M.

    2005-01-01

    Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

  20. Evolution of a localized vortex in plane nonparallel viscous flows with constant velocity shear. I. Hyperbolic flow

    NASA Astrophysics Data System (ADS)

    Shukhman, I. G.

    2006-09-01

    The framework of the linear theory is employed to study the evolution of an initial compact vortical disturbance in unbounded plane nonparallel viscous incompressible flows with constant velocity gradients. Two types of such flows are known to be possible: hyperbolical and elliptical (as well as an intermediate case of the well-studied parallel Couette flow). The results presented here are obtained for a hyperbolical flow. (Results concerning the elliptical flow are to be issued in a separate publication.) This paper is a development of earlier work by R. R. Lagnado, N. Phan-Thien, and L. G. Leal [Phys. Fluids 27, 1094 (1984)] studying the stability of a hyperbolical flow relative to the simplest perturbations in the form of plane waves with a time-dependent wave vector. The dynamics of vortex intensity is investigated as well as the evolution of its geometrical form and orientation. The results are discussed in the context of the problem of hairpin vortex formation.

  1. The (3000), (4000) and (5000) stretching overtone bands of silane—I. The effect of local-mode vibration on rotational constants

    NASA Astrophysics Data System (ADS)

    Zhu, Qingshi; Zhang, Baoshu; Ma, Yueren; Qian, Haibo

    The (4000) stretching overtone band of SiH 4 has been observed near 8347 cm -1. A symmetric top rotational structure, similar to that observed in the (3000) band of GeH 4: Q.-S. Zhu, B. A. Thrush and A. G. Robiette, Chem. Phys. Lett. 150, 181 (1988); Q.-S. Zhu and B. A. Thrush, J. Chem. Phys. 92, 2691 (1990) [1], and the (3000) and (5000) bands of SiH 4: Q.-S. Zhu, B.-S. Zhang, Y.-R. Ma and H.-B. Qian, Chem. Phys. Lett. 164, 596 (1989) [2], are clearly demonstrated. Three local-mode bands of SiH 4, (3000), (4000) and (5000) are analysed in the symmetric top model. A striking effect of local-mode vibration on rotational constants is observed and accounted for in a classical picture of vibrational localization.

  2. A New Green's Function for the Wake Potential Calculation of the SLAC S-band Constant Gradient Accelerating Section

    SciTech Connect

    Novokhatski, A,; /SLAC

    2012-02-17

    The behavior of the longitudinal wake fields excited by a very short bunch in the SLAC S-band constant gradient accelerating structures has been studied. Wake potential calculations were performed for a bunch length of 10 microns using the author's code to obtain a numerical solution of Maxwell's equations in the time domain. We have calculated six accelerating sections in the series (60-ft) to find the stationary solution. While analyzing the computational results we have found a new formula for the Green's function. Wake potentials, which are calculated using this Green's function are in amazingly good agreement with numerical results over a wide range of bunch lengths. The Green's function simplifies the wake potential calculations and can be easily incorporated into the tracking codes. This is very useful for beam dynamics studies of the linear accelerators of LCLS and FACET.

  3. Local quality functions for graph clustering with non-negative matrix factorization

    NASA Astrophysics Data System (ADS)

    van Laarhoven, Twan; Marchiori, Elena

    2014-12-01

    Many graph clustering quality functions suffer from a resolution limit, namely the inability to find small clusters in large graphs. So-called resolution-limit-free quality functions do not have this limit. This property was previously introduced for hard clustering, that is, graph partitioning. We investigate the resolution-limit-free property in the context of non-negative matrix factorization (NMF) for hard and soft graph clustering. To use NMF in the hard clustering setting, a common approach is to assign each node to its highest membership cluster. We show that in this case symmetric NMF is not resolution-limit free, but that it becomes so when hardness constraints are used as part of the optimization. The resulting function is strongly linked to the constant Potts model. In soft clustering, nodes can belong to more than one cluster, with varying degrees of membership. In this setting resolution-limit free turns out to be too strong a property. Therefore we introduce locality, which roughly states that changing one part of the graph does not affect the clustering of other parts of the graph. We argue that this is a desirable property, provide conditions under which NMF quality functions are local, and propose a novel class of local probabilistic NMF quality functions for soft graph clustering.

  4. Initial Sensorimotor and Cardiovascular Data Acquired from Soyuz Landings: Establishing a Functional Performance Recovery Time Constant

    NASA Technical Reports Server (NTRS)

    Reschke, M. F.; Kozlovskaya, I. B.; Kofman, I. S.; Tomilovskaya, E. S.; Cerisano, J. M.; Bloomberg, J. J.; Stenger, M. B.; Platts, S. H.; Rukavishnikov, I. V.; Fomina, E. V.; Lee, S. M. C.; Wood, S. J.; Mulavara, A. P.; Feiveson, A. H.; Fisher, E. A.

    2015-01-01

    INTRODUCTION Testing of crew responses following long-duration flights has not been previously possible until a minimum of more than 24 hours after landing. As a result, it has not been possible to determine the trend of the early recovery process, nor has it been possible to accurately assess the full impact of the decrements associated with long-duration flight. To overcome these limitations, both the Russian and U.S. programs have implemented joint testing at the Soyuz landing site. This International Space Station research effort has been identified as the functional Field Test, and represents data collect on NASA, Russian, European Space Agency, and Japanese Aerospace Exploration Agency crews. RESEARCH The primary goal of this research is to determine functional abilities associated with long-duration space flight crews beginning as soon after landing as possible on the day of landing (typically within 1 to 1.5 hours). This goal has both sensorimotor and cardiovascular elements. To date, a total of 15 subjects have participated in a 'pilot' version of the full 'field test'. The full version of the 'field test' will assess functional sensorimotor measurements included hand/eye coordination, standing from a seated position (sit-to-stand), walking normally without falling, measurement of dynamic visual acuity, discriminating different forces generated with the hands (both strength and ability to judge just noticeable differences of force), standing from a prone position, coordinated walking involving tandem heel-to-toe placement (tested with eyes both closed and open), walking normally while avoiding obstacles of differing heights, and determining postural ataxia while standing (measurement of quiet stance). Sensorimotor performance has been obtained using video records, and data from body worn inertial sensors. The cardiovascular portion of the investigation has measured blood pressure and heart rate during a timed stand test in conjunction with postural ataxia

  5. Host microbiota constantly control maturation and function of microglia in the CNS.

    PubMed

    Erny, Daniel; Hrabě de Angelis, Anna Lena; Jaitin, Diego; Wieghofer, Peter; Staszewski, Ori; David, Eyal; Keren-Shaul, Hadas; Mahlakoiv, Tanel; Jakobshagen, Kristin; Buch, Thorsten; Schwierzeck, Vera; Utermöhlen, Olaf; Chun, Eunyoung; Garrett, Wendy S; McCoy, Kathy D; Diefenbach, Andreas; Staeheli, Peter; Stecher, Bärbel; Amit, Ido; Prinz, Marco

    2015-07-01

    As the tissue macrophages of the CNS, microglia are critically involved in diseases of the CNS. However, it remains unknown what controls their maturation and activation under homeostatic conditions. We observed substantial contributions of the host microbiota to microglia homeostasis, as germ-free (GF) mice displayed global defects in microglia with altered cell proportions and an immature phenotype, leading to impaired innate immune responses. Temporal eradication of host microbiota severely changed microglia properties. Limited microbiota complexity also resulted in defective microglia. In contrast, recolonization with a complex microbiota partially restored microglia features. We determined that short-chain fatty acids (SCFA), microbiota-derived bacterial fermentation products, regulated microglia homeostasis. Accordingly, mice deficient for the SCFA receptor FFAR2 mirrored microglia defects found under GF conditions. These findings suggest that host bacteria vitally regulate microglia maturation and function, whereas microglia impairment can be rectified to some extent by complex microbiota.

  6. Range Separation and Local Hybridization in Density Functional Theory†

    PubMed Central

    Henderson, Thomas M.; Janesko, Benjamin G.; Scuseria, Gustavo E.

    2016-01-01

    Kohn–Sham density functional theory has become a standard method for modeling energetic, spectroscopic, and chemical reactivity properties of large molecules and solids. Density functional theory provides a rigorous theoretical framework for modeling the many-body exchange-correlation effects that dominate the computational cost of traditional wave function approaches. The advent of hybrid exchange-correlation functionals which incorporate a fraction of nonlocal exact exchange has solidified the prominence of density functional theory within computational chemistry. Hybrids provide accurate treatments of properties such as thermochemistry and molecular geometry. But they also exhibit some rather spectacular failures, and often contain multiple empirical parameters. This article reviews our work on developing novel exchange-correlation functionals that build upon the successes of global hybrids. We focus on more flexible functional forms, including local and range-separated hybrid functionals, constructed to obey known exact constraints and (ideally) to incorporate a minimum of empirical parametrization. The article places our work within the context of some other new approximate density functionals and discusses prospects for future work. PMID:19006280

  7. Velocity analysis with local event slopes related probability density function

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Lu, Wenkai; Zhang, Yingqiang

    2015-12-01

    Macro velocity model plays a key role in seismic imaging and inversion. The performance of traditional velocity analysis methods is degraded by multiples and amplitude-versus-offset (AVO) anomalies. Local event slopes, containing the subsurface velocity information, have been widely used to accomplish common time-domain seismic processing, imaging and velocity estimation. In this paper, we propose a method for velocity analysis with probability density function (PDF) related to local event slopes. We first estimate local event slopes with phase information in the Fourier domain. An adaptive filter is applied to improve the performance of slopes estimator in the low signal-to-noise ratio (SNR) situation. Second, the PDF is approximated with the histogram function, which is related to attributes derived from local event slopes. As a graphical representation of the data distribution, the histogram function can be computed efficiently. By locating the ray path of the first arrival on the semblance image with straight-ray segments assumption, automatic velocity picking is carried out to establish velocity model. Unlike local event slopes based velocity estimation strategies such as averaging filters and image warping, the proposed method does not make the assumption that the errors of mapped velocity values are symmetrically distributed or that the variation of amplitude along the offset is slight. Extension of the method to prestack time-domain migration velocity estimation is also given. With synthetic and field examples, we demonstrate that our method can achieve high resolution, even in the presence of multiples, strong amplitude variations and polarity reversals.

  8. Structure and Possible Functions of Constant-Frequency Calls in Ariopsis seemanni (Osteichthyes, Ariidae)

    PubMed Central

    Schmidtke, Daniel; Schulz, Jochen; Hartung, Jörg; Esser, Karl-Heinz

    2013-01-01

    In the 1970s, Tavolga conducted a series of experiments in which he found behavioral evidence that the vocalizations of the catfish species Ariopsis felis may play a role in a coarse form of echolocation. Based on his findings, he postulated a similar function for the calls of closely related catfish species. Here, we describe the physical characteristics of the predominant call-type of Ariopsis seemanni. In two behavioral experiments, we further explore whether A. seemanni uses these calls for acoustic obstacle detection by testing the hypothesis that the call-emission rate of individual fish should increase when subjects are confronted with novel objects, as it is known from other vertebrate species that use pulse-type signals to actively probe the environment. Audio-video monitoring of the fish under different obstacle conditions did not reveal a systematic increase in the number of emitted calls in the presence of novel objects or in dependence on the proximity between individual fish and different objects. These negative findings in combination with our current understanding of directional hearing in fishes (which is a prerequisite for acoustic obstacle detection) make it highly unlikely that A. seemanni uses its calls for acoustic obstacle detection. We argue that the calls are more likely to play a role in intra- or interspecific communication (e.g. in school formation or predator deterrence) and present results from a preliminary Y-maze experiment that are indicative for a positive phonotaxis of A. seemanni towards the calls of conspecifics. PMID:23741408

  9. Local Paley Wiener theorems for functions analytic on unit spheres

    NASA Astrophysics Data System (ADS)

    Damelin, S. B.; Devaney, A. J.

    2007-04-01

    The purpose of this paper is to provide new and simplified statements of local Paley-Wiener theorems on the (n - 1)-dimensional unit sphere realized as a subset of n = 2, 3 Euclidean space. More precisely, given a function f:{\\bb C}^n\\to {\\bb C}, n=2,3 , whose restriction to an n - 1 sphere is analytic, we establish necessary and sufficient conditions determining whether f is the Fourier transform of a compactly supported, bounded function F:{\\bb R}^n\\to{\\bb C} . The essence of this investigation is that, because of the local nature of the problem, the mapping f → F is not in general invertible and so the problem cannot be studied via a Fourier integral. Our proofs are new.

  10. Global functions in global-local finite-element analysis of localized stresses in prismatic structures

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

    An important consideration in the global local finite-element method (GLFEM) is the availability of global functions for the given problem. The role and mathematical requirements of these global functions in a GLFEM analysis of localized stress states in prismatic structures are discussed. A method is described for determining these global functions. Underlying this method are theorems due to Toupin and Knowles on strain energy decay rates, which are related to a quantitative expression of Saint-Venant's principle. It is mentioned that a mathematically complete set of global functions can be generated, so that any arbitrary interface condition between the finite element and global subregions can be represented. Convergence to the true behavior can be achieved with increasing global functions and finite-element degrees of freedom. Specific attention is devoted to mathematically two-dimensional and three-dimensional prismatic structures. Comments are offered on the GLFEM analysis of NASA flat panel with a discontinuous stiffener. Methods for determining global functions for other effects are also indicated, such as steady-state dynamics and bodies under initial stress.

  11. Investigation of Biodiesel Through Photopyroelectric and Dielectric-Constant Measurements as a Function of Temperature: Freezing/Melting Interval

    NASA Astrophysics Data System (ADS)

    Zanelato, E. B.; Machado, F. A. L.; Rangel, A. B.; Guimarães, A. O.; Vargas, H.; da Silva, E. C.; Mansanares, A. M.

    2015-06-01

    Biodiesel is a promising option for alternative fuels since it derives from natural and renewable materials; it is biodegradable and less polluting than fossil fuels. A gradual replacement of diesel by biodiesel has been adopted by many countries, making necessary the investigation of the physical properties of biodiesel and of its mixture in diesel. Photothermal techniques, specifically the photopyroelectric technique (PPE), have proved to be suitable in the characterization of biodiesel and of its precursor oils, as well as of the biodiesel/diesel mixtures. In this paper, we investigate thermal and electrical properties of animal fat-based biodiesel as a function of temperature, aiming to characterize the freezing/melting interval and the changes in the physical properties from the solid to the liquid phase. The samples were prepared using the transesterification method, by the ethylic route. Optical transmittance experiments were carried out in order to confirm the phase transition interval. Solid and liquid phases present distinct thermal diffusivities and conductivities, as well as dielectric constants. The PPE signal amplitude is governed by the changes in the thermal diffusivity/conductivity. As a consequence, the amplitude of the signal becomes like a step function, which is smoothed and sometimes delayed by the nucleation processes during cooling. A similar behavior is found in the dielectric constant data, which is higher in the liquid phase since the molecules have a higher degree of freedom. Both methods (PPE/dielectric constant) proved to be useful in the characterization of the freezing/melting interval, as well as to establish the distinction in the physical properties of solid and liquid phases. The methodology allowed a discussion of the cloud point and the pour point of the samples in the temperature variation interval.

  12. Influence of metallothionein-1 localization on its function.

    PubMed Central

    Levadoux-Martin, M; Hesketh, J E; Beattie, J H; Wallace, H M

    2001-01-01

    Metallothioneins (MTs) have a major role to play in metal metabolism, and may also protect DNA against oxidative damage. MT protein has been found localized in the nucleus during S-phase. The mRNA encoding the MT-1 isoform has a perinuclear localization, and is associated with the cytoskeleton; this targeting, due to signals within the 3'-untranslated region (3'-UTR), facilitates nuclear localization of MT-1 during S-phase [Levadoux, Mahon, Beattie, Wallace and Hesketh (1999) J. Biol. Chem. 274, 34961-34966]. Using cells transfected with MT gene constructs differing in their 3'-UTRs, the role of MT protein in the nucleus has been studied. Chinese hamster ovary cells were transfected with either the full MT gene (MTMT cells) or with the MT 5'-UTR and coding region linked to the 3'-UTR of glutathione peroxidase (MTGSH cells). Cell survival following exposure to oxidative stress and chemical agents was higher in cells expressing the native MT gene than in cells where MT localization was disrupted, or in untransfected cells. Also, MTMT cells showed less DNA damage than MTGSH cells in response to either hydrogen peroxide or mutagen. After exposure to UV light or mutagen, MTMT cells showed less apoptosis than MTGSH cells, as assessed by DNA fragmentation and flow cytometry. The data indicate that the perinuclear localization of MT mRNA is important for the function of MT in a protective role against DNA damage and apoptosis induced by external stress. PMID:11284736

  13. Computation of Local and Global Properties of the Electron Localization Function Topology in Crystals.

    PubMed

    Contreras-García, J; Pendás, A Martín; Recio, J M; Silvi, B

    2009-01-13

    We present a novel computational procedure, general, automated, and robust, for the analysis of local and global properties of the electron localization function (ELF) in crystalline solids. Our algorithm successfully faces the two main shortcomings of the ELF analysis in crystals: (i) the automated identification and characterization of the ELF induced topology in periodic systems, which is impeded by the great number and concentration of critical points in crystalline cells, and (ii) the localization of the zero flux surfaces and subsequent integration of basins, whose difficulty is due to the diverse (in many occasions very flat or very steep) ELF profiles connecting the set of critical points. Application of the new code to representative crystals exhibiting different bonding patterns is carried out in order to show the performance of the algorithm and the conceptual possibilities offered by the complete characterization of the ELF topology in solids.

  14. Hydrogen Abstraction Reactions from Phenolic Compounds by Peroxyl Radicals: Multireference Character and Density Functional Theory Rate Constants.

    PubMed

    Galano, Annia; Muñoz-Rugeles, Leonardo; Alvarez-Idaboy, Juan Raul; Bao, Junwei Lucas; Truhlar, Donald G

    2016-07-14

    An assessment of multireference character in transition states is considered to be an important component in establishing the expected reliability of various electronic structure methods. In the present work, the multireference characters of the transition states and the forming and breaking of bonds for a large set of hydrogen abstraction reactions from phenolic compounds by peroxyl radicals have been analyzed using the T1, M, B1, and GB1 diagnostics. The extent of multireference character depends on the system and on the conditions under which the reaction takes place, and some systematic trends are observed. In particular, the multireference character is found to be reduced by solvation, the size of the phenolic compound, and deprotonation in aqueous solution. However, the deviations of calculated rate constants from experimental ones are not correlated with the extent of multireference character. The performance of single-determinant density functional theory was investigated for the kinetics of these reactions by comparing calculated rate constants to experimental data; the results from these analyses showed that the M05 functional performs well for the task at hand.

  15. Exponentially localized Wannier functions in periodic zero flux magnetic fields

    NASA Astrophysics Data System (ADS)

    De Nittis, G.; Lein, M.

    2011-11-01

    In this work, we investigate conditions which ensure the existence of an exponentially localized Wannier basis for a given periodic hamiltonian. We extend previous results [Panati, G., Ann. Henri Poincare 8, 995-1011 (2007), 10.1007/s00023-007-0326-8] to include periodic zero flux magnetic fields which is the setting also investigated by Kuchment [J. Phys. A: Math. Theor. 42, 025203 (2009), 10.1088/1751-8113/42/2/025203]. The new notion of magnetic symmetry plays a crucial rôle; to a large class of symmetries for a non-magnetic system, one can associate "magnetic" symmetries of the related magnetic system. Observing that the existence of an exponentially localized Wannier basis is equivalent to the triviality of the so-called Bloch bundle, a rank m hermitian vector bundle over the Brillouin zone, we prove that magnetic time-reversal symmetry is sufficient to ensure the triviality of the Bloch bundle in spatial dimension d = 1, 2, 3. For d = 4, an exponentially localized Wannier basis exists provided that the trace per unit volume of a suitable function of the Fermi projection vanishes. For d > 4 and d ⩽ 2m (stable rank regime) only the exponential localization of a subset of Wannier functions is shown; this improves part of the analysis of Kuchment [J. Phys. A: Math. Theor. 42, 025203 (2009), 10.1088/1751-8113/42/2/025203]. Finally, for d > 4 and d > 2m (unstable rank regime) we show that the mere analysis of Chern classes does not suffice in order to prove triviality and thus exponential localization.

  16. Global and local curvature in density functional theory

    NASA Astrophysics Data System (ADS)

    Zhao, Qing; Ioannidis, Efthymios I.; Kulik, Heather J.

    2016-08-01

    Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.

  17. Functional brain networks develop from a "local to distributed" organization.

    PubMed

    Fair, Damien A; Cohen, Alexander L; Power, Jonathan D; Dosenbach, Nico U F; Church, Jessica A; Miezin, Francis M; Schlaggar, Bradley L; Petersen, Steven E

    2009-05-01

    The mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions. Studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks. In this report, we combine resting state functional connectivity MRI (rs-fcMRI), graph analysis, community detection, and spring-embedding visualization techniques to analyze four separate networks defined in earlier studies. As we have previously reported, we find, across development, a trend toward 'segregation' (a general decrease in correlation strength) between regions close in anatomical space and 'integration' (an increased correlation strength) between selected regions distant in space. The generalization of these earlier trends across multiple networks suggests that this is a general developmental principle for changes in functional connectivity that would extend to large-scale graph theoretic analyses of large-scale brain networks. Communities in children are predominantly arranged by anatomical proximity, while communities in adults predominantly reflect functional relationships, as defined from adult fMRI studies. In sum, over development, the organization of multiple functional networks shifts from a local anatomical emphasis in children to a more "distributed" architecture in young adults. We argue that this "local to distributed" developmental characterization has important implications for understanding the development of neural systems underlying cognition. Further, graph metrics (e.g., clustering coefficients and average path lengths) are similar in child and adult graphs, with both showing "small-world"-like properties, while community detection by modularity optimization reveals stable communities within the graphs that are clearly different between young children and young adults. These observations suggest that early school age children and adults both have

  18. Melanocortin MC₄ receptor expression sites and local function.

    PubMed

    Siljee-Wong, Jacqueline E

    2011-06-11

    The melanocortin MC(4) receptor plays an important role in energy metabolism, but also affects blood pressure, heart rate and erectile function. Localization of the receptors that fulfill these distinct roles is only partially known. Mapping of the melanocortin MC(4) receptor has been stymied by the absence of a functional antibody. Several groups have examined mRNA expression of the melanocortin MC(4) receptor in the rodent brain and transgenic approaches have also been utilized to visualize melanocortin MC(4) receptor expression sites within the brain. Ligand expression and binding studies have provided additional information on the areas of the brain where this elusive receptor is functionally expressed. Finally, microinjection of melanocortin MC(4) receptor ligands in specific nuclei has further served to elucidate the function of melanocortin MC(4) receptors in these nuclei. These combined approaches have helped link the anatomy and function of this receptor, such as the role of paraventricular hypothalamic nucleus melanocortin MC(4) receptor in the regulation of food intake. Intriguingly, however, numerous expression-sites have been identified that have not been linked to a specific receptor function such as those along the optic tract and olfactory tubercle. Further research is needed to clarify the function of the melanocortin MC(4) receptor at these sites.

  19. Cancer-Related Functions and Subcellular Localizations of Septins

    PubMed Central

    Poüs, Christian; Klipfel, Laurence; Baillet, Anita

    2016-01-01

    Since the initial discovery of septin family GTPases, the understanding of their molecular organization and cellular roles keeps being refined. Septins have been involved in many physiological processes and the misregulation of specific septin gene expression has been implicated in diverse human pathologies, including neurological disorders and cancer. In this minireview, we focus on the importance of the subunit composition and subcellular localization of septins relevant to tumor initiation, progression, and metastasis. We especially underline the importance of septin polymer composition and of their association with the plasma membrane, actin, or microtubules in cell functions involved in cancer and in resistance to cancer therapies. Through their scaffolding role, their function in membrane compartmentalization or through their protective function against protein degradation, septins also emerge as critical organizers of membrane-associated proteins and of signaling pathways implicated in cancer-associated angiogenesis, apoptosis, polarity, migration, proliferation, and in metastasis. Also, the question as to which of the free monomers, hetero-oligomers, or filaments is the functional form of mammalian septins is raised and the control over their spatial and temporal localization is discussed. The increasing amount of crosstalks identified between septins and cellular signaling mediators reinforces the exciting possibility that septins could be new targets in anti-cancer therapies or in therapeutic strategies to limit drug resistance. PMID:27878118

  20. Effects of Local Compression on Peroneal Nerve Function in Humans

    NASA Technical Reports Server (NTRS)

    Hargens, Alan R.; Botte, Michael J.; Swenson, Michael R.; Gelberman, Richard H.; Rhoades, Charles E.; Akeson, Wayne H.

    1993-01-01

    A new apparatus was developed to compress the anterior compartment selectively and reproducibly in humans. Thirty-five normal volunteers were studied to determine short-term thresholds of local tissue pressure that produce significant neuromuscular dysfunction. Local tissue fluid pressure adjacent to the deep peroneal nerve was elevated by the compression apparatus and continuously monitored for 2-3 h by the slit catheter technique. Elevation of tissue fluid pressure to within 35-40 mm Hg of diastolic blood pressure (approx. 40 mm Hg of in situ pressure in our subjects) elicited a consistent progression of neuromuscular deterioration including, in order, (a) gradual loss of sensation, as assessed by Semmes-Weinstein monofilaments, (b) subjective complaints, (c) reduced nerve conduction velocity, (d) decreased action potential amplitude of the extensor digitorum brevis muscle, and (e) motor weakness of muscles within the anterior compartment. Generally, higher intracompartment at pressures caused more rapid deterioration of neuromuscular function. In two subjects, when in situ compression levels were 0 and 30 mm Hg, normal neuromuscular function was maintained for 3 h. Threshold pressures for significant dysfunction were not always the same for each functional parameter studied, and the magnitudes of each functional deficit did not always correlate with compression level. This variable tolerance to elevated pressure emphasizes the need to monitor clinical signs and symptoms carefully in the diagnosis of compartment syndromes. The nature of the present studies was short term; longer term compression of myoneural tissues may result in dysfunction at lower pressure thresholds.

  1. Effect of local anesthetics on serotonin1A receptor function.

    PubMed

    Rao, Bhagyashree D; Shrivastava, Sandeep; Chattopadhyay, Amitabha

    2016-12-01

    The fundamental mechanism behind the action of local anesthetics is still not clearly understood. Phenylethanol (PEtOH) is a constituent of essential oils with a pleasant odor and can act as a local anesthetic. In this work, we have explored the effect of PEtOH on the function of the hippocampal serotonin1A receptor, a representative neurotransmitter receptor belonging to the G protein-coupled receptor (GPCR) family. Our results show that PEtOH induces reduction in ligand binding to the serotonin1A receptor due to lowering of binding affinity, along with a concomitant decrease in the degree of G-protein coupling. Analysis of membrane order using the environment-sensitive fluorescent probe DPH revealed decrease in membrane order with increasing PEtOH concentration, as evident from reduction in rotational correlation time of the probe. Analysis of results obtained shows that the action of local anesthetics could be attributed to the combined effects of specific interaction of the receptor with anesthetics and alteration of membrane properties (such as membrane order). These results assume relevance in the perspective of anesthetic action and could be helpful to achieve a better understanding of the possible role of anesthetics in the function of membrane receptors.

  2. Avoiding coral reef functional collapse requires local and global action.

    PubMed

    Kennedy, Emma V; Perry, Chris T; Halloran, Paul R; Iglesias-Prieto, Roberto; Schönberg, Christine H L; Wisshak, Max; Form, Armin U; Carricart-Ganivet, Juan P; Fine, Maoz; Eakin, C Mark; Mumby, Peter J

    2013-05-20

    Coral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification. While the abundance of coral has declined in recent decades, the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services.

  3. Determination of plasma frequency, damping constant, and size distribution from the complex dielectric function of noble metal nanoparticles

    SciTech Connect

    Mendoza Herrera, Luis J.; Arboleda, David Muñetón; Schinca, Daniel C.; Scaffardi, Lucía B.

    2014-12-21

    This paper develops a novel method for simultaneously determining the plasma frequency ω{sub P}   and the damping constant γ{sub free} in the bulk damped oscillator Drude model, based on experimentally measured real and imaginary parts of the metal refractive index in the IR wavelength range, lifting the usual approximation that restricts frequency values to the UV-deep UV region. Our method was applied to gold, silver, and copper, improving the relative uncertainties in the final values for ω{sub p} (0.5%–1.6%) and for γ{sub free} (3%–8%), which are smaller than those reported in the literature. These small uncertainties in ω{sub p} and γ{sub free} determination yield a much better fit of the experimental complex dielectric function. For the case of nanoparticles (Nps), a series expansion of the Drude expression (which includes ω{sub p} and γ{sub free} determined using our method) enables size-dependent dielectric function to be written as the sum of three terms: the experimental bulk dielectric function plus two size corrective terms, one for free electron, and the other for bound-electron contributions. Finally, size distribution of nanometric and subnanometric gold Nps in colloidal suspension was determined through fitting its experimental optical extinction spectrum using Mie theory based on the previously determined dielectric function. Results are compared with size histogram obtained from Transmission Electron Microscopy (TEM)

  4. Spectroscopic constants of diatomic molecules computed correcting Hartree-Fock or general-valence-bond potential-energy curves with correlation-energy functionals

    NASA Astrophysics Data System (ADS)

    Pérez-Jordá, José M.; San-Fabián, Emilio; Moscardó, Federico

    1992-04-01

    The Kohn-Sham energy with exact exchange [using the exact Hartree-Fock (HF) exchange but an approximate correlation-energy functional] may be computed very accurately by adding the correlation obtained from the HF density to the total HF energy. Three density functionals are used: local spin density (LSD), LSD with self-interaction correction, and LSD with generalized gradient correction. This scheme has been extended (Lie-Clementi, Colle-Salvetti, and Moscardo-San-Fabian) to be used with general-valence-bond (GVB) energies and wave functions, so that the extra correlation included in the GVB energy is not counted again. The effect of all these approximate correlations on HF or GVB spectroscopic constants (Re,ωe, and De) is studied. Approximate relations showing how correlation affects them are derived, and may be summarized as follows: (1) the effect on Re and ωe depends only on the correlation derivative at Re, and (2) the effect on De depends mainly on the correlation difference between quasidissociated and equilibrium geometries. A consequence is that all the correlation corrections tested here give larger ωe and De and shorter Re than the uncorrected HF or GVB values. This trend is correct for De for both HF and GVB. For Re and ωe, it is correct in most cases for GVB, but it often fails for the HF cases. A comparison is made with Kohn-Sham calculations with both exchange and correlation approximated. As a final conclusion, it is found that, within the present scheme, a qualitatively correct HF or GVB potential-energy curve, together with a correlation-energy approximation with correct dissociation behavior, is crucial for obtaining good estimates of spectroscopic constants.

  5. Local and linear chemical reactivity response functions at finite temperature in density functional theory.

    PubMed

    Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto

    2015-12-28

    We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

  6. Local and linear chemical reactivity response functions at finite temperature in density functional theory

    SciTech Connect

    Franco-Pérez, Marco E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Ayers, Paul W. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Gázquez, José L. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Vela, Alberto E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx

    2015-12-28

    We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

  7. Imaging local brain function with emission computed tomography

    SciTech Connect

    Kuhl, D.E.

    1984-03-01

    Positron emission tomography (PET) using /sup 18/F-fluorodeoxyglucose (FDG) was used to map local cerebral glucose utilization in the study of local cerebral function. This information differs fundamentally from structural assessment by means of computed tomography (CT). In normal human volunteers, the FDG scan was used to determine the cerebral metabolic response to conrolled sensory stimulation and the effects of aging. Cerebral metabolic patterns are distinctive among depressed and demented elderly patients. The FDG scan appears normal in the depressed patient, studded with multiple metabolic defects in patients with multiple infarct dementia, and in the patients with Alzheimer disease, metabolism is particularly reduced in the parietal cortex, but only slightly reduced in the caudate and thalamus. The interictal FDG scan effectively detects hypometabolic brain zones that are sites of onset for seizures in patients with partial epilepsy, even though these zones usually appear normal on CT scans. The future prospects of PET are discussed.

  8. Localization using nonindividualized head-related transfer functions

    NASA Astrophysics Data System (ADS)

    Wenzel, Elizabeth M.; Arruda, Marianne; Kistler, Doris J.; Wightman, Frederic L.

    1993-07-01

    The paper investigates the accuracy of localization by inexperienced listeners of the direction (azimuth and elevation) of wideband noisebursts presented in the free-field or over headphones, with headphone stimuli being synthesized using head-related transfer functions (HRTFs) from a representative subject of Wightman and Kistler (1989). Many subjects showed high rates of front-back and up-down confusions that increased significantly for virtual sources compared to the free-field stimuli. When confusions were resolved, localization of virtual sources was quite accurate and comparable to the free-field sources for 12 out of 16 subjects. The results of this study suggest that, while the interaural cues to horizontal location are robust, the spectral cues considered important for resolving location along a particular cone-of-confusion are distorted by a synthesis process that uses nonindividualized HRTFs.

  9. Comparing Teacher-Directed and Computer-Assisted Constant Time Delay for Teaching Functional Sight Words to Students with Moderate Intellectual Disability

    ERIC Educational Resources Information Center

    Coleman, Mari Beth; Hurley, Kevin J.; Cihak, David F.

    2012-01-01

    The purpose of this study was to compare the effectiveness and efficiency of teacher-directed and computer-assisted constant time delay strategies for teaching three students with moderate intellectual disability to read functional sight words. Target words were those found in recipes and were taught via teacher-delivered constant time delay or…

  10. Impact of twin boundaries on bulk elastic constants: Density-functional theory data for Young׳s modulus of Ag.

    PubMed

    Klöffel, Tobias; Bitzek, Erik; Meyer, Bernd

    2015-06-01

    Experimental and theoretical studies on nanowires have reported a size-dependence of the Young׳s modulus in the axial direction, which has been attributed to the increasing influence of surface stresses with decreasing wire diameter. Internal interfaces and their associated interface stresses could lead to similar changes in the elastic properties. In Kobler et al. [1], however, we reported results from atomistic calculations which showed for Ag that twin boundaries have a negligible effect on the Young׳s modulus. Here, we present data of density-functional theory calculations of elastic constants and Young׳s modulus for defect-free bulk Ag as well as for bulk Ag containing dense arrays of twin boundaries. It is shown that rigorous convergence tests are required in order to be able to deduce changes in the elastic properties due to bulk defects in a reliable way.

  11. SNAP-Tag Technology: A Useful Tool To Determine Affinity Constants and Other Functional Parameters of Novel Antibody Fragments.

    PubMed

    Niesen, Judith; Sack, Markus; Seidel, Melanie; Fendel, Rolf; Barth, Stefan; Fischer, Rainer; Stein, Christoph

    2016-08-17

    Antibody derivatives, such as the single chain fragment variable (scFv), can be developed as diagnostic and therapeutic tools in cancer research, especially in the form of fusion proteins. Such derivatives are easier to produce and modify than monoclonal antibodies (mAbs) and achieve better tissue/tumor penetration. The genetic modification of scFvs is also much more straightforward than the challenging chemical modification of mAbs. Therefore, we constructed two scFvs derived from the approved monoclonal antibodies cetuximab (scFv2112) and panitumumab (scFv1711), both of which are specific for the epidermal growth factor receptor (EGFR), a well-characterized solid tumor antigen. Both scFvs were genetically fused to the SNAP-tag, an engineered version of the human DNA repair enzyme O(6)-alkylguanine DNA alkyltransferase that allows the covalent coupling of benzylguanine (BG)-modified substrates such as fluorescent dyes. The SNAP-tag achieves controllable and irreversible protein modification and is an important tool for experimental studies in vitro and in vivo. The affinity constant of a scFv is a key functional parameter, especially in the context of a fusion protein. Therefore, we developed a method to define the affinity constants of scFv-SNAP fusion proteins by surface plasmon resonance (SPR) spectroscopy. We could confirm that both scFvs retained their functionality after fusion to the SNAP-tag in a variety of procedures and assays, including ELISA, flow cytometry, and confocal microscopy. The experimental procedures described herein, and the new protocol for affinity determination by SPR spectroscopy, are suitable for the preclinical evaluation of diverse antibody formats and derivatives.

  12. Insulin in the brain: sources, localization and functions.

    PubMed

    Ghasemi, Rasoul; Haeri, Ali; Dargahi, Leila; Mohamed, Zahurin; Ahmadiani, Abolhassan

    2013-02-01

    Historically, insulin is best known for its role in peripheral glucose homeostasis, and insulin signaling in the brain has received less attention. Insulin-independent brain glucose uptake has been the main reason for considering the brain as an insulin-insensitive organ. However, recent findings showing a high concentration of insulin in brain extracts, and expression of insulin receptors (IRs) in central nervous system tissues have gathered considerable attention over the sources, localization, and functions of insulin in the brain. This review summarizes the current status of knowledge of the peripheral and central sources of insulin in the brain, site-specific expression of IRs, and also neurophysiological functions of insulin including the regulation of food intake, weight control, reproduction, and cognition and memory formation. This review also considers the neuromodulatory and neurotrophic effects of insulin, resulting in proliferation, differentiation, and neurite outgrowth, introducing insulin as an attractive tool for neuroprotection against apoptosis, oxidative stress, beta amyloid toxicity, and brain ischemia.

  13. Semiparametric Bayesian local functional models for diffusion tensor tract statistics☆

    PubMed Central

    Hua, Zhaowei; Dunson, David B.; Gilmore, John H.; Styner, Martin A.; Zhu, Hongtu

    2012-01-01

    We propose a semiparametric Bayesian local functional model (BFM) for the analysis of multiple diffusion properties (e.g., fractional anisotropy) along white matter fiber bundles with a set of covariates of interest, such as age and gender. BFM accounts for heterogeneity in the shape of the fiber bundle diffusion properties among subjects, while allowing the impact of the covariates to vary across subjects. A nonparametric Bayesian LPP2 prior facilitates global and local borrowings of information among subjects, while an infinite factor model flexibly represents low-dimensional structure. Local hypothesis testing and credible bands are developed to identify fiber segments, along which multiple diffusion properties are significantly associated with covariates of interest, while controlling for multiple comparisons. Moreover, BFM naturally group subjects into more homogeneous clusters. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. A simulation study is performed to evaluate the finite sample performance of BFM. We apply BFM to investigate the development of white matter diffusivities along the splenium of the corpus callosum tract and the right internal capsule tract in a clinical study of neurodevelopment in new born infants. PMID:22732565

  14. Cloning, localization, and axonemal function of Tetrahymena centrin.

    PubMed

    Guerra, Charles; Wada, Yuuko; Leick, Vagn; Bell, Aaron; Satir, Peter

    2003-01-01

    Centrin, an EF hand Ca(2+) binding protein, has been cloned in Tetrahymena thermophila. It is a 167 amino acid protein of 19.4 kDa with a unique N-terminal region, coded by a single gene containing an 85-base pair intron. It has > 80% homology to other centrins and high homology to Tetrahymena EF hand proteins calmodulin, TCBP23, and TCBP25. Specific cellular localizations of the closely related Tetrahymena EF hand proteins are different from centrin. Centrin is localized to basal bodies, cortical fibers in oral apparatus and ciliary rootlets, the apical filament ring and to inner arm (14S) dynein (IAD) along the ciliary axoneme. The function of centrin in Ca(2+) control of IAD activity was explored using in vitro microtubule (MT) motility assays. Ca(2+) or the Ca(2+)-mimicking peptide CALP1, which binds EF hand proteins in the absence of Ca(2+), increased MT sliding velocity. Antibodies to centrin abrogated this increase. This is the first demonstration of a specific centrin function associated with axonemal dynein. It suggests that centrin is a key regulatory protein for Tetrahymena axonemal Ca(2+) responses, including ciliary reversal or chemotaxis.

  15. Local functional descriptors for surface comparison based binding prediction

    PubMed Central

    2012-01-01

    Background Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface. Results We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces. Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions. Our approach uses a variety of physical, chemical, and geometric properties, adaptively weighting these properties as appropriate for different regions of the interface. Our approach builds a classifier based on a training corpus of examples of binding sites of the target ligand. The constructed classifiers can be applied to a query protein providing a probability for each position on the protein that the position is part of a binding interface. We demonstrate the effectiveness of the approach on a number of benchmarks, demonstrating performance that is comparable to the state-of-the-art, with an approach with more generality than these prior methods. Conclusions Local functional descriptors offer a new method for protein surface comparison that is sufficiently flexible to serve in a variety of applications. PMID:23176080

  16. Serial assessment of local peripheral vascular function after eccentric exercise.

    PubMed

    Stacy, Mitchel R; Bladon, Kallie J; Lawrence, Jennifer L; McGlinchy, Sarah A; Scheuermann, Barry W

    2013-12-01

    Muscle damage is a common response to unaccustomed eccentric exercise; however, the effects of skeletal muscle damage on local vascular function and blood flow are poorly understood. This study examined serial local vascular responses to flow-mediated (endothelial-dependent) and nitroglycerin-mediated (endothelial-independent) dilation in the brachial artery after strenuous eccentric exercise and serially assessed resting blood flow. Ten healthy males performed 50 maximal eccentric unilateral arm contractions to induce muscle damage to the biceps brachii. Changes in maximal isometric strength and vascular responses were assessed 1, 24, 48, and 96 h after exercise. Mean blood velocities and arterial diameters, measured with Doppler ultrasound, were used to calculate blood flow and shear stress (expressed as area under the curve). Eccentric exercise resulted in impaired maximal isometric strength for up to 96 h (p < 0.001). Reductions in flow-mediated dilation (before exercise, 9.4% ± 2.6%; 1 h after exercise, 5.1% ± 2.2%) and nitroglycerin responses (before exercise, 26.3% ± 6.5%; 1 h after exercise, 20.7% ± 4.7%) were observed in the 1 h after exercise and remained lower for 96 h (p < 0.05). The shear stress response was attenuated immediately after exercise and remained impaired for 48 h (p < 0.05). Resting blood pressure and muscle blood flow remained similar throughout the study. Results suggest that muscle damage from eccentric exercise leads to impaired local endothelial and vascular smooth muscle function. Lower shear stress after exercise might contribute to the observed reduction in flow-mediated dilation responses, but the mechanism responsible for the attenuated endothelial-independent vasodilation remains unclear.

  17. Localization using nonindividualized head-related transfer functions.

    PubMed

    Wenzel, E M; Arruda, M; Kistler, D J; Wightman, F L

    1993-07-01

    A recent development in human-computer interfaces is the virtual acoustic display, a device that synthesizes three-dimensional, spatial auditory information over headphones using digital filters constructed from head-related transfer functions (HRTFs). The utility of such a display depends on the accuracy with which listeners can localize virtual sound sources. A previous study [F. L. Wightman and D. J. Kistler, J. Acoust. Soc. Am. 85, 868-878 (1989)] observed accurate localization by listeners for free-field sources and for virtual sources generated from the subjects' own HRTFs. In practice, measurement of the HRTFs of each potential user of a spatial auditory display may not be feasible. Thus, a critical research question is whether listeners can obtain adequate localization cues from stimuli based on nonindividualized transforms. Here, inexperienced listeners judged the apparent direction (azimuth and elevation) of wideband noisebursts presented in the free-field or over headphones; headphone stimuli were synthesized using HRTFs from a representative subject of Wightman and Kistler. When confusions were resolved, localization of virtual sources was quite accurate and comparable to the free-field sources for 12 of the 16 subjects. Of the remaining subjects, 2 showed poor elevation accuracy in both stimulus conditions, and 2 showed degraded elevation accuracy with virtual sources. Many of the listeners also showed high rates of front-back and up-down confusions that increased significantly for virtual sources compared to the free-field stimuli. These data suggest that while the interaural cues to horizontal location are robust, the spectral cues considered important for resolving location along a particular cone-of-confusion are distorted by a synthesis process that uses nonindividualized HRTFs.

  18. Exact density functional and wave function embedding schemes based on orbital localization

    NASA Astrophysics Data System (ADS)

    Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

    2016-08-01

    Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

  19. Testing local position and fundamental constant invariance due to periodic gravitational and boost using long-term comparison of the SYRTE atomic fountains and H-masers

    NASA Astrophysics Data System (ADS)

    Tobar, M. E.; Stanwix, P. L.; McFerran, J. J.; Guéna, J.; Abgrall, M.; Bize, S.; Clairon, A.; Laurent, Ph.; Rosenbusch, P.; Rovera, D.; Santarelli, G.

    2013-06-01

    The frequencies of three separate Cs fountain clocks and one Rb fountain clock have been compared to various hydrogen masers to search for periodic changes correlated with the changing solar gravitational potential at the Earth and boost with respect to the cosmic microwave background rest frame. The data sets span over more than 8 yr. The main sources of long-term noise in such experiments are the offsets and linear drifts associated with the various H-masers. The drift can vary from nearly immeasurable to as high as 1.3×10-15 per day. To circumvent these effects, we apply a numerical derivative to the data, which significantly reduces the standard error when searching for periodic signals. We determine a standard error for the putative local position invariance coefficient with respect to gravity for a Cs-fountain H-maser comparison of |βH-βCs|≤4.8×10-6 and |βH-βRb|≤10-5 for a Rb-Fountain H-maser comparison. From the same data, the putative boost local position invariance coefficients were measured to a precision of up to parts in 1011 with respect to the cosmic microwave background rest frame. By combining these boost invariance experiments to a cryogenic sapphire oscillator vs H-maser comparison, independent limits on all nine coefficients of the boost-violation vector with respect to fundamental constant invariance, Bα, Be, and Bq (fine structure constant, electron mass, and quark mass, respectively), were determined to a precision of parts up to 1010.

  20. Functional implications of local DNA structures in regulatory motifs.

    PubMed

    Xiang, Qian

    2013-01-01

    The three-dimensional structure of DNA has been proposed to be a major determinant for functional transcription factors (TFs) and DNA interaction. Here, we use hydroxyl radical cleavage pattern as a measure of local DNA structure. We compared the conservation between DNA sequence and structure in terms of information content and attempted to assess the functional implications of DNA structures in regulatory motifs. We used statistical methods to evaluate the structural divergence of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. The following are our major observations: (i) we observed more information in structural alignment than in the corresponding sequence alignment for most of the transcriptional factors; (ii) for each TF, majority of positions have more information in the structural alignment as compared to the sequence alignment; (iii) we further defined a DNA structural divergence score (SD score) for each wild-type and mutant pair that is distinguished by single-base mutation. The SD score for benign mutations is significantly lower than that of switch mutations. This indicates structural conservation is also important for TFBS to be functional and DNA structures will provide previously unappreciated information for TF to realize the binding specificity.

  1. Multicolour localization microscopy by point-spread-function engineering

    NASA Astrophysics Data System (ADS)

    Shechtman, Yoav; Weiss, Lucien E.; Backer, Adam S.; Lee, Maurice Y.; Moerner, W. E.

    2016-09-01

    Super-resolution microscopy has revolutionized cellular imaging in recent years. Methods that rely on sequential localization of single point emitters enable spatial tracking at a resolution of ˜10-40 nm. Moreover, tracking and imaging in three dimensions is made possible by various techniques, including point-spread-function (PSF) engineering—namely, encoding the axial (z) position of a point source in the shape that it creates in the image plane. However, efficient multicolour imaging remains a challenge for localization microscopy—a task of the utmost importance for contextualizing biological data. Normally, multicolour imaging requires sequential imaging, multiple cameras or segmented dedicated fields of view. Here, we demonstrate an alternate strategy: directly encoding the spectral information (colour), in addition to three-dimensional position, in the image. By exploiting chromatic dispersion we design a new class of optical phase masks that simultaneously yield controllably different PSFs for different wavelengths, enabling simultaneous multicolour tracking or super-resolution imaging in a single optical path.

  2. A mapping of the electron localization function for earth materials

    NASA Astrophysics Data System (ADS)

    Gibbs, G. V.; Cox, D. F.; Ross, N. L.; Crawford, T. D.; Burt, J. B.; Rosso, K. M.

    2005-06-01

    The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies

  3. A Mapping of the Electron Localization Function for Earth Materials

    SciTech Connect

    Gibbs, Gerald V.; Cox, David F.; Ross, Nancy; Crawford, T Daniel; Burt, Jason; Rosso, Kevin M.

    2005-06-01

    The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies

  4. Are Fundamental Constants Really Constant?

    ERIC Educational Resources Information Center

    Swetman, T. P.

    1972-01-01

    Dirac's classical conclusions, that the values of e2, M and m are constants and the quantity of G decreases with time. Evoked considerable interest among researchers and traces historical development by which further experimental evidence points out that both e and G are constant values. (PS)

  5. Empirical Method to Estimate Hydrogen Embrittlement of Metals as a Function of Hydrogen Gas Pressure at Constant Temperature

    NASA Technical Reports Server (NTRS)

    Lee, Jonathan A.

    2010-01-01

    High pressure Hydrogen (H) gas has been known to have a deleterious effect on the mechanical properties of certain metals, particularly, the notched tensile strength, fracture toughness and ductility. The ratio of these properties in Hydrogen as compared to Helium or Air is called the Hydrogen Environment Embrittlement (HEE) Index, which is a useful method to classify the severity of H embrittlement and to aid in the material screening and selection for safety usage H gas environment. A comprehensive world-wide database compilation, in the past 50 years, has shown that the HEE index is mostly collected at two conveniently high H pressure points of 5 ksi and 10 ksi near room temperature. Since H embrittlement is directly related to pressure, the lack of HEE index at other pressure points has posed a technical problem for the designers to select appropriate materials at a specific H pressure for various applications in aerospace, alternate and renewable energy sectors for an emerging hydrogen economy. Based on the Power-Law mathematical relationship, an empirical method to accurately predict the HEE index, as a function of H pressure at constant temperature, is presented with a brief review on Sievert's law for gas-metal absorption.

  6. On the Khinchin Constant

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Borwein, Jonathan M.; Crandall, Richard E.; Craw, James M. (Technical Monitor)

    1995-01-01

    We prove known identities for the Khinchin constant and develop new identities for the more general Hoelder mean limits of continued fractions. Any of these constants can be developed as a rapidly converging series involving values of the Riemann zeta function and rational coefficients. Such identities allow for efficient numerical evaluation of the relevant constants. We present free-parameter, optimizable versions of the identities, and report numerical results.

  7. The black hole mass function derived from local spiral galaxies

    SciTech Connect

    Davis, Benjamin L.; Berrier, Joel C.; Shields, Douglas W.; Kennefick, Daniel; Kennefick, Julia; Seigar, Marc S.; Lacy, Claud H. S.; Hartley, Matthew T.

    2014-07-10

    We present our determination of the nuclear supermassive black hole (SMBH) mass function for spiral galaxies in the local universe, established from a volume-limited sample consisting of a statistically complete collection of the brightest spiral galaxies in the southern (δ < 0°) hemisphere. Our SMBH mass function agrees well at the high-mass end with previous values given in the literature. At the low-mass end, inconsistencies exist in previous works that still need to be resolved, but our work is more in line with expectations based on modeling of black hole evolution. This low-mass end of the spectrum is critical to our understanding of the mass function and evolution of black holes since the epoch of maximum quasar activity. The sample is defined by a limiting luminosity (redshift-independent) distance, D{sub L} = 25.4 Mpc (z = 0.00572) and a limiting absolute B-band magnitude, M{sub B}=−19.12. These limits define a sample of 140 spiral galaxies, with 128 measurable pitch angles to establish the pitch angle distribution for this sample. This pitch-angle distribution function may be useful in the study of the morphology of late-type galaxies. We then use an established relationship between the logarithmic spiral arm pitch angle and the mass of the central SMBH in a host galaxy in order to estimate the mass of the 128 respective SMBHs in this volume-limited sample. This result effectively gives us the distribution of mass for SMBHs residing in spiral galaxies over a lookback time, t{sub L} ≤ 82.1 h{sub 67.77}{sup −1} Myr and contained within a comoving volume, V{sub C} = 3.37 × 10{sup 4} h{sub 67.77}{sup −3} Mpc{sup 3}. We estimate that the density of SMBHs residing in spiral galaxies in the local universe is ρ=5.54{sub −2.73}{sup +6.55} × 10{sup 4} h{sub 67.77}{sup 3} M{sub ☉} Mpc{sup –3}. Thus, our derived cosmological SMBH mass density for spiral galaxies is Ω{sub BH}=4.35{sub −2.15}{sup +5.14} × 10{sup –7} h{sub 67.77}. Assuming that

  8. Four-Component Relativistic Density-Functional Theory Calculations of Nuclear Spin-Rotation Constants: Relativistic Effects in p-Block Hydrides.

    PubMed

    Komorovsky, Stanislav; Repisky, Michal; Malkin, Elena; Demissie, Taye B; Ruud, Kenneth

    2015-08-11

    We present an implementation of the nuclear spin-rotation (SR) constants based on the relativistic four-component Dirac-Coulomb Hamiltonian. This formalism has been implemented in the framework of the Hartree-Fock and Kohn-Sham theory, allowing assessment of both pure and hybrid exchange-correlation functionals. In the density-functional theory (DFT) implementation of the response equations, a noncollinear generalized gradient approximation (GGA) has been used. The present approach enforces a restricted kinetic balance condition for the small-component basis at the integral level, leading to very efficient calculations of the property. We apply the methodology to study relativistic effects on the spin-rotation constants by performing calculations on XHn (n = 1-4) for all elements X in the p-block of the periodic table and comparing the effects of relativity on the nuclear SR tensors to that observed for the nuclear magnetic shielding tensors. Correlation effects as described by the density-functional theory are shown to be significant for the spin-rotation constants, whereas the differences between the use of GGA and hybrid density functionals are much smaller. Our calculated relativistic spin-rotation constants at the DFT level of theory are only in fair agreement with available experimental data. It is shown that the scaling of the relativistic effects for the spin-rotation constants (varying between Z(3.8) and Z(4.5)) is as strong as for the chemical shieldings but with a much smaller prefactor.

  9. Chemistry as a function of the fine-structure constant and the electron-proton mass ratio

    SciTech Connect

    King, Rollin A.; Siddiqi, Ali; Allen, Wesley D.; Schaefer, Henry F. III

    2010-04-15

    In standard computations in theoretical quantum chemistry the accepted values of the fundamental physical constants are assumed. Alternatively, the tools of computational quantum chemistry can be used to investigate hypothetical chemistry that would result from different values of these constants, given the same physical laws. In this work, the dependence of a variety of basic chemical quantities on the values of the fine-structure constant and the electron-proton mass ratio is explored. In chemistry, the accepted values of both constants may be considered small, in the sense that their increase must be substantial to seriously impact bond energies. It is found that if the fine-structure constant were larger, covalent bonds between light atoms would be weaker, and the dipole moment and hydrogen-bonding ability of water would be reduced. Conversely, an increase in the value of the electron-proton mass ratio increases dissociation energies in molecules such as H{sub 2}, O{sub 2}, and CO{sub 2}. Specifically, a sevenfold increase in the fine-structure constant decreases the strength of the O-H bond in the water molecule by 7 kcal mol{sup -1} while reducing its dipole moment by at least 10%, whereas a 100-fold increase in the electron-proton mass ratio increases the same bond energy by 11 kcal mol{sup -1}.

  10. Neuropeptide Y system in the retina: From localization to function.

    PubMed

    Santos-Carvalho, Ana; Ambrósio, António Francisco; Cavadas, Cláudia

    2015-07-01

    The retina is a highly complex structure where several types of cells communicate through countless different molecules to codify visual information. Each type of cells plays unique roles in the retina, presenting a singular expression of neurotransmitters. Some neurotransmitter systems in the retina are well understood, while others need to be better explored to unravel the intricate signaling system involved. Neuropeptide Y (NPY), a 36 amino acid peptide, is one of the most common peptide neurotransmitter in the CNS and a highly conserved peptide among species. We review the localization of NPY and NPY receptors (mainly NPY Y1, Y2, Y4 and Y5) in retinal cells. Common features of the expression of NPY and NPY receptors in mammalian and non-mammalian species indicate universal roles of this system in the retina. In the present review, we highlight the putative roles of NPY receptor activation in the retina, discussing, in particular, their involvement in retinal development, neurotransmitter release modulation, neuroprotection, microglia and Muller cells function, retinal pigmented epithelium changes, retinal endothelial physiology and proliferation of retinal progenitor cells. Further studies are needed to confirm that targeting the NPY system might be a potential therapeutic strategy for retinal degenerative diseases.

  11. Localization and function of three monothiol glutaredoxins in Schizosaccharomyces pombe

    SciTech Connect

    Chung, Woo-Hyun; Kim, Kyoung-Dong; Roe, Jung-Hye . E-mail: jhroe@plaza.snu.ac.kr

    2005-05-06

    The fission yeast Schizosaccharomyces pombe contains two dithiol glutaredoxins (Grx1 and Grx2) and genes for three putative monothiol glutaredoxins (grx3, 4, and 5). We investigated the expression, sub-cellular localization, and functions of the three monothiol glutaredoxins. Fluorescence microscopy revealed that Grx3 is targeted to nuclear rim and endoplasmic reticulum, Grx4 primarily to the nucleus, and Grx5 to mitochondria. Null mutation of grx3 did not significantly affect growth and resistance against various oxidants, whereas grx5 mutation caused slow growth and sensitivity toward oxidants such as hydrogen peroxide, paraquat, and diamide. The grx2grx5 double mutation, deficient in all mitochondrial glutaredoxins, caused further retardation in growth and severe sensitivity toward all the oxidants tested. The grx4 mutation was not viable, suggesting a critical role of Grx4 for the physiology of S. pombe. Overproduction of Grx3 and Grx5, but not the truncated form of Grx5 without mitochondrial target sequence, severely retarded growth as Grx2 did, supporting the idea that Grx2, 3, and 5 are targeted to organellar compartments. Our results propose a distinct role for each glutaredoxin to maintain thiol redox balance, and hence the growth and stress resistance, of the fission yeast.

  12. Non-locality, adiabaticity, thermodynamics and electron energy probability functions

    NASA Astrophysics Data System (ADS)

    Boswell, Roderick; Zhang, Yunchao; Charles, Christine; Takahashi, Kazunori

    2016-09-01

    Thermodynamic properties are revisited for electrons that are governed by nonlocal electron energy probability functions in a plasma of low collisionality. Measurements in a laboratory helicon double layer experiment have shown that the effective electron temperature and density show a polytropic correlation with an index of γe = 1 . 17 +/- 0 . 02 along the divergent magnetic field, implying a nearly isothermal plasma (γe = 1) with heat being brought into the system. However, the evolution of electrons along the divergent magnetic field is essentially an adiabatic process, which should have a γe = 5 / 3 . The reason for this apparent contradiction is that the nearly collisionless plasma is very far from local thermodynamic equilibrium and the electrons behave nonlocally. The corresponding effective electron enthalpy has a conservation relation with the potential energy, which verifies that there is no heat transferred into the system during the electron evolution. The electrons are shown in nonlocal momentum equilibrium under the electric field and the gradient of the effective electron pressure. The convective momentum of ions, which can be assumed as a cold species, is determined by the effective electron pressure and the effective electron enthalpy is shown to be the source for ion acceleration. For these nearly collisionless plasmas, the use of traditional thermodynamic concepts can lead to very erroneous conclusions regarding the thermal conductivity.

  13. Towards a Density Functional Theory Exchange-Correlation Functional able to describe localization/delocalization

    NASA Astrophysics Data System (ADS)

    Mattsson, Ann E.; Wills, John M.

    2013-03-01

    The inability to computationally describe the physics governing the properties of actinides and their alloys is the poster child of failure of existing Density Functional Theory exchange-correlation functionals. The intricate competition between localization and delocalization of the electrons, present in these materials, exposes the limitations of functionals only designed to properly describe one or the other situation. We will discuss the manifestation of this competition in real materials and propositions on how to construct a functional able to accurately describe properties of these materials. I addition we will discuss both the importance of using the Dirac equation to describe the relativistic effects in these materials, and the connection to the physics of transition metal oxides. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  14. Many-body Localization Transition in Rokhsar-Kivelson-type wave functions

    NASA Astrophysics Data System (ADS)

    Chen, Xiao; Yu, Xiongjie; Cho, Gil Young; Clark, Bryan; Fradkin, Eduardo

    We construct a family of many-body wave functions to study the many-body localization phase transition. The wave functions have a Rokhsar-Kivelson form, in which the weight for the configurations are chosen from the Gibbs weights of a classical spin glass model, known as the Random Energy Model, multiplied by a random sign structure to represent a highly excited state. These wave functions show a phase transition into an MBL phase. In addition, we see three regimes of entanglement scaling with subsystem size: scaling with entanglement corresponding to an infinite temperature thermal phase, constant scaling, and a sub-extensive scaling between these limits. Near the phase transition point, the fluctuations of the Renyi entropies are non-Gaussian. We find that Renyi entropies with different Renyi index transition into the MBL phase at different points and have different scaling behavior, suggesting a multifractal behavior. This work was supported in part by DMR-1064319 and DMR-1408713 (XC,GYC,EF) at the University of Illinois, PHY11-25915 at KITP (EF), DOE, SciDAC FG02-12ER46875 (BKC and XY), and the Brain Korea 21 PLUS Project of Korea Government (GYC).

  15. Determination of Henry's law constants of organochlorine pesticides in deionized and saline water as a function of temperature

    NASA Astrophysics Data System (ADS)

    Cetin, Banu; Ozer, Serdar; Sofuoglu, Aysun; Odabasi, Mustafa

    The Henry's law constant ( H) is an important parameter that is required to estimate the air-water exchange of semi-volatile organic compounds. Henry's law constants for 17 banned/restricted/currently used organochlorine pesticides (OCPs) were experimentally determined using a gas-stripping technique in deionized and saline water (3%) over a temperature range of 5-35 °C. H values (at 25 °C) ranged between 0.066±0.037 Pa m 3 mol -1 (endosulfan II) and 62.0±24.2 Pa m 3 mol -1 (heptachlor) in deionized water while the range in saline water was 0.28±0.03 Pa m 3 mol -1 ( γ-HCH) and 135.2±31.3 Pa m 3 mol -1 (heptachlor). The increase in dimensionless Henry's law constants ( H') for OCPs over the studied temperature range was between 3 ( γ-HCH)-19 times (chlorpyrifos) and 3 (endosulfan II)-80 times ( trans-nonachlor) in deionized and saline water, respectively. The calculated enthalpies of phase change (Δ HH) were within the ranges previously reported for OCPs and other organic compounds (23.8-100.2 kJ mol -1). The salting-out constant, ks, ranged between 0.04 ( γ-HCH) and 1.80 L mol -1 (endosulfan II) indicating the importance of assessing the H values of OCPs in saline water to accurately determine their partitioning and fate in seawater.

  16. Local field effect as a function of pulse duration

    SciTech Connect

    Novitsky, Denis V.

    2010-07-15

    In this brief report we give semiclassical consideration to the role of pulse duration in the observation of local field effects in the regime of optical switching. We show that the main parameter governing local field influence is the ratio of peak Rabi frequency corresponding to medium inversion and Lorentz frequency of the medium. To obtain significant local field effect, this parameter should be near unity that is valid only for long enough pulses. We also discuss the role of relaxation and pulse shape in this process.

  17. Stability constants for the formation of rare earth-inorganic complexes as a function of ionic strength

    NASA Astrophysics Data System (ADS)

    Millero, Frank J.

    1992-08-01

    Recent studies have been made on the distribution of the rare earths (La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) in natural waters relative to their concentration in shales. These metals have also been used as models for the behavior of the trivalent actinides. The speciation of the rare earths in natural waters is modelled by using ionic interaction models which require reliable stability constants. In this paper the stability constants for the formation of lanthanide complexes ( k mx∗) with Cl -, NO 3-, SO 42-, OH -, HCO 3-, H 2PO 4-, HPO 42-, and CO 32- determined in NaClO 44 at various ionic strengths have been extrapolated to infinite dilution using the Pitzer interaction model. The activity coefficients for free ions ( γM, γx) needed for this extrapolation have been estimated from the Pitzer equations. The thermodynamic stability constants ( KMX) and activity coefficients of the various ion pairs ( γMX) were determined from In ( solK MX∗/γ Mγ x) = In K mx+ In (γ MX). The activity coefficients of the ion pairs have been used to determine Pitzer parameters ( BMX) for the rare earth complexes. The values of BMX were found to be the same for complexes of the same charge. These results make it possible to estimate the stability constants for the formation of rare earth complexes over a wide range of ionic strengths. The stability constants have been used to determine the speciation of the lanthanides in seawater and in brines. The carbonate complexes dominate for all natural waters where the carbonate alkalinity is greater than 0.001 eq/L at a pH near 8.

  18. Transverse isospin response function of asymmetric nuclear matter from a local isospin density functional

    NASA Astrophysics Data System (ADS)

    Lipparini, Enrico; Pederiva, Francesco

    2016-08-01

    The time dependent local isospin density approximation (TDLIDA) has been extended to the study of the transverse isospin response function in nuclear matter with an arbitrary neutron-proton asymmetry parameter ξ . The energy density functional has been chosen in order to fit existing accurate quantum Monte Carlo calculations with a density dependent potential. The evolution of the response with ξ in the Δ Tz=±1 channels is quite different. While the strength of the Δ Tz=+1 channel disappears rather quickly by increasing the asymmetry, the Δ Tz=-1 channel develops a stronger and stronger collective mode that in the regime typical of neutron star matter at β equilibrium almost completely exhausts the excitation spectrum of the system. The neutrino mean free paths obtained from the TDLIDA responses are strongly dependent on ξ and on the presence of collective modes, leading to a sizable difference with respect to the prediction of the Fermi gas model.

  19. Accurate determination of pyridine-poly(amidoamine) dendrimer absolute binding constants with the OPLS-AA force field and direct integration of radial distribution functions.

    PubMed

    Peng, Yong; Kaminski, George A

    2005-08-11

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to amino group (NH2) and amide group hydrogen atoms in and first generation poly(amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2-2.0 range).

  20. Accurate Determination of Pyridine -- Poly (Amidoamine) Dendrimer Absolute Binding Constants with the OPLS-AA Force Field and Direct Integration of Radial Distribution Functions

    NASA Astrophysics Data System (ADS)

    Peng, Yong; Kaminski, George

    2006-03-01

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to NH2 and amide group hydrogen atoms in 0th and 1st generation poly (amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 kcal/mol and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2 -- 2.0 range).

  1. Functional Lagrange formalism for time-non-local Lagrangians

    NASA Astrophysics Data System (ADS)

    Ferialdi, L.; Bassi, A.

    2012-05-01

    We develop a time-non-local (TNL) formalism based on variational calculus, which allows for the analysis of TNL Lagrangians. We derive the generalized Euler-Lagrange equations starting from the Hamilton's principle and, by defining a generalized momentum, we introduce the corresponding Hamiltonian formalism. We apply the formalism to second order TNL Lagrangians and we show that it reproduces standard results in the time-local limit. An example will show how the formalism works, and will provide an interesting insight on the non-standard features of TNL equations.

  2. Enhancement of piezoelectric constants induced by cation-substitution and two-dimensional strain effects on ZnO predicted by density functional perturbation theory

    NASA Astrophysics Data System (ADS)

    Nakamura, Kaoru; Higuchi, Sadao; Ohnuma, Toshiharu

    2016-03-01

    Using density functional perturbation theory, we investigated the effect of various substitutional dopant elements and in-plane strain on the piezoelectric properties of ZnO. The piezoelectric stress constant e33 of doped ZnO was found to depend on the formal charge of the substitutional dopant. By decomposing the piezoelectric stress constant e33 into the individual atomic contributions, the change in the piezoelectric properties was found to originate from a change in the coupling between the atomic displacement and the strain. Furthermore, we found that in-plane tensile strain along the a axis, which is specific to the thin film, can enhance the piezoelectric constant of ZnO. A phase transition from wurtzite to h-BN-type structure was found to occur with increasing in-plane tensile. The piezoelectric strain constant d33 was predicted to reach ˜200 pC/N for 2.78 at. % V-substituted ZnO at 5.5% in-plane strain, just before the phase transition. These theoretical results suggest that the piezoelectric constant of ZnO can be enhanced by controlling the in-plane strain via selection of the substrate material and dopant element.

  3. Intracellular localization of human cytidine deaminase. Identification of a functional nuclear localization signal.

    PubMed

    Somasekaram, A; Jarmuz, A; How, A; Scott, J; Navaratnam, N

    1999-10-01

    The cytidine deaminases belong to the family of multisubunit enzymes that catalyze the hydrolytic deamination of their substrate to a corresponding uracil product. They play a major role in pyrimidine nucleoside and nucleotide salvage. The intracellular distribution of cytidine deaminase and related enzymes has previously been considered to be cytosolic. Here we show that human cytidine deaminase (HCDA) is present in the nucleus. A highly specific, affinity purified polyclonal antibody against HCDA was used to analyze the intracellular localization of native HCDA in a variety of mammalian cells by in situ immunochemistry. Native HCDA was found to be present in the nucleus as well as the cytoplasm in several cell types. Indirect immunofluorescence microscopy indicated a predominantly nuclear localization of FLAG-tagged HCDA overexpressed in these cells. We have identified an amino-terminal bipartite nuclear localization signal that is both necessary and sufficient to direct HCDA and a non-nuclear reporter protein to the nucleus. We also show HCDA binding to the nuclear import receptor, importin alpha. Similar putative bipartite nuclear localization sequences are found in other cytidine/deoxycytidylate deaminases. The results presented here suggest that the pyrimidine nucleotide salvage pathway may operate in the nucleus. This localization may have implications in the regulation of nucleoside and nucleotide metabolism and nucleic acid biosynthesis.

  4. Functional genomics of physiological plasticity and local adaptation in killifish.

    PubMed

    Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F

    2011-01-01

    Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.

  5. Stability Analysis and Stabilization of Nonlinear Systems via Locally Defined Density Functions

    NASA Astrophysics Data System (ADS)

    Masubuchi, Izumi

    This paper considers local stability analysis of nonlinear systems with deriving a positively invariant set based on the Rantzer's stability theory by using density functions. We define a notion of locally defined density functions around an equilibrium that give monotonously increasing positive measures near the equilibrium of a nonlinear system. Under certain assumptions, it is shown that some level set of a locally defined density function is a positively invariant set where almost all of the system trajectories converge to the equilibrium. We also mention an SOS (sum-of-squares) formulation for synthesis of a nonlinear gain via locally defined density functions.

  6. Validation of local hybrid functionals for TDDFT calculations of electronic excitation energies

    NASA Astrophysics Data System (ADS)

    Maier, Toni M.; Bahmann, Hilke; Arbuznikov, Alexei V.; Kaupp, Martin

    2016-02-01

    The first systematic evaluation of local hybrid functionals for the calculation of electronic excitation energies within linear-response time-dependent density functional theory (TDDFT) is reported. Using our recent efficient semi-numerical TDDFT implementation [T. M. Maier et al., J. Chem. Theory Comput. 11, 4226 (2015)], four simple, thermochemically optimized one-parameter local hybrid functionals based on local spin-density exchange are evaluated against a database of singlet and triplet valence excitations of organic molecules, and against a mixed database including also Rydberg, intramolecular charge-transfer (CT) and core excitations. The four local hybrids exhibit comparable performance to standard global or range-separated hybrid functionals for common singlet valence excitations, but several local hybrids outperform all other functionals tested for the triplet excitations of the first test set, as well as for relative energies of excited states. Evaluation for the combined second test set shows that local hybrids can also provide excellent Rydberg and core excitations, in the latter case rivaling specialized functionals optimized specifically for such excitations. This good performance of local hybrids for different excitation types could be traced to relatively large exact-exchange (EXX) admixtures in a spatial region intermediate between valence and asymptotics, as well as close to the nucleus, and lower EXX admixtures in the valence region. In contrast, the tested local hybrids cannot compete with the best range-separated hybrids for intra- and intermolecular CT excitation energies. Possible directions for improvement in the latter category are discussed. As the used efficient TDDFT implementation requires essentially the same computational effort for global and local hybrids, applications of local hybrid functionals to excited-state problems appear promising in a wide range of fields. Influences of current-density dependence of local kinetic

  7. Influencing uptake and localization of aminoglycoside-functionalized peptoids.

    PubMed

    Lee, Melissa M; French, Jonathan M; Disney, Matthew D

    2011-08-01

    The development of small-molecule therapeutics that target RNA remains a promising field but one hampered with considerable challenges that include programming high affinity, specificity, cell permeability, and favorable pharmacokinetic profiles. Previously, we employed the use of peptoids to modularly display RNA-binding modules to enhance binding affinity and specificity by altering valency and the distance between ligand modules. Herein, factors that affect uptake, localization, and toxicity of peptoids that display a kanamycin derivative into a variety of mammalian cells lines are reported. A series of peptoids that display various spacing modules was synthesized to determine if the spacing module affects permeability and localization. The spacing module does affect cellular permeability into C2C12, A549, HeLa, and MCF7 cell lines but not into Jurkat cells. Moreover, the modularly assembled peptoids carrying the kanamycin cargo localize in the cytoplasm and perinuclear region of C2C12 and A549 cells and throughout HeLa cells, including the nucleus. These studies could contribute to the development of general strategies to afford cell permeable, modularly assembled small molecules that specifically target RNAs present in a variety of cell types.

  8. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    PubMed

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-03-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  9. (1)JCH NMR Profile: Identification of Key Structural Features and Functionalities by Visual Observation and Direct Measurement of One-Bond Proton-Carbon Coupling Constants.

    PubMed

    Marcó, Núria; Souza, Alexandre A; Nolis, Pau; Cobas, Carlos; Gil, Roberto R; Parella, Teodor

    2017-02-17

    A user-friendly NMR interface for the visual and accurate determination of experimental one-bond proton-carbon coupling constants ((1)JCH) in small molecules is presented. This intuitive (1)JCH profile correlates directly to δ((1)H), and (1)JCH facilitates the rapid identification and assignment of (1)H signals belonging to key structural elements and functional groups. Illustrative examples are provided for some target molecules, including terminal alkynes, strained rings, electronegative substituents, or lone-pair-bearing heteronuclei.

  10. Protein function annotation by local binding site surface similarity.

    PubMed

    Spitzer, Russell; Cleves, Ann E; Varela, Rocco; Jain, Ajay N

    2014-04-01

    Hundreds of protein crystal structures exist for proteins whose function cannot be confidently determined from sequence similarity. Surflex-PSIM, a previously reported surface-based protein similarity algorithm, provides an alternative method for hypothesizing function for such proteins. The method now supports fully automatic binding site detection and is fast enough to screen comprehensive databases of protein binding sites. The binding site detection methodology was validated on apo/holo cognate protein pairs, correctly identifying 91% of ligand binding sites in holo structures and 88% in apo structures where corresponding sites existed. For correctly detected apo binding sites, the cognate holo site was the most similar binding site 87% of the time. PSIM was used to screen a set of proteins that had poorly characterized functions at the time of crystallization, but were later biochemically annotated. Using a fully automated protocol, this set of 8 proteins was screened against ∼60,000 ligand binding sites from the PDB. PSIM correctly identified functional matches that predated query protein biochemical annotation for five out of the eight query proteins. A panel of 12 currently unannotated proteins was also screened, resulting in a large number of statistically significant binding site matches, some of which suggest likely functions for the poorly characterized proteins.

  11. Local Hamiltonians for quantitative Green's function embedding methods

    NASA Astrophysics Data System (ADS)

    Rusakov, Alexander A.; Phillips, Jordan J.; Zgid, Dominika

    2014-11-01

    Embedding calculations that find approximate solutions to the Schrödinger equation for large molecules and realistic solids are performed commonly in a three step procedure involving (i) construction of a model system with effective interactions approximating the low energy physics of the initial realistic system, (ii) mapping the model system onto an impurity Hamiltonian, and (iii) solving the impurity problem. We have developed a novel procedure for parametrizing the impurity Hamiltonian that avoids the mathematically uncontrolled step of constructing the low energy model system. Instead, the impurity Hamiltonian is immediately parametrized to recover the self-energy of the realistic system in the limit of high frequencies or short time. The effective interactions parametrizing the fictitious impurity Hamiltonian are local to the embedded regions, and include all the non-local interactions present in the original realistic Hamiltonian in an implicit way. We show that this impurity Hamiltonian can lead to excellent total energies and self-energies that approximate the quantities of the initial realistic system very well. Moreover, we show that as long as the effective impurity Hamiltonian parametrization is designed to recover the self-energy of the initial realistic system for high frequencies, we can expect a good total energy and self-energy. Finally, we propose two practical ways of evaluating effective integrals for parametrizing impurity models.

  12. A Tomographic Method for the Reconstruction of Local Probability Density Functions

    NASA Technical Reports Server (NTRS)

    Sivathanu, Y. R.; Gore, J. P.

    1993-01-01

    A method of obtaining the probability density function (PDF) of local properties from path integrated measurements is described. The approach uses a discrete probability function (DPF) method to infer the PDF of the local extinction coefficient from measurements of the PDFs of the path integrated transmittance. The local PDFs obtained using the method are compared with those obtained from direct intrusive measurements in propylene/air and ethylene/air diffusion flames. The results of this comparison are good.

  13. Approximate forms of the pair-density-functional kinetic energy on the basis of a rigorous expression with coupling-constant integration

    NASA Astrophysics Data System (ADS)

    Higuchi, Katsuhiko; Higuchi, Masahiko

    2014-12-01

    We propose approximate kinetic energy (KE) functionals of the pair-density (PD)-functional theory on the basis of the rigorous expression with the coupling-constant integration (RECCI) that has been recently derived [Phys. Rev. A 85, 062508 (2012), 10.1103/PhysRevA.85.062508]. These approximate functionals consist of the noninteracting KE and correlation energy terms. It is found that the Thomas-Fermi-Weizsäcker functional is shown to be better as the noninteracting KE term than the Thomas-Fermi and Gaussian model functionals. It is also shown that the correlation energy term is also indispensable for the reduction of the KE error, i.e., reductions of both inappropriateness of the approximate functional and error of the resultant PD. Concerning the correlation energy term, we further propose an approximate functional in addition to using the existing familiar functionals. This functional satisfies the scaling property of the KE functional, and yields a reasonable PD in a sense that the KE, electron-electron interaction, and potentials energies tend to be improved with satisfying the virial theorem. The present results not only suggest the usefulness of the RECCI but also provide the guideline for the further improvement of the RECCI-based KE functional.

  14. Protein function prediction using local 3D templates.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-08-19

    The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.

  15. Local hybrid functionals with orbital-free mixing functions and balanced elimination of self-interaction error

    SciTech Connect

    Silva, Piotr de E-mail: clemence.corminboeuf@epfl.ch; Corminboeuf, Clémence E-mail: clemence.corminboeuf@epfl.ch

    2015-02-21

    The recently introduced density overlap regions indicator (DORI) [P. de Silva and C. Corminboeuf, J. Chem. Theory Comput. 10(9), 3745–3756 (2014)] is a density-dependent scalar field revealing regions of high density overlap between shells, atoms, and molecules. In this work, we exploit its properties to construct local hybrid exchange-correlation functionals aiming at balanced reduction of the self-interaction error. We show that DORI can successfully replace the ratio of the von Weizsäcker and exact positive-definite kinetic energy densities, which is commonly used in mixing functions of local hybrids. Additionally, we introduce several semi-empirical parameters to control the local and global admixture of exact exchange. The most promising of our local hybrids clearly outperforms the underlying semi-local functionals as well as their global hybrids.

  16. Local hybrid functionals with orbital-free mixing functions and balanced elimination of self-interaction error

    NASA Astrophysics Data System (ADS)

    de Silva, Piotr; Corminboeuf, Clémence

    2015-02-01

    The recently introduced density overlap regions indicator (DORI) [P. de Silva and C. Corminboeuf, J. Chem. Theory Comput. 10(9), 3745-3756 (2014)] is a density-dependent scalar field revealing regions of high density overlap between shells, atoms, and molecules. In this work, we exploit its properties to construct local hybrid exchange-correlation functionals aiming at balanced reduction of the self-interaction error. We show that DORI can successfully replace the ratio of the von Weizsäcker and exact positive-definite kinetic energy densities, which is commonly used in mixing functions of local hybrids. Additionally, we introduce several semi-empirical parameters to control the local and global admixture of exact exchange. The most promising of our local hybrids clearly outperforms the underlying semi-local functionals as well as their global hybrids.

  17. Communication: Hole localization in Al-doped quartz SiO{sub 2} within ab initio hybrid-functional DFT

    SciTech Connect

    Gerosa, Matteo; Bottani, Carlo Enrico

    2015-09-21

    We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO{sub 2}, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.

  18. Dissecting the Structure-Function Relationship of a Fungicidal Peptide Derived from the Constant Region of Human Immunoglobulins

    PubMed Central

    Ciociola, Tecla; Pertinhez, Thelma A.; Giovati, Laura; Sperindè, Martina; Magliani, Walter; Ferrari, Elena; Gatti, Rita; D'Adda, Tiziana; Spisni, Alberto; Polonelli, Luciano

    2016-01-01

    Synthetic peptides encompassing sequences related to the complementarity-determining regions of antibodies or derived from their constant region (Fc peptides) were proven to exert differential antimicrobial, antiviral, antitumor, and/or immunomodulatory activities in vitro and/or in vivo, regardless of the specificity and isotype of the parental antibody. Alanine substitution derivatives of these peptides exhibited unaltered, increased, or decreased candidacidal activities in vitro. The bioactive IgG-derived Fc N10K peptide (NQVSLTCLVK) spontaneously self-assembles, a feature previously recognized as relevant for the therapeutic activity of another antibody-derived peptide. We evaluated the contribution of each residue to the peptide self-assembling capability by circular-dichroism spectroscopy. The interaction of the N10K peptide and its derivatives with Candida albicans cells was studied by confocal, transmission, and scanning electron microscopy. The apoptosis and autophagy induction profiles in yeast cells treated with the peptides were evaluated by flow cytometry, and the therapeutic efficacy against candidal infection was studied in a Galleria mellonella model. Overall, the results indicate a critical role for some residues in the self-assembly process and a correlation of that capability with the candidacidal activities of the peptides in vitro and their therapeutic effects in vivo. PMID:26856836

  19. Structural changes of anodic layer on titanium in sulfate solution as a function of anodization duration in constant current mode

    NASA Astrophysics Data System (ADS)

    Komiya, Shinji; Sakamoto, Kouta; Ohtsu, Naofumi

    2014-03-01

    The present study investigated the effect of anodization time, in constant current mode, on the anodic oxide layer formed on titanium (Ti). Anodization of the Ti substrate was carried out in a 0.1 M (NH4)2SO4 aqueous solution with reaction times of various durations, after which the characteristics and photocatalytic activity were investigated in detail. The TiO2 layer fabricated in a short duration exhibited comparatively flat surface morphology and an anatase-type crystal structure. This layer acted as a photocatalyst only under ultraviolet light (UV) illumination. Upon prolonging the anodization, the layer structure changed drastically. The surface morphology became rough, and the crystal structure changed to rutile-type TiO2. Furthermore, the layer showed photocatalytic activity both under UV and visible light illumination. Further anodization increased the amount of methylene blue (MB) adsorbed on the surface, but did not cause additional change to the structure of the anodic layer. The surface morphology and crystal structure of the anodic layer were predominantly controlled by the anodization time; thus, the anodization time is an important parameter for controlling the characteristics of the anodic layer.

  20. Dissecting the Structure-Function Relationship of a Fungicidal Peptide Derived from the Constant Region of Human Immunoglobulins.

    PubMed

    Ciociola, Tecla; Pertinhez, Thelma A; Giovati, Laura; Sperindè, Martina; Magliani, Walter; Ferrari, Elena; Gatti, Rita; D'Adda, Tiziana; Spisni, Alberto; Conti, Stefania; Polonelli, Luciano

    2016-04-01

    Synthetic peptides encompassing sequences related to the complementarity-determining regions of antibodies or derived from their constant region (Fc peptides) were proven to exert differential antimicrobial, antiviral, antitumor, and/or immunomodulatory activitiesin vitroand/orin vivo, regardless of the specificity and isotype of the parental antibody. Alanine substitution derivatives of these peptides exhibited unaltered, increased, or decreased candidacidal activitiesin vitro The bioactive IgG-derived Fc N10K peptide (NQVSLTCLVK) spontaneously self-assembles, a feature previously recognized as relevant for the therapeutic activity of another antibody-derived peptide. We evaluated the contribution of each residue to the peptide self-assembling capability by circular-dichroism spectroscopy. The interaction of the N10K peptide and its derivatives withCandida albicanscells was studied by confocal, transmission, and scanning electron microscopy. The apoptosis and autophagy induction profiles in yeast cells treated with the peptides were evaluated by flow cytometry, and the therapeutic efficacy against candidal infection was studied in aGalleria mellonellamodel. Overall, the results indicate a critical role for some residues in the self-assembly process and a correlation of that capability with the candidacidal activities of the peptidesin vitroand their therapeutic effectsin vivo.

  1. Dynamics of localized particles from density functional theory

    NASA Astrophysics Data System (ADS)

    Reinhardt, J.; Brader, J. M.

    2012-01-01

    A fundamental assumption of the dynamical density functional theory (DDFT) of colloidal systems is that a grand-canonical free-energy functional may be employed to generate the thermodynamic driving forces. Using one-dimensional hard rods as a model system, we analyze the validity of this key assumption and show that unphysical self-interactions of the tagged particle density fields, arising from coupling to a particle reservoir, are responsible for the excessively fast relaxation predicted by the theory. Moreover, our findings suggest that even employing a canonical functional would not lead to an improvement for many-particle systems, if only the total density is considered. We present several possible schemes to suppress these effects by incorporating tagged densities. When applied to confined systems, we demonstrate, using a simple example, that DDFT necessarily leads to delocalized tagged particle density distributions, which do not respect the fundamental geometrical constraints apparent in Brownian dynamics simulation data. The implication of these results for possible applications of DDFT to treat the glass transition are discussed.

  2. Resolving the Sedimentary Basin Structure from Oklahoma with Local Receiver Function

    NASA Astrophysics Data System (ADS)

    Zheng, D.; Ni, S.

    2015-12-01

    The teleseismic receiver function is defined as the radial component of P wave being deconvoluted from the vertical component of the earthquakes with magnitude larger than 5.5 at teleseismic distances. It has successfully been applied in resolving the structure of the crust and upper mantle in many regions. The receiver function can also be used to determine the thickness of sedimentary basin. However the corner frequency of the P waves from the teleseismic events (M>5.5) is relatively low and the high frequency content in the teleseismic P waves is attenuated, thus, the teleseismic receiver function is usually not sufficient to reveal details of sedimentary basin structure. Instead, local small earthquake (~ M3) generates P waves of short duration waveforms with high frequency content, which can be used to calculate receiver functions (called local receiver function). As a case study, we study waveform data from local earthquakes in Oklahoma. We first explore feasibility of local receiver function for different magnitude, focal depth, epicentral distance, filtering band and time window length. After local receiver functions are computed, we search the best velocity model to fit the local receiver function waveforms with the Differential Evolution (DE) algorithm which is a global optimization method. We invert the sedimentary basin structure in Oklahoma and find that this method is suitable for other area for the sedimentary basin structure where local seismic waveforms are available.

  3. A surface work function measurement technique utilizing constant deflected grazing electron trajectories: oxygen uptake on Cu(001).

    PubMed

    Ermakov, A V; Ciftlikli, E Z; Syssoev, S E; Shuttleworth, I G; Hinch, B J

    2010-10-01

    We report on the application of a novel nondestructive in-vacuum technique for relative work function measurements, employing a grazing incidence electron deflection above a sample with a planar surface. Two deflected electron beam detectors are used as a position sensitive detector to control feedback to the sample potential as the sample work function changes. With feedback the sample potential exactly follows the surface sample-size averaged work function variation, so that the deflected beam trajectory remains stable. We also discuss methods to optimize the initial electron trajectories for this method, so as to minimize unwanted effects such as from uncontrolled external magnetic fields. As the electron beam does not impinge on the surface in this new technique electron induced desorption, ionization, dissociation, and/or decomposition is not induced at the interface. Importantly also the technique allows for free access to the surfaces enabling simultaneous deposition/evaporation and/or application of other surface characterization methods. We demonstrate its application in concurrent measurements of helium atom reflectivity and work function changes taking place during molecular oxygen exposure of a Cu(001) surface. A work function measurement sensitivity and stability is demonstrated at ∼10 mV at a sampling rate of 1 Hz and after application of an ∼7 s smoothing routine. In comparison to the helium atom reflectivity measurements, the work function measurements are more sensitive to the initial O uptake, and less so to the final coverage variations and possible surface reordering at higher O coverages.

  4. Magnetosensory function in rats: localization using positron emission tomography.

    PubMed

    Frilot, Clifton; Carrubba, Simona; Marino, Andrew A

    2009-05-01

    The aim of this study was to show that low-strength electromagnetic fields (EMFs) produced evoked potentials in rats and to localize the activated region in the brain. In response to a 2.5-G, 60-Hz stimulus, onset- and offset-evoked potentials were detected (P < 0.05 in each of the 10 animals studied); the evoked potentials had the same magnitude, latency, and nonlinear relationship to the field seen in previous studies on rabbits and human subjects. The neuroanatomical region of activation associated with the electrophysiological effect was identified by positron emission tomography using fluorodeoxyglucose. Paired emission scans (the same animal with and without field treatment) from 10 additional rats were differenced and averaged to produce a t-statistic image using the pooled variance; the t value of each voxel was compared with a calculated critical t value to identify the activated voxels (P < 0.05). A brain volume of 13 mm(3) (15 voxels) located in the posterior, central cerebellum was found to have been activated by exposure to the field. Taken together, the results indicated that magnetosensory evoked potentials in the rats were associated with increased glucose utilization in the cerebellum, thereby supporting earlier evidence that EMF transduction occurred in the brain.

  5. The binding of cytochrome c peroxidase and ferricytochrome c. A spectrophotometric determination of the equilibrium association constant as a function of ionic strength.

    PubMed

    Erman, J E; Vitello, L B

    1980-07-10

    Complex formation between cytochrome c peroxidase and ferricytochrome c perturbs the optical absorption spectrum in the Soret band by about 2%. This perturbation can be utilized as a measure of the complex formed in solution and permits the determination of the stoichiometry and the equilibrium association constant for this reaction. At pH 6, in cacodylate/KNO3 buffers, only a 1:1 complex between cytochrome c peroxidase and ferricytochrome c is detected. The equilibrium association constant for the complex has been determined as a function of ionic strength and varies between (6.0 +/- 3.6) x 10(6) M-1 and (2.2 +/- 1.9) x 10(6) M-1 over the ionic strength range 0.01 M to 0.20 M.

  6. Calculation of the magnetic circular dichroism B term from the imaginary part of the Verdet constant using damped time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Krykunov, Mykhaylo; Seth, Michael; Ziegler, Tom; Autschbach, Jochen

    2007-12-01

    A time-dependent density functional theory (TDDFT) formalism with damping for the calculation of the magnetic optical rotatory dispersion and magnetic circular dichroism (MCD) from the complex Verdet constant is presented. For a justification of such an approach, we have derived the TDDFT analog of the sum-over-states formula for the Verdet constant. The results of the MCD calculations by this method for ethylene, furan, thiophene, selenophene, tellurophene, and pyrrole are in good agreement with our previous theoretical sum-over-states MCD spectra. For the π →π* transition of propene, we have obtained a positive Faraday B term. It is located between the two negative B terms. This finding is in agreement with experiment in the range of 6-8eV.

  7. Label-Free Kinetics: Exploiting Functional Hemi-Equilibrium to Derive Rate Constants for Muscarinic Receptor Antagonists.

    PubMed

    Riddy, Darren M; Valant, Celine; Rueda, Patricia; Charman, William N; Sexton, Patrick M; Summers, Roger J; Christopoulos, Arthur; Langmead, Christopher J

    2015-10-01

    Drug receptor kinetics is as a key component in drug discovery, development, and efficacy; however, determining kinetic parameters has historically required direct radiolabeling or competition with a labeled tracer. Here we present a simple approach to determining the kinetics of competitive antagonists of G protein-coupled receptors by exploiting the phenomenon of hemi-equilibrium, the state of partial re-equilibration of agonist, antagonist, and receptor in some functional assays. Using functional [Ca(2+)]i-flux and extracellular kinases 1 and 2 phosphorylation assays that have short incubation times and therefore are prone to hemi-equilibrium "behaviors," we investigated a wide range of structurally and physicochemically distinct muscarinic acetylcholine receptor antagonists. Using a combined operational and hemi-equilibrium model of antagonism to both simulate and analyze data, we derived estimates of association and dissociation rates for the test set of antagonists, identifying both rapidly dissociating (4-DAMP, himbacine) and slowly dissociating (tiotropium, glycopyrrolate) ligands. The results demonstrate the importance of assay incubation time and the degree of receptor reserve in applying the analytical model. There was an excellent correlation between estimates of antagonist pK(B), k(on), and k(off) from functional assays and those determined by competition kinetics using whole-cell [(3)H]N-methylscopolamine binding, validating this approach as a rapid and simple method to functionally profile receptor kinetics of competitive antagonists in the absence of a labeled tracer.

  8. [Cognitive functions and personality traits in patients with brain tumors: the role of lesion localization].

    PubMed

    Razumnikova, O M; Perfil'ev, A M; Stupak, V V

    2014-01-01

    Personality traits and cognitive functions were studied depending on a tumor localization in the brain in 21 neurosurgical patients and the results were compared with a control group. In patients with brain damage, mostly affected were personality traits associated with emotion regulation and social interaction (neuroticism, psychoticism and social conformity). Increases in psychoticism and decreases in neuroticism were more expressed in patients with a left-hemisphere localization of tumors. The tumor-induced decrease in cognitive abilities was more presented in performing figurative tasks and less in verbal ones. Verbal functions were more decreased in the group with frontal localization of tumor compared to that with parietal localization.

  9. Influence of local vibration on finger functions of forest workers.

    PubMed

    Tanaka, M; Nakamura, K; Sato, K; Tanaka, K

    1997-07-01

    We physically examined of forest workers in the northern part of Fukushima District, Japan. The main purpose of this study was to survey the state of finger functions, especially the differences between the functions of right and left fingers of forest workers. This physical examination was conducted in winter. The items of the physical examination were hand grip strength, finger skin temperature, vibration sensation threshold, nail pressure test of the finger. Subjects were classified into A and B groups on the base of the results of the physical examination. A group is normal or slight disorder, and B group is disorder or illness. Hand grip strength was measured five times at five-second intervals. The decrease ratio of the left hand grip strength was greater than that of the right hand grip strength. Although there were significant differences among each finger of A and B groups, there were no big differences in the skin temperatures of the fingers in each group. Vibration sensation threshold was measured for II, III and IV fingers. The vibration sensation threshold of the index finger was the most sensitive and that of IV finger was the least sensitive. The vibration sensation threshold of the right fingers was more sensitive than that of the left fingers. The reaction times of the nail pressure test of the right fingers were generally faster than those of the left fingers. Forestry workers in Japan become elderly. There are big differences among the physical reactions or strengths of elderly people. Standard values for the measuring items for ageing are needed.

  10. On the local fractional derivative of everywhere non-differentiable continuous functions on intervals

    NASA Astrophysics Data System (ADS)

    Liu, Cheng-shi

    2017-01-01

    We first prove that for a continuous function f(x) defined on an open interval, the Kolvankar-Gangal's (or equivalently Chen-Yan-Zhang's) local fractional derivative f(α)(x) is not continuous, and then prove that it is impossible that the KG derivative f(α)(x) exists everywhere on the interval and satisfies f(α)(x) ≠ 0 in the same time. In addition, we give a criterion of the nonexistence of the local fractional derivative of everywhere non-differentiable continuous functions. Furthermore, we construct two simple nowhere differentiable continuous functions on (0, 1) and prove that they have no the local fractional derivatives everywhere.

  11. Density functional theory with alternative spin densities: application to magnetic systems with localized spins.

    PubMed

    Pérez-Jiménez, Angel J; Pérez-Jordá, José M; Illas, Francesc

    2004-01-01

    A new method to improve the excess spin density obtained from unrestricted Hartree-Fock wave functions in terms of natural orbitals is proposed. Using this modified excess spin density to evaluate the correlation energy by means of density functionals leads to large improvements in the computed magnetic coupling constants of several materials without need to modify the exchange contribution. This is important because it reconciles the density functional theory description with the one provided by multi-determinant wave functions. Using the present approach, the leading contribution to the magnetic coupling constant arises from electron correlation effects. The performance of the new method is illustrated on various materials including high-critical-temperature superconductors parent compounds.

  12. METALLICITY DISTRIBUTION FUNCTIONS OF FOUR LOCAL GROUP DWARF GALAXIES

    SciTech Connect

    Ross, Teresa L.; Holtzman, Jon; Saha, Abhijit; Anthony-Twarog, Barbara J. E-mail: holtz@nmsu.edu

    2015-06-15

    We present stellar metallicities in Leo I, Leo II, IC 1613, and Phoenix dwarf galaxies derived from medium (F390M) and broad (F555W, F814W) band photometry using the Wide Field Camera 3 instrument on board the Hubble Space Telescope. We measured metallicity distribution functions (MDFs) in two ways, (1) matching stars to isochrones in color–color diagrams and (2) solving for the best linear combination of synthetic populations to match the observed color–color diagram. The synthetic technique reduces the effect of photometric scatter and produces MDFs 30%–50% narrower than the MDFs produced from individually matched stars. We fit the synthetic and individual MDFs to analytical chemical evolution models (CEMs) to quantify the enrichment and the effect of gas flows within the galaxies. Additionally, we measure stellar metallicity gradients in Leo I and II. For IC 1613 and Phoenix our data do not have the radial extent to confirm a metallicity gradient for either galaxy. We find the MDF of Leo I (dwarf spheroidal) to be very peaked with a steep metal-rich cutoff and an extended metal-poor tail, while Leo II (dwarf spheroidal), Phoenix (dwarf transition), and IC 1613 (dwarf irregular) have wider, less peaked MDFs than Leo I. A simple CEM is not the best fit for any of our galaxies; therefore we also fit the “Best Accretion Model” of Lynden-Bell. For Leo II, IC 1613, and Phoenix we find similar accretion parameters for the CEM even though they all have different effective yields, masses, star formation histories, and morphologies. We suggest that the dynamical history of a galaxy is reflected in the MDF, where broad MDFs are seen in galaxies that have chemically evolved in relative isolation and narrowly peaked MDFs are seen in galaxies that have experienced more complicated dynamical interactions concurrent with their chemical evolution.

  13. Localizing the site of magnetic brain stimulation by functional MRI.

    PubMed

    Terao, Y; Ugawa, Y; Sakai, K; Miyauchi, S; Fukuda, H; Sasaki, Y; Takino, R; Hanajima, R; Furubayashi, T; Pütz, B; Kanazawa, I

    1998-07-01

    In order to locate the site of action of transcranial magnetic stimulation (TMS) within the human motor cortices, we investigated how the optimal positions for evoking motor responses over the scalp corresponded to the hand and leg primary-motor areas. TMS was delivered with a figure-8 shaped coil over each point of a grid system constructed on the skull surface, each separated by 1 cm, to find the optimal site for obtaining motor-evoked potentials (MEPs) in the contralateral first dorsal interosseous (FDI) and tibialis anterior (TA) muscles. Magnetic resonance imaging scans of the brain were taken for each subject with markers placed over these sites, the positions of which were projected onto the cortical region just beneath. On the other hand, cortical areas where blood flow increased during finger tapping or leg movements were identified on functional magnetic resonance images (fMRI), which should include the hand and leg primary-motor areas. The optimal location for eliciting MEPs in FDI, regardless of their latency, lay just above the bank of the precentral gyrus, which coincided with the activated region during finger tapping in fMRI studies. The direction of induced current preferentially eliciting MEPs with the shortest latency in each subject was nearly perpendicular to the course of the precentral gyrus at this position. The optimal site for evoking motor responses in TA was also located just above the activated area during leg movements identified within the anterior portion of the paracentral lobule. The results suggest that, for magnetic stimulation, activation occurs in the primary hand and leg motor area (Brodmann area 4), which is closest in distance to the optimal scalp position for evoking motor responses.

  14. Towards improved local hybrid functionals by calibration of exchange-energy densities

    SciTech Connect

    Arbuznikov, Alexei V. E-mail: martin.kaupp@tu-berlin.de; Kaupp, Martin E-mail: martin.kaupp@tu-berlin.de

    2014-11-28

    A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.

  15. Local electric dipole moments for periodic systems via density functional theory embedding

    SciTech Connect

    Luber, Sandra

    2014-12-21

    We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

  16. Metallicity Distribution Functions of Four Local Group Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    Ross, Teresa L.; Holtzman, Jon; Saha, Abhijit; Anthony-Twarog, Barbara J.

    2015-06-01

    We present stellar metallicities in Leo I, Leo II, IC 1613, and Phoenix dwarf galaxies derived from medium (F390M) and broad (F555W, F814W) band photometry using the Wide Field Camera 3 instrument on board the Hubble Space Telescope. We measured metallicity distribution functions (MDFs) in two ways, (1) matching stars to isochrones in color-color diagrams and (2) solving for the best linear combination of synthetic populations to match the observed color-color diagram. The synthetic technique reduces the effect of photometric scatter and produces MDFs 30%-50% narrower than the MDFs produced from individually matched stars. We fit the synthetic and individual MDFs to analytical chemical evolution models (CEMs) to quantify the enrichment and the effect of gas flows within the galaxies. Additionally, we measure stellar metallicity gradients in Leo I and II. For IC 1613 and Phoenix our data do not have the radial extent to confirm a metallicity gradient for either galaxy. We find the MDF of Leo I (dwarf spheroidal) to be very peaked with a steep metal-rich cutoff and an extended metal-poor tail, while Leo II (dwarf spheroidal), Phoenix (dwarf transition), and IC 1613 (dwarf irregular) have wider, less peaked MDFs than Leo I. A simple CEM is not the best fit for any of our galaxies; therefore we also fit the “Best Accretion Model” of Lynden-Bell. For Leo II, IC 1613, and Phoenix we find similar accretion parameters for the CEM even though they all have different effective yields, masses, star formation histories, and morphologies. We suggest that the dynamical history of a galaxy is reflected in the MDF, where broad MDFs are seen in galaxies that have chemically evolved in relative isolation and narrowly peaked MDFs are seen in galaxies that have experienced more complicated dynamical interactions concurrent with their chemical evolution. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is

  17. Vicinal 1H-1H NMR coupling constants from density functional theory as reliable tools for stereochemical analysis of highly flexible multichiral center molecules.

    PubMed

    López-Vallejo, Fabian; Fragoso-Serrano, Mabel; Suárez-Ortiz, Gloria Alejandra; Hernández-Rojas, Adriana C; Cerda-García-Rojas, Carlos M; Pereda-Miranda, Rogelio

    2011-08-05

    A protocol for stereochemical analysis, based on the systematic comparison between theoretical and experimental vicinal (1)H-(1)H NMR coupling constants, was developed and applied to a series of flexible compounds (1-8) derived from the 6-heptenyl-5,6-dihydro-2H-pyran-2-one framework. The method included a broad conformational search, followed by geometry optimization at the DFT B3LYP/DGDZVP level, calculation of the vibrational frequencies, thermochemical parameters, magnetic shielding tensors, and the total NMR spin-spin coupling constants. Three scaling factors, depending on the carbon atom hybridizations, were found for the (1)H-C-C-(1)H vicinal coupling constants: f((sp3)-(sp3)) = 0.910, f((sp3)-(sp2)) = 0.929, and f((sp2)-(sp2))= 0.977. A remarkable correlation between the theoretical (J(pre)) and experimental (1)H-(1)H NMR (J(exp)) coupling constants for spicigerolide (1), a cytotoxic natural product, and some of its synthetic stereoisomers (2-4) demonstrated the predictive value of this approach for the stereochemical assignment of highly flexible compounds containing multiple chiral centers. The stereochemistry of two natural 6-heptenyl-5,6-dihydro-2H-pyran-2-ones (14 and 15) containing diverse functional groups in the heptenyl side chain was also analyzed by application of this combined theoretical and experimental approach, confirming its reliability. Additionally, a geometrical analysis for the conformations of 1-8 revealed that weak hydrogen bonds substantially guide the conformational behavior of the tetraacyloxy-6-heptenyl-2H-pyran-2-ones.

  18. Relationship Between Nutrient Enrichment and Benthic Function: Local Effects and Spatial Patterns

    EPA Science Inventory

    Eutrophication-induced changes to benthic structure and function are problems of enormous ecological and economic significance. Understanding the relationships between nutrient enrichment and effects, modifying factors such as localized transport time, and symptoms of eutrophica...

  19. Dielectric Constant of Suspensions

    NASA Astrophysics Data System (ADS)

    Mendelson, Kenneth S.; Ackmann, James J.

    1997-03-01

    We have used a finite element method to calculate the dielectric constant of a cubic array of spheres. Extensive calculations support preliminary conclusions reported previously (K. Mendelson and J. Ackmann, Bull. Am. Phys. Soc. 41), 657 (1996).. At frequencies below 100 kHz the real part of the dielectric constant (ɛ') shows oscillations as a function of the volume fraction of suspension. These oscillations disappear at low conductivities of the suspending fluid. Measurements of the dielectric constant (J. Ackmann, et al., Ann. Biomed. Eng. 24), 58 (1996). (H. Fricke and H. Curtis, J. Phys. Chem. 41), 729 (1937). are not sufficiently sensitive to show oscillations but appear to be consistent with the theoretical results.

  20. Reconstruction of the Orientation Distribution Function in Single and Multiple Shell Q-Ball Imaging within Constant Solid Angle

    PubMed Central

    Aganj, Iman; Lenglet, Christophe; Sapiro, Guillermo; Yacoub, Essa; Ugurbil, Kamil; Harel, Noam

    2010-01-01

    Q-ball imaging (QBI) is a high angular resolution diffusion imaging (HARDI) technique which has been proven very successful in resolving multiple intravoxel fiber orientations in MR images. The standard computation of the orientation distribution function (ODF, the probability of diffusion in a given direction) from q-ball data uses linear radial projection, neglecting the change in the volume element along each direction. This results in spherical distributions that are different from the true ODFs. For instance, they are neither normalized nor as sharp as expected, and generally require post-processing, such as artificial sharpening. In this paper, a new technique is proposed that, by considering the solid angle factor, uses the mathematically correct definition of the ODF and results in a dimensionless and normalized ODF expression. Our model is flexible enough so that ODFs can be estimated either from single q-shell datasets, or by exploiting the greater information available from multiple q-shell acquisitions. We show that the latter can be achieved by using a more accurate multi-exponential model for the diffusion signal. The improved performance of the proposed method is demonstrated on artificial examples and high-resolution HARDI data acquired on a 7T magnet. PMID:20535807

  1. γδTCR immunoglobulin constant region domain exchange in human αβTCRs improves TCR pairing without altering TCR gene-modified T cell function.

    PubMed

    Tao, Changli; Shao, Hongwei; Zhang, Wenfeng; Bo, Huaben; Wu, Fenglin; Shen, Han; Huang, Shulin

    2017-02-15

    The adoptive genetic transfer of T cell receptors (TCRs) has been shown to be overall feasible and offer clinical potential as a treatment for different types of cancer. However, this promising clinical approach is limited by the serious potential consequence that exogenous TCR mispairing with endogenous TCR chains may lead to the risk of self-reactivity. In the present study, domain‑exchange and three‑dimensional modeling strategies were used to create a set of chimeric TCR variants, which were used to exchange the partial or complete constant region of αβTCR with corresponding γδTCR domains. The expression, assembly and function of the chimeric TCR variants were examined in Jurkat T cells and peripheral mononuclear blood cells (PBMCs). Genetically‑encoded chimeras were fused with a pair of fluorescent proteins (ECFP/EYFP) to monitor expression and the pairing between chimeric TCRα chains and TCRβ chains. The fluorescence energy transfer based on confocal laser scanning microscopy showed that the introduction of γδTCR constant sequences into the αβTCR did not result in a global reduction of mispairing with endogenous TCR. However, the TCR harboring the immunoglobulin‑like domain of the γδTCR constant region (i.e., TCR∆IgC), showed a higher expression and preferential pairing, compared with wild‑type (wt)TCR. The function analysis showed that TCR∆IgC exhibited the same levels of interferon-γ production and cytotoxic activity, compared with wtTCR. Furthermore, these modified TCR-transduced T cells retained the classic human leukocyte antigen restriction of the original TCR. The other two chimeric TCRs, had either exchange of the cp+tm+ic domain or exchange of the whole C domain (Fig. 1). Ultimately, exchange of these domains demonstrated defective function in the transduced T cells. Taken together, these findings may provide further understanding of the γδTCR constant domain with implications for the improvement of TCR gene transfer

  2. EVALUATION OF ANATOMICAL INTEGRITY USING ULTRASOUND EXAMINATION, AND FUNCTIONAL INTEGRITY USING THE CONSTANT & MURLEY SCORE, OF THE ROTATOR CUFF FOLLOWING ARTHROSCOPIC REPAIR

    PubMed Central

    Godinho, Glaydson Gomes; França, Flavio de Oliveira; Alves, Freitas José Marcio; Watanabe, Fábio Nagato; Nobre, Leonardo Oliveira; De Almeida Neto, Manoel Augusto; Mendes Da Silva, Marcos André

    2015-01-01

    Objective: To evaluate the functional and anatomical results from surgical treatment via arthroscopy in cases of complete rupture of the rotator cuff, using ultrasound images and the Constant and Murley functional index to investigate the correlation between them. Methods: 100 patients (110 shoulders) were evaluated. The mean follow-up was 48.8 ± 33.28 months (12 to 141 months). The mean age was 60.25 ± 10.09 (36 to 81 years). Rupture of the supraspinal tendon alone occurred in 85 cases (77%), and in association with the infraspinatus in 20 cases (18%) and subscapularis in four shoulders (4%). An association of supraspinatus, infraspinatus and subscapularis lesions was found in one shoulder (1%). The lesions were classified according to DeOrio and Cofield scores as small/medium in 85 shoulders (77%) and large/extensive in 25 (23%). The clinical results were assessed in accordance with the Constant and Murley criteria. The ultrasound results relate to reports issued by different radiologists. Statistical analysis was carried out using the chi-square test, Fisher's exact test, Student's t test, Pearson's correlation, Kruskal-Wallis correlation and logistic regression (significance: p < 0.05). Results: The mean Constant evaluation was 85.3 ± 10.06 in the normal shoulders and 83.96 ± 8.67 in the operated shoulders (p = 0.224). Excellent and good results were found in 74 shoulders (67%), satisfactory and moderate results in 32 (29%) and poor results in four (4%). The ultrasound evaluation showed 38 shoulders with re-rupture (35%) and absence of rupture in 71 (65%). Among the 74 shoulders (67%) with excellent/good results, 22 (30%) presented re-rupture in the ultrasound report (p = 0.294). Among the four shoulders (4%) with poor results, two (50%) presented reports of intact tendons (p = 0.294). Conclusion: There was no statistically valid correlation between the ultrasound diagnosis and the clinical evaluation of results among the patients who underwent arthroscopic

  3. Adsorption energies of mercury-containing species on CaO and temperature effects on equilibrium constants predicted by density functional theory calculations.

    PubMed

    Kim, Bo Gyeong; Li, Xinxin; Blowers, Paul

    2009-03-03

    The adsorption of Hg, HgCl, and HgCl2 on the CaO surface was investigated theoretically so the fundamental interactions between Hg species and this potential sorbent can be explored. Surface models of a 4 x 4 x 2 cluster, a 5 x 5 x 2 cluster, and a periodic structure using density functional theory calculations with LDA/PWC and GGA/BLYP functionals, as employed in the present work, offer a useful description for the thermodynamic properties of adsorption on metal oxides. The effect of temperature on the equilibrium constant for the adsorption of mercury-containing species on the CaO (0 0 1) surface was investigated with GGA/BLYP calculations in the temperature range of 250-600 K. Results show that, at low coverage of elemental mercury, adsorption on the surface is physisorption while the two forms of oxidized mercury adsorption undergo stronger adsorption. The adsorption energies decrease with increasing coverage for elemental mercury on the surfaces. The chlorine atom enhances the adsorption capacity and adsorbs mercury to the CaO surface more strongly. The adsorption energy is changed as the oxidation state varies, and the equilibrium constant decreases as the temperature increases, in good agreement with data for exothermic adsorption systems.

  4. Change in blood coagulation indices as a function of the incubation period of plasma in a constant magnetic field. [considering heparin tolerance and recalcification

    NASA Technical Reports Server (NTRS)

    Yepishina, S. G.

    1974-01-01

    The influence of a constant magnetic field (CMF) with a strength of 250 and 2500 oersteds on the recalcification reaction and the tolerance of plasma to heparin was studied as a function of the exposure time of the plasma to the CMF. The maximum and reliable change in the activation of the coagulatory system of the blood was observed after a 20-hour incubation of the plasma in a CMF. As the exposure time increased, the recalcification reaction changed insigificantly; the difference between the mean arithmetic of the experiment and control values was not statistically reliable. The tolerance of the plasma to heparin as a function of the exposure time to the CMF of the plasma was considerably modified, an was statistically reliable.

  5. Uncertainty in measurement: a review of monte carlo simulation using microsoft excel for the calculation of uncertainties through functional relationships, including uncertainties in empirically derived constants.

    PubMed

    Farrance, Ian; Frenkel, Robert

    2014-02-01

    The Guide to the Expression of Uncertainty in Measurement (usually referred to as the GUM) provides the basic framework for evaluating uncertainty in measurement. The GUM however does not always provide clearly identifiable procedures suitable for medical laboratory applications, particularly when internal quality control (IQC) is used to derive most of the uncertainty estimates. The GUM modelling approach requires advanced mathematical skills for many of its procedures, but Monte Carlo simulation (MCS) can be used as an alternative for many medical laboratory applications. In particular, calculations for determining how uncertainties in the input quantities to a functional relationship propagate through to the output can be accomplished using a readily available spreadsheet such as Microsoft Excel. The MCS procedure uses algorithmically generated pseudo-random numbers which are then forced to follow a prescribed probability distribution. When IQC data provide the uncertainty estimates the normal (Gaussian) distribution is generally considered appropriate, but MCS is by no means restricted to this particular case. With input variations simulated by random numbers, the functional relationship then provides the corresponding variations in the output in a manner which also provides its probability distribution. The MCS procedure thus provides output uncertainty estimates without the need for the differential equations associated with GUM modelling. The aim of this article is to demonstrate the ease with which Microsoft Excel (or a similar spreadsheet) can be used to provide an uncertainty estimate for measurands derived through a functional relationship. In addition, we also consider the relatively common situation where an empirically derived formula includes one or more 'constants', each of which has an empirically derived numerical value. Such empirically derived 'constants' must also have associated uncertainties which propagate through the functional relationship

  6. Extension of local-type inequality for the higher order correlation functions

    SciTech Connect

    Suyama, Teruaki; Yokoyama, Shuichiro E-mail: shu@a.phys.nagoya-u.ac.jp

    2011-07-01

    For the local-type primordial perturbation, it is known that there is an inequality between the bispectrum and the trispectrum. By using the diagrammatic method, we develop a general formalism to systematically construct the similar inequalities up to any order correlation function. As an application, we explicitly derive all the inequalities up to six and eight-point functions.

  7. Use of localized performance-based functions for the specification and correction of hybrid imaging systems

    NASA Astrophysics Data System (ADS)

    Lisson, Jerold B.; Mounts, Darryl I.; Fehniger, Michael J.

    1992-08-01

    Localized wavefront performance analysis (LWPA) is a system that allows the full utilization of the system optical transfer function (OTF) for the specification and acceptance of hybrid imaging systems. We show that LWPA dictates the correction of wavefront errors with the greatest impact on critical imaging spatial frequencies. This is accomplished by the generation of an imaging performance map-analogous to a map of the optic pupil error-using a local OTF. The resulting performance map a function of transfer function spatial frequency is directly relatable to the primary viewing condition of the end-user. In addition to optimizing quality for the viewer it will be seen that the system has the potential for an improved matching of the optical and electronic bandpass of the imager and for the development of more realistic acceptance specifications. 1. LOCAL WAVEFRONT PERFORMANCE ANALYSIS The LWPA system generates a local optical quality factor (LOQF) in the form of a map analogous to that used for the presentation and evaluation of wavefront errors. In conjunction with the local phase transfer function (LPTF) it can be used for maximally efficient specification and correction of imaging system pupil errors. The LOQF and LPTF are respectively equivalent to the global modulation transfer function (MTF) and phase transfer function (PTF) parts of the OTF. The LPTF is related to difference of the average of the errors in separated regions of the pupil. Figure

  8. Nocturnal illumination maintains reproductive function and simulates the period-lengthening effect of constant light in the mature male Djungarian hamster (Phodopus sungorus)

    NASA Technical Reports Server (NTRS)

    Ferraro, J. S.

    1990-01-01

    Mature male Djungarian hamsters (Phodopus sungorus) were placed in individual light-tight, sound attenuated chambers and exposed to one of four lighting conditions for a duration of approximately seven weeks. The four lighting conditions were: constant light (LL); constant dark (DD); feedback lighting (LDFB; a condition that illuminates the cage in response to locomotor activity); or a feedback lighting neighbor control (LDFB NC; the animal receives the same light pattern as a paired animal in feedback lighting, but has no control over it). Exposure of hamsters to LL or LDFB produced significantly and similarly longer free-running periods of the locomotor activity rhythm than exposure of animals to DD. Hamsters exposed to LDFB NC did not free-run or entrain, but rather displayed "relative coordination". The paired testes and sex accessory glands weights suggest that in the Djungarian hamster, LL and LDFB exposed animals maintained reproductive function, whereas DD exposed animals did not. Animals exposed to LDFB NC had intermediate paired testes weights. Since several previous studies have demonstrated that short pulses of light, which are coincident with the subjective night, are photostimulatory, it is not surprising that LDFB maintained reproductive function in the mature Djungarian hamster. Feedback lighting, however, has been shown to be an insufficient stimulus to maintain reproductive function of mature male and female Syrian hamsters, and to the reproductive maturation of immature Djungarian hamsters. The results suggest that there may be slight, but significant differences in the way these two species interpret photoperiod, as well as a developmental change in the photoperiodic response of Djungarian hamsters.

  9. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

    SciTech Connect

    Ponomarenko, Natalia; Belogurov, Alexey Jr; Fedorova, Olga S.; Dubina, Michael; Golovin, Andrey; Lamzin, Victor; Makarov, Alexander A.; Wilmanns, Matthias

    2014-03-01

    Catalytic antibody variants with κ and λ light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates. The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the V{sub L} and V{sub H} domains. These V{sub L}/V{sub H} domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.

  10. The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Sargolzaei, M.; Afshar, M.; Sadeghi, M. S.; Kavee, M.

    2014-07-01

    In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu--Ala-Lys+ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (p K a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic p K a of lysine amino acid.

  11. Electron localization function in full-potential representation for crystalline materials.

    PubMed

    Ormeci, A; Rosner, H; Wagner, F R; Kohout, M; Grin, Yu

    2006-01-26

    The electron localization function (ELF) is implemented in the first-principles, all-electron, full-potential local orbital method. This full-potential implementation increases the accuracy with which the ELF can be computed for crystalline materials. Some representative results obtained are presented and compared with the results of other methods. Although for crystal structures with directed bonding only minor differences are found, in simple elemental metals, there are differences in the valence region, which give rise to different ELF topologies.

  12. Local Release of Highly Loaded Antibodies from Functionalized Nanoporous Support for Cancer Immunotherapy

    SciTech Connect

    Lei, Chenghong; Liu, P.; Chen, Baowei; Mao, Yumeng; Engelmann, Heather E.; Shin, Yongsoon; Jaffar, Jade; Hellstrom, Ingegerd; Liu, Jun; Hellstrom, Karl E.

    2010-05-26

    We report that antibodies can be loaded in functionalized mesoporous silica (FMS) with super-high density to provide long-lasting local release at a given site. Preliminary data indicate that FMS-antibody injected directly into a mouse melanoma induces a greater inhibition of tumor growth than seen in various controls, including the antibody injected intraperitoneally. Our findings introduce a novel approach for local delivery of therapeutically active proteins to tumors and potentially, other diseases.

  13. An analysis through order variant Planck's constant over 2pi(2) of a surface hopping expansion of the nonadiabatic wave function.

    PubMed

    Herman, Michael F; Wu, Yinghua

    2008-03-21

    It is shown that a surface hopping expansion of the semiclassical wave function formally satisfies the time independent Schrodinger equation for many-state, multidimensional problems. This wave function includes terms involving hops between different adiabatic quantum states as well as momentum changes without change of state at each point along classical trajectories. The single-state momentum changes correct for the order variant Planck's constant over 2pi(2) errors due to the semiclassical approximation that are present even in single surface problems. A prescription is provided for the direction of this momentum change and the amplitude associated with it. The direction of the momentum change for energy conserving hops between adiabatic states is required to be in the direction of the nonadiabatic coupling vector. The magnitude of the posthop momentum in this direction is determined by the energy, but the sign is not. Hops with both signs of this momentum component are required in order for the wave function to formally satisfy the Schrodinger equation. Numerical results are presented which illustrate how the surface hopping expansion can be implemented and the accuracy that can be obtained.

  14. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

    PubMed Central

    Ponomarenko, Natalia; Chatziefthimiou, Spyros D.; Kurkova, Inna; Mokrushina, Yuliana; Mokrushina, Yuliana; Stepanova, Anastasiya; Smirnov, Ivan; Avakyan, Marat; Bobik, Tatyana; Mamedov, Azad; Mitkevich, Vladimir; Belogurov, Alexey; Fedorova, Olga S.; Dubina, Michael; Golovin, Andrey; Lamzin, Victor; Friboulet, Alain; Makarov, Alexander A.; Wilmanns, Matthias; Gabibov, Alexander

    2014-01-01

    The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophos­phate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions. PMID:24598740

  15. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody.

    PubMed

    Ponomarenko, Natalia; Chatziefthimiou, Spyros D; Kurkova, Inna; Mokrushina, Yuliana; Mokrushina, Yuliana; Stepanova, Anastasiya; Smirnov, Ivan; Avakyan, Marat; Bobik, Tatyana; Mamedov, Azad; Mitkevich, Vladimir; Belogurov, Alexey; Fedorova, Olga S; Dubina, Michael; Golovin, Andrey; Lamzin, Victor; Friboulet, Alain; Makarov, Alexander A; Wilmanns, Matthias; Gabibov, Alexander

    2014-03-01

    The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.

  16. Analysis of agonism and inverse agonism in functional assays with constitutive activity: estimation of orthosteric ligand affinity constants for active and inactive receptor states.

    PubMed

    Ehlert, Frederick J; Suga, Hinako; Griffin, Michael T

    2011-08-01

    We describe a modification of receptor theory for the estimation of observed affinities (K(obs)) and relative efficacies of orthosteric ligands in functional assays that exhibit constitutive activity. Our theory includes parameters for the fractions of the occupied receptor population in the active (intrinsic efficacy, ε) and inactive (ε(i)) states and analogous parameters for the fractions of the free receptor population in the active (ε(sys)) and inactive (ε(i-sys)) states. The total stimulus represents the summation of the active states of the free and occupied receptor populations. A modified operational model is developed that expresses the response as a logistic function of the total stimulus. This function includes the standard parameters related to affinity and efficacy (K(obs) and τ) as well as a parameter proportional to the activity of the free receptor complex, τ(sys). Two related parameters are proportional to the fraction of the free (τ(i-sys)) and occupied (τ(i)) receptor populations in the inactive state. We show that the estimates of the affinity constants of orthosteric ligands for the active (K(b)) and inactive (K(a)) states of the receptor are equivalent to τK(obs)/τ(sys) and τ(i)K(obs)/τ(i-sys), respectively. We verify our method with computer simulation techniques and apply it to the analysis of M(2) and M(3) muscarinic receptors. Our method is applicable in the analysis of ligand bias in drug discovery programs.

  17. Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology.

    PubMed

    Sommer, Felix; Bäckhed, Fredrik

    2016-05-01

    Interactions between the host and its associated microbiota differ spatially and the local cross talk determines organ function and physiology. Animals and their organs are not uniform but contain several functional and cellular compartments and gradients. In the intestinal tract, different parts of the gut carry out different functions, tissue structure varies accordingly, epithelial cells are differentially distributed and gradients exist for several physicochemical parameters such as nutrients, pH, or oxygen. Consequently, the microbiota composition also differs along the length of the gut, but also between lumen and mucosa of the same intestinal segment, and even along the crypt-villus axis in the epithelium. Thus, host-microbiota interactions are highly site-specific and the local cross talk determines intestinal function and physiology. Here we review recent advances in our understanding of site-specific host-microbiota interactions and discuss their functional relevance for host physiology.

  18. Quantifying local exciton, charge resonance, and multiexciton character in correlated wave functions of multichromophoric systems

    SciTech Connect

    Casanova, David; Krylov, Anna I.

    2016-01-07

    A new method for quantifying the contributions of local excitation, charge resonance, and multiexciton configurations in correlated wave functions of multichromophoric systems is presented. The approach relies on fragment-localized orbitals and employs spin correlators. Its utility is illustrated by calculations on model clusters of hydrogen, ethylene, and tetracene molecules using adiabatic restricted-active-space configuration interaction wave functions. In addition to the wave function analysis, this approach provides a basis for a simple state-specific energy correction accounting for insufficient description of electron correlation. The decomposition scheme also allows one to compute energies of the diabatic states of the local excitonic, charge-resonance, and multi-excitonic character. The new method provides insight into electronic structure of multichromophoric systems and delivers valuable reference data for validating excitonic models.

  19. Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests.

    PubMed

    Wang, Xugao; Wiegand, Thorsten; Swenson, Nathan G; Wolf, Amy T; Howe, Robert W; Hao, Zhanqing; Lin, Fei; Ye, Ji; Yuan, Zuoqiang

    2015-04-01

    Although trait information has been widely used to explore underlying mechanisms of forest community structure, most studies have focused on local patterns of phylogenetic or functional alpha diversity. Investigations of functional beta diversity, on the other hand, have not been conducted at local scales in a spatially explicit way. In this study, we provide a powerful methodology based on recent advances in spatial point pattern analysis using fully mapped data of large and small trees in two large temperate forest plots. This approach allowed us to assess the relative importance of different ecological processes and mechanisms for explaining patterns of local phylogenetic and functional beta diversity. For both forests and size classes, we found a clear hierarchy of scales: habitat filtering accounted for patterns of phylogenetic and functional beta diversity at larger distances (150-250 m), dispersal limitation accounted for the observed decline in beta diversity at distances below 150 m, and species interactions explained small departures from functional and phylogenetic beta diversity at the immediate plant-neighborhood scale (below 20 m). Thus, both habitat filtering and dispersal limitation influenced the observed patterns in phylogenetic and functional beta diversity at local scales. This result contrasts with a previous study from the same forests, where dispersal limitation alone approximated the observed species beta diversity for distances up to 250 m. In addition, species interactions were relatively unimportant for predicting phylogenetic and functional beta diversity. Our analysis suggests that phylogenetic and functional beta diversity can provide insights into the mechanisms of local community assembly that are missed by studies focusing exclusively on species beta diversity.

  20. Subcellular Localization of RPB5-Mediating Protein and Its Putative Functional Partner

    PubMed Central

    Delgermaa, Luvsanjav; Hayashi, Naoyuki; Dorjsuren, Dorjbal; Nomura, Takahiro; Thuy, Le Thi-Thu; Murakami, Seishi

    2004-01-01

    We previously identified a novel cellular protein, RPB5-mediating protein (RMP), that retains corepressor activity and functionally antagonizes transcriptional modulation via hepatitis B virus X protein. The subcellular localization of RMP was examined using green fluorescent protein-fused protein forms. We found that a nuclear localization signal (NLS) and a coiled-coil (CC) domain functioning as a cytoplasmic localization signal (CLS) are important for the subcellular localization of RMP. The CLS apparently acts dominantly, since RMP was mostly localized in the cytoplasm with weak and diffuse signals in the nucleus, and the NLS was indispensable for the nuclear localization of RMP only in the absence of the CLS. Using a yeast two-hybrid method, we isolated a putative corepressor, DNA methyltransferase 1-associating protein (DMAP1), which was found to bind to the CC domain of RMP. DMAP1 facilitated the nuclear localization of RMP and the corepressor activity of RMP in a dose-dependent manner by interacting with the CC domain of RMP. These results are discussed in light of a recent paper showing a novel evolutionarily conserved role of URI in the TOR signaling pathway. PMID:15367675

  1. Some Critical Observations of the Test Information Function as a Measure of Local Accuracy in Ability Estimation.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    1994-01-01

    Using the constant information model, constant amounts of test information, and a finite interval of ability, simulated data were produced for 8 ability levels and 20 numbers of test items. Analyses suggest that it is desirable to consider modifying test information functions when they measure accuracy in ability estimation. (SLD)

  2. Percolation with Constant Freezing

    NASA Astrophysics Data System (ADS)

    Mottram, Edward

    2014-06-01

    We introduce and study a model of percolation with constant freezing ( PCF) where edges open at constant rate , and clusters freeze at rate independently of their size. Our main result is that the infinite volume process can be constructed on any amenable vertex transitive graph. This is in sharp contrast to models of percolation with freezing previously introduced, where the limit is known not to exist. Our interest is in the study of the percolative properties of the final configuration as a function of . We also obtain more precise results in the case of trees. Surprisingly the algebraic exponent for the cluster size depends on the degree, suggesting that there is no lower critical dimension for the model. Moreover, even for , it is shown that finite clusters have algebraic tail decay, which is a signature of self organised criticality. Partial results are obtained on , and many open questions are discussed.

  3. The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons

    PubMed Central

    Holt, Christine E.; Schuman, Erin M.

    2013-01-01

    The elaborate morphology of neurons together with the information processing that occurs in remote dendritic and axonal compartments makes the use of decentralized cell biological machines necessary. Recent years have witnessed a revolution in our understanding of signaling in neuronal compartments and the manifold functions of a variety of RNA molecules that regulate protein translation and other cellular functions. Here we discuss the view that mRNA localization and RNA-regulated and localized translation underlie many fundamental neuronal processes and highlight key issues for future experiments. PMID:24183017

  4. Si dielectric function in a local basis representation: Optical properties, local field effects, excitons, and stopping power

    NASA Astrophysics Data System (ADS)

    Gómez, M.; González, P.; Ortega, J.; Flores, F.

    2014-11-01

    An atomiclike basis representation is used to analyze the dielectric function ɛ (q ⃗+G ⃗,q ⃗+G⃗';ω ) of Si. First, we show that a s p3d5 local basis set yields good results for the electronic band structure of this crystal and, then, we analyze the Si optical properties including local field and excitonic effects. In our formulation, we follow Hanke and Sham [W. Hanke and L. J. Sham, Phys. Rev. B 12, 4501 (1975), 10.1103/PhysRevB.12.4501; Phys. Rev. B 21, 4656 (1980), 10.1103/PhysRevB.21.4656], and introduce excitonic effects using a many-body formulation that incorporates a static screened electron-hole interaction. Dynamical effects in this interaction are also analyzed and shown to introduce non-negligible corrections in the optical spectrum. Our results are found in reasonable agreement with the experimental evidence and with other theoretical results calculated with the computationally more demanding plane-wave representation. Finally, calculations for the stopping power of Si are also presented.

  5. Dual effect of local anesthetics on the function of excitable rod outer segment disk membrane

    SciTech Connect

    Mashimo, T.; Abe, K.; Yoshiya, I.

    1986-04-01

    The effects of local anesthetics and a divalent cation, Ca2+, on the function of rhodopsin were estimated from the measurements of light-induced proton uptake. The light-induced proton uptake by rhodopsin in the rod outer segment disk membrane was enhanced at lower pH (4) but depressed at higher pHs (6 to 8) by the tertiary amine local anesthetics lidocaine, bupivacaine, tetracaine, and dibucaine. The order of local anesthetic-induced depression of the proton uptake followed that of their clinical anesthetic potencies. The depression of the proton uptake versus the concentration of the uncharged form of local anesthetic nearly describes the same curve for small and large dose of added anesthetic. Furthermore, a neutral local anesthetic, benzocaine, depressed the proton uptake at all pHs between 4 and 7. These results indicate that the depression of the proton uptake is due to the effect of only the uncharged form. It is hypothesized that the uncharged form of local anesthetics interacts hydrophobically with the rhodopsin in the disk membrane. The dual effect of local anesthetics on the proton uptake, on the other hand, suggests that the activation of the function of rhodopsin may be caused by the charged form. There was no significant change in the light-induced proton uptake by rhodopsin when 1 mM of Ca2+ was introduced into the disk membrane at varying pHs in the absence or presence of local anesthetics. This fact indicates that Ca2+ ion does not influence the diprotonating process of metarhodopsin; neither does it interfere with the local anesthetic-induced changes in the rhodopsin molecule.

  6. Localization of function in anterior cingulate cortex: from psychosurgery to functional neuroimaging.

    PubMed

    Gasquoine, Philip Gerard

    2013-03-01

    Early localizationists linked anterior cingulate cortex (ACC: Brodmann's area 24 and adjacent regions) with emotional behavior, paving the way for bilateral cingulotomy psychosurgery in severe, treatment resistant, cases of obsessive-compulsive disorder, chronic pain, depression, and substance abuse. Neuropsychological follow-up of such cases demonstrated executive function impairment. Abnormal neuroimaged activity in ACC has been found in many psychiatric conditions, including obsessive-compulsive disorder, chronic pain, substance abuse, and schizophrenia. With healthy participants, increased neuroimaged activity in ACC has been linked with challenging executive function tasks, homeostatically incongruous physical states, and the encoding of the pleasant/averseness of stimuli. There is disagreement on the cortical substrate subsumed by the term ACC, the existence of functionally distinct ACC subregions (e.g., dorsal: cognitive vs. ventral: emotion), and the interpretation of functional neuroimaging studies. Synthesis of neuropsychological and functional neuroimaging studies suggests ACC contributes to behavior by modifying responses especially in reaction to challenging cognitive and physical states that require additional effortful cognitive control. This is accomplished by monitoring the emotional salience of stimuli, exerting control over the autonomic nervous system, and modulating cognitive activity.

  7. Static dielectric constants and molecular dipole distributions of liquid water and ice-Ih investigated by the PAW-PBE exchange-correlation functional.

    PubMed

    Rusnak, Andrew J; Pinnick, Eric R; Calderon, Camilo E; Wang, Feng

    2012-07-21

    The static dielectric constants, ε(s), of ice-Ih and liquid water were calculated using density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the projector-augmented-wave (PAW) approach. Proton disordered ice configurations and uncorrelated liquid configurations were sampled with the electrostatic switching method using force fields specially designed to facilitate the ab initio free energy perturbation calculations. Our results indicate that PAW-PBE underestimates the ε(s) of both ice-Ih and liquid water but predicts the ratio of ice and water ε(s) in good agreement with experimental measurements. PAW-PBE gives average water dipole moments of 2.50 D in ice-Ih and 2.48 D in the liquid. Our results show that the fixed-charge water models developed by adaptive force matching can reproduce the PAW-PBE dipole moments with an error of approximately 5%. The ice and liquid models created in this work have polarizabilities of 1.32 Å(3) and 1.30 Å(3), respectively, along the HOH bisector direction.

  8. Microscopic description of large-amplitude shape-mixing dynamics with local QRPA inertial functions

    SciTech Connect

    Hinohara, Nobuo; Yoshida, Kenichi; Nakatsukasa, Takashi; Sato, Koichi; Matsuo, Masayuki

    2011-05-06

    We introduce a microscopic approach to derive all the inertial functions in the five-dimensional quadrupole collective Hamiltonian. Local normal modes are evaluated on the constrained mean field in the quasiparticle random-phase approximation in order to derive the inertial functions. The collective Hamiltonians for neutron-rich Mg isotopes are determined with use of this approach, and the shape coexistence/mixing around the N = 20 region is analyzed.

  9. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A.

    PubMed

    Bateman, Nicholas W; Shoji, Yutaka; Conrads, Kelly A; Stroop, Kevin D; Hamilton, Chad A; Darcy, Kathleen M; Maxwell, George L; Risinger, John I; Conrads, Thomas P

    2016-01-01

    AT-rich interactive domain-containing protein 1A (ARID1A) is a recently identified nuclear tumor suppressor frequently altered in solid tumor malignancies. We have identified a bipartite-like nuclear localization sequence (NLS) that contributes to nuclear import of ARID1A not previously described. We functionally confirm activity using GFP constructs fused with wild-type or mutant NLS sequences. We further show that cyto-nuclear localized, bipartite NLS mutant ARID1A exhibits greater stability than nuclear-localized, wild-type ARID1A. Identification of this undescribed functional NLS within ARID1A contributes vital insights to rationalize the impact of ARID1A missense mutations observed in patient tumors.

  10. Gestalt Perception and Local-Global Processing in High-Functioning Autism

    ERIC Educational Resources Information Center

    Bolte, Sven; Holtmann, Martin; Poustka, Fritz; Scheurich, Armin; Schmidt, Lutz

    2007-01-01

    This study examined gestalt perception in high-functioning autism (HFA) and its relation to tasks indicative of local visual processing. Data on of gestalt perception, visual illusions (VI), hierarchical letters (HL), Block Design (BD) and the Embedded Figures Test (EFT) were collected in adult males with HFA, schizophrenia, depression and…

  11. [Progress of clinical application of functional MRI in the localization of brain language area].

    PubMed

    Zhang, Nan; Lu, Junfeng; Wu, Jinsong

    2016-02-01

    For surgical operation in the functional area in the brain, it's commonly demanded to resect the lesion to the maximal extent on the basis of preserve the normal neural function, thus the precise localization of functional area is extremely important. As for the advantages of being widely available, easy to grasp and non-invasive, the functional MRI (fMRI) has come into wide use, while the application of language fMRI is still in the initial stage. It's important to choose appropriate fMRI task according to the individual condition of the subject, the commonly-adopted tasks include verb generation, picture naming, word recognition, word generation, etc. However, the effectiveness of using fMRI to localize language area is not totally satisfactory, adopting multiple task is an effective approach to improve the sensitivity of this technique. The application of resting state fMRI in the localization of language area and the further research of the role of fMRI in localizing the Chinese language area are the important future directions.

  12. Independent component analysis of localized resting-state functional magnetic resonance imaging reveals specific motor subnetworks.

    PubMed

    Sohn, William Seunghyun; Yoo, Kwangsun; Jeong, Yong

    2012-01-01

    Recent studies have shown that blood oxygen level-dependent low-frequency (<0.1 Hz) fluctuations (LFFs) during a resting-state exhibit a high degree of correlation with other regions that share cognitive function. Initial studies of resting-state network mapping have focused primarily on major networks such as the default mode network, primary motor, somatosensory, visual, and auditory networks. However, more specific or subnetworks, including those associated with specific motor functions, have yet to be properly addressed. We performed independent component analysis (ICA) in a specific target region of the brain, a process we name, "localized ICA." We demonstrated that when ICA is applied to localized fMRI data, it can be used to distinguish resting-state LFFs associated with specific motor functions (e.g., finger tapping, foot movement, or bilateral lip pulsing) in the primary motor cortex. These ICA components generated from localized data can then be used as functional regions of interest to map whole-brain connectivity. In addition, this method can be used to visualize inter-regional connectivity by expanding the localized region and identifying components that show connectivity between the two regions.

  13. Functional Hemispheric Differences for the Categorization of Global and Local Information in Naturalistic Stimuli

    ERIC Educational Resources Information Center

    Hubner, Ronald; Studer, Tobias

    2009-01-01

    Up to now functional hemispheric asymmetries for global/local processing have mainly been investigated with hierarchical letters as stimuli. In the present study, three experiments were conducted to examine whether corresponding visual-field (VF) effects can also be obtained with more naturalistic stimuli. To this end, images of animals with a…

  14. Local ζ -functions, stress-energy tensor, field fluctuations, and all that, in curved static spacetime

    NASA Astrophysics Data System (ADS)

    Moretti, Valter

    This is a quick review on some technology concerning the local zeta function applied to Quantum Field Theory in curved static (thermal) spacetime to regularize the stress energy tensor and the field fluctuations. Dedicated to Prof. Emilio Elizalde on the occasion of his 60th birthday.

  15. Local sleep homeostasis in the avian brain: convergence of sleep function in mammals and birds?

    PubMed

    Lesku, John A; Vyssotski, Alexei L; Martinez-Gonzalez, Dolores; Wilzeck, Christiane; Rattenborg, Niels C

    2011-08-22

    The function of the brain activity that defines slow wave sleep (SWS) and rapid eye movement (REM) sleep in mammals is unknown. During SWS, the level of electroencephalogram slow wave activity (SWA or 0.5-4.5 Hz power density) increases and decreases as a function of prior time spent awake and asleep, respectively. Such dynamics occur in response to waking brain use, as SWA increases locally in brain regions used more extensively during prior wakefulness. Thus, SWA is thought to reflect homeostatically regulated processes potentially tied to maintaining optimal brain functioning. Interestingly, birds also engage in SWS and REM sleep, a similarity that arose via convergent evolution, as sleeping reptiles and amphibians do not show similar brain activity. Although birds deprived of sleep show global increases in SWA during subsequent sleep, it is unclear whether avian sleep is likewise regulated locally. Here, we provide, to our knowledge, the first electrophysiological evidence for local sleep homeostasis in the avian brain. After staying awake watching David Attenborough's The Life of Birds with only one eye, SWA and the slope of slow waves (a purported marker of synaptic strength) increased only in the hyperpallium--a primary visual processing region--neurologically connected to the stimulated eye. Asymmetries were specific to the hyperpallium, as the non-visual mesopallium showed a symmetric increase in SWA and wave slope. Thus, hypotheses for the function of mammalian SWS that rely on local sleep homeostasis may apply also to birds.

  16. Adding local components to global functions for continuous covariates in multivariable regression modeling.

    PubMed

    Binder, H; Sauerbrei, W

    2010-03-30

    When global techniques, based on fractional polynomials (FPs), are employed for modeling potentially nonlinear effects of several continuous covariates on a response, accessible model equations are obtained. However, local features might be missed. Therefore, a procedure is introduced, which systematically checks model fits, obtained by the multivariable fractional polynomial (MFP) approach, for overlooked local features. Statistically significant local polynomials are then parsimoniously added. This approach, called MFP + L, is seen to result in an effective control of the Type I error with respect to the addition of local components in a small simulation study with univariate and multivariable settings. Prediction performance is compared with that of a penalized regression spline technique. In a setting unfavorable for FPs, the latter outperforms the MFP approach, if there is much information in the data. However, the addition of local features reduces this performance difference. There is only a small detrimental effect in settings where the MFP approach performs better. In an application example with children's respiratory health data, fits from the spline-based approach indicate many local features, but MFP + L adds only few significant features, which seem to have good support in the data. The proposed approach may be expected to be superior in settings with local features, but retains the good properties of the MFP approach in a large number of settings where global functions are sufficient.

  17. Activity-Dependent Palmitoylation Controls SynDIG1 Stability, Localization, and Function

    PubMed Central

    Kaur, Inderpreet; Yarov-Yarovoy, Vladimir; Kirk, Lyndsey M.; Plambeck, Kristopher E.; Barragan, Eden V.; Ontiveros, Eric S.

    2016-01-01

    Synapses are specialized contacts between neurons. Synapse differentiation-induced gene I (SynDIG1) plays a critical role during synapse development to regulate AMPA receptor (AMPAR) and PSD-95 content at excitatory synapses. Palmitoylation regulates the localization and function of many synaptic proteins, including AMPARs and PSD-95. Here we show that SynDIG1 is palmitoylated, and investigate the effects of palmitoylation on SynDIG1 stability and localization. Structural modeling of SynDIG1 suggests that the membrane-associated region forms a three-helical bundle with two cysteine residues located at positions 191 and 192 in the juxta-transmembrane region exposed to the cytoplasm. Site-directed mutagenesis reveals that C191 and C192 are palmitoylated in heterologous cells and positively regulates dendritic targeting in neurons. Like PSD-95, activity blockade in a rat hippocampal slice culture increases SynDIG1 palmitoylation, which is consistent with our prior demonstration that SynDIG1 localization at synapses increases upon activity blockade. These data demonstrate that palmitoylation of SynDIG1 is regulated by neuronal activity, and plays a critical role in regulating its stability and subcellular localization, and thereby its function. SIGNIFICANCE STATEMENT Palmitoylation is a reversible post-translation modification that has recently been recognized as playing a critical role in the localization and function of many synaptic proteins. Here we show that activity-dependent palmitoylation of the atypical AMPA receptor auxiliary transmembrane protein SynDIG1 regulates its stability and localization at synapses to regulate function and synaptic strength. PMID:27445135

  18. Systematic offset of kV and MV localization systems as a function of gantry angle.

    PubMed

    Mullins, John P; Herman, Michael G

    2010-11-09

    Mechanical flex of the gantry and mounted imaging panels leads to systematic offsets in localization image isocenter as a function of gantry angle for linear accelerator-mounted image guidance systems. Subsequently, object positions obtained from localization radiographs may be offset, resulting in greater target positioning uncertainty. While current QA procedures measure kV/MV image agreement, these measurements do not provide insight to apparent isocenter position for either single imaging system as a function of gantry rotation. This study measures offset as a function of gantry angle in kV and MV imaging systems on four treatment machines to investigate the magnitude of systematic offsets and their reproducibility between systems and machines, as well as over time. It is shown that each machine and energy has a reproducible pattern of offset as a function of gantry angle that is independent of kV/MV agreement, and it varies by machine. kV and MV offset ranges are on the order of 1.5 mm in the R/L and A/P directions, and 0.5 mm in the S/I direction. Variability of kV-MV agreement is on the order of 0.7 mm. At certain angles, combinations of localization images could show a compounded offset of over 2 mm, exceeding the desired certainty threshold. Since these trends are persistent over time for each machine, online correction for image offsets as a function of gantry angle could improve the margin of positioning uncertainty.

  19. Local and Regional Determinants of an Uncommon Functional Group in Freshwater Lakes and Ponds

    PubMed Central

    McCann, Michael James

    2015-01-01

    A combination of local and regional factors and stochastic forces is expected to determine the occurrence of species and the structure of communities. However, in most cases, our understanding is incomplete, with large amounts of unexplained variation. Using functional groups rather than individual species may help explain the relationship between community composition and conditions. In this study, I used survey data from freshwater lakes and ponds to understand factors that determine the presence of the floating plant functional group in the northeast United States. Of the 176 water bodies surveyed, 104 (59.1%) did not contain any floating plant species. The occurrence of this functional group was largely determined by local abiotic conditions, which were spatially autocorrelated across the region. A model predicting the presence of the floating plant functional group performed similarly to the best species-specific models. Using a permutation test, I also found that the observed prevalence of floating plants is no different than expected by random assembly from a species pool of its size. These results suggest that the size of the species pool interacts with local conditions in determining the presence of a functional group. Nevertheless, a large amount of unexplained variation remains, attributable to either stochastic species occurrence or incomplete predictive models. The simple permutation approach in this study can be extended to test alternative models of community assembly. PMID:26121636

  20. Comparison of Local Information Indices Applied in Resting State Functional Brain Network Connectivity Prediction

    PubMed Central

    Cheng, Chen; Chen, Junjie; Cao, Xiaohua; Guo, Hao

    2016-01-01

    Anatomical distance has been widely used to predict functional connectivity because of the potential relationship between structural connectivity and functional connectivity. The basic implicit assumption of this method is “distance penalization.” But studies have shown that one-parameter model (anatomical distance) cannot account for the small-worldness, modularity, and degree distribution of normal human brain functional networks. Two local information indices–common neighbor (CN) and preferential attachment index (PA), are introduced into the prediction model as another parameter to emulate many key topological of brain functional networks in the previous study. In addition to these two indices, many other local information indices can be chosen for investigation. Different indices evaluate local similarity from different perspectives. Currently, we still have no idea about how to select local information indices to achieve higher predicted accuracy of functional connectivity. Here, seven local information indices are chosen, including CN, hub depressed index (HDI), hub promoted index (HPI), Leicht-Holme-Newman index (LHN-I), Sørensen index (SI), PA, and resource allocation index (RA). Statistical analyses were performed on eight network topological properties to evaluate the predictions. Analysis shows that different prediction models have different performances in terms of simulating topological properties and most of the predicted network properties are close to the real data. There are four topological properties whose average relative error is less than 5%, including characteristic path length, clustering coefficient, global efficiency, and local efficiency. CN model shows the most accurate predictions. Statistical analysis reveals that five properties within the CN-predicted network do not differ significantly from the real data (P > 0.05, false-discovery rate method corrected for seven comparisons). PA model shows the worst prediction performance

  1. Functional classification of protein 3D structures from predicted local interaction sites.

    PubMed

    Parasuram, Ramya; Lee, Joslynn S; Yin, Pengcheng; Somarowthu, Srinivas; Ondrechen, Mary Jo

    2010-12-01

    A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.

  2. On the regulation, function, and localization of the DNA-dependent ATPase PICH.

    PubMed

    Kaulich, Manuel; Cubizolles, Fabien; Nigg, Erich A

    2012-08-01

    The putative chromatin remodeling enzyme Plk1-interacting checkpoint helicase (PICH) was discovered as an interaction partner and substrate of the mitotic kinase Plk1. During mitosis PICH associates with centromeres and kinetochores and, most interestingly, constitutes a robust marker for ultrafine DNA bridges (UFBs) that connect separating chromatids in anaphase cells. The precise roles of PICH remain to be clarified. Here, we have used antibody microinjection and siRNA-rescue experiments to study PICH function and localization during M phase progression, with particular emphasis on the role of the predicted ATPase domain and the regulation of PICH localization by Plk1. We show that interference with PICH function results in chromatin bridge formation and micronucleation and that ATPase activity is critical for PICH function. Interestingly, an intact ATPase domain of PICH is required for prevention of chromatin bridge formation but not for UFB resolution, and quantitative analyses of UFB and chromatin bridge frequencies suggest that these structures are of different etiologies. We also show that the ATPase activity of PICH is required for temporal and spatial control of PICH localization to chromatin and that Plk1 likely controls PICH localization through phosphorylation of proteins distinct from PICH itself. This work strengthens the view that PICH is an important, Plk1-regulated enzyme, whose ATPase activity is essential for maintenance of genome integrity. Although not required for the spindle assembly checkpoint, PICH is clearly important for faithful chromosome segregation.

  3. Comparison of the influence of two different constant-rate infusions (dexmedetomidine versus morphine) on anaesthetic requirements, cardiopulmonary function and recovery quality in isoflurane anaesthetized horses.

    PubMed

    Gozalo-Marcilla, Miguel; Steblaj, Barbara; Schauvliege, Stijn; Duchateau, Luc; Gasthuys, Frank

    2013-12-01

    Twenty adult healthy horses undergoing elective surgery were involved in this prospective, blinded, clinical study. Horses were randomly allocated to receive a constant rate infusion (CRI) of morphine or dexmedetomidine. After induction, anaesthesia was maintained with isoflurane in oxygen/air and mechanical ventilation applied. The end-tidal isoflurane concentration (FÉISO) was initially set at 0.9% and adjusted by the anaesthetist, to maintain a light surgical plane of anaesthesia, according to an objective flow-chart. The cardiopulmonary function was only minimally different between groups and maintained within clinically normal ranges. Less ketamine was required, FÉISO was lower after 1h and fewer alterations in the anaesthetic depth were needed in horses receiving dexmedetomidine, with better recoveries. One horse receiving morphine developed post-operative colic and pulmonary oedema and two showed box-walking behaviour. This study showed that a dexmedetomidine CRI produced a more stable anaesthetic depth, reduced isoflurane requirements and better recoveries, without post-operative complications compared with a morphine CRI.

  4. Radical scavenging ability of gallic acid toward OH and OOH radicals. Reaction mechanism and rate constants from the density functional theory.

    PubMed

    Marino, Tiziana; Galano, Annia; Russo, Nino

    2014-09-04

    Gallic acid is a ubiquitous compound, widely distributed in the vegetal kingdom and frequently found in the human diet. In the present work, its primary antioxidant activity has been investigated using the density functional theory (DFT), and the quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA) protocol. It was found that gallic acid is a better antioxidant than the reference compound, Trolox, regardless of the polarity of the environment. In addition, gallic acid is predicted to be among the best peroxyl radical scavengers identified so far in nonpolar (lipid) media. This compound is capable of scavenging hydroxyl radicals at diffusion-limited rates, and hydroperoxyl radicals with rate constants in the order of 10(5) M(-1) s(-1). The deprotonation of gallic acid, in aqueous solution, is predicted to increase the protective action of this compound against oxidative stress. Gallic acid was also identified as a versatile scavenger, capable of rapidly deactivating a wide variety of reactive oxygen species (ROS) and reactive nitrogen species (RNS) via electron transfer at physiological pH.

  5. Non Lyapunov stability of a constant spatially developing 2-D gas flow

    NASA Astrophysics Data System (ADS)

    Balint, Agneta M.; Balint, Stefan; Tanasie, Loredana

    2017-01-01

    Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 2-D gas flow are analyzed in a particular phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the plane. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].

  6. Localization of electronic states in finite ladder models: Participation ratio and localization length as measures of the wave-function extension

    NASA Astrophysics Data System (ADS)

    Carrillo-Nuñez, H.; Schulz, Peter A.

    2008-12-01

    In this work we discuss and compare different definitions for localization of electronic states in low-dimensional systems. We choose a heuristic model for DNA-like molecules as a system prototype in order to establish ranges of equivalence for the localization length obtained from both the conductance and participation ratios. The results suggest also criteria to infer the extension of wave function in mesoscopic systems within the diffusive transport regime as complementary information to the localization length.

  7. Functional localization of a "Time Keeper" function separate from attentional resources and task strategy.

    PubMed

    Tracy, J I; Faro, S H; Mohamed, F B; Pinsk, M; Pinus, A

    2000-03-01

    The functional neuroanatomy of time estimation has not been well-documented. This research investigated the fMRI measured brain response to an explicit, prospective time interval production (TIP) task. The study tested for the presence of brain activity reflecting a primary time keeper function, distinct from the brain systems involved either in conscious strategies to monitor time or attentional resource and other cognitive processes to accomplish the task. In the TIP task participants were given a time interval and asked to indicate when it elapsed. Two control tasks (counting forwards, backwards) were administered, in addition to a dual task format of the TIP task. Whole brain images were collected at 1.5 Tesla. Analyses (n = 6) yielded a statistical parametric map (SPM ¿z¿) reflecting time keeping and not strategy (counting, number manipulation) or attention resource utilization. Additional SPM ¿z¿s involving activation associated with the accuracy and magnitude the of time estimation response are presented. Results revealed lateral cerebellar and inferior temporal lobe activation were associated with primary time keeping. Behavioral data provided evidence that the procedures for the explicit time judgements did not occur automatically and utilized controlled processes. Activation sites associated with accuracy, magnitude, and the dual task provided indications of the other structures involved in time estimation that implemented task components related to controlled processing. The data are consistent with prior proposals that the cerebellum is a repository of codes for time processing, but also implicate temporal lobe structures for this type of time estimation task.

  8. Local Atomic Structure of Semiconductor Alloys Using Pair Distribution Function Analysis

    SciTech Connect

    Billinge, S.J.L.; Thorpe, M.F.

    2002-06-24

    We have been taking advantage of recent experimental developments, which involve utilizing diffraction data from x-rays or neutrons out to very large wave-vectors, to obtain a detailed structural characterization of semiconductor alloys. This approach allows an accurate Pair Distribution Function (PDF) to be obtained to 20A and beyond and reveals the local structure of the alloy directly. These data can be modeled explicitly to learn about local correlations and short-range order in materials. We are combining theory, modeling and experiments to study a range of materials from semiconductors to thermoelectrics and proton conductors.

  9. MinFinder: Locating all the local minima of a function

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-01-01

    A new stochastic clustering algorithm is introduced that aims to locate all the local minima of a multidimensional continuous and differentiable function inside a bounded domain. The accompanying software (MinFinder) is written in ANSI C++. However, the user may code his objective function either in C++, C or Fortran 77. We compare the performance of this new method to the performance of Multistart and Topographical Multilevel Single Linkage Clustering on a set of benchmark problems. Program summaryTitle of program:MinFinder Catalogue identifier:ADWU Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which is has been tested:The tool is designed to be portable in all systems running the GNU C++ compiler Installation:University of Ioannina, Greece Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data:200 KB No. of bits in a word:32 No. of processors used:1 Has the code been vectorized or parallelized?:no No. of lines in distributed program, including test data, etc.:5797 No. of bytes in distributed program, including test data, etc.:588 121 Distribution format:gzipped tar file Nature of the physical problem:A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be trapped in any local minimum. Global optimization is then the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zero. Method of solution:Using a uniform pdf, points are sampled from the

  10. Rational Conformal Correlation Functions of Gauge-Invariant Local Fields in Four Dimensions

    SciTech Connect

    Nikolov, N.M.; Stanev, Ya.S.; Todorov, I.T.

    2005-11-01

    Global conformal invariance in Minkowski space and the Wightman axioms imply strong locality (Huygens principle) and rationality of correlation functions, thus providing an extension of the concept of a vertex algebra to higher (even) dimensions D. We (p)review current work on a model of a Hermitian scalar field L of scale dimension 4 (D = 4) which can be interpreted as the Lagrangian of a gauge field theory that generates the algebra of gauge-invariant local observables in a conformally invariant renormalization group fixed point.

  11. Fractal dimensions of wave functions and local spectral measures on the Fibonacci chain

    NASA Astrophysics Data System (ADS)

    Macé, Nicolas; Jagannathan, Anuradha; Piéchon, Frédéric

    2016-05-01

    We present a theoretical framework for understanding the wave functions and spectrum of an extensively studied paradigm for quasiperiodic systems, namely the Fibonacci chain. Our analytical results, which are obtained in the limit of strong modulation of the hopping amplitudes, are in good agreement with published numerical data. In the perturbative limit, we show a symmetry of wave functions under permutation of site and energy indices. We compute the wave-function renormalization factors and from them deduce analytical expressions for the fractal exponents corresponding to individual wave functions, as well as their global averages. The multifractality of wave functions is seen to appear at next-to-leading order in ρ . Exponents for the local spectral density are given, in extremely good accord with numerical calculations. Interestingly, our analytical results for exponents are observed to describe the system rather well even for values of ρ well outside the domain of applicability of perturbation theory.

  12. Investigation of the resonance-assisted hydrogen bond in model β-diketones through localized molecular orbital analysis of the spin-spin coupling constants related to the O-H···O hydrogen bond.

    PubMed

    Zarycz, M Natalia C; Provasi, Patricio F

    2015-02-01

    The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.

  13. Identification of a functional nuclear localization signal within the human USP22 protein

    SciTech Connect

    Xiong, Jianjun; Wang, Yaqin; Gong, Zhen; Liu, Jianyun; Li, Weidong

    2014-06-20

    Highlights: • USP22 was accumulated in nucleus. • We identified of a functional USP22 NLS. • The KRRK amino acid residues are indispensable in NLS. • The KRRK motif is conserved in USP22 homologues. - Abstract: Ubiquitin-specific processing enzyme 22 (USP22), a member of the deubiquitinase family, is over-expressed in most human cancers and has been implicated in tumorigenesis. Because it is an enzymatic subunit of the human SAGA transcriptional cofactor, USP22 deubiquitylates histone H2A and H2B in the nucleus, thus participating in gene regulation and cell-cycle progression. However, the mechanisms regulating its nuclear translocation have not yet been elucidated. It was here demonstrated that USP22 is imported into the nucleus through a mechanism mediated by nuclear localization signal (NLS). The bipartite NLS sequence KRELELLKHNPKRRKIT (aa152–168), was identified as the functional NLS for its nuclear localization. Furthermore, a short cluster of basic amino acid residues KRRK within this bipartite NLS plays the primary role in nuclear localization and is evolutionarily conserved in USP22 homologues. In the present study, a functional NLS and the minimal sequences required for the active targeting of USP22 to the nucleus were identified. These findings may provide a molecular basis for the mechanism underlying USP22 nuclear trafficking and function.

  14. Poly-cyclodextrin functionalized porous bioceramics for local chemotherapy and anticancer bone reconstruction.

    PubMed

    Chai, Feng; Abdelkarim, Mohamed; Laurent, Thomas; Tabary, Nicolas; Degoutin, Stephanie; Simon, Nicolas; Peters, Fabian; Blanchemain, Nicolas; Martel, Bernard; Hildebrand, Hartmut F

    2014-08-01

    The progress in bone cancer surgery and multimodal treatment concept achieve only modest improvement in the overall survival, due to failure in clearing out residual cancer cells at the surgical margin and extreme side-effects of adjuvant postoperative treatments. Our study aims to propose a new method based on cyclodextrin polymer (polyCD) functionalized hydroxyapatite (HA) for achieving a high local drug concentration with a sustained release profile and a better control of residual malignant cells via local drug delivery and promotion of the reconstruction of bone defects. PolyCD, a versatile carrier for therapeutic molecules, can be incorporated into HA (bone regeneration scaffold) through thermal treatment. The parameters of polyCD treatment on the macroporous HA (porosity 65%) were characterized via thermogravimetric analysis. Good cytocompatibility of polyCD functionalized bioceramics was demonstrated on osteoblast cells by cell vitality assay. An antibiotic (gentamicin) and an anticancer agent (cisplatin) were respectively loaded on polyCD functionalized bioceramics for drug release test. The results show that polyCD functionalization leads to significantly improved drug loading quantity (30% more concerning gentamicin and twice more for cisplatin) and drug release duration (7 days longer concerning gentamicin and 3 days longer for cisplatin). Conclusively, this study offers a safe and reliable drug delivery system for bioceramic matrices, which can load anticancer agents (or/and antibiotics) to reduce local recurrence (or/and infection).

  15. A generalized finite element method with global-local enrichment functions for confined plasticity problems

    NASA Astrophysics Data System (ADS)

    Kim, D.-J.; Duarte, C. A.; Proenca, S. P.

    2012-11-01

    The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J 2 plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

  16. Locally Estimated Hemodynamic Response Function and Activation Detection Sensitivity in Heroin-Cue Reactivity Study

    PubMed Central

    Maleki-Balajoo, Somayeh; Hossein-Zadeh, Gholam-Ali; Soltanian-Zadeh, Hamid; Ekhtiari, Hamed

    2016-01-01

    Introduction: A fixed hemodynamic response function (HRF) is commonly used for functional magnetic resonance imaging (fMRI) analysis. However, HRF may vary from region to region and subject to subject. We investigated the effect of locally estimated HRF (in functionally homogenous parcels) on activation detection sensitivity in a heroin cue reactivity study. Methods: We proposed a novel exploratory method for brain parcellation based on a probabilistic model to segregate the brain into spatially connected and functionally homogeneous components. Then, we estimated HRF and detected activated regions in response to an experimental task in each parcel using a joint detection estimation (JDE) method. We compared the proposed JDE method with the general linear model (GLM) that uses a fixed HRF and is implemented in FEAT (as a part of FMRIB Software Library, version 4.1). Results: 1) Regions detected by JDE are larger than those detected by fixed HRF, 2) In group analysis, JDE found areas of activation not detected by fixed HRF. It detected drug craving a priori “regions-of-interest” in the limbic lobe (anterior cingulate cortex [ACC], posterior cingulate cortex [PCC] and cingulate gyrus), basal ganglia, especially striatum (putamen and head of caudate), and cerebellum in addition to the areas detected by the fixed HRF method, 3) JDE obtained higher Z-values of local maxima compared to those obtained by fixed HRF. Conclusion: In our study of heroin cue reactivity, our proposed method (that estimates HRF locally) outperformed the conventional GLM that uses a fixed HRF. PMID:27872691

  17. Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

    PubMed

    Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

    2015-08-03

    The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

  18. Locally optimal control under unknown dynamics with learnt cost function: application to industrial robot positioning

    NASA Astrophysics Data System (ADS)

    Guérin, Joris; Gibaru, Olivier; Thiery, Stéphane; Nyiri, Eric

    2017-01-01

    Recent methods of Reinforcement Learning have enabled to solve difficult, high dimensional, robotic tasks under unknown dynamics using iterative Linear Quadratic Gaussian control theory. These algorithms are based on building a local time-varying linear model of the dynamics from data gathered through interaction with the environment. In such tasks, the cost function is often expressed directly in terms of the state and control variables so that it can be locally quadratized to run the algorithm. If the cost is expressed in terms of other variables, a model is required to compute the cost function from the variables manipulated. We propose a method to learn the cost function directly from the data, in the same way as for the dynamics. This way, the cost function can be defined in terms of any measurable quantity and thus can be chosen more appropriately for the task to be carried out. With our method, any sensor information can be used to design the cost function. We demonstrate the efficiency of this method through simulating, with the V-REP software, the learning of a Cartesian positioning task on several industrial robots with different characteristics. The robots are controlled in joint space and no model is provided a priori. Our results are compared with another model free technique, consisting in writing the cost function as a state variable.

  19. Localization of focal epileptic discharges using functional connectivity magnetic resonance imaging

    PubMed Central

    Stufflebeam, Steven M.; Liu, Hesheng; Sepulcre, Jorge; Tanaka, Naoaki; Buckner, Randy L.; Madsen, Joseph R.

    2011-01-01

    Object In patients with medically refractory epilepsy the accurate localization of the seizure onset zone is critical for successful surgical treatment. The object of this study was to investigate whether the degree of coupling of spontaneous brain activity as measured with functional connectivity MR imaging (fcMR imaging) can accurately identify and localize epileptic discharges. Methods The authors studied 6 patients who underwent fcMR imaging presurgical mapping and subsequently underwent invasive electroencephalography. Results Focal regions of statistically significant increases in connectivity were identified in 5 patients when compared with an ad hoc normative sample of 300 controls. The foci identified by fcMR imaging overlapped the epileptogenic areas identified by invasive encephalography in all 5 patients. Conclusions These results suggest that fcMR imaging may provide an effective high–spatial resolution and noninvasive method of localizing epileptic discharges in patients with refractory epilepsy. PMID:21351832

  20. Meshless Local Petrov-Galerkin Method for Shallow Shells with Functionally Graded and Orthotropic Material Properties

    NASA Astrophysics Data System (ADS)

    Sladek, J.; Sladek, V.; Zhang, Ch.

    2008-02-01

    A meshless local Petrov-Galerkin (MLPG) formulation is presented for analysis of shear deformable shallow shells with orthotropic material properties and continuously varying material properties through the shell thickness. Shear deformation of shells described by the Reissner theory is considered. Analyses of shells under static and dynamic loads are given here. For transient elastodynamic case the Laplace-transform is used to eliminate the time dependence of the field variables. A weak formulation with a unit test function transforms the set of the governing equations into local integral equations on local subdomains in the plane domain of the shell. The meshless approximation based on the Moving Least-Squares (MLS) method is employed for the implementation.

  1. A comparison of memory function following local and general anaesthesia for extraction of senile cataract.

    PubMed

    Karhunen, U; Jönn, G

    1982-08-01

    The memory performance of 60 female patients, scheduled for either local or general anaesthesia and extraction of senile cataract, was investigated. Six subtests of the Wechsler Memory Scale and four items of memory tests according to Luria were performed. One week postoperatively there was a diminution in the performance of the Wechsler Memory Scale and Luria tests. Comparison of the pre- and postoperative diminutions between the local and general anaesthesia groups was statistically significant only in the Luria tests. According to this study general anaesthesia does not affect memory function more profoundly than local anaesthesia supplemented with tranquilizing and/or analgesic drugs. In this respect, the advantages of general anesthesia should be utilized, at least in patients without clearcut contraindications.

  2. The cerebral ventricles, the animal spirits and the dawn of brain localization of function.

    PubMed

    Manzoni, T

    1998-03-01

    This paper reviews the early history of brain localization of function. It analyses the doctrines professed in ancient times by philosophers and physicians, who believed that brain functions were carried out in the cerebral ventricles by the psychic pneuma, or animal spirit, a sort of special and light substance endowed with the power to perform sensory, motor and mental activities. This theory, conceived in the Classic Age and called "ventricular-pneumatic doctrine", evolved in the 4th-5th centuries A.D. into the "three-cell theory", according to which each cerebral ventricle was the seat of a specific function, and contained a unique type of spirit with the power to perform that function. The three-cell theory represents the earliest attempt to localize different mind functions in separate brain sites and was held true by Byzantine, Arabian and Western Latin scholars well beyond the Renaissance. The paper is subdivided into an Introduction and eight sections. The first two sections report a brief history of the philosophical and medical doctrines about the pneuma as mediator of all vital functions, the ventricular-pneumatic doctrine elaborated by Galen of Pergamon, and his theory of nerve physiology based on the assumption that the pneuma, set in motion by active brain movements and flowing in the hollow nerves, could transfer sensations from the sense organs to the anterior ventricles, and motor commands from the posterior ventricle to the muscles. The third and fourth sections trace the ways in which these doctrines were transmitted to the Byzantine physicians and then to the Arabs, until they reached the Latin West. Here, throughout the Middle Ages they not only formed the background of medical and natural philosophy, but also influenced Christian theologians. The fifth section is devoted to the ventricular localization of mind faculties, called internal senses by Arabian and Western Latin scholars. Most authors recognized three basic internal senses

  3. Evaluation of iris functional capillary density in experimental local and systemic inflammation.

    PubMed

    Arora, N; Islam, S; Wafa, K; Zhou, J; Toguri, J T; Cerny, V; Lehmann, C

    2017-04-01

    The ocular microcirculation represents an important target to treat inflammatory diseases of eye, where impairment of microvascular blood flow plays key role as, for example, in anterior uveitis. To evaluate novel interventions targeting the microcirculation, appropriate and reliable tools to study this particular microvascular bed are needed. Intravital microscopy (IVM) belongs to several methods allowing evaluation of microcirculation experimentally, even in small animals. The aim of our study was to examine the iridial microcirculation (IMIC) in uveitis induced by local or systemic endotoxin administration in rats and mice by IVM and to propose new parameters to quantify the changes within the IMIC. Systemic inflammation was induced in rats by intravenous endotoxin administration, control group received normal saline intravenously. Local inflammation was induced in mice by intravitreal endotoxin administration, the control group received normal saline intravitreally. IVM of IMIC was performed in animals receiving systemic endotoxin prior injection and 1 and 2 h afterwards, respectively, in animals receiving intravitreal endotoxin/saline prior local injection and 5 h afterwards. Obtained video recordings were analyzed off-line. Functional capillary density (FCD) and dysfunctional capillary density (DCD) were evaluated for description of IMIC, and calculation of FCD/DCD ratio was performed. In systemic inflammation, FCD was significantly decreased compared to control animals. In local inflammation, the number of functional capillaries in the IMIC was significantly reduced following the endotoxin challenge. Analysis of the DCD revealed a significant increase in capillaries with reduced perfusion after intravitreal endotoxin administration and right shift of the FCD/DCD ratio was observed after endotoxin local injection. Detecting and quantifying changes in IMIC during systemic or local inflammation in experimental animals by IVM was feasible. Therefore, IVM of the

  4. Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma

    PubMed Central

    Faura Tellez, Grissel; Willemse, Brigitte W. M.; Brouwer, Uilke; Nijboer-Brinksma, Susan; Vandepoele, Karl; Noordhoek, Jacobien A.; Heijink, Irene; de Vries, Maaike; Smithers, Natalie P.; Postma, Dirkje S.; Timens, Wim; Wiffen, Laura; van Roy, Frans; Holloway, John W.; Lackie, Peter M.; Nawijn, Martijn C.; Koppelman, Gerard H.

    2016-01-01

    Background The asthma gene PCDH1 encodes Protocadherin-1, a putative adhesion molecule of unknown function expressed in the airway epithelium. Here, we characterize the localization, differential expression, homotypic adhesion specificity and function of PCDH1 in airway epithelial cells in asthma. Methods We performed confocal fluorescence microscopy to determine subcellular localization of PCDH1 in 16HBE cells and primary bronchial epithelial cells (PBECs) grown at air-liquid interface. Next, to compare PCDH1 expression and localization in asthma and controls we performed qRT-PCR and fluorescence microscopy in PBECs and immunohistochemistry on airway wall biopsies. We examined homotypic adhesion specificity of HEK293T clones overexpressing fluorescently tagged-PCDH1 isoforms. Finally, to evaluate the role for PCDH1 in epithelial barrier formation and repair, we performed siRNA knockdown-studies and measured epithelial resistance. Results PCDH1 localized to the cell membrane at cell-cell contact sites, baso-lateral to adherens junctions, with increasing expression during epithelial differentiation. No differences in gene expression or localization of PCDH1 isoforms expressing the extracellular domain were observed in either PBECs or airway wall biopsies between asthma patients and controls. Overexpression of PCDH1 mediated homotypic interaction, whereas downregulation of PCDH1 reduced epithelial barrier formation, and impaired repair after wounding. Conclusions In conclusion, PCDH1 is localized to the cell membrane of bronchial epithelial cells baso-lateral to the adherens junction. Expression of PCDH1 is not reduced nor delocalized in asthma even though PCDH1 contributes to homotypic adhesion, epithelial barrier formation and repair. PMID:27701444

  5. Ejaculatory Function After Permanent {sup 125}I Prostate Brachytherapy for Localized Prostate Cancer

    SciTech Connect

    Huyghe, Eric Delannes, Martine; Wagner, Fabien M.; Delaunay, Boris; Nohra, Joe; Thoulouzan, Matthieu; Shut-Yee, J. Yeung; Plante, Pierre; Soulie, Michel; Thonneau, Patrick; Bachaud, Jean Marc

    2009-05-01

    Purpose: Ejaculatory function is an underreported aspect of male sexuality in men treated for prostate cancer. We conducted the first detailed analysis of ejaculatory function in patients treated with permanent {sup 125}I prostate brachytherapy for localized prostate cancer. Patients and Methods: Of 270 sexually active men with localized prostate cancer treated with permanent {sup 125}I prostate brachytherapy, 241 (89%), with a mean age of 65 years (range, 43-80), responded to a mailed questionnaire derived from the Male Sexual Health Questionnaire regarding ejaculatory function. Five aspects of ejaculatory function were examined: frequency, volume, dry ejaculation, pleasure, and pain. Results: Of the 241 sexually active men, 81.3% had conserved ejaculatory function after prostate brachytherapy; however, the number of patients with rare/absent ejaculatory function was double the pretreatment number (p < .0001). The latter finding was correlated with age (p < .001) and the preimplant International Index of Erectile Function score (p < .001). However, 84.9% of patients with maintained ejaculatory function after implantation reported a reduced volume of ejaculate compared with 26.9% before (p < .001), with dry ejaculation accounting for 18.7% of these cases. After treatment, 30.3% of the patients experienced painful ejaculation compared with 12.9% before (p = .0001), and this was associated with a greater number of implanted needles (p = .021) and the existence of painful ejaculation before implantation (p < .0001). After implantation, 10% of patients who continued to be sexually active experienced no orgasm compared with only 1% before treatment. in addition, more patients experienced late/difficult or weak orgasms (p = .001). Conclusion: Most men treated with brachytherapy have conserved ejaculatory function after prostate brachytherapy. However, most of these men experience a reduction in volume and a deterioration in orgasm.

  6. Introducing anisotropic Minkowski functionals and quantitative anisotropy measures for local structure analysis in biomedical imaging

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; De, Titas; Lochmüller, Eva; Eckstein, Felix; Nagarajan, Mahesh B.

    2013-03-01

    The ability of Minkowski Functionals to characterize local structure in different biological tissue types has been demonstrated in a variety of medical image processing tasks. We introduce anisotropic Minkowski Functionals (AMFs) as a novel variant that captures the inherent anisotropy of the underlying gray-level structures. To quantify the anisotropy characterized by our approach, we further introduce a method to compute a quantitative measure motivated by a technique utilized in MR diffusion tensor imaging, namely fractional anisotropy. We showcase the applicability of our method in the research context of characterizing the local structure properties of trabecular bone micro-architecture in the proximal femur as visualized on multi-detector CT. To this end, AMFs were computed locally for each pixel of ROIs extracted from the head, neck and trochanter regions. Fractional anisotropy was then used to quantify the local anisotropy of the trabecular structures found in these ROIs and to compare its distribution in different anatomical regions. Our results suggest a significantly greater concentration of anisotropic trabecular structures in the head and neck regions when compared to the trochanter region (p < 10-4). We also evaluated the ability of such AMFs to predict bone strength in the femoral head of proximal femur specimens obtained from 50 donors. Our results suggest that such AMFs, when used in conjunction with multi-regression models, can outperform more conventional features such as BMD in predicting failure load. We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding directional attributes of local structure, which may be useful in a wide scope of biomedical imaging applications.

  7. Imaging the static dielectric constant in vitro and in living cells by a bioconjugable GFP chromophore analog.

    PubMed

    Signore, Giovanni; Abbandonato, Gerardo; Storti, Barbara; Stöckl, Martin; Subramaniam, Vinod; Bizzarri, Ranieri

    2013-02-28

    A fluorescent probe structurally similar to the GFP chromophore is demonstrated to report the local static dielectric constant. This probe can be chemically functionalized for selective targeting at the intracellular level.

  8. Organelle DB: a cross-species database of protein localization and function.

    PubMed

    Wiwatwattana, Nuwee; Kumar, Anuj

    2005-01-01

    To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu.

  9. Local Field Distribution Function and High Order Field Moments for metal-dielectric composites.

    NASA Astrophysics Data System (ADS)

    Genov, Dentcho A.; Sarychev, Andrey K.; Shalaev, Vladimir M.

    2001-11-01

    In a span of two decades the physics of nonlinear optics saw vast improvement in our understanding of optical properties for various inhomogeneous mediums. One such medium is the metal-dielectric composite, where the metal inclusions have a surface coverage fraction of p, while the rest (1-p) is assumed to represent the dielectric host. The computations carried out by using different theoretical models and the experimental data show existence of giant local electric and magnetic field fluctuations. In this presentation we will introduce a new developed 2D model that determines exactly the Local Field Distribution Function (LFDF) and all other relevant parameters of the film. The LFDF for small filling factors will be shown to transform from lognormal distribution into a single-dipole distribution function. We also will confirm the predictions of the scaling theory for the high field moments, which have a power law dependence on the loss factor.

  10. Influence of the local-spin-density correlation functional on the stability of bcc ferromagnetic iron

    NASA Astrophysics Data System (ADS)

    Singh, D.; Clougherty, D. P.; MacLaren, J. M.; Albers, R. C.; Wang, C. S.

    1991-10-01

    The influence of local-spin-dependent correlation effects on the predicted stable ground-state phase of iron is reexamined with use of general-potential linearized augmented-plane-wave calculations. Differences in the form of the Vosko-Wilk-Nusair (VWN) local-spin-density functional used in previous studies are noted, since in previous studies significant additional approximations were made with respect to those of Vosko, Wilk, and Nusan [Can. J. Phys. 58, 1200 (1980)] and of MacLaren, Clougherty, and Albers [Phys. Rev. B 42, 3205 (1990)]. While the results of previous linear muffin-tin orbital calculations using the VWN functional predict a bcc ferromagnetic ground state, the present calculations show that the VWN spin-correlation effects fail to stabilize a bcc ground state. Considerable sensitivity to the form of the spin interpolation is found.

  11. Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.

    PubMed

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-01-14

    Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.

  12. Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities

    SciTech Connect

    Rodriguez, Brian; Kalinin, Sergei V; Jesse, Stephen; Thompson, G. L.; Vertegel, Alexey; Hohlbauch, Sophia; Proksch, Roger

    2008-01-01

    Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.

  13. Local and global processing of music in high-functioning persons with autism: beyond central coherence?

    PubMed

    Mottron, L; Peretz, I; Ménard, E

    2000-11-01

    A multi-modal abnormality in the integration of parts and whole has been proposed to account for a bias toward local stimuli in individuals with autism (Frith, 1989; Mottron & Belleville, 1993). In the current experiment, we examined the utility of hierarchical models in characterising musical information processing in autistic individuals. Participants were 13 high-functioning individuals with autism and 13 individuals of normal intelligence matched on chronological age, nonverbal IQ, and laterality, and without musical experience. The task consisted of same-different judgements of pairs of melodies. Differential local and global processing was assessed by manipulating the level, local or global, at which modifications occurred. No deficit was found in the two measures of global processing. In contrast, the clinical group performed better than the comparison group in the detection of change in nontransposed, contour-preserved melodies that tap local processing. These findings confirm the existence of a "local bias" in music perception in individuals with autism, but challenge the notion that it is accounted for by a deficit in global music processing. The present study suggests that enhanced processing of elementary physical properties of incoming stimuli, as found previously in the visual modality, may also exist in the auditory modality.

  14. Functional assays of local connectivity in the somatosensory cortex of individuals with autism.

    PubMed

    Coskun, Mehmet Akif; Loveland, Katherine A; Pearson, Deborah A; Papanicolaou, Andrew C; Sheth, Bhavin R

    2013-06-01

    Emerging evidence for differences between individuals with autism spectrum disorder (ASD) and neurotypical (NT) individuals in somatic processing and brain response to touch suggests somatosensory cortex as a promising substrate for elucidating differences in functional brain connectivity between individuals with and without autism. Signals from adjacent digits project to neighboring locations or representations in somatosensory cortex. When a digit is stimulated, i.e. touched, its representation in cortex is directly activated; local intracortical connections indirectly activate nonprimary cortical representations corresponding to adjacent digits. The response of the nonprimary cortical representations is thus a proxy for connection strength. Local overconnectivity in autism implies that the nonprimary/primary response ratios of the ASD group will be higher than those of the NT group. D1 and D2 of the dominant hand of the participant were individually stimulated while we recorded neural responses using magnetoencephalography. The cortical representations of D1 and D2 (somatosensory-evoked fields) were computed from the ensemble-averaged data using (a) dipole model fits and (b) singular value decomposition. Individual adjacent/primary response ratios were measured, and group response ratio data were fitted with straight lines. Local overconnectivity in autism implies steeper ASD vs. NT group slopes. Our findings did not support local overconnectivity. Slopes were found to be significantly shallower for the ASD group than the NT group. Our findings support the idea of local underconnectivity in the somatosensory cortex of the brains of individuals with ASD.

  15. The local projection in the density functional theory plus U approach: A critical assessment.

    PubMed

    Wang, Yue-Chao; Chen, Ze-Hua; Jiang, Hong

    2016-04-14

    Density-functional theory plus the Hubbard U correction (DFT + U) method is widely used in first-principles studies of strongly correlated systems, as it can give qualitatively (and sometimes, semi-quantitatively) correct description of energetic and structural properties of many strongly correlated systems with similar computational cost as local density approximation or generalized gradient approximation. On the other hand, the DFT + U approach is limited both theoretically and practically in several important aspects. In particular, the results of DFT + U often depend on the choice of local orbitals (the local projection) defining the subspace in which the Hubbard U correction is applied. In this work we have systematically investigated the issue of the local projection by considering typical transition metal oxides, β-MnO2 and MnO, and comparing the results obtained from different implementations of DFT + U. We found that the choice of the local projection has significant effects on the DFT + U results, which are more significant for systems with stronger covalent bonding (e.g., MnO2) than those with more ionic bonding (e.g., MnO). These findings can help to clarify some confusion arising from the practical use of DFT + U and may also provide insights for the development of new first-principles approaches beyond DFT + U.

  16. Local voltage drop in a single functionalized graphene sheet characterized by Kelvin probe force microscopy.

    PubMed

    Yan, Liang; Punckt, Christian; Aksay, Ilhan A; Mertin, Wolfgang; Bacher, Gerd

    2011-09-14

    We studied the local voltage drop in functionalized graphene sheets of subμm size under external bias conditions by Kelvin probe force microscopy. Using this noninvasive experimental approach, we measured ohmic current-voltage characteristics and an intrinsic conductivity of about 3.7 × 10(5) S/m corresponding to a sheet resistance of 2.7 kΩ/sq under ambient conditions for graphene produced via thermal reduction of graphite oxide. The contact resistivity between functionalized graphene and metal electrode was found to be <6.3 × 10(-7) Ωcm(2).

  17. Solutions to Kuessner's integral equation in unsteady flow using local basis functions

    NASA Technical Reports Server (NTRS)

    Fromme, J. A.; Halstead, D. W.

    1975-01-01

    The computational procedure and numerical results are presented for a new method to solve Kuessner's integral equation in the case of subsonic compressible flow about harmonically oscillating planar surfaces with controls. Kuessner's equation is a linear transformation from pressure to normalwash. The unknown pressure is expanded in terms of prescribed basis functions and the unknown basis function coefficients are determined in the usual manner by satisfying the given normalwash distribution either collocationally or in the complex least squares sense. The present method of solution differs from previous ones in that the basis functions are defined in a continuous fashion over a relatively small portion of the aerodynamic surface and are zero elsewhere. This method, termed the local basis function method, combines the smoothness and accuracy of distribution methods with the simplicity and versatility of panel methods. Predictions by the local basis function method for unsteady flow are shown to be in excellent agreement with other methods. Also, potential improvements to the present method and extensions to more general classes of solutions are discussed.

  18. Building Local Infrastructure for Community Adoption of Science-Based Prevention: The Role of Coalition Functioning

    PubMed Central

    Hawkins, J. David; Oesterle, Sabrina

    2015-01-01

    The widespread adoption of science-based prevention requires local infrastructures for prevention service delivery. Communities That Care (CTC) is a tested prevention service delivery system that enables a local coalition of community stakeholders to use a science-based approach to prevention and improve the behavioral health of young people. This paper uses data from the Community Youth Development Study (CYDS), a community-randomized trial of CTC, to examine the extent to which better internal team functioning of CTC coalitions increases the community-wide adoption of science-based prevention within 12 communities, relative to 12 matched comparison communities. Specifically, this paper examines the potential of both a direct relationship between coalition functioning and the community-wide adoption of science-based prevention and a direct relationship between functioning and the coalition capacities that ultimately enable the adoption of science-based prevention. Findings indicate no evidence of a direct relationship between four dimensions of coalition functioning and the community-wide adoption of a science-based approach to prevention, but suggest a relationship between coalition functioning and coalition capacities (building new member skills and establishing external linkages with existing community organizations) that enable science-based prevention. PMID:26017632

  19. Building Local Infrastructure for Community Adoption of Science-Based Prevention: The Role of Coalition Functioning.

    PubMed

    Shapiro, Valerie B; Hawkins, J David; Oesterle, Sabrina

    2015-11-01

    The widespread adoption of science-based prevention requires local infrastructures for prevention service delivery. Communities That Care (CTC) is a tested prevention service delivery system that enables a local coalition of community stakeholders to use a science-based approach to prevention and improve the behavioral health of young people. This paper uses data from the Community Youth Development Study (CYDS), a community-randomized trial of CTC, to examine the extent to which better internal team functioning of CTC coalitions increases the community-wide adoption of science-based prevention within 12 communities, relative to 12 matched comparison communities. Specifically, this paper examines the potential of both a direct relationship between coalition functioning and the community-wide adoption of science-based prevention and a direct relationship between functioning and the coalition capacities that ultimately enable the adoption of science-based prevention. Findings indicate no evidence of a direct relationship between four dimensions of coalition functioning and the community-wide adoption of a science-based approach to prevention, but suggest a relationship between coalition functioning and coalition capacities (building new member skills and establishing external linkages with existing community organizations) that enable science-based prevention.

  20. Functional diversity of Arabidopsis organelle-localized RNA-recognition motif-containing proteins.

    PubMed

    Shi, Xiaowen; Hanson, Maureen R; Bentolila, Stephane

    2017-03-29

    RNA-Binding Proteins (RBPs) play key roles in plant gene expression and regulation. RBPs contain a variety of RNA-binding motifs, the most abundant and most widespread one in eukaryotes is the RNA recognition motif (RRM). Many nucleus-encoded RRM-containing proteins are transported into chloroplasts and/or mitochondria, and participate in various RNA-related processes in plant organelles. Loss of these proteins can have a detrimental effect on some critical processes such as photosynthesis and respiration, sometimes leading to lethality. Progress has been made in the last few years in understanding the function of particular organelle-localized RRM-containing proteins. Members of the Organelle RRM protein (ORRM, some also characterized as Glycine-Rich RNA-Binding Proteins) family and the Chloroplast RiboNucleoProtein (cpRNP) family, are involved in various types of RNA metabolism, including RNA editing, RNA stability and RNA processing. Organelle-localized RRM proteins also function in plant development and stress responses, in some conditions acting as protein or RNA chaperones. There has been recent progress in characterizing the function of organelle-localized RRM proteins in RNA-related processes and how RRM proteins contribute to the normal growth and development of plants. For further resources related to this article, please visit the WIREs website.

  1. Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

    PubMed Central

    Warren, Ian A.; Ciborowski, Kate L.; Casadei, Elisa; Hazlerigg, David G.; Martin, Sam; Jordan, William C.; Sumner, Seirian

    2014-01-01

    Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favored by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole-genome duplications are sparse although one example is the salmonids, which have undergone a whole-genome duplication event within the last 100 Myr. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here, we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high-throughput sequencing to characterize the transcriptomes of three key organs involved in regulating migration in S. salar: Brain, pituitary, and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences and designed an analytic workflow to distinguish between paralogs originating from local gene duplication events or from whole-genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event. Many of the identified paralog pairs have either diverged in function or become noncoding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle. PMID:24951567

  2. Maximally--localized Wannier Functions in Mott Insulators: the Case of MnO.

    NASA Astrophysics Data System (ADS)

    Posternak, M.; Baldereschi, A.; Marzari, N.

    2000-03-01

    Wannier functions can be considered a generalization of ``localized molecular orbitals'' to the case of extended systems. As such, they allow for a clear description of chemical bonds, and provide a convenient basis to study correlation effects. The localization algorithm of Marzari and Vanderbilt(N. Marzari and D. Vanderbilt, Phys. Rev. B 56) 12847 (1997). is combined here with the all--electron FLAPW method, and then applied to the case of antiferromagnetic MnO, a half--filled d shell Mott insulator. Two different one-electron schemes have been explored: local spin density (LSD), and LSD+U. In the latter case, the screened on--site Coulomb interaction U is explicitly included. The observed mixed charge--transfer/Mott--Hubbard character of MnO, as well as the mechanism of superexchange, are discussed in terms of the calculated Wannier functions, which display O 2p/Mn 3d bonding character. The centers of these Wannier functions are either on the Mn sites, or close to the O sites. Finally, their individual contributions to the Born effective charges are also presented.

  3. Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon.

    PubMed

    Warren, Ian A; Ciborowski, Kate L; Casadei, Elisa; Hazlerigg, David G; Martin, Sam; Jordan, William C; Sumner, Seirian

    2014-06-19

    Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favored by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole-genome duplications are sparse although one example is the salmonids, which have undergone a whole-genome duplication event within the last 100 Myr. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here, we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high-throughput sequencing to characterize the transcriptomes of three key organs involved in regulating migration in S. salar: Brain, pituitary, and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences and designed an analytic workflow to distinguish between paralogs originating from local gene duplication events or from whole-genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event. Many of the identified paralog pairs have either diverged in function or become noncoding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle.

  4. Abnormal functional global and local brain connectivity in female patients with anorexia nervosa

    PubMed Central

    Geisler, Daniel; Borchardt, Viola; Lord, Anton R.; Boehm, Ilka; Ritschel, Franziska; Zwipp, Johannes; Clas, Sabine; King, Joseph A.; Wolff-Stephan, Silvia; Roessner, Veit; Walter, Martin; Ehrlich, Stefan

    2016-01-01

    Background Previous resting-state functional connectivity studies in patients with anorexia nervosa used independent component analysis or seed-based connectivity analysis to probe specific brain networks. Instead, modelling the entire brain as a complex network allows determination of graph-theoretical metrics, which describe global and local properties of how brain networks are organized and how they interact. Methods To determine differences in network properties between female patients with acute anorexia nervosa and pairwise matched healthy controls, we used resting-state fMRI and computed well-established global and local graph metrics across a range of network densities. Results Our analyses included 35 patients and 35 controls. We found that the global functional network structure in patients with anorexia nervosa is characterized by increases in both characteristic path length (longer average routes between nodes) and assortativity (more nodes with a similar connectedness link together). Accordingly, we found locally decreased connectivity strength and increased path length in the posterior insula and thalamus. Limitations The present results may be limited to the methods applied during preprocessing and network construction. Conclusion We demonstrated anorexia nervosa–related changes in the network configuration for, to our knowledge, the first time using resting-state fMRI and graph-theoretical measures. Our findings revealed an altered global brain network architecture accompanied by local degradations indicating wide-scale disturbance in information flow across brain networks in patients with acute anorexia nervosa. Reduced local network efficiency in the thalamus and posterior insula may reflect a mechanism that helps explain the impaired integration of visuospatial and homeostatic signals in patients with this disorder, which is thought to be linked to abnormal representations of body size and hunger. PMID:26252451

  5. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

    PubMed

    Parasuram, Ramya; Mills, Caitlyn L; Wang, Zhouxi; Somasundaram, Saroja; Beuning, Penny J; Ondrechen, Mary Jo

    2016-01-15

    Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural

  6. Varying Constants, Gravitation and Cosmology.

    PubMed

    Uzan, Jean-Philippe

    2011-01-01

    Fundamental constants are a cornerstone of our physical laws. Any constant varying in space and/or time would reflect the existence of an almost massless field that couples to matter. This will induce a violation of the universality of free fall. Thus, it is of utmost importance for our understanding of gravity and of the domain of validity of general relativity to test for their constancy. We detail the relations between the constants, the tests of the local position invariance and of the universality of free fall. We then review the main experimental and observational constraints that have been obtained from atomic clocks, the Oklo phenomenon, solar system observations, meteorite dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic microwave background and big bang nucleosynthesis. At each step we describe the basics of each system, its dependence with respect to the constants, the known systematic effects and the most recent constraints that have been obtained. We then describe the main theoretical frameworks in which the low-energy constants may actually be varying and we focus on the unification mechanisms and the relations between the variation of different constants. To finish, we discuss the more speculative possibility of understanding their numerical values and the apparent fine-tuning that they confront us with.

  7. Local climate and cultivation, but not ploidy, predict functional trait variation in Bouteloua gracilis (Poaceae)

    USGS Publications Warehouse

    Butterfield, Bradley J.; Wood, Troy E.

    2015-01-01

    Efforts to improve the diversity of seed 18 resources for important restoration species has become a high priority for land managers in many parts of the world. Relationships between functional trait values and the environment from which seed sources are collected can provide important insights into patterns of local adaptation and guidelines for seed transfer. However, little is known about which functional traits exhibit genetic differentiation across populations of restoration species and thus may contribute to local adaptation. Here, we report the results of a common garden experiment aimed at assessing genetic (including ploidy level) and environmental regulation of several functional traits among populations of Bouteloua gracilis, a dominant C4 grass and the most highly utilized restoration species across much of the Colorado Plateau. We found that leaf size and specific leaf area (SLA) varied significantly among populations, and were strongly correlated with the source population environment from which seeds were collected. However, variation in ploidy level had no significant effect on functional traits. Leaves of plants grown from commercial seed releases were significantly larger and had lower SLA than those from natural populations, a result that is concordant with the overall relation between climate and these two functional traits. We suggest that the patterns of functional trait variation shown here may extend to other grass species in the western USA, and may serve as useful proxies for more extensive genecology research. Furthermore, we argue that care should be taken to develop commercial seed lines with functional trait values that match those of natural populations occupying climates similar to target restoration sites.

  8. A spectroscopic approach toward depression diagnosis: local metabolism meets functional connectivity.

    PubMed

    Demenescu, Liliana Ramona; Colic, Lejla; Li, Meng; Safron, Adam; Biswal, B; Metzger, Coraline Danielle; Li, Shijia; Walter, Martin

    2017-03-01

    Abnormal anterior insula (AI) response and functional connectivity (FC) is associated with depression. In addition to clinical features, such as severity, AI FC and its metabolism further predicted therapeutic response. Abnormal FC between anterior cingulate and AI covaried with reduced glutamate level within cingulate cortex. Recently, deficient glial glutamate conversion was found in AI in major depression disorder (MDD). We therefore postulate a local glutamatergic mechanism in insula cortex of depressive patients, which is correlated with symptoms severity and itself influences AI's network connectivity in MDD. Twenty-five MDD patients and 25 healthy controls (HC) matched on age and sex underwent resting state functional magnetic resonance imaging and magnetic resonance spectroscopy scans. To determine the role of local glutamate-glutamine complex (Glx) ratio on whole brain AI FC, we conducted regression analysis with Glx relative to creatine (Cr) ratio as factor of interest and age, sex, and voxel tissue composition as nuisance factors. We found that in MDD, but not in HC, AI Glx/Cr ratio correlated positively with AI FC to right supramarginal gyrus and negatively with AI FC toward left occipital cortex (p < 0.05 family wise error). AI Glx/Cr level was negatively correlated with HAMD score (p < 0.05) in MDD patients. We showed that the local AI ratio of glutamatergic-creatine metabolism is an underlying candidate subserving functional network disintegration of insula toward low level and supramodal integration areas, in MDD. While causality cannot directly be inferred from such correlation, our finding helps to define a multilevel network of response-predicting regions based on local metabolism and connectivity strength.

  9. Globus Pallidus Interna in Tourette Syndrome: Decreased Local Activity and Disrupted Functional Connectivity

    PubMed Central

    Ji, Gong-Jun; Liao, Wei; Yu, Yang; Miao, Huan-Huan; Feng, Yi-Xuan; Wang, Kai; Feng, Jian-Hua; Zang, Yu-Feng

    2016-01-01

    Globus pallidus interna (GPi) is an effective deep brain stimulation site for the treatment of Tourette syndrome (TS), and plays a crucial role in the pathophysiology of TS. To investigate the functional network feature of GPi in TS patients, we retrospectively studied 24 boys with ‘pure’ TS and 32 age-/education-matched healthy boys by resting state functional magnetic resonance images. Amplitude of low-frequency fluctuation (ALFF) and functional connectivity were used to estimate the local activity in GPi and its functional coordinate with the whole brain regions, respectively. We found decreased ALFF in patients’ bilateral GPi, which was also negatively correlated with clinical symptoms. Functional connectivity analysis indicated abnormal regions within motor and motor-control networks in patients (inferior part of sensorimotor area, cerebellum, prefrontal cortex, cingulate gyrus, caudate nucleus, and brain stem). Transcranial magnetic stimulation sites defined by previous studies (“hand knob” area, premotor area, and supplementary motor area) did not show significantly different functional connectivity with GPi between groups. In summary, this study characterized the disrupted functional network of GPi and provided potential regions-of-interest for further basic and clinical studies on TS. PMID:27799898

  10. An accurate solution of elastodynamic problems by numerical local Green's functions

    NASA Astrophysics Data System (ADS)

    Loureiro, F. S.; Silva, J. E. A.; Mansur, W. J.

    2015-09-01

    Green's function based methodologies for elastodynamics in both time and frequency domains, which can be either numerical or analytical, appear in many branches of physics and engineering. Thus, the development of exact expressions for Green's functions is of great importance. Unfortunately, such expressions are known only for relatively few kinds of geometry, medium and boundary conditions. In this way, due to the difficulty in finding exact Green's functions, specially in the time domain, the present paper presents a solution of the transient elastodynamic equations by a time-stepping technique based on the Explicit Green's Approach method written in terms of the Green's and Step response functions, both being computed numerically by the finite element method. The major feature is the computation of these functions separately by the central difference time integration scheme and locally owing to the principle of causality. More precisely, Green's functions are computed only at t = Δt adopting two time substeps while Step response functions are computed directly without substeps. The proposed time-stepping method shows to be quite accurate with distinct numerical properties not presented in the standard central difference scheme as addressed in the numerical example.

  11. Cellular localization, expression and functional implications of the utero-placental endothelin system during maintenance and termination of canine gestation.

    PubMed

    Gram, Aykut; Boos, Alois; Kowalewski, Mariusz P

    2017-02-20

    Utero-placental (Ut-Pl) angiogenesis and blood flow are fundamental for successful outcome of pregnancy. They are controlled by numerous vasodilator and vasoconstrictor systems such as endothelins (EDNs) and the renin angiotensin system. Dogs possess an invasive type of placentation, classified as endotheliochorial. Despite increasing knowledge regarding canine Ut-Pl function, little information exists on uterine and placental vascular activity during initiation, maintenance and termination of pregnancy in this species. The current study investigated expression of EDNs and their receptors (EDNRA and EDNRB) in the pre-implantation uterus and Ut-Pl compartments during gestation and at normal parturition, as well as in mid-pregnant dogs treated with the antigestagen aglepristone. The Ut-Pl mRNA expression of EDN1 and EDNRA was constant until mid-gestation and increased significantly during prepartum luteolysis. In contrast, EDN2 was highest pre-implantation and decreased following placentation, remaining low thereafter. Expression of the EDN-activating enzyme ECE1 and mRNA of EDNRB increased towards mid-gestation and was further elevated at prepartum luteolysis. Antigestagen treatment resulted in increased levels of EDN1 and EDNRA. At the cellular level, the uterine expression of EDN1, ECE1 and EDNRB was found predominantly in the endometrial surface and glandular epithelial cells; uterine signals for EDNRA were weak. In Ut-Pl all targets were mainly localized in the placenta fetalis, with syncytiotrophoblast staining stronger for ECE1 and EDNRB. In contrast, EDNRA stained strongly at the base of the placental labyrinth. Expression and localization of EDNs (EDN-1, -2), EDN receptors and ECE1 in the placenta fetalis suggests their involvement in the trophoblast invasion and proliferation.

  12. Cosmological constant, fine structure constant and beyond

    NASA Astrophysics Data System (ADS)

    Wei, Hao; Zou, Xiao-Bo; Li, Hong-Yu; Xue, Dong-Ze

    2017-01-01

    In the present work, we consider the cosmological constant model Λ ∝ α ^{-6}, which is well motivated from three independent approaches. As is well known, the hint of varying fine structure constant α was found in 1998. If Λ ∝ α ^{-6} is right, it means that the cosmological constant Λ should also be varying. Here, we try to develop a suitable framework to model this varying cosmological constant Λ ∝ α ^{-6}, in which we view it from an interacting vacuum energy perspective. Then we consider the observational constraints on these models by using the 293 Δ α /α data from the absorption systems in the spectra of distant quasars. We find that the model parameters can be tightly constrained to the very narrow ranges of O(10^{-5}) typically. On the other hand, we can also view the varying cosmological constant model Λ ∝ α ^{-6} from another perspective, namely it can be equivalent to a model containing "dark energy" and "warm dark matter", but there is no interaction between them. We find that this is also fully consistent with the observational constraints on warm dark matter.

  13. Assessing lung function and respiratory health in schoolchildren as a means to improve local environmental conditions.

    PubMed

    Hutter, Hans-Peter; Borsoi, Livia; Wallner, Peter; Moshammer, Hanns; Kundi, Michael

    2009-07-01

    In response to the World Health Organization Children's Environment and Health Action Plan for Europe (CEHAPE), a town near Vienna initiated a health survey of schoolchildren. To create recommendations for the community's decision makers, the health survey tried to identify the environmental factors influencing the respiratory health of children. The survey consisted of a questionnaire and spirometry. For 186 of 207 children of first and second grade, parents consented to include their children and answered a questionnaire. Spirometry was performed in 177 children. Results of lung function testing revealed that lung function was significantly reduced in children with visible mould infestation at home and living on a street with frequent lorry traffic. Larger family size and living in a rural area had positive effects on lung function. Our study provides an example for a feasible strategy to provide local decision makers with recommendations based on scientific evidence and actual observations and to help them implement measures in accordance with CEHAPE.

  14. The local counting function of operators of Dirac and Laplace type

    NASA Astrophysics Data System (ADS)

    Li, Liangpan; Strohmaier, Alexander

    2016-06-01

    Let P be a non-negative self-adjoint Laplace type operator acting on sections of a hermitian vector bundle over a closed Riemannian manifold. In this paper we review the close relations between various P-related coefficients such as the mollified spectral counting coefficients, the heat trace coefficients, the resolvent trace coefficients, the residues of the spectral zeta function as well as certain Wodzicki residues. We then use the Wodzicki residue to obtain results about the local counting function of operators of Dirac and Laplace type. In particular, we express the second term of the mollified spectral counting function of Dirac type operators in terms of geometric quantities and characterize those Dirac type operators for which this coefficient vanishes.

  15. Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins.

    PubMed

    Michishita, Eriko; Park, Jean Y; Burneskis, Jenna M; Barrett, J Carl; Horikawa, Izumi

    2005-10-01

    Sir2 is a NAD+-dependent protein deacetylase that extends lifespan in yeast and worms. This study examines seven human proteins homologous to Sir2 (SIRT1 through SIRT7) for cellular localization, expression profiles, protein deacetylation activity, and effects on human cell lifespan. We found that: 1) three nuclear SIRT proteins (SIRT1, SIRT6, and SIRT7) show different subnuclear localizations: SIRT6 and SIRT7 are associated with heterochromatic regions and nucleoli, respectively, where yeast Sir2 functions; 2) SIRT3, SIRT4, and SIRT5 are localized in mitochondria, an organelle that links aging and energy metabolism; 3) cellular p53 is a major in vivo substrate of SIRT1 deacetylase, but not the other six SIRT proteins; 4) SIRT1, but not the other two nuclear SIRT proteins, shows an in vitro deacetylase activity on histone H4 and p53 peptides; and 5) overexpression of any one of the seven SIRT proteins does not extend cellular replicative lifespan in normal human fibroblasts or prostate epithelial cells. This study supports the notion that multiple human SIRT proteins have evolutionarily conserved and nonconserved functions at different cellular locations and reveals that the lifespan of normal human cells, in contrast to that of lower eukaryotes, cannot be manipulated by increased expression of a single SIRT protein.

  16. Local glucocorticoid production in lymphoid organs of mice and birds: Functions in lymphocyte development.

    PubMed

    Taves, Matthew D; Hamden, Jordan E; Soma, Kiran K

    2017-02-01

    Circulating glucocorticoids (GCs) are powerful regulators of immunity. Stress-induced GC secretion by the adrenal glands initially enhances and later suppresses the immune response. GC targets include lymphocytes of the adaptive immune system, which are well known for their sensitivity to GCs. Less appreciated, however, is that GCs are locally produced in lymphoid organs, such as the thymus, where GCs play a critical role in selection of the T cell antigen receptor (TCR) repertoire. Here, we review the roles of systemic and locally-produced GCs in T lymphocyte development, which has been studied primarily in laboratory mice. By antagonizing TCR signaling in developing T cells, thymus-derived GCs promote selection of T cells with stronger TCR signaling. This results in increased T cell-mediated immune responses to a range of antigens. We then compare local and systemic GC patterns in mice to those in several bird species. Taken together, these studies suggest that a combination of adrenal and lymphoid GC production might function to adaptively regulate lymphocyte development and selection, and thus antigen-specific immune reactivity, to optimize survival under different environmental conditions. Future studies should examine how lymphoid GC patterns vary across other vertebrates, how GCs function in B lymphocyte development in the bone marrow, spleen, and the avian bursa of Fabricius, and whether GCs adaptively program immunity in free-living animals.

  17. An Essential Role for COPI in mRNA Localization to Mitochondria and Mitochondrial Function.

    PubMed

    Zabezhinsky, Dmitry; Slobodin, Boris; Rapaport, Doron; Gerst, Jeffrey E

    2016-04-19

    Nuclear-encoded mRNAs encoding mitochondrial proteins (mMPs) can localize directly to the mitochondrial surface, yet how mMPs target mitochondria and whether RNA targeting contributes to protein import into mitochondria and cellular metabolism are unknown. Here, we show that the COPI vesicle coat complex is necessary for mMP localization to mitochondria and mitochondrial function. COPI inactivation leads to reduced mMP binding to COPI itself, resulting in the dissociation of mMPs from mitochondria, a reduction in mitochondrial membrane potential, a decrease in protein import in vivo and in vitro, and severe deficiencies in mitochondrial respiration. Using a model mMP (OXA1), we observed that COPI inactivation (or mutation of the potential COPI-interaction site) led to altered mRNA localization and impaired cellular respiration. Overall, COPI-mediated mMP targeting is critical for mitochondrial protein import and function, and transcript delivery to the mitochondria or endoplasmic reticulum is regulated by cis-acting RNA sequences and trans-acting proteins.

  18. Eight-choice sound localization by manatees: performance abilities and head related transfer functions.

    PubMed

    Colbert-Luke, Debborah E; Gaspard, Joseph C; Reep, Roger L; Bauer, Gordon B; Dziuk, Kimberly; Cardwell, Adrienne; Mann, David A

    2015-02-01

    Two experiments investigated the ability and means by which two male Florida manatees (Trichechus manatus latirostris) may determine the direction of a sound source. An eight-choice discrimination paradigm was used to determine the subjects' sound localization abilities of five signal conditions covering a range of frequencies, durations, and levels. Subjects performed above the 12.5% chance level for all broadband frequencies and were able to localize sounds over a large level range. Errors were typically located to either side of the signal source location when presented in the front 180° but were more dispersed when presented from locations behind the subject. Front-to-back confusions were few and accuracy was greater when signals originated from the front 180°. Head-related transfer functions were measured to determine if frequencies were filtered by the manatee body to create frequency-specific interaural level differences (ILDs). ILDs were found for all frequencies as a function of source location, although they were largest with frequencies above 18 kHz and when signals originated to either side of the subjects. Larger ILDs were found when the signals originated behind the subjects. A shadowing-effect produced by the body may explain the relatively low occurrence of front-back confusions in the localization study.

  19. Structural and functional characterization of human telomerase RNA processing and cajal body localization signals.

    PubMed

    Theimer, Carla A; Jády, Beáta E; Chim, Nicholas; Richard, Patricia; Breece, Katherine E; Kiss, Tamás; Feigon, Juli

    2007-09-21

    The RNA component of human telomerase (hTR) includes H/ACA and CR7 domains required for 3' end processing, localization, and accumulation. The terminal loop of the CR7 domain contains the CAB box (ugAG) required for targeting of scaRNAs to Cajal bodies (CB) and an uncharacterized sequence required for accumulation and processing. To dissect out the contributions of the CR7 stem loop to hTR processing and localization, we solved the solution structures of the 3' terminal stem loops of hTR CR7 and U64 H/ACA snoRNA, and the 5' terminal stem loop of U85 C/D-H/ACA scaRNA. These structures, together with analysis of localization, processing, and accumulation of hTRs containing nucleotide substitutions in the CR7 domain, identified the sequence and structural requirements of the hTR processing and CB localization signals and showed that these signals are functionally independent. Further, 3' end processing was found to be a prerequisite for translocation of hTR to CBs.

  20. Small but Powerful: Top Predator Local Extinction Affects Ecosystem Structure and Function in an Intermittent Stream

    PubMed Central

    Rodríguez-Lozano, Pablo; Verkaik, Iraima; Rieradevall, Maria; Prat, Narcís

    2015-01-01

    Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators’ extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a ‘mesopredator release’, affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to ‘mesopredator release’, and also to ‘prey release’ despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem’s structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers’ extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been

  1. Small but powerful: top predator local extinction affects ecosystem structure and function in an intermittent stream.

    PubMed

    Rodríguez-Lozano, Pablo; Verkaik, Iraima; Rieradevall, Maria; Prat, Narcís

    2015-01-01

    Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators' extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a 'mesopredator release', affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to 'mesopredator release', and also to 'prey release' despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem's structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers' extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore

  2. Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

    PubMed

    Kristensen, David M; Chen, Brian Y; Fofanov, Viacheslav Y; Ward, R Matthew; Lisewski, Andreas Martin; Kimmel, Marek; Kavraki, Lydia E; Lichtarge, Olivier

    2006-06-01

    The annotation of protein function has not kept pace with the exponential growth of raw sequence and structure data. An emerging solution to this problem is to identify 3D motifs or templates in protein structures that are necessary and sufficient determinants of function. Here, we demonstrate the recurrent use of evolutionary trace information to construct such 3D templates for enzymes, search for them in other structures, and distinguish true from spurious matches. Serine protease templates built from evolutionarily important residues distinguish between proteases and other proteins nearly as well as the classic Ser-His-Asp catalytic triad. In 53 enzymes spanning 33 distinct functions, an automated pipeline identifies functionally related proteins with an average positive predictive power of 62%, including correct matches to proteins with the same function but with low sequence identity (the average identity for some templates is only 17%). Although these template building, searching, and match classification strategies are not yet optimized, their sequential implementation demonstrates a functional annotation pipeline which does not require experimental information, but only local molecular mimicry among a small number of evolutionarily important residues.

  3. The Local [C ii] 158 μm Emission Line Luminosity Function

    NASA Astrophysics Data System (ADS)

    Hemmati, Shoubaneh; Yan, Lin; Diaz-Santos, Tanio; Armus, Lee; Capak, Peter; Faisst, Andreas; Masters, Daniel

    2017-01-01

    We present, for the first time, the local [C ii] 158 μm emission line luminosity function measured using a sample of more than 500 galaxies from the Revised Bright Galaxy Sample. [C ii] luminosities are measured from the Herschel PACS observations of the Luminous Infrared Galaxies (LIRGs) in the Great Observatories All-sky LIRG Survey and estimated for the rest of the sample based on the far-infrared (far-IR) luminosity and color. The sample covers 91.3% of the sky and is complete at S60 μm > 5.24 Jy. We calculate the completeness as a function of [C ii] line luminosity and distance, based on the far-IR color and flux densities. The [C ii] luminosity function is constrained in the range ∼107–9 L⊙ from both the 1/Vmax and a maximum likelihood methods. The shape of our derived [C ii] emission line luminosity function agrees well with the IR luminosity function. For the CO(1-0) and [C ii] luminosity functions to agree, we propose a varying ratio of [C ii]/CO(1-0) as a function of CO luminosity, with larger ratios for fainter CO luminosities. Limited [C ii] high-redshift observations as well as estimates based on the IR and UV luminosity functions are suggestive of an evolution in the [C ii] luminosity function similar to the evolution trend of the cosmic star formation rate density. Deep surveys using the Atacama Large Millimeter Array with full capability will be able to confirm this prediction.

  4. Gestalt perception and local-global processing in high-functioning autism.

    PubMed

    Bölte, Sven; Holtmann, Martin; Poustka, Fritz; Scheurich, Armin; Schmidt, Lutz

    2007-09-01

    This study examined gestalt perception in high-functioning autism (HFA) and its relation to tasks indicative of local visual processing. Data on of gestalt perception, visual illusions (VI), hierarchical letters (HL), Block Design (BD) and the Embedded Figures Test (EFT) were collected in adult males with HFA, schizophrenia, depression and normative controls. Individuals with HFA processed gestalt stimuli less in accord with gestalt laws, particularly regarding the principle of similarity. Gestalt processing correlated positively with global processing of the HL. EFT and BD performance correlated negatively with VI susceptibility in HFA. All clinical groups succumbed less to VI than the normative sample. Results suggest decreased gestalt perception in HFA, being associated with a more general local visual processing bias.

  5. Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages.

    PubMed

    Redrejo-Rodríguez, Modesto; Muñoz-Espín, Daniel; Holguera, Isabel; Mencía, Mario; Salas, Margarita

    2012-11-06

    A number of prokaryotic proteins have been shown to contain nuclear localization signals (NLSs), although its biological role remains sometimes unclear. Terminal proteins (TPs) of bacteriophages prime DNA replication and become covalently linked to the genome ends. We predicted NLSs within the TPs of bacteriophages from diverse families and hosts and, indeed, the TPs of Φ29, Nf, PRD1, Bam35, and Cp-1, out of seven TPs tested, were found to localize to the nucleus when expressed in mammalian cells. Detailed analysis of Φ29 TP led us to identify a bona fide NLS within residues 1-37. Importantly, gene delivery into the eukaryotic nucleus is enhanced by the presence of Φ29 TP attached to the 5' DNA ends. These findings show a common feature of TPs from diverse bacteriophages targeting the eukaryotic nucleus and suggest a possible common function by facilitating the horizontal transfer of genes between prokaryotes and eukaryotes.

  6. Localization using nonindividualized head-related transfer functions. [for auditory interfaces in virtual environments

    NASA Technical Reports Server (NTRS)

    Wenzel, Elizabeth M.; Arruda, Marianne; Kistler, Doris J.; Wightman, Frederic L.

    1993-01-01

    The paper investigates the accuracy of localization by inexperienced listeners of the direction (azimuth and elevation) of wideband noisebursts presented in the free-field or over headphones, with headphone stimuli being synthesized using head-related transfer functions (HRTFs) from a representative subject of Wightman and Kistler (1989). Many subjects showed high rates of front-back and up-down confusions that increased significantly for virtual sources compared to the free-field stimuli. When confusions were resolved, localization of virtual sources was quite accurate and comparable to the free-field sources for 12 out of 16 subjects. The results of this study suggest that, while the interaural cues to horizontal location are robust, the spectral cues considered important for resolving location along a particular cone-of-confusion are distorted by a synthesis process that uses nonindividualized HRTFs.

  7. Localized operator partitioning method for electronic excitation energies in the time-dependent density functional formalism.

    PubMed

    Nagesh, Jayashree; Frisch, Michael J; Brumer, Paul; Izmaylov, Artur F

    2016-12-28

    We extend the localized operator partitioning method (LOPM) [J. Nagesh, A. F. Izmaylov, and P. Brumer, J. Chem. Phys. 142, 084114 (2015)] to the time-dependent density functional theory framework to partition molecular electronic energies of excited states in a rigorous manner. A molecular fragment is defined as a collection of atoms using Becke's atomic partitioning. A numerically efficient scheme for evaluating the fragment excitation energy is derived employing a resolution of the identity to preserve standard one- and two-electron integrals in the final expressions. The utility of this partitioning approach is demonstrated by examining several excited states of two bichromophoric compounds: 9-((1- naphthyl)- methyl)- anthracene and 4-((2- naphthyl)- methyl)- benzaldehyde. The LOPM is found to provide nontrivial insights into the nature of electronic energy localization that is not accessible using a simple density difference analysis.

  8. Effects of adaptation of vestibulo-ocular reflex function on manual target localization

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Merkle, L. A.; Barry, S. R.; Huebner, W. P.; Cohen, H. S.; Mueller, S. A.; Fordice, J.

    2000-01-01

    The goal of the present study was to determine if adaptive modulation of vestibulo-ocular reflex (VOR) function is associated with commensurate alterations in manual target localization. To measure the effects of adapted VOR on manual responses we developed the Vestibular-Contingent Pointing Test (VCP). In the VCP test, subjects pointed to a remembered target following passive whole body rotation in the dark. In the first experiment, subjects performed VCP before and after wearing 0.5X minifying lenses that adaptively attenuate horizontal VOR gain. Results showed that adaptive reduction in horizontal VOR gain was accompanied by a commensurate change in VCP performance. In the second experiment, bilaterally labyrinthine deficient (LD) subjects were tested to confirm that vestibular cues were central to the spatial coding of both eye and hand movements during VCP. LD subjects performed significantly worse than normal subjects. These results demonstrate that adaptive change in VOR can lead to alterations in manual target localization.

  9. Local description of closed submodules of a special module of entire functions of exponential type

    SciTech Connect

    Krasichkov-Ternovskii, I F; Shishkin, A B

    2001-12-31

    Let {pi}{sub 1}(z),...,{pi}{sub q}(z) be a system of polynomials of the complex variable z. In connection with the problem of spectral synthesis for systems of differential operators {pi}{sub 1}(D),...,{pi}{sub q}(D), D=d/dz, the problem of the local description of closed submodules is considered for a special module of entire functions over the ring C[{pi}{sub 1},...,{pi}{sub q}]. It is shown that this problem can be reduced to the local description over the ring C[l], where l is the Luroth polynomial associated with the system {pi}{sub 1}(z),...,{pi}{sub q}(z)

  10. Sucrose Transporter Localization and Function in Phloem Unloading in Developing Stems1[OPEN

    PubMed Central

    Rae, Anne L.; Reinders, Anke

    2017-01-01

    How sucrose transporters (SUTs) regulate phloem unloading in monocot stems is poorly understood and particularly so for species storing high Suc concentrations. To this end, Sorghum bicolor SUTs SbSUT1 and SbSUT5 were characterized by determining their transport properties heterologously expressed in yeast or Xenopus laevis oocytes, and their in planta cellular and subcellular localization. The plasma membrane-localized SbSUT1 and SbSUT5 exhibited a strong selectivity for Suc and high Suc affinities in X. laevis oocytes at pH 5—SbSUT1, 6.3 ± 0.7 mm, and SbSUT5, 2.4 ± 0.5 mm Suc. The Suc affinity of SbSUT1 was dependent on membrane potential and pH. In contrast, SbSUT5 Suc affinity was independent of membrane potential and pH but supported high transport rates at neutral pH. Suc transport by the tonoplast localized SbSUT4 could not be detected using yeast or X. laevis oocytes. Across internode development, SUTs, other than SbSUT4, were immunolocalized to sieve elements, while for elongating and recently elongated internodes, SUTs also were detected in storage parenchyma cells. We conclude that apoplasmic Suc unloading from de-energized protophloem sieve elements in meristematic zones may be mediated by reversal of SbSUT1 and/or by uniporting SWEETs. Storage parenchyma localized SbSUT1 and SbSUT5 may accumulate Suc from the stem apoplasms of elongating and recently elongated internodes, whereas SbSUT4 may function to release Suc from vacuoles. Transiting from an apoplasmic to symplasmic unloading pathway as the stem matures, SbSUT1 and SbSUT5 increasingly function in Suc retrieval into metaphloem sieve elements to maintain a high turgor to drive symplasmic unloading by bulk flow. PMID:27986867

  11. A possible functional localizer for identifying brain regions sensitive to sentence-level prosody.

    PubMed

    Fedorenko, Evelina; Hsieh, Po-Jang; Balewski, Zuzanna

    Investigations of how we produce and perceive prosodic patterns are not only interesting in their own right but can inform fundamental questions in language research. We here argue that functional magnetic resonance imaging (fMRI) in general - and the functional localization approach in particular (e.g., Kanwisher et al., 1997; Saxe et al., 2006; Fedorenko et al., 2010; Nieto-Castañon & Fedorenko, 2012) - has the potential to help address open research questions in prosody research and at the intersection of prosody and other domains. Critically, this approach can go beyond questions like "where in the brain does mental process x produce activation" and toward questions that probe the nature of the representations and computations that subserve different mental abilities. We describe one way to functionally define regions sensitive to sentence-level prosody in individual subjects. This or similar "localizer" contrasts can be used in future studies to test hypotheses about the precise contributions of prosody-sensitive brain regions to prosodic processing and cognition more broadly.

  12. A functional nuclear localization sequence in the C. elegans TRPV channel OCR-2.

    PubMed

    Ezak, Meredith J; Ferkey, Denise M

    2011-01-01

    The ability to modulate gene expression in response to sensory experience is critical to the normal development and function of the nervous system. Calcium is a key activator of the signal transduction cascades that mediate the process of translating a cellular stimulus into transcriptional changes. With the recent discovery that the mammalian Ca(v)1.2 calcium channel can be cleaved, enter the nucleus and act as a transcription factor to control neuronal gene expression, a more direct role for the calcium channels themselves in regulating transcription has begun to be appreciated. Here we report the identification of a nuclear localization sequence (NLS) in the C. elegans transient receptor potential vanilloid (TRPV) cation channel OCR-2. TRPV channels have previously been implicated in transcriptional regulation of neuronal genes in the nematode, although the precise mechanism remains unclear. We show that the NLS in OCR-2 is functional, being able to direct nuclear accumulation of a synthetic cargo protein as well as the carboxy-terminal cytosolic tail of OCR-2 where it is endogenously found. Furthermore, we discovered that a carboxy-terminal portion of the full-length channel can localize to the nucleus of neuronal cells. These results suggest that the OCR-2 TRPV cation channel may have a direct nuclear function in neuronal cells that was not previously appreciated.

  13. A Functional Nuclear Localization Sequence in the C. elegans TRPV Channel OCR-2

    PubMed Central

    Ezak, Meredith J.; Ferkey, Denise M.

    2011-01-01

    The ability to modulate gene expression in response to sensory experience is critical to the normal development and function of the nervous system. Calcium is a key activator of the signal transduction cascades that mediate the process of translating a cellular stimulus into transcriptional changes. With the recent discovery that the mammalian Cav1.2 calcium channel can be cleaved, enter the nucleus and act as a transcription factor to control neuronal gene expression, a more direct role for the calcium channels themselves in regulating transcription has begun to be appreciated. Here we report the identification of a nuclear localization sequence (NLS) in the C. elegans transient receptor potential vanilloid (TRPV) cation channel OCR-2. TRPV channels have previously been implicated in transcriptional regulation of neuronal genes in the nematode, although the precise mechanism remains unclear. We show that the NLS in OCR-2 is functional, being able to direct nuclear accumulation of a synthetic cargo protein as well as the carboxy-terminal cytosolic tail of OCR-2 where it is endogenously found. Furthermore, we discovered that a carboxy-terminal portion of the full-length channel can localize to the nucleus of neuronal cells. These results suggest that the OCR-2 TRPV cation channel may have a direct nuclear function in neuronal cells that was not previously appreciated. PMID:21957475

  14. On-board SPECT for localizing functional targets: a simulation study.

    PubMed

    Roper, Justin; Bowsher, James; Yin, Fang-Fang

    2009-05-01

    Single photon emission computed tomography (SPECT) was investigated for imaging on-board radiation therapy machines in order to localize functional and molecular targets. A computer-simulated female NCAT phantom was positioned supine on a flat-top treatment couch. Twenty tumor locations were defined in the upper torso. The eight lung tumors were subject to the effects of respiratory motion. Tumor diameters of 10.8, 14.4, and 21.6 mm were simulated for tumor-to-background ratios of 3:1 and 6:1 that are characteristic of the radiotracer 99mTc-sestamibi. Projection images representing scan times of 4, 8, and 20 min were simulated for an anterior, half-circular trajectory. Images were reconstructed with attenuation correction by ordered-subsets expectation maximization (OSEM) using six subsets and five iterations. Contrast-to-noise ratios (CNRs) were calculated from ensembles of 25 images. Cross correlation with a noise-free tumor template was used to select the most suspicious tumor location within a 14.4-mm-radius search volume surrounding each tumor, with only that one tumor in each search volume. Localization accuracy was assessed by calculating average distances between measured and true tumor locations. Localization accuracy and CNRs were strongly affected by tumor location relative to the detector trajectory. For example, CNR values near the chest wall were greater by a factor of 3.5 than for tumors near the spine and posterior ribs, a much greater effect than the factor of 1.6 difference in CNR between 6:1 and 3:1 tumor uptakes. Typically, tumors of 6:1 uptake were localized as accurately with 4 min of scan time as tumors of 3:1 uptake that had been imaged for 20 min. Using 4 min scans, 14.4 and 21.6 mm anterior tumors of 6:1 uptake were localized within 2 mm. These results suggest that SPECT, on-board radiation therapy machines, may be a viable modality for localizing certain functional and molecular targets using relatively short scan times.

  15. Functional analysis of the Cucumber mosaic virus 2b protein: pathogenicity and nuclear localization.

    PubMed

    Wang, Yongzeng; Tzfira, Tzvi; Gaba, Victor; Citovsky, Vitaly; Palukaitis, Peter; Gal-On, Amit

    2004-10-01

    The 2b protein encoded by Cucumber mosaic virus (CMV) has been shown to be a silencing suppressor and pathogenicity determinant in solanaceous hosts, but a movement determinant in cucumber. In addition, synergistic interactions between CMV and Zucchini yellow mosaic virus (ZYMV) have been described in several cucurbit species. Here, it was shown that deletion of the 2b gene from CMV prevented extensive systemic movement of the virus in zucchini squash, which could not be complemented by co-infection with ZYMV. Thus, ZYMV expressing a silencing suppressor with a different target could not complement the CMV 2b-specific movement function. Expression of the 2b protein from an attenuated ZYMV vector resulted in a synergistic response, largely restoring infection symptoms of wild-type ZYMV in several cucurbit species. Deletion or alteration of either of two nuclear localization signals (NLSs) did not affect nuclear localization in two assays, but did affect pathogenicity in several cucurbit species, whilst deletion of both NLSs led to loss of nuclear localization. The 2b protein interacted with an Arabidopsis thaliana karyopherin alpha protein (AtKAPalpha) in the yeast two-hybrid system, as did each of the two single NLS-deletion mutants. However, 2b protein containing a deletion of both NLSs was unable to interact with AtKAPalpha. These data suggest that the 2b protein localizes to the nucleus by using the karyopherin alpha-mediated system, but demonstrate that nuclear localization was insufficient for enhancement of the 2b-mediated pathogenic response in cucurbit hosts. Thus, the sequences corresponding to the two NLSs must have another role leading to pathogenicity enhancement.

  16. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain

    PubMed Central

    Hatayama, Minoru; Tomizawa, Tadashi; Sakai-Kato, Kumiko; Bouvagnet, Patrice; Kose, Shingo; Imamoto, Naoko; Yokoyama, Shigeyuki; Utsunomiya-Tate, Naoko; Mikoshiba, Katsuhiko; Kigawa, Takanori; Aruga, Jun

    2008-01-01

    Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy. Here we revealed the structural and functional basis of the nuclear localization signal (NLS) of ZIC3 and investigated its relationship to the defect caused by ZF1 mutation. The ZIC3 NLS was located in the ZF2 and ZF3 regions, rather than ZF1. Several basic residues interspersed throughout these regions were responsible for the nuclear localization, but R320, K337 and R350 were particularly important. NMR structure analysis revealed that ZF1–4 had a similar structure to GLI ZF, and the basic side chains of the NLS clustered together in two regions on the protein surface, similar to classical bipartite NLSs. Among the residues for the ZF1 mutations, C253 and H286 were positioned for the metal chelation, whereas W255 was positioned in the hydrophobic core formed by ZF1 and ZF2. Tryptophan 255 was a highly conserved inter-finger connector and formed part of a structural motif (tandem CXW-C-H-H) that is shared with GLI, Glis and some fungal ZF proteins. Furthermore, we found that knockdown of Karyopherin α1/α6 impaired ZIC3 nuclear localization, and physical interactions between the NLS and the nuclear import adapter proteins were disturbed by mutations in the NLS but not by W255G. These results indicate that ZIC3 is imported into the cell nucleus by the Karyopherin (Importin) system and that the impaired nuclear localization by the ZF1 mutation is not due to a direct influence on the NLS. PMID:18716025

  17. Making assessment locally relevant: measuring functioning for maternal depression in Khayelitsha, Cape Town

    PubMed Central

    Baron, Emily; Davies, Thandi; Bass, Judith; Lund, Crick

    2015-01-01

    Purpose We developed a locally relevant functioning assessment instrument (FAI) for pregnant women and mothers of young babies to complement a widely validated instrument—the World Health Organization’s Disability Assessment Schedule (WHODAS) 12-item version. The FAI is an outcome measure in a randomised controlled trial on the effectiveness of a lay counsellor administered intervention for distressed pregnant women in Khayelitsha, Cape Town. Methods Nine items most commonly reported by 40 pregnant women or mothers with young babies in qualitative interviews were selected for the instrument, with a 10th item ‘Other’. The FAI was validated with 142 pregnant women and mothers in Khayelitsha. Analysis was conducted to assess internal reliability, exploratory factor analysis and convergent validity. Results The FAI had good internal reliability (Cronbach’s alpha = 0.77) and the explanatory factor analysis showed a clear 3-factor solution, relating to domestic, childcare and social activities. The FAI scores showed floor effects, but were positively correlated with the two measures of functioning (WHODAS 2.0 and Washington Group Short Set). The FAI scores also correlated with the measure of depression (Edinburgh Postnatal Depression Scale—EPDS), reflecting increased functional limitations associated with increased depressive symptoms. Conclusion The results show that the FAI has good internal reliability, and good convergent and construct validity as a measure of functioning for this context. This paper reports on the process of developing an instrument and highlights the importance of using instruments that are locally relevant to ensure accurate measurement of functional status. PMID:25567235

  18. Constrained localized-warping-reduced registration errors due to lesions in functional neuroimages

    NASA Astrophysics Data System (ADS)

    Radau, Perry E.; Slomka, Piotr J.; Julin, Per; Svensson, Leif; Wahlund, Lars-Olof

    2001-07-01

    The constrained, localized warping (CLW) algorithm was developed to minimize the registration errors caused by hypoperfusion lesions. SPECT brain perfusion images from 21 Alzheimer patients and 35 controls were analyzed. CLW automatically determines homologous landmarks on patient and template images. CLW was constrained by anatomy and where lesions were probable. CLW was compared with 3rd-degree, polynomial warping (AIR 3.0). Accuracy was assessed by correlation, overlap, and variance. 16 lesion types were simulated, repeated with 5 images. The errors in defect volume and intensity after registration were estimated by comparing the images resulting from warping transforms calculated when the defects were or were not present. Registration accuracy of normal studies was very similar between CLW and polynomial warping methods, and showed marked improvement over linear registration. The lesions had minimal effect on the CLW algorithm accuracy, with small errors in volume (> -4%) and intensity (< +2%). The accuracy improvement compared with not warping was nearly constant regardless of defect: +1.5% overlap and +0.001 correlation. Polynomial warping caused larger errors in defect volume (< -10%) and intensity (> +2.5%) for most defects. CLW is recommended because it caused small errors in defect estimation and improved the registration accuracy in all cases.

  19. Stellar mass functions: methods, systematics and results for the local Universe

    NASA Astrophysics Data System (ADS)

    Weigel, Anna K.; Schawinski, Kevin; Bruderer, Claudio

    2016-06-01

    We present a comprehensive method for determining stellar mass functions, and apply it to samples in the local Universe. We combine the classical 1/Vmax approach with STY, a parametric maximum likelihood method and step-wise maximum likelihood, a non-parametric maximum likelihood technique. In the parametric approach, we are assuming that the stellar mass function can be modelled by either a single or a double Schechter function and we use a likelihood ratio test to determine which model provides a better fit to the data. We discuss how the stellar mass completeness as a function of z biases the three estimators and how it can affect, especially the low-mass end of the stellar mass function. We apply our method to Sloan Digital Sky Survey DR7 data in the redshift range from 0.02 to 0.06. We find that the entire galaxy sample is best described by a double Schechter function with the following parameters: log (M*/M⊙) = 10.79 ± 0.01, log (Φ ^{{ast }}_1/h^3 Mpc^{-3}) = -3.31 ± 0.20, α1 = -1.69 ± 0.10, log (Φ ^{{ast }}_2/h^3 Mpc^{-3}) = -2.01 ± 0.28 and α2 = -0.79 ± 0.04. We also use morphological classifications from Galaxy Zoo and halo mass, overdensity, central/satellite, colour and specific star formation rate measurements to split the galaxy sample into over 130 subsamples. We determine and present the stellar mass functions and the best-fitting Schechter function parameters for each of these subsamples.

  20. Electron affinities for rare gases and some actinides from local-spin-density-functional theory

    SciTech Connect

    Guo, Y.; Wrinn, M.C.; Whitehead, M.A. )

    1989-12-01

    The negative ions of the rare gases (He, Ne, Ar, Kr, Xe, and Rn) and some actinides (Pu, Am, Bk, Cf, and Es) have been calculated self-consistently by the generalized exchange local-spin-density-functional theory with self-interaction correction and correlation. The electron affinities were obtained as the differences between the statistical total energies of the negative ions and neutral atoms; the electron affinities were positive around several millirydbergs. Consequently, the negative ions are predicted stable for the rare gases and actinides.

  1. Using an iterative eigensolver to compute vibrational energies with phase-spaced localized basis functions

    SciTech Connect

    Brown, James Carrington, Tucker

    2015-07-28

    Although phase-space localized Gaussians are themselves poor basis functions, they can be used to effectively contract a discrete variable representation basis [A. Shimshovitz and D. J. Tannor, Phys. Rev. Lett. 109, 070402 (2012)]. This works despite the fact that elements of the Hamiltonian and overlap matrices labelled by discarded Gaussians are not small. By formulating the matrix problem as a regular (i.e., not a generalized) matrix eigenvalue problem, we show that it is possible to use an iterative eigensolver to compute vibrational energy levels in the Gaussian basis.

  2. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M local duality.

  3. EPW: Electron-phonon coupling, transport and superconducting properties using maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Poncé, S.; Margine, E. R.; Verdi, C.; Giustino, F.

    2016-12-01

    The EPW (Electron-Phonon coupling using Wannier functions) software is a Fortran90 code that uses density-functional perturbation theory and maximally localized Wannier functions for computing electron-phonon couplings and related properties in solids accurately and efficiently. The EPW v4 program can be used to compute electron and phonon self-energies, linewidths, electron-phonon scattering rates, electron-phonon coupling strengths, transport spectral functions, electronic velocities, resistivity, anisotropic superconducting gaps and spectral functions within the Migdal-Eliashberg theory. The code now supports spin-orbit coupling, time-reversal symmetry in non-centrosymmetric crystals, polar materials, and k and q-point parallelization. Considerable effort was dedicated to optimization and parallelization, achieving almost a ten times speedup with respect to previous releases. A computer test farm was implemented to ensure stability and portability of the code on the most popular compilers and architectures. Since April 2016, version 4 of the EPW code is fully integrated in and distributed with the Quantum ESPRESSO package, and can be downloaded through QE-forge at http://qe-forge.org/gf/project/q-e.

  4. Functional role of unmyelinated tactile afferents in human hairy skin: sympathetic response and perceptual localization.

    PubMed

    Olausson, Håkan; Cole, Jonathan; Rylander, Karin; McGlone, Francis; Lamarre, Yves; Wallin, B Gunnar; Krämer, Heidrun; Wessberg, Johan; Elam, Mikael; Bushnell, M Catherine; Vallbo, Ake

    2008-01-01

    In addition to A-beta fibres the human hairy skin has unmyelinated (C) fibres responsive to light touch. Previous functional magnetic resonance imaging (fMRI) studies in a subject with a neuronopathy who specifically lacks A-beta afferents indicated that tactile C afferents (CT) activate insular cortex, whereas no response was seen in somatosensory areas 1 and 2. Psychophysical tests suggested that CT afferents give rise to an inconsistent perception of weak and pleasant touch. By examining two neuronopathy subjects as well as control subjects we have now demonstrated that CT stimulation can elicit a sympathetic skin response. Further, the neuronopathy subjects' ability to localize stimuli which activate CT afferents was very poor but above chance level. The findings support the interpretation that the CT system is well suited to underpin affective rather than discriminative functions of tactile sensations.

  5. Functional mapping of cell surface proteins with localized stimulation of single cells

    NASA Astrophysics Data System (ADS)

    Sun, Bingyun; Chiu, Daniel T.

    2003-11-01

    This paper describes the development of using individual micro and nano meter-sized vesicles as delivery vessels to functionally map the distribution of cell surface proteins at the level of single cells. The formation of different sizes of vesicles from tens of nanometers to a few micrometers in diameter that contain the desired molecules is addressed. An optical trap is used to manipulate the loaded vesicle to specific cell morphology of interest, and a pulsed UV laser is used to photo-release the stimuli onto the cell membrane. Carbachol activated cellular calcium flux, upon binding to muscarinic acetylcholine receptors, is studied by this method, and the potential of using this method for the functional mapping of localized proteins on the cell surface membrane is discussed.

  6. First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

    NASA Astrophysics Data System (ADS)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-04-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

  7. Approaching many-body localization from disordered Luttinger liquids via the functional renormalization group

    NASA Astrophysics Data System (ADS)

    Karrasch, C.; Moore, J. E.

    2015-09-01

    We study the interplay of interactions and disorder in a one-dimensional fermion lattice coupled adiabatically to infinite reservoirs. We employ both the functional renormalization group (FRG) as well as matrix product state techniques, which serve as an accurate benchmark for small systems. Using the FRG, we compute the length- and temperature-dependence of the conductance averaged over 104 samples for lattices as large as 105 sites. We identify regimes in which non-Ohmic power law behavior can be observed and demonstrate that the corresponding exponents can be understood by adapting earlier predictions obtained perturbatively for disordered Luttinger liquids. In the presence of both disorder and isolated impurities, the conductance has a universal single-parameter scaling form. This lays the groundwork for an application of the functional renormalization group to the realm of many-body localization.

  8. Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

    PubMed Central

    2013-01-01

    Background Most proteins have evolved in specific cellular compartments that limit their functions and potential interactions. On the other hand, motifs define amino acid arrangements conserved between protein family members and represent powerful tools for assigning function to protein sequences. The ideal motif would identify all members of a protein family but in practice many motifs identify both family members and unrelated proteins, referred to as True Positive (TP) and False Positive (FP) sequences, respectively. Results To address the relationship between protein motifs, protein function and cellular localization, we systematically assigned subcellular localization data to motif sequences from the comprehensive PROSITE sequence motif database. Using this data we analyzed relationships between localization and function. We find that TPs and FPs have a strong tendency to localize in different compartments. When multiple localizations are considered, TPs are usually distributed between related cellular compartments. We also identified cases where FPs are concentrated in particular subcellular regions, indicating possible functional or evolutionary relationships with TP sequences of the same motif. Conclusions Our findings suggest that the systematic examination of subcellular localization has the potential to uncover evolutionary and functional relationships between motif-containing sequences. We believe that this type of analysis complements existing motif annotations and could aid in their interpretation. Our results shed light on the evolution of cellular organelles and potentially establish the basis for new subcellular localization and function prediction algorithms. PMID:23865897

  9. Local network structure of a-SiC:H and its correlation with dielectric function

    SciTech Connect

    Kageyama, Shota; Matsuki, Nobuyuki; Fujiwara, Hiroyuki

    2013-12-21

    The microscopic disordered structures of hydrogenated amorphous silicon carbide (a-Si{sub 1−x}C{sub x}:H) layers with different carbon contents have been determined based on the correlations between the dielectric function in the ultraviolet/visible region and the local bonding states studied by high-sensitivity infrared attenuated total reflection spectroscopy. We find that the microscopic structure of the a-Si{sub 1−x}C{sub x}:H layers fabricated by plasma-enhanced chemical vapor deposition shows a sharp structural transition at a boundary of x = 6.3 at. %. In the regime of x ≤ 6.3 at. %, (i) the amplitude of the a-SiC:H dielectric function reduces and (ii) the SiH{sub 2} content increases drastically with x, even though most of the C atoms are introduced into the tetrahedral sites without bonding with H. In the regime of x > 6.3 at. %, on the other hand, (i) the amplitude of the dielectric function reduces further and (ii) the concentration of the sp{sup 3} CH{sub n} (n = 2,3) groups increases. Moreover, we obtained the direct evidence that the sp{sup 2} C bonding state in the a-SiC matrix exists in the configuration of C = CH{sub 2} and the generation of the graphite-like C = CH{sub 2} unit suppresses the band gap widening significantly. At high C contents of x > 6.3 at. %, the a-SiC:H layers show quite porous structures due to the formation of microvoids terminated with the SiH{sub 2}/CH{sub n} groups. By taking the SiH{sub 2}/CH{sub n} microvoid generation in the network and the high-energy shift of the dielectric function by the local bonding states into account, the a-SiC:H dielectric function model has been established. From the analysis using this model, we have confirmed that the a-SiC:H optical properties in the ultraviolet/visible region are determined almost completely by the local network structures.

  10. Effect of skin sympathetic response to local or systemic cold exposure on thermoregulatory functions in humans.

    PubMed

    Sawasaki, N; Iwase, S; Mano, T

    2001-03-23

    We studied how, sympathetic response to cold exposure determines thermoregulatory function. Three female and seven male volunteers (age, 23.2+/-1.9 years) were exposed to abrupt local cooling and gradual systemic cooling with recording of microneurographic skin sympathetic nerve activity tSSNA), skill temperatures (Ts), tympanic temperature (Tty), skin blood flow measured by laser Doppler flowmetry, and sweating rate measured with a ventilated capsule. Local cooling induced an abrupt vasoconstrictor SSNA increase and Tty rise. There was a significant positive correlation between the increase in the vasoconstrictor SSNA and the change rate of Tty. Systemic cooling at 0.2 degrees C/min enhanced SSNA but gradually decreased Tty, and a significant negative correlation was observed between them. A 10-min delay separated the SSNA rise from the subsequent Tty rise following local cooling. A delay of less than 1 min preceded the SSNA increase after the Tty fall induced by systemic cooling. These findings suggested that subjects with a good SSNA response to cold stress can maintain core temperature, but 10 min is necessary to raise the core temperature by reducing heat loss from the skin surface. In contrast. vasoconstrictor SSNA responds linearly to a fall in core temperature with a delay of less than 1 min.

  11. Efficient Approximation of Head-Related Transfer Functions in Subbands for Accurate Sound Localization

    PubMed Central

    Marelli, Damián; Baumgartner, Robert; Majdak, Piotr

    2015-01-01

    Head-related transfer functions (HRTFs) describe the acoustic filtering of incoming sounds by the human morphology and are essential for listeners to localize sound sources in virtual auditory displays. Since rendering complex virtual scenes is computationally demanding, we propose four algorithms for efficiently representing HRTFs in subbands, i.e., as an analysis filterbank (FB) followed by a transfer matrix and a synthesis FB. All four algorithms use sparse approximation procedures to minimize the computational complexity while maintaining perceptually relevant HRTF properties. The first two algorithms separately optimize the complexity of the transfer matrix associated to each HRTF for fixed FBs. The other two algorithms jointly optimize the FBs and transfer matrices for complete HRTF sets by two variants. The first variant aims at minimizing the complexity of the transfer matrices, while the second one does it for the FBs. Numerical experiments investigate the latency-complexity trade-off and show that the proposed methods offer significant computational savings when compared with other available approaches. Psychoacoustic localization experiments were modeled and conducted to find a reasonable approximation tolerance so that no significant localization performance degradation was introduced by the subband representation. PMID:26681930

  12. A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

    PubMed

    Saad, Ziad S; Glen, Daniel R; Chen, Gang; Beauchamp, Michael S; Desai, Rutvik; Cox, Robert W

    2009-02-01

    Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

  13. Vector-Valued Localizing Basis Functions on the Sphere for Satellite Geomagnetic Data Analysis

    NASA Astrophysics Data System (ADS)

    Plattner, A.; Simons, F. J.; Wei, L.

    2011-12-01

    For the analysis and inversion of scalar (potential) fields on the sphere, spatiospectrally localized ``Slepian'' functions have proven to be a viable tool, enjoying a growing popularity, especially in geodesy but also in seismology and geodynamics. These functions, linear combinations of spherical harmonics, are typically spectrally bandlimited while spatially concentrated, by quadratic optimization, to a target region on the sphere. The family of functions that is obtained in this manner remains a globally orthornomal basis but is also orthogonal over the area of interest, which makes them suitable for the representation and analysis of global as well as regional data sets, even those showing features that warrant a multiresolution approach. Localized spherical analysis of vector fields such as would be demanded by geomagnetic satellite missions has not been attempted in this consistent framework. In this presentation we construct bandlimited vector-spherical-harmonics based Slepian basis sets for the study of such data, on regular symmetric and irregularly shaped domains on the surface of the sphere. These will be ideally suited for the separation of lithospheric and deeper sources of the magnetic field from processed solutions of the terrestrial magnetic field, in new inversions for crustal magnetization from primary data, in the analysis of solar flares, and so on. We pay special attention to algorithmic and numerical efficiency in the construction of the vectorial Slepian basis even to high degrees, and present several alternative approaches by which they can be computed depending on the application of interest and the acquisition geometry of the data. A first example of their use in an inversion scheme will use a Slepian basis set that, by judicious truncation, provides a natural regularization and hence an alternative solution to the traditional damped least-squares vector-spherical-harmonic approaches that are computationally more demanding and numerically

  14. Functional redundancies, distinct localizations and interactions among three fission yeast homologs of centromere protein-B.

    PubMed Central

    Irelan, J T; Gutkin, G I; Clarke, L

    2001-01-01

    Several members of protein families that are conserved in higher eukaryotes are known to play a role in centromere function in the fission yeast Schizosaccharomyces pombe, including two homologs of the mammalian centromere protein CENP-B, Abp1p and Cbh1p. Here we characterize a third S. pombe CENP-B homolog, Cbh2p (CENP-B homolog 2). cbh2Delta strains exhibited a modest elevation in minichromosome loss, similar to cbh1Delta or abp1Delta strains. cbh2Delta cbh1Delta strains showed little difference in growth or minichromosome loss rate when compared to single deletion strains. In contrast, cbh2Delta abp1Delta strains displayed dramatic morphological and chromosome segregation defects, as well as enhancement of the slow-growth phenotype of abp1Delta strains, indicating partial functional redundancy between these proteins. Both cbh2Delta abp1Delta and cbh1Delta abp1Delta strains also showed strongly enhanced sensitivity to a microtubule-destabilizing drug, consistent with a mitotic function for these proteins. Cbh2p was localized to the central core and core-associated repeat regions of centromeric heterochromatin, but not at several other centromeric and arm locations tested. Thus, like its mammalian counterpart, Cbh2p appeared to be localized exclusively to a portion of centromeric heterochromatin. In contrast, Abp1p was detected in both centromeric heterochromatin and in chromatin at two of three replication origins tested. Cbh2p and Abp1p homodimerized in the budding yeast two-hybrid assay, but did not interact with each other. These results suggest that indirect cooperation between different CENP-B-like DNA binding proteins with partially overlapping chromatin distributions helps to establish a functional centromere. PMID:11238404

  15. Neuronal ClC-3 Splice Variants Differ in Subcellular Localizations, but Mediate Identical Transport Functions.

    PubMed

    Guzman, Raul E; Miranda-Laferte, Erick; Franzen, Arne; Fahlke, Christoph

    2015-10-23

    ClC-3 is a member of the CLC family of anion channels and transporters, for which multiple functional properties and subcellular localizations have been reported. Since alternative splicing often results in proteins with diverse properties, we investigated to what extent alternative splicing might influence subcellular targeting and function of ClC-3. We identified three alternatively spliced ClC-3 isoforms, ClC-3a, ClC-3b, and ClC-3c, in mouse brain, with ClC-3c being the predominant splice variant. Whereas ClC-3a and ClC-3b are present in late endosomes/lysosomes, ClC-3c is targeted to recycling endosomes via a novel N-terminal isoleucine-proline (IP) motif. Surface membrane insertion of a fraction of ClC-3c transporters permitted electrophysiological characterization of this splice variant through whole-cell patch clamping on transfected mammalian cells. In contrast, neutralization of the N-terminal dileucine-like motifs was required for functional analysis of ClC-3a and ClC-3b. Heterologous expression of ClC-3a or ClC-3b carrying mutations in N-terminal dileucine motifs as well as WTClC-3c in HEK293T cells resulted in outwardly rectifying Cl(-) currents with significant capacitive current components. We conclude that alternative splicing of Clcn3 results in proteins with different subcellular localizations, but leaves the transport function of the proteins unaffected.

  16. Neuronal ClC-3 Splice Variants Differ in Subcellular Localizations, but Mediate Identical Transport Functions*

    PubMed Central

    Guzman, Raul E.; Miranda-Laferte, Erick; Franzen, Arne; Fahlke, Christoph

    2015-01-01

    ClC-3 is a member of the CLC family of anion channels and transporters, for which multiple functional properties and subcellular localizations have been reported. Since alternative splicing often results in proteins with diverse properties, we investigated to what extent alternative splicing might influence subcellular targeting and function of ClC-3. We identified three alternatively spliced ClC-3 isoforms, ClC-3a, ClC-3b, and ClC-3c, in mouse brain, with ClC-3c being the predominant splice variant. Whereas ClC-3a and ClC-3b are present in late endosomes/lysosomes, ClC-3c is targeted to recycling endosomes via a novel N-terminal isoleucine-proline (IP) motif. Surface membrane insertion of a fraction of ClC-3c transporters permitted electrophysiological characterization of this splice variant through whole-cell patch clamping on transfected mammalian cells. In contrast, neutralization of the N-terminal dileucine-like motifs was required for functional analysis of ClC-3a and ClC-3b. Heterologous expression of ClC-3a or ClC-3b carrying mutations in N-terminal dileucine motifs as well as WTClC-3c in HEK293T cells resulted in outwardly rectifying Cl− currents with significant capacitive current components. We conclude that alternative splicing of Clcn3 results in proteins with different subcellular localizations, but leaves the transport function of the proteins unaffected. PMID:26342074

  17. Probing Local Ionic Dynamics in Functional Oxides: From Nanometer to Atomic Scale

    NASA Astrophysics Data System (ADS)

    Kalinin, Sergei

    2014-03-01

    Vacancy-mediated electrochemical reactions in oxides underpin multiple applications ranging from electroresistive memories, to chemical sensors to energy conversion systems such as fuel cells. Understanding the functionality in these systems requires probing reversible (oxygen reduction/evolution reaction) and irreversible (cathode degradation and activation, formation of conductive filaments) electrochemical processes. In this talk, I summarize recent advances in probing and controlling these transformations locally on nanometer level using scanning probe microscopy. The localized tip concentrates the electric field in the nanometer scale volume of material, inducing local transition. Measured simultaneously electromechanical response (piezoresponse) or current (conductive AFM) provides the information on the bias-induced changes in material. Here, I illustrate how these methods can be extended to study local electrochemical transformations, including vacancy dynamics in oxides such as titanates, LaxSr1-xCoO3, BiFeO3, and YxZr1-xO2. The formation of electromechanical hysteresis loops and their bias-, temperature- and environment dependences provide insight into local electrochemical mechanisms. In materials such as lanthanum-strontium cobaltite, mapping both reversible vacancy motion and vacancy ordering and static deformation is possible, and can be corroborated by post mortem STEM/EELS studies. In ceria, a broad gamut of electrochemical behaviors is observed as a function of temperature and humidity. The possible strategies for elucidation ionic motion at the electroactive interfaces in oxides using high-resolution electron microscopy and combined ex-situ and in-situ STEM-SPM studies are discussed. In the second part of the talk, probing electrochemical phenomena on in-situ grown surfaces with atomic resolution is illustrated. I present an approach based on the multivariate statistical analysis of the coordination spheres of individual atoms to reveal

  18. Structure and functionalization of mesoporous bioceramics for bone tissue regeneration and local drug delivery.

    PubMed

    Vallet-Regí, María; Izquierdo-Barba, Isabel; Colilla, Montserrat

    2012-03-28

    This review article describes the importance of structure and functionalization in the performance of mesoporous silica bioceramics for bone tissue regeneration and local drug delivery purposes. Herein, we summarize the pivotal features of mesoporous bioactive glasses, also known as 'templated glasses' (TGs), which present chemical compositions similar to those of conventional bioactive sol-gel glasses and the added value of an ordered mesopore arrangement. An in-depth study concerning the possibility of tailoring the structural and textural characteristics of TGs at the nanometric scale and their influence on bioactive behaviour is discussed. The highly ordered mesoporous arrangement of cavities allows these materials to confine drugs to be subsequently released, acting as drug delivery devices. The functionalization of mesoporous silica walls has been revealed as the cornerstone in the performance of these materials as controlled release systems. The synergy between the improved bioactive behaviour and local sustained drug release capability of mesostructured materials makes them suitable to manufacture three-dimensional macroporous scaffolds for bone tissue engineering. Finally, this review tackles the possibility of covalently grafting different osteoinductive agents to the scaffold surface that act as attracting signals for bone cells to promote the bone regeneration process.

  19. Deep brain stimulation mechanisms: beyond the concept of local functional inhibition.

    PubMed

    Deniau, Jean-Michel; Degos, Bertrand; Bosch, Clémentine; Maurice, Nicolas

    2010-10-01

    Deep brain electrical stimulation has become a recognized therapy in the treatment of a variety of motor disorders and has potentially promising applications in a wide range of neurological diseases including neuropsychiatry. Behavioural observation that electrical high-frequency stimulation of a given brain area induces an effect similar to a lesion suggested a mechanism of functional inhibition. In vitro and in vivo experiments as well as per operative recordings in patients have revealed a variety of effects involving local changes of neuronal excitability as well as widespread effects throughout the connected network resulting from activation of axons, including antidromic activation. Here we review current data regarding the local and network activity changes induced by high-frequency stimulation of the subthalamic nucleus and discuss this in the context of motor restoration in Parkinson's disease. Stressing the important functional consequences of axonal activation in deep brain stimulation mechanisms, we highlight the importance of developing anatomical knowledge concerning the fibre connections of the putative therapeutic targets.

  20. Evidence for local relaxin ligand-receptor expression and function in arteries.

    PubMed

    Novak, Jacqueline; Parry, Laura J; Matthews, Julianna E; Kerchner, Laurie J; Indovina, Kimberly; Hanley-Yanez, Karen; Doty, Ketah D; Debrah, Dan O; Shroff, Sanjeev G; Conrad, Kirk P

    2006-11-01

    Relaxin is a 6 kDa protein hormone produced by the corpus luteum and secreted into the blood during pregnancy in rodents and humans. Growing evidence indicates that circulating relaxin causes vasodilatation and increases in arterial compliance, which may be among its most important actions during pregnancy. Here we investigated whether there is local expression and function of relaxin and relaxin receptor in arteries of nonpregnant females and males. Relaxin-1 and its major receptor, Lgr7, mRNA are expressed in thoracic aortas, small renal and mesenteric arteries from mice and rats of both sexes, as well as in small renal arteries from female tammar wallabies (an Australian marsupial). Using available antibodies for rat and mouse Lgr7 receptor and rat relaxin, we also identified protein expression in arteries. Small renal arteries isolated from relaxin-1 gene-deficient mice demonstrate enhanced myogenic reactivity and decreased passive compliance relative to wild-type (WT) and heterozygous mice. Taken together, these findings reveal an arterial-derived, relaxin ligand-receptor system that acts locally to regulate arterial function.

  1. Functional Local Renin-Angiotensin System in Human and Rat Periodontal Tissue

    PubMed Central

    Santos, Carlos F.; Morandini, Ana C.; Dionísio, Thiago J.; Faria, Flávio A.; Lima, Marta C.; Figueiredo, Caio M.; Colombini-Ishikiriama, Bella L.; Sipert, Carla R.; Maciel, Rubens P.; Akashi, Ana P.; Souza, Gabriela P.; Garlet, Gustavo P.; Rodini, Camila O.; Amaral, Sandra L.; Becari, Christiane; Salgado, Maria C.; Oliveira, Eduardo B.; Matus, Isaac; Didier, Daniela N.; Greene, Andrew S.

    2015-01-01

    The initiation or progression of periodontitis might involve a local renin-angiotensin system (RAS) in periodontal tissue. The aim of this study was to further characterize the local RAS in human and rat periodontal tissues between healthy and periodontally-affected tissue. Components of the RAS were investigated using in vitro, ex vivo and in vivo experiments involving both human and Wistar rat periodontium. Although not upregulated when challenged with P. gingivalis-lipopolysaccharide, human gingival and periodontal ligament fibroblasts expressed RAS components. Likewise, healthy and inflamed human gingiva expressed RAS components, some of which were shown to be functional, yet no differences in expression were found between healthy and diseased gingiva. However, in inflamed tissue the immunoreactivity was greater for the AT1R compared to AT2R in fibroblasts. When compared to healthy tissue, ACE activity was increased in human gingiva from volunteers with gingivitis. Human-gingiva homogenates generated Ang II, Ang 1-9 and Ang 1-7 when incubated with precursors. In gingiva homogenates, Ang II formation from Ang I was nearly abolished only when captopril and chymostatin were combined. Ang 1-7 formation was significantly greater when human gingiva homogenates were incubated with chymostatin alone compared to incubation without any inhibitor, only captopril, or captopril and chymostatin. In rat gingiva, RAS components were also found; their expression was not different between healthy and experimentally induced periodontitis (EP) groups. However, renin inhibition (aliskiren) and an AT1R antagonist (losartan) significantly blocked EP-alveolar-bone loss in rats. Collectively, these data are consistent with the hypothesis that a local RAS system is not only present but is also functional in both human and rat periodontal tissue. Furthermore, blocking AT1R and renin can significantly prevent periodontal bone loss induced by EP in rats. PMID:26244896

  2. Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites

    PubMed Central

    Park, Jae-Sook; Thorsness, Mary K.; Policastro, Robert; McGoldrick, Luke L.; Hollingsworth, Nancy M.; Thorsness, Peter E.; Neiman, Aaron M.

    2016-01-01

    The Vps13 protein family is highly conserved in eukaryotic cells. Mutations in human VPS13 genes result in a variety of diseases, such as chorea acanthocytosis (ChAc), but the cellular functions of Vps13 proteins are not well defined. In yeast, there is a single VPS13 orthologue, which is required for at least two different processes: protein sorting to the vacuole and sporulation. This study demonstrates that VPS13 is also important for mitochondrial integrity. In addition to preventing transfer of DNA from the mitochondrion to the nucleus, VPS13 suppresses mitophagy and functions in parallel with the endoplasmic reticulum–mitochondrion encounter structure (ERMES). In different growth conditions, Vps13 localizes to endosome–mitochondrion contacts and to the nuclear–vacuole junctions, indicating that Vps13 may function at membrane contact sites. The ability of VPS13 to compensate for the absence of ERMES correlates with its intracellular distribution. We propose that Vps13 is present at multiple membrane contact sites and that separation-of-function mutants are due to loss of Vps13 at specific junctions. Introduction of VPS13A mutations identified in ChAc patients at cognate sites in yeast VPS13 are specifically defective in compensating for the lack of ERMES, suggesting that mitochondrial dysfunction might be the basis for ChAc. PMID:27280386

  3. Modelling Stream-Fish Functional Traits in Reference Conditions: Regional and Local Environmental Correlates

    PubMed Central

    Oliveira, João M.; Segurado, Pedro; Santos, José M.; Teixeira, Amílcar; Ferreira, Maria T.; Cortes, Rui V.

    2012-01-01

    Identifying the environmental gradients that control the functional structure of biological assemblages in reference conditions is fundamental to help river management and predict the consequences of anthropogenic stressors. Fish metrics (density of ecological guilds, and species richness) from 117 least disturbed stream reaches in several western Iberia river basins were modelled with generalized linear models in order to investigate the importance of regional- and local-scale abiotic gradients to variation in functional structure of fish assemblages. Functional patterns were primarily associated with regional features, such as catchment elevation and slope, rainfall, and drainage area. Spatial variations of fish guilds were thus associated with broad geographic gradients, showing (1) pronounced latitudinal patterns, affected mainly by climatic factors and topography, or (2) at the basin level, strong upstream-downstream patterns related to stream position in the longitudinal gradient. Maximum native species richness was observed in midsize streams in accordance with the river continuum concept. The findings of our study emphasized the need to use a multi-scale approach in order to fully assess the factors that govern the functional organization of biotic assemblages in ‘natural’ streams, as well as to improve biomonitoring and restoration of fluvial ecosystems. PMID:23029242

  4. Electron Attachment to POCl3: Measurement and Theoretical Analysis of Rate Constants and Branching Ratios as a Function of Gas Pressure and Temperature, Electron Temperature, and Electron Energy

    DTIC Science & Technology

    2006-03-31

    the pulse along the flow tube axis variation in the total rate constant with temperature.2 In con- with the Langmuir probe . In the electron-He+-Ar...calculations 5 reported in Ref. 4 and should cylindrical Langmuir probe . The plasma velocity is measured be reliable within ±0.1 eV. Electron attachment...increasing temperature decreased diffusion. the amount of parent ion substantially in flowing - afterglow In the present work, POCI3 gas was added

  5. Effect of occupational exposure to local powdered tobacco (snuff) on pulmonary function in south eastern Nigerians.

    PubMed

    Maduka, S O; Osim, E E; Nneli, R O; Anyabolu, A E

    2009-12-01

    The effect of occupational exposure to local powdered tobacco (snuff) on pulmonary function was studied. Snuff industry workers in Onitsha and Enugu markets were studied and compared with age, weight, and height-matched control not exposed to any known air pollutant. The pulmonary indices studied include forced vital capacity [FVC], forced expiratory volume in one second [FEV1] and ratio of FEV1/FVC as percentage using a vitalograph spirometer and Peak Expiratory Flow Rate [PEFR], using a mini Wright Peak Expiratory Flow Meter. The respiratory and non-respiratory symptoms frequently associated with these workers were also analyzed and dust sampling in both test and control environments was also done. The mean anthropometric parameters, [age, height and body weight] between the two groups were not statistically different. The results obtained showed statistically significant impairment of lung function of workers chronically exposed to snuff. FVC, FEV1 and PEFR in the exposed [test] subjects were significantly decreased in comparison with the control subjects [P<0.05]. However, the mean value of FEV1/FVC [%] of the test subjects was 86.8% which was within the normal range and was not significantly different from control. This signified that the test subjects had restrictive pattern of lung function defect. All respiratory symptoms, such as cough, chest tightness had a higher prevalence in test subjects than their control group. The lung function indices of snuff-producing workers proportionately decreased with their length of exposure in the industry. The respirable dust level in the vicinity [indoor] of the snuff-workers [1.11+/-0.35 mg/m3] was significantly [P<0.001] higher than in the control environment[0.37+/-0.086 mg/m3]. Although it was not possible to determine all the factors that may be responsible for lung function impairment, the dust sampling result showed that chronic exposure to Nigerian snuff [powered tobacco] dust impairs lung function and the

  6. Harmonic undulator radiations with constant magnetic field

    NASA Astrophysics Data System (ADS)

    Jeevakhan, Hussain; Mishra, G.

    2015-01-01

    Harmonic undulators has been analysed in the presence of constant magnetic field along the direction of main undulator field. The spectrum modifications in harmonic undulator radiations and intensity degradation as a function of constant magnetic field magnitude at fundamental and third harmonics have been evaluated with a numerical integration method and generalised Bessel function. The role of harmonic field to overcome the intensity reduction due to constant magnetic field and energy spread in electron beam has also been demonstrated.

  7. Linking human brain local activity fluctuations to structural and functional network architectures

    PubMed Central

    Baria, A.T.; Mansour, A.; Huang, L.; Baliki, M.N.; Cecchi, G.A.; Mesulam, M.M.; Apkarian, A.V.

    2013-01-01

    Activity of cortical local neuronal populations fluctuates continuously, and a large proportion of these fluctuations are shared across populations of neurons. Here we seek organizational rules that link these two phenomena. Using neuronal activity, as identified by functional MRI (fMRI) and for a given voxel or brain region, we derive a single measure of full bandwidth brain-oxygenation-level-dependent (BOLD) fluctuations by calculating the slope, α, for the log-linear power spectrum. For the same voxel or region, we also measure the temporal coherence of its fluctuations to other voxels or regions, based on exceeding a given threshold, Θ, for zero lag correlation, establishing functional connectivity between pairs of neuronal populations. From resting state fMRI, we calculated whole-brain group-averaged maps for α and for functional connectivity. Both maps showed similar spatial organization, with a correlation coefficient of 0.75 between the two parameters across all brain voxels, as well as variability with hodology. A computational model replicated the main results, suggesting that synaptic low-pass filtering can account for these interrelationships. We also investigated the relationship between α and structural connectivity, as determined by diffusion tensor imaging-based tractography. We observe that the correlation between α and connectivity depends on attentional state; specifically, α correlated more highly to structural connectivity during rest than while attending to a task. Overall, these results provide global rules for the dynamics between frequency characteristics of local brain activity and the architecture of underlying brain networks. PMID:23396160

  8. Function and subcellular localization of Gcn5, a histone acetyltransferase in Candida albicans.

    PubMed

    Chang, Peng; Fan, Xueyi; Chen, Jiangye

    2015-08-01

    Candida albicans is an opportunistic fungal pathogen commonly found in humans. It has the ability to switch reversibly between three growth forms: budding yeast, pseudohypha, and hypha. The transition between yeast and hyphal growth forms is critical for the pathogenesis of C. albicans. During the yeast-to-hypha morphologic transition, gene expression is regulated by transcriptional regulators including histone modifying complexes and chromatin remodeling complexes. We previously reported that Esa1, a catalytic subunit in the histone acetyltransferase complex NuA4, is essential for the hyphal development of C. albicans. In this study, we analyzed the functional roles of Gcn5, a catalytic subunit in the histone acetyltransferase complex SAGA, in C. albicans. Gcn5 is required for the invasive and filamentous growth of C. albicans. Deletion of GCN5 impaired hyphal elongation in sensing serum and attenuated the virulence of C. albicans in a mouse systemic infection model. The C. albicans gcn5/gcn5 mutant cells also exhibited sensitivity to cell wall stress. Functional analysis showed that the HAT domain and Bromodomain in Gcn5 play distinct roles in morphogenesis and cell wall stress response of C. albicans. Our results show that the conserved residue Glu188 is crucial for the Gcn5 HAT activity and for Gcn5 function during filamentous growth. In addition, the subcellular distribution of ectopically expressed GFP-Gcn5 correlates with the different growth states of C. albicans. In stationary phase, Gcn5 accumulated in the nucleus, while during vegetative growth it localized in the cytoplasm in a morpha-independent manner. Our results suggest that the nuclear localization of Gcn5 depends on the existence of its N-terminal NLS and HAT domains.

  9. On the local theory of stellar convection with μ-gradient using one-point correlation functions

    NASA Astrophysics Data System (ADS)

    Umezu, Minoru

    2008-12-01

    The local equations of Xiong's theory of convection with one-point correlation functions contain the equations for an extended mixing length theory of convection with helium flux by Umezu & Nakakita. The equations also contain the equations for overstable convection of Kato. Similar equations can be derived from those of Grossman et al. and Canuto. The local convection and the overstable convection can be treated in a unified way with their localized equations.

  10. Fundamental Physical Constants

    National Institute of Standards and Technology Data Gateway

    SRD 121 CODATA Fundamental Physical Constants (Web, free access)   This site, developed in the Physics Laboratory at NIST, addresses three topics: fundamental physical constants, the International System of Units (SI), which is the modern metric system, and expressing the uncertainty of measurement results.

  11. TESTING FOR A LARGE LOCAL VOID BY INVESTIGATING THE NEAR-INFRARED GALAXY LUMINOSITY FUNCTION

    SciTech Connect

    Keenan, R. C.; Wang, W.-H.; Barger, A. J.; Wold, I.; Cowie, L. L.; Trouille, L.

    2012-08-01

    Recent cosmological modeling efforts have shown that a local underdensity on scales of a few hundred Mpc (out to z {approx} 0.1) could produce the apparent acceleration of the expansion of the universe observed via Type Ia supernovae. Several studies of galaxy counts in the near-infrared (NIR) have found that the local universe appears underdense by {approx}25%-50% compared with regions a few hundred Mpc distant. Galaxy counts at low redshifts sample primarily L {approx} L* galaxies. Thus, if the local universe is underdense, then the normalization of the NIR galaxy luminosity function (LF) at z > 0.1 should be higher than that measured for z < 0.1. Here we present a highly complete (>90%) spectroscopic sample of 1436 galaxies selected in the H band (1.6 {mu}m) to study the normalization of the NIR LF at 0.1 < z < 0.3 and address the question of whether or not we reside in a large local underdensity. Our survey sample consists of all galaxies brighter than 18th magnitude in the H band drawn from six widely separated fields at high Galactic latitudes, which cover a total of {approx}2 deg{sup 2} on the sky. We find that for the combination of our six fields, the product {phi}*L* at 0.1 < z < 0.3 is {approx}30% higher than that measured at lower redshifts. While our statistical errors in this measurement are on the {approx}10% level, we find the systematics due to cosmic variance may be larger still. We investigate the effects of cosmic variance on our measurement using the COSMOS cone mock catalogs from the Millennium Simulation and recent empirical estimates of cosmic variance. We find that our survey is subject to systematic uncertainties due to cosmic variance at the 15% level (1{sigma}), representing an improvement by a factor of {approx}2 over previous studies in this redshift range. We conclude that observations cannot yet rule out the possibility that the local universe is underdense at z < 0.1. The fields studied in this work have a large amount of publicly

  12. The local stellar luminosity function and mass-to-light ratio in the near-infrared

    NASA Astrophysics Data System (ADS)

    Just, A.; Fuchs, B.; Jahreiß, H.; Flynn, C.; Dettbarn, C.; Rybizki, J.

    2015-07-01

    A new sample of stars, representative of the solar neighbourhood luminosity function (LF), is constructed from the Hipparcos catalogue and the Fifth Catalogue of Nearby Stars. We have cross-matched to sources in the Two Micron All Sky Survey catalogue so that for all stars individually determined near-infrared (NIR) photometry is available on a homogeneous system (typically Ks). The spatial completeness of the sample has been carefully determined by statistical methods, and the NIR LF of the stars has been derived by direct star counts. We find a local volume luminosity of 0.121 ± 0.004 LK⊙ pc-3, corresponding to a volumetric mass-to-light ratio (M/L) of M/L_K = 0.31 ± 0.02 {M}_{⊙}/L_{K⊙}, where giants contribute 80 per cent to the light but less than 2 per cent to the stellar mass. We derive the surface brightness of the solar cylinder with the help of a vertical disc model. We find a surface brightness of 99 LK⊙ pc-2 with an uncertainty of approximately 10 per cent. This corresponds to an M/L for the solar cylinder of M/L_K = 0.34 {M}_{⊙}/L_{K⊙}. The M/L for the solar cylinder is only 10 per cent larger than the local value despite the fact that the local population has a much larger contribution of young stars. It turns out that the effective scaleheights of the lower main sequence carrying most of the mass is similar to that of the giants, which are dominating the NIR light. The corresponding colour for the solar cylinder is V - K = 2.89 mag compared to the local value of V - K = 2.46 mag. An extrapolation of the local surface brightness to the whole Milky Way yields a total luminosity of MK = -24.2 mag. The Milky Way falls in the range of K band Tully-Fisher relations from the literature.

  13. An alternative local collocation strategy for high-convergence meshless PDE solutions, using radial basis functions

    NASA Astrophysics Data System (ADS)

    Stevens, D.; Power, H.; Meng, C. Y.; Howard, D.; Cliffe, K. A.

    2013-12-01

    This work proposes an alternative decomposition for local scalable meshless RBF collocation. The proposed method operates on a dataset of scattered nodes that are placed within the solution domain and on the solution boundary, forming a small RBF collocation system around each internal node. Unlike other meshless local RBF formulations that are based on a generalised finite difference (RBF-FD) principle, in the proposed "finite collocation" method the solution of the PDE is driven entirely by collocation of PDE governing and boundary operators within the local systems. A sparse global collocation system is obtained not by enforcing the PDE governing operator, but by assembling the value of the field variable in terms of the field value at neighbouring nodes. In analogy to full-domain RBF collocation systems, communication between stencils occurs only over the stencil periphery, allowing the PDE governing operator to be collocated in an uninterrupted manner within the stencil interior. The local collocation of the PDE governing operator allows the method to operate on centred stencils in the presence of strong convective fields; the reconstruction weights assigned to nodes in the stencils being automatically adjusted to represent the flow of information as dictated by the problem physics. This "implicit upwinding" effect mitigates the need for ad-hoc upwinding stencils in convective dominant problems. Boundary conditions are also enforced within the local collocation systems, allowing arbitrary boundary operators to be imposed naturally within the solution construction. The performance of the method is assessed using a large number of numerical examples with two steady PDEs; the convection-diffusion equation, and the Lamé-Navier equations for linear elasticity. The method exhibits high-order convergence in each case tested (greater than sixth order), and the use of centred stencils is demonstrated for convective-dominant problems. In the case of linear elasticity

  14. First principles calculations for liquids and solids using maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Swartz, Charles W., VI

    The field of condensed matter computational physics has seen an explosion of applicability over the last 50+ years. Since the very first calculations with ENIAC and MANIAC the field has continued to pushed the boundaries of what is possible; from the first large-scale molecular dynamics simulation, to the implementation of Density Functional Theory and large scale Car-Parrinello molecular dynamics, to million-core turbulence calculations by Standford. These milestones represent not only technological advances but theoretical breakthroughs and algorithmic improvements as well. The work in this thesis was completed in the hopes of furthering such advancement, even by a small fraction. Here we will focus mainly on the calculation of electronic and structural properties of solids and liquids, where we shall implement a wide range of novel approaches that are both computational efficient and physically enlightening. To this end we routinely will work with maximally localized Wannier functions (MLWFs) which have recently seen a revival in mainstream scientific literature. MLWFs present us with interesting opportunity to calculate a localized orbital within the planewave formalism of atomistic simulations. Such a localization will prove to be invaluable in the construction of layer-based superlattice models, linear scaling hybrid functional schemes and model quasiparticle calculations. In the first application of MLWF we will look at modeling functional piezoelectricity in superlattices. Based on the locality principle of insulating superlattices, we apply the method of Wu et al to the piezoelectric strains of individual layers under iifixed displacement field. For a superlattice of arbitrary stacking sequence an accurate model is acquired for predicting piezoelectricity. By applying the model in the superlattices where ferroelectric and antiferrodistortive modes are in competition, functional piezoelectricity can be achieved. A strong nonlinear effect is observed and can

  15. Evidence for a Non-Uniform Initial Mass Function in the Local Universe

    NASA Astrophysics Data System (ADS)

    Meurer, Gerhardt R.; Wong, O. I.; Kim, J. H.; Hanish, D. J.; SUNGG; SINGG

    2009-01-01

    Many results in modern astrophysics rest on the notion that the Initial Mass Function (IMF) is universal. Our observations of a sample of HI selected galaxies in the light of Halpha and the far-ultraviolet (FUV) challenge this result. The extinction corrected flux ratio Halpha/FUV from these two tracers of star formation shows strong correlations with the surface-brightness in Halpha and the R band: Low Surface Brightness (LSB) galaxies have lower Halpha/FUV compared to High Surface Brightness (HSB) galaxies as well as compared to expectations from equilibrium models of constant star formation rate (SFR) using commonly favored IMF parameters. We demonstrate that the correlations are not caused by our corrections for dust absorption, and that models of variable star formation including "bursts" or "gasps" can not explain these correlations. While our data do not rule out systematic variations in the escape fraction of ionizing photons driving the correlations, this would require LSB galaxies to have a higher escape fraction than HSB galaxies which, counter to naive expectations. The most plausible explanation for the correlations is for systematic variations of the upper mass limit or the slope which define the upper end of the IMF. We outline a scenario of pressure driving the correlations and discuss implications of our results. Primary support for the work presented here was obtained through NASA Galex Guest Investigator grant GALEXGI04-0105-0009 and NASA LTSA grant NAG5-13083.

  16. Localization of recombination proteins and Srs2 reveals anti-recombinase function in vivo.

    PubMed

    Burgess, Rebecca C; Lisby, Michael; Altmannova, Veronika; Krejci, Lumir; Sung, Patrick; Rothstein, Rodney

    2009-06-15

    Homologous recombination (HR), although an important DNA repair mechanism, is dangerous to the cell if improperly regulated. The Srs2 "anti-recombinase" restricts HR by disassembling the Rad51 nucleoprotein filament, an intermediate preceding the exchange of homologous DNA strands. Here, we cytologically characterize Srs2 function in vivo and describe a novel mechanism for regulating the initiation of HR. We find that Srs2 is recruited separately to replication and repair centers and identify the genetic requirements for recruitment. In the absence of Srs2 activity, Rad51 foci accumulate, and surprisingly, can form in the absence of Rad52 mediation. However, these Rad51 foci do not represent repair-proficient filaments, as determined by recombination assays. Antagonistic roles for Rad52 and Srs2 in Rad51 filament formation are also observed in vitro. Furthermore, we provide evidence that Srs2 removes Rad51 indiscriminately from DNA, while the Rad52 protein coordinates appropriate filament reformation. This constant breakdown and rebuilding of filaments may act as a stringent quality control mechanism during HR.

  17. Local structure investigation of oxide ion and proton defects in Ge-apatites by pair distribution function analysis.

    PubMed

    Malavasi, Lorenzo; Orera, Alodia; Slater, Peter R; Panchmatia, Pooja M; Islam, M Saiful; Siewenie, Joan

    2011-01-07

    In this communication we provide a direct insight into the local structure and defects of oxygen excess Ge-apatites, in both dry and deuterated states, by means of pair distribution function analysis.

  18. Direct localization of poles of a meromorphic function from measurements on an incomplete boundary

    NASA Astrophysics Data System (ADS)

    Nara, Takaaki; Ando, Shigeru

    2010-01-01

    This paper proposes an algebraic method to reconstruct the positions of multiple poles in a meromorphic function field from measurements on an arbitrary simple arc in it. A novel issue is the exactness of the algorithm depending on whether the arc is open or closed, and whether it encloses or does not enclose the poles. We first obtain a differential equation that can equivalently determine the meromorphic function field. From it, we derive linear equations that relate the elementary symmetric polynomials of the pole positions to weighted integrals of the field along the simple arc and end-point terms of the arc when it is an open one. Eliminating the end-point terms based on an appropriate choice of weighting functions and a combination of the linear equations, we obtain a simple system of linear equations for solving the elementary symmetric polynomials. We also show that our algorithm can be applied to a 2D electric impedance tomography problem. The effects of the proximity of the poles, the number of measurements and noise on the localization accuracy are numerically examined.

  19. Statistical properties of the Green function in finite size for Anderson localization models with multifractal eigenvectors

    NASA Astrophysics Data System (ADS)

    Monthus, Cécile

    2017-03-01

    For Anderson localization models with multifractal eigenvectors on disordered samples containing N sites, we analyze in a unified framework the consequences for the statistical properties of the Green function. We focus in particular on the imaginary part of the Green function at coinciding points GxxI≤ft(E-\\text{i}η \\right) and study the scaling with the size N of the moments of arbitrary indices q when the broadening follows the scaling η =\\frac{c}{{{N}δ}} . For the standard scaling regime δ =1 , we find in the two limits c\\ll 1 and c\\gg 1 that the moments are governed by the anomalous exponents Δ (q) of individual eigenfunctions, without the assumption of strong correlations between the weights of consecutive eigenstates at the same point. For the non-standard scaling regimes 0<δ <1 , we obtain that the imaginary Green function follows some Fréchet distribution in the typical region, while rare events are important to obtain the scaling of the moments. We describe the application to the case of Gaussian multifractality and to the case of linear multifractality.

  20. Presynaptic DLG regulates synaptic function through the localization of voltage-activated Ca2+ Channels

    PubMed Central

    Astorga, César; Jorquera, Ramón A.; Ramírez, Mauricio; Kohler, Andrés; López, Estefanía; Delgado, Ricardo; Córdova, Alex; Olguín, Patricio; Sierralta, Jimena

    2016-01-01

    The DLG-MAGUK subfamily of proteins plays a role on the recycling and clustering of glutamate receptors (GLUR) at the postsynaptic density. discs-large1 (dlg) is the only DLG-MAGUK gene in Drosophila and originates two main products, DLGA and DLGS97 which differ by the presence of an L27 domain. Combining electrophysiology, immunostaining and genetic manipulation at the pre and postsynaptic compartments we study the DLG contribution to the basal synaptic-function at the Drosophila larval neuromuscular junction. Our results reveal a specific function of DLGS97 in the regulation of the size of GLUR fields and their subunit composition. Strikingly the absence of any of DLG proteins at the presynaptic terminal disrupts the clustering and localization of the calcium channel DmCa1A subunit (Cacophony), decreases the action potential-evoked release probability and alters short-term plasticity. Our results show for the first time a crucial role of DLG proteins in the presynaptic function in vivo. PMID:27573697

  1. Estimation of the receptor-state affinity constants of ligands in functional studies using wild type and constitutively active mutant receptors: Implications for estimation of agonist bias.

    PubMed

    Ehlert, Frederick J; Stein, Richard S L

    We describe a method for estimating the affinities of ligands for active and inactive states of a G protein-coupled receptor (GPCR). Our protocol involves measuring agonist-induced signaling responses of a wild type GPCR and a constitutively active mutant of it under control conditions and after partial receptor inactivation or reduced receptor expression. Our subsequent analysis is based on the assumption that the activating mutation increases receptor isomerization into the active state without affecting the affinities of ligands for receptor states. A means of confirming this assumption is provided. Global nonlinear regression analysis yields estimates of 1) the active (Kact) and inactive (Kinact) receptor-state affinity constants, 2) the isomerization constant of the unoccupied receptor (Kq-obs), and 3) the sensitivity constant of the signaling pathway (KE-obs). The latter two parameters define the output response of the receptor, and hence, their ratio (Kq-obs/KE) is a useful measure of system bias. If the cellular system is reasonably stable and the Kq-obs and KE-obs values of the signaling pathway are known, the Kact and Kinact values of additional agonists can be estimated in subsequent experiments on cells expressing the wild type receptor. We validated our method through computer simulation, an analytical proof, and analysis of previously published data. Our approach provides 1) a more meaningful analysis of structure-activity relationships, 2) a means of validating in silico docking experiments on active and inactive receptor structures and 3) an absolute, in contrast to relative, measure of agonist bias.

  2. Dissociation between neural and vascular responses to sympathetic stimulation : contribution of local adrenergic receptor function

    NASA Technical Reports Server (NTRS)

    Jacob, G.; Costa, F.; Shannon, J.; Robertson, D.; Biaggioni, I.

    2000-01-01

    Sympathetic activation produced by various stimuli, eg, mental stress or handgrip, evokes regional vascular responses that are often nonhomogeneous. This phenomenon is believed to be the consequence of the recruitment of differential central neural pathways or of a sympathetically mediated vasodilation. The purpose of this study was to determine whether a similar heterogeneous response occurs with cold pressor stimulation and to test the hypothesis that local differences in adrenergic receptor function could be in part responsible for this diversity. In 8 healthy subjects, local norepinephrine spillover and blood flow were measured in arms and legs at baseline and during sympathetic stimulation induced by baroreflex mechanisms (nitroprusside infusion) or cold pressor stimulation. At baseline, legs had higher vascular resistance (27+/-5 versus 17+/-2 U, P=0.05) despite lower norepinephrine spillover (0.28+/-0.04 versus 0.4+/-0.05 mg. min(-1). dL(-1), P=0.03). Norepinephrine spillover increased similarly in both arms and legs during nitroprusside infusion and cold pressor stimulation. On the other hand, during cold stimulation, vascular resistance increased in arms but not in legs (20+/-9% versus -7+/-4%, P=0.03). Increasing doses of isoproterenol and phenylephrine were infused intra-arterially in arms and legs to estimate beta-mediated vasodilation and alpha-induced vasoconstriction, respectively. beta-Mediated vasodilation was significantly lower in legs compared with arms. Thus, we report a dissociation between norepinephrine spillover and vascular responses to cold stress in lower limbs characterized by a paradoxical decrease in local resistance despite increases in sympathetic activity. The differences observed in adrenergic receptor responses cannot explain this phenomenon.

  3. EPW: A program for calculating the electron-phonon coupling using maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Noffsinger, Jesse; Giustino, Feliciano; Malone, Brad D.; Park, Cheol-Hwan; Louie, Steven G.; Cohen, Marvin L.

    2010-12-01

    EPW ( Electron- Phonon coupling using Wannier functions) is a program written in Fortran90 for calculating the electron-phonon coupling in periodic systems using density-functional perturbation theory and maximally localized Wannier functions. EPW can calculate electron-phonon interaction self-energies, electron-phonon spectral functions, and total as well as mode-resolved electron-phonon coupling strengths. The calculation of the electron-phonon coupling requires a very accurate sampling of electron-phonon scattering processes throughout the Brillouin zone, hence reliable calculations can be prohibitively time-consuming. EPW combines the Kohn-Sham electronic eigenstates and the vibrational eigenmodes provided by the Quantum ESPRESSO package (see Giannozzi et al., 2009 [1]) with the maximally localized Wannier functions provided by the wannier90 package (see Mostofi et al., 2008 [2]) in order to generate electron-phonon matrix elements on arbitrarily dense Brillouin zone grids using a generalized Fourier interpolation. This feature of EPW leads to fast and accurate calculations of the electron-phonon coupling, and enables the study of the electron-phonon coupling in large and complex systems. Program summaryProgram title: EPW Catalogue identifier: AEHA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License No. of lines in distributed program, including test data, etc.: 304 443 No. of bytes in distributed program, including test data, etc.: 1 487 466 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any architecture with a Fortran 90 compiler Operating system: Any environment with a Fortran 90 compiler Has the code been vectorized or parallelized?: Yes, optimized for 1 to 64 processors RAM: Heavily system dependent, as small as a few MB Supplementary material: A copy of the "EPW/examples" directory

  4. A Time-Frequency Functional Model for Locally Stationary Time Series Data

    PubMed Central

    Qin, Li; Guo, Wensheng; Litt, Brian

    2009-01-01

    Unlike traditional time series analysis that focuses on one long time series, in many biomedical experiments, it is common to collect multiple time series and focus on how the design covariates impact the patterns of stochastic variation over time. In this article, we propose a time-frequency functional model for a family of time series indexed by a set of covariates. This model can be used to compare groups of time series in terms of the patterns of stochastic variation and to estimate the covariate effects. We focus our development on locally stationary time series and propose the covariate-indexed locally stationary setting, which include stationary processes as special cases. We use smoothing spline ANOVA models for the time-frequency coefficients. A two-stage procedure is introduced for estimation. To reduce the computational demand, we develop an equivalent state space model to the proposed model with an efficient algorithm. We also propose a new simulation method to generate replicated time series from their design spectra. An epileptic intracranial electroencephalogram (IEEG) dataset is analyzed for illustration. PMID:20228961

  5. Cholesterol increase in mitochondria: its effect on inner-membrane functions, submitochondrial localization and ultrastructural morphology.

    PubMed Central

    Echegoyen, S; Oliva, E B; Sepulveda, J; Díaz-Zagoya, J C; Espinosa-García, M T; Pardo, J P; Martínez, F

    1993-01-01

    The effect of cholesterol incorporation on some functions of the mitochondrial inner membrane and on the morphology of rat liver mitochondria was studied. Basal ATPase and succinate dehydrogenase activities remained unchanged after cholesterol was incorporated into the mitochondria; however, uncoupled ATPase activity was partially inhibited. The presence of several substrates and inhibitors did not change the amount of cholesterol incorporated, which was localized mostly in the outer membrane. Electron-microscope observations revealed the presence of vesicles between the outer and inner membranes; these vesicles increased in number with the amount of cholesterol incorporated. The data suggest that cholesterol induces the formation of vesicles from the outer membrane, and modifies the activity of stimulated ATPase. Images Figure 4 PMID:8435069

  6. Induced pH-dependent shift by local surface plasmon resonance in functionalized gold nanorods

    PubMed Central

    2013-01-01

    Localized surface plasmon resonance (LSPR) spectroscopy of metallic nanoparticles is a powerful tool for chemical and biological sensing experiments. In this study, we observed LSPR shifts of 11-mercaptoundecanoic acid modified gold nanorods (GNR-MUA) for the pH range of 6.41 to 8.88. We proposed a mechanism involving changes of the dipole moment after protonation/deprotonation carboxylic groups of 11-mercaptoundecanoic acid (MUA) which plays an important role by modulating LSPR around the functionalized GNR. Such a stable and easily prepared GNR-MUA has potential to become one of the most efficient and promising pH nanosensors to study intra- or extra-cellular pH in a wide range of chemical or biological systems. PMID:23432999

  7. The bond ionicity in ANB8-N compounds from maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Qteish, Abdallah

    2015-07-01

    The bond ionicity in seventy two ANB8-N compounds is investigated according to the recently introduced first-principles ionicity scale, based on the centers of the maximally localized Wannier functions, which has several interesting features. The obtained bond ionicities (qi) are found to exhibit the expected trends, according to electronegativity arguments. In particular, the bond ionicity in the alkaline-earth oxides increases by going from MgO to BaO. A strong crystal structure dependence of qi is observed. A critical value of qi (of 0.91) that separates between the tetrahedrally and octahedrally coordinated systems is inferred directly from the calculated values of qi. The volume dependence of qi is investigated for all the considered compounds and found to reduce by volume decrease for most of the studied systems. The adopted ionicity scale is established as a very strong competitor to the most widely accepted Phillips and Pauling ionicity measures.

  8. Regulation of mammalian microRNA processing and function by cellular signaling and subcellular localization

    PubMed Central

    Smalheiser, Neil R.

    2008-01-01

    For many microRNAs, in many normal tissues and in cancer cells, the cellular levels of mature microRNAs are not simply determined by transcription of microRNA genes. This mini-review will discuss how microRNA biogenesis and function can be regulated by various nuclear and cytoplasmic processing events, including emerging evidence that microRNA pathway components can be selectively regulated by control of their subcellular localization and by modifications that occur during dynamic cellular signaling. Finally, I will briefly summarize studies of microRNAs in synaptic fractions of adult mouse forebrain, which may serve as a model for other cell types as well. PMID:18433727

  9. The HI Content of Galaxies as a Function of Local Density and Large-Scale Environment

    NASA Astrophysics Data System (ADS)

    Thoreen, Henry; Cantwell, Kelly; Maloney, Erin; Cane, Thomas; Brough Morris, Theodore; Flory, Oscar; Raskin, Mark; Crone-Odekon, Mary; ALFALFA Team

    2017-01-01

    We examine the HI content of galaxies as a function of environment, based on a catalogue of 41527 galaxies that are part of the 70% complete Arecibo Legacy Fast-ALFA (ALFALFA) survey. We use nearest-neighbor methods to characterize local environment, and a modified version of the algorithm developed for the Galaxy and Mass Assembly (GAMA) survey to classify large-scale environment as group, filament, tendril, or void. We compare the HI content in these environments using statistics that include both HI detections and the upper limits on detections from ALFALFA. The large size of the sample allows to statistically compare the HI content in different environments for early-type galaxies as well as late-type galaxies. This work is supported by NSF grants AST-1211005 and AST-1637339, the Skidmore Faculty-Student Summer Research program, and the Schupf Scholars program.

  10. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    SciTech Connect

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  11. "Recognizing Numerical Constants"

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Craw, James M. (Technical Monitor)

    1995-01-01

    The advent of inexpensive, high performance computer and new efficient algorithms have made possible the automatic recognition of numerically computed constants. In other words, techniques now exist for determining, within certain limits, whether a computed real or complex number can be written as a simple expression involving the classical constants of mathematics. In this presentation, some of the recently discovered techniques for constant recognition, notably integer relation detection algorithms, will be presented. As an application of these methods, the author's recent work in recognizing "Euler sums" will be described in some detail.

  12. The cosmological constant problem

    SciTech Connect

    Dolgov, A.D.

    1989-05-01

    A review of the cosmological term problem is presented. Baby universe model and the compensating field model are discussed. The importance of more accurate data on the Hubble constant and the Universe age is stressed. 18 refs.

  13. Science Is Constantly Cool.

    ERIC Educational Resources Information Center

    Eichinger, John

    1996-01-01

    Presents an activity in which students attempt to keep water at a constant temperature. Helps students in grades three to six hone their skills in prediction, observation, measurement, data collection, graphing, data analysis, and communication. (JRH)

  14. Requirements of fission yeast septins for complex formation, localization, and function.

    PubMed

    An, Hanbing; Morrell, Jennifer L; Jennings, Jennifer L; Link, Andrew J; Gould, Kathleen L

    2004-12-01

    Septins are GTP binding proteins important for cytokinesis in many eukaryotes. The Schizosaccaromyces pombe genome sequence predicts orthologues of four of five Saccharomyces cerevisiae septins involved in cytokinesis and these are named Spns1-4p. That spns1-4 are not essential genes permitted the application of a combined genetic and proteomics approach to determine their functional relationships. Our findings indicate that Spns1-4p are present throughout interphase as a diffusely localized approximately 8.5S complex containing two copies of each septin linked together as a chain in the order Spn3p-Spn4p-Spn1p-Spn2p. Septin recruitment to the medial region of the cell is genetically separable from ring formation, and whereas it is normally restricted to mitosis, it can be promoted without activation of the mitotic cell cycle machinery. Coalescence into ring structures requires Spn1p and Spn4p associate with at least one other septin subunit and the expression of Mid2p that is normally restricted to mitosis. This study establishes the functional requirements for septin complex organization in vivo.

  15. Requirements of Fission Yeast Septins for Complex Formation, Localization, and FunctionD⃞

    PubMed Central

    An, Hanbing; Morrell, Jennifer L.; Jennings, Jennifer L.; Link, Andrew J.; Gould, Kathleen L.

    2004-01-01

    Septins are GTP binding proteins important for cytokinesis in many eukaryotes. The Schizosaccaromyces pombe genome sequence predicts orthologues of four of five Saccharomyces cerevisiae septins involved in cytokinesis and these are named Spns1-4p. That spns1-4 are not essential genes permitted the application of a combined genetic and proteomics approach to determine their functional relationships. Our findings indicate that Spns1-4p are present throughout interphase as a diffusely localized ∼8.5S complex containing two copies of each septin linked together as a chain in the order Spn3p-Spn4p-Spn1p-Spn2p. Septin recruitment to the medial region of the cell is genetically separable from ring formation, and whereas it is normally restricted to mitosis, it can be promoted without activation of the mitotic cell cycle machinery. Coalescence into ring structures requires Spn1p and Spn4p associate with at least one other septin subunit and the expression of Mid2p that is normally restricted to mitosis. This study establishes the functional requirements for septin complex organization in vivo. PMID:15385632

  16. Ligand-dependent localization and function of ORP-VAP complexes at membrane contact sites.

    PubMed

    Weber-Boyvat, Marion; Kentala, Henriikka; Peränen, Johan; Olkkonen, Vesa M

    2015-05-01

    Oxysterol-binding protein/OSBP-related proteins (ORPs) constitute a conserved family of sterol/phospholipid-binding proteins with lipid transporter or sensor functions. We investigated the spatial occurrence and regulation of the interactions of human OSBP/ORPs or the S. cerevisiae orthologs, the Osh (OSBP homolog) proteins, with their endoplasmic reticulum (ER) anchors, the VAMP-associated proteins (VAPs), by employing bimolecular fluorescence complementation and pull-down set-ups. The ORP-VAP interactions localize frequently at distinct subcellular sites, shown in several cases to represent membrane contact sites (MCSs). Using established ORP ligand-binding domain mutants and pull-down assays with recombinant proteins, we show that ORP liganding regulates the ORP-VAP association, alters the subcellular targeting of ORP-VAP complexes, or modifies organelle morphology. There is distinct protein specificity in the effects of the mutants on subcellular targeting of ORP-VAP complexes. We provide evidence that complexes of human ORP2 and VAPs at ER-lipid droplet interfaces regulate the hydrolysis of triglycerides and lipid droplet turnover. The data suggest evolutionarily conserved, complex ligand-dependent functions of ORP-VAP complexes at MCSs, with implications for cellular lipid homeostasis and signaling.

  17. Spitzer Local Volume Legacy (LVL) Star-Forming Regions: Luminosity Functions

    NASA Astrophysics Data System (ADS)

    Cook, David O.; Dale, Daniel A.; Lee, Janice C.; LVL Team

    2015-01-01

    The conversion of gas into stars is one of the most fundamental processes in the universe, yet the effects of environmental conditions are poorly constrained. Observations of star-forming regions (young star clusters and HII regions) have shown evidence of a fractal pattern in their mass and luminosity distributions. The Mass Function (MF), and similarly the Luminosity Function (LF), of star-forming regions can be approximated as a power-law and is characterized by the power-law slope. A consistent slope of -2 has been observed across numerous galaxies, however, systematic deviations from this canonical slope have been measured across different environments. We present the LF slopes for 258 nearby galaxies in the Local Volume Legacy (LVL) sample utilizing tens of thousands of Hα- and FUV-selected sources. We test any relationships between LF slope and global galaxy properties to quantify the effect of environment on the star formation process. In addition, we combine the entire star-forming region sample in an attempt to characterize a previously proposed break in the HII region LF power-law at L˜38.6 erg/s.

  18. How to use fMRI functional localizers to improve EEG/MEG source estimation

    PubMed Central

    Cottereau, Benoit R.; Ales, Justin M.; Norcia, Anthony M.

    2015-01-01

    EEG and MEG have excellent temporal resolution, but the estimation of the neural sources that generate the signals recorded by the sensors is a difficult, ill-posed problem. The high spatial resolution of functional MRI makes it an ideal tool to improve the localization of the EEG/MEG sources using data fusion. However, the combination of the two techniques remains challenging, as the neural generators of the EEG/MEG and BOLD signals might in some cases be very different. Here we describe a data fusion approach that was developed by our team over the last decade in which fMRI is used to provide source constraints that are based on functional areas defined individually for each subject. This mini-review describes the different steps that are necessary to perform source estimation using this approach. It also provides a list of pitfalls that should be avoided when doing fMRI-informed EEG/MEG source imaging. Finally, it describes the advantages of using a ROI-based approach for group-level analysis and for the study of sensory systems. PMID:25088693

  19. Two-state model based on the block-localized wave function method

    NASA Astrophysics Data System (ADS)

    Mo, Yirong

    2007-06-01

    The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense π →π* transition for formamide upon solvation undergoes a redshift of 0.3eV, compared with the experimental data (0.40-0.5eV).

  20. Cerebral localization of functions and the neurology of language: fact versus fiction or is it something else?

    PubMed

    Ross, Elliott D

    2010-06-01

    Over the last 15 years there has been a burgeoning number of publications using functional brain imaging (>40,000 articles based on an ISI/Web of Science search) to localize behavioral and cognitive processes to specific areas in the human brain that are often not confirmed by traditional, lesion-based studies. Thus, there is a need to reassess what cerebral localization of functions is and is not. Otherwise, there is no rational way to interpret the escalating claims of localization in the functional imaging literature that is taking on the appearance of neurophysiologic "phrenology". This article will present arguments to suggest that functional localization in the brain is a robust but very dynamic, four-dimensional process. It is a learned phenomenon driven over time by large-scale, spatially distributed, neural networks seeking to efficiently maximize the processing, storage, and manipulation of information for cognitive and behavioral operations. Because of historical considerations and space limitations, the main focus will be on localization of language-related functions whose theoretical neurological basis can be generalized for any complex cognitive-behavioral function.

  1. Median-plane sound localization as a function of the number of spectral channels using a channel vocoder.

    PubMed

    Goupell, Matthew J; Majdak, Piotr; Laback, Bernhard

    2010-02-01

    Using a vocoder, median-plane sound localization performance was measured in eight normal-hearing listeners as a function of the number of spectral channels. The channels were contiguous and logarithmically spaced in the range from 0.3 to 16 kHz. Acutely testing vocoded stimuli showed significantly worse localization compared to noises and 100 pulses click trains, both of which were tested after feedback training. However, localization for the vocoded stimuli was better than chance. A second experiment was performed using two different 12-channel spacings for the vocoded stimuli, now including feedback training. One spacing was from experiment 1. The second spacing (called the speech-localization spacing) assigned more channels to the frequency range associated with speech. There was no significant difference in localization between the two spacings. However, even with training, localizing 12-channel vocoded stimuli remained worse than localizing virtual wideband noises by 4.8 degrees in local root-mean-square error and 5.2% in quadrant error rate. Speech understanding for the speech-localization spacing was not significantly different from that for a typical spacing used by cochlear-implant users. These experiments suggest that current cochlear implants have a sufficient number of spectral channels for some vertical-plane sound localization capabilities, albeit worse than normal-hearing listeners, without loss of speech understanding.

  2. Median-plane sound localization as a function of the number of spectral channels using a channel vocoder

    PubMed Central

    Goupell, Matthew J.; Majdak, Piotr; Laback, Bernhard

    2010-01-01

    Using a vocoder, median-plane sound localization performance was measured in eight normal-hearing listeners as a function of the number of spectral channels. The channels were contiguous and logarithmically spaced in the range from 0.3 to 16 kHz. Acutely testing vocoded stimuli showed significantly worse localization compared to noises and 100 pulse∕s click trains, both of which were tested after feedback training. However, localization for the vocoded stimuli was better than chance. A second experiment was performed using two different 12-channel spacings for the vocoded stimuli, now including feedback training. One spacing was from experiment 1. The second spacing (called the speech-localization spacing) assigned more channels to the frequency range associated with speech. There was no significant difference in localization between the two spacings. However, even with training, localizing 12-channel vocoded stimuli remained worse than localizing virtual wideband noises by 4.8° in local root-mean-square error and 5.2% in quadrant error rate. Speech understanding for the speech-localization spacing was not significantly different from that for a typical spacing used by cochlear-implant users. These experiments suggest that current cochlear implants have a sufficient number of spectral channels for some vertical-plane sound localization capabilities, albeit worse than normal-hearing listeners, without loss of speech understanding. PMID:20136221

  3. Localized Programmable Gas Phase Electrodeposition Yielding Functional Nanostructured Materials and Molecular Arrays

    NASA Astrophysics Data System (ADS)

    Lin, En-Chiang

    This thesis focuses on nanomanufacturing processes for the heterogeneous integration of nanomaterials and molecules. We demonstrate and discovered a novel gas phase method to control material flux at specific points on a surface which is based on the interplay of high mobility gas ions and lower mobility nanoparticles and molecules in the presence of a patterned substrate. The thesis is divided into two parts describing applications of the discovered process for the localized deposition of (A) metallic and semiconducting particles producing functional nanostructured deposits including multimaterial sensor arrays and nanostructured electrodes for photovoltaic applications and, (B) molecules for gas sensor application demonstrating improved collection efficiencies and sensitivity over previously methods. Section (A) begins with the description of an arc discharge based method to produce a flux of charged nanoparticles (<5nm particles Au, Ag, Pt, W, TiO2, ZnO and Ge) which are characterized using various methods. It then describes a process to locally deposit the charged particles into extended two and three dimensional metallic and semiconducting nanostructured deposits. The thesis describes the use externally-biased electrodes to achieve an electronic shutter to turn ON/OFF the deposition in selected domains. Subsequently it explores and describes the use of patterned dielectrics whereby the patterned dielectrics are charged to define arrays of electrodynamic lenses. Incorporation of these lensing structures was found to enable nanostructured deposits with sub 100nm lateral resolution. The utility of the discovered processes are demonstrated in two areas. For the first application, semiconducting nanomaterial are sequentially deposited on the same substrate to fabricate a multi-material/multi-functional sensor array on a single substrate in a single deposition process. The process eliminates critical alignment and masking steps and has a higher material efficiency

  4. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions

    NASA Astrophysics Data System (ADS)

    Zhao, Yan; Truhlar, Donald G.

    2006-11-01

    We present a new local density functional, called M06-L, for main-group and transition element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed.

  5. Cellular localization and functional significance of CYP3A4 in the human epileptic brain

    PubMed Central

    Ghosh, Chaitali; Marchi, Nicola; Desai, Nirav K.; Puvenna, Vikram; Hossain, Mohammed; Gonzalez-Martinez, Jorge; Alexopoulos, Andreas V.; Janigro, Damir

    2011-01-01

    Summary Purpose Compelling evidence supports the presence of P450 enzymes (CYPs) in the central nervous system (CNS). However, little information is available on the localization and function of CYPs in the drug-resistant epileptic brain. We have evaluated the pattern of expression of the specific enzyme CYP3A4 and studied its co-localization with MDR1. We also determined whether an association exists between CYP3A4 expression and cell survival. Methods Brain specimens were obtained from eight patients undergoing resection to relieve drug-resistant seizures or to remove a cavernous angioma. Each specimen was partitioned for either immunostaining or primary culture of human endothelial cells and astrocytes. Immunostaining was performed using anti-CYP3A4, MDR1, GFAP, or NeuN antibodies. High performance liquid chromatography–ultraviolet (HPLC-UV) analysis was used to quantify carbamazepine (CBZ) metabolism by these cells. CYP3A4 expression was correlated to DAPI condensation, a marker of cell viability. Human embryonic kidney (HEK) cells were transfected with CYP3A4 to further evaluate the link between CYP3A4 levels, CBZ metabolism, and cell viability. Key Findings CYP3A4 was expressed by blood–brain barrier (BBB) endothelial cells and by the majority of neurons (75 ± 10%). Fluorescent immunostaining showed coexpression of CYP3A4 and MDR1 in endothelial cells and neurons. CYP3A4 expression inversely correlated with DAPI nuclear condensation. CYP3A4 overexpression in HEK cells conferred resistance to cytotoxic levels of carbamazepine. CYP3A4 levels positively correlated with the amount of CBZ metabolized. Significance CYP3A4 brain expression is not only associated with drug metabolism but may also represent a cytoprotective mechanism. Coexpression of CYP3A4 and MDR1 may be involved in cell survival in the diseased brain. PMID:21294720

  6. Biological function of hpsh4590 localized in the plasticity zone of Helicobacter pylori.

    PubMed

    Gu, Yu-feng; Li, Yu; Song, Yu; Chang, Xin; Qu, Ye-Min; Wang, Ming-Yi; Gao, Xiao-Zhong

    2016-04-01

    The aim of this study was to determine the biological function of hpsh4590 in Helicobacter pylori. After Hpsh4590 was expressed using a prokaryotic expression system, the cytotoxic effects and IL-8 production of Hpsh4590 were analyzed by co-culturing with GES-1 cells. Meanwhile, the antibody of rHpsh4590, produced by immunizing rabbit, was used for localization and protein interaction studies. Hpsh4590 fusion protein was expressed successfully in Escherichia coli Rosetta (DE3), and the polyclonal antibody was produced at high titers. The MTT assay showed that the inhibition ratio of GES-1 cells cultured with 0.1 μg/mL rHpsh4590 (3.02% ± 0.02%) was significantly lower than that of 20 μg/mL rHpsh4590 (57.57% ± 0.03%, p < 0.01), while DAPI staining showed the cytotoxic effects of rHpsh4590 for GES-1 cells. The up-regulation of cleaved caspase-3 and cleaved PARP was observed after GES-1 cells co-cultured with rHpsh4590 by Western blot. Co-culturing of GES-1 cells with rHpsh0459 (20 μg/mL) led to significant production of IL-8 at 12 h(1097.74 ± 212.37 pg/mL) and 24 h (1379.55 ± 209.58 pg/mL) then at 6 h(134.68 ± 14.64 pg/mL, p < 0.01). These observations suggest that the cytotoxicity of Hpsh4590 occurred in a concentration dependent manner, which is related with IL-8 secretion from gastric mucosal epithelial cells. Hpsh4590 was found localized in the membrane and the periplasm of H. pylori, interacted with zinc finger protein and methionine ABC transporter ATP-binding protein, and potentially regulates DNA uptake or transfer.

  7. Automatic variance reduction for Monte Carlo simulations via the local importance function transform

    SciTech Connect

    Turner, S.A.

    1996-02-01

    The author derives a transformed transport problem that can be solved theoretically by analog Monte Carlo with zero variance. However, the Monte Carlo simulation of this transformed problem cannot be implemented in practice, so he develops a method for approximating it. The approximation to the zero variance method consists of replacing the continuous adjoint transport solution in the transformed transport problem by a piecewise continuous approximation containing local biasing parameters obtained from a deterministic calculation. He uses the transport and collision processes of the transformed problem to bias distance-to-collision and selection of post-collision energy groups and trajectories in a traditional Monte Carlo simulation of ``real`` particles. He refers to the resulting variance reduction method as the Local Importance Function Transform (LIFI) method. He demonstrates the efficiency of the LIFT method for several 3-D, linearly anisotropic scattering, one-group, and multigroup problems. In these problems the LIFT method is shown to be more efficient than the AVATAR scheme, which is one of the best variance reduction techniques currently available in a state-of-the-art Monte Carlo code. For most of the problems considered, the LIFT method produces higher figures of merit than AVATAR, even when the LIFT method is used as a ``black box``. There are some problems that cause trouble for most variance reduction techniques, and the LIFT method is no exception. For example, the author demonstrates that problems with voids, or low density regions, can cause a reduction in the efficiency of the LIFT method. However, the LIFT method still performs better than survival biasing and AVATAR in these difficult cases.

  8. Charge transport calculations by a wave-packet dynamical approach using maximally localized Wannier functions based on density functional theory: Application to high-mobility organic semiconductors

    NASA Astrophysics Data System (ADS)

    Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

    2017-01-01

    We present a wave-packet dynamical approach to charge transport using maximally localized Wannier functions based on density functional theory including van der Waals interactions. We apply it to the transport properties of pentacene and rubrene single crystals and show the temperature-dependent natures from bandlike to thermally activated behaviors as a function of the magnitude of external static disorder. We compare the results with those obtained by the conventional band and hopping models and experiments.

  9. The HerMES submillimetre local and low-redshift luminosity functions

    NASA Astrophysics Data System (ADS)

    Marchetti, L.; Vaccari, M.; Franceschini, A.; Arumugam, V.; Aussel, H.; Béthermin, M.; Bock, J.; Boselli, A.; Buat, V.; Burgarella, D.; Clements, D. L.; Conley, A.; Conversi, L.; Cooray, A.; Dowell, C. D.; Farrah, D.; Feltre, A.; Glenn, J.; Griffin, M.; Hatziminaoglou, E.; Heinis, S.; Ibar, E.; Ivison, R. J.; Nguyen, H. T.; O'Halloran, B.; Oliver, S. J.; Page, M. J.; Papageorgiou, A.; Pearson, C. P.; Pérez-Fournon, I.; Pohlen, M.; Rigopoulou, D.; Roseboom, I. G.; Rowan-Robinson, M.; Schulz, B.; Scott, Douglas; Seymour, N.; Shupe, D. L.; Smith, A. J.; Symeonidis, M.; Valtchanov, I.; Viero, M.; Wang, L.; Wardlow, J.; Xu, C. K.; Zemcov, M.

    2016-02-01

    We used wide-area surveys over 39 deg2 by the HerMES (Herschel Multi-tiered Extragalactic Survey) collaboration, performed with the Herschel Observatory SPIRE multiwavelength camera, to estimate the low-redshift, 0.02 < z < 0.5, monochromatic luminosity functions (LFs) of galaxies at 250, 350 and 500 μm. Within this redshift interval, we detected 7087 sources in five independent sky areas, ˜40 per cent of which have spectroscopic redshifts, while for the remaining objects photometric redshifts were used. The SPIRE LFs in different fields did not show any field-to-field variations beyond the small differences to be expected from cosmic variance. SPIRE flux densities were also combined with Spitzer photometry and multiwavelength archival data to perform a complete spectral energy distribution fitting analysis of SPIRE detected sources to calculate precise k-corrections, as well as the bolometric infrared (IR; 8-1000 μm) LFs and their low-z evolution from a combination of statistical estimators. Integration of the latter prompted us to also compute the local luminosity density and the comoving star formation rate density (SFRD) for our sources, and to compare them with theoretical predictions of galaxy formation models. The LFs show significant and rapid luminosity evolution already at low redshifts, 0.02 < z < 0.2, with L_{IR}^{*} ∝ (1+z)^{6.0± 0.4} and Φ _{IR}^{*} ∝ (1+z)^{-2.1± 0.4}, L_{250}^{*} ∝ (1+z)^{5.3± 0.2} and Φ _{250}^{*} ∝ (1+z)^{-0.6± 0.4} estimated using the IR bolometric and the 250 μm LFs, respectively. Converting our IR LD estimate into an SFRD assuming a standard Salpeter initial mass function and including the unobscured contribution based on the UV dust-uncorrected emission from local galaxies, we estimate an SFRD scaling of SFRD0 + 0.08z, where SFRD0 ≃ (1.9 ± 0.03) × 10-2 [M⊙ Mpc-3] is our total SFRD estimate at z ˜ 0.02.

  10. The shortcomings of semi-local and hybrid functionals: what we can learn from surface science studies

    NASA Astrophysics Data System (ADS)

    Stroppa, A.; Kresse, G.

    2008-06-01

    A study of the adsorption of CO on late 4d and 5d transition metal (111) surfaces (Ru, Rh, Pd, Ag, Os, Ir and Pt) considering atop and hollow site adsorption is presented. The applied functionals include the gradient-corrected Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) functionals, and the corresponding hybrid Hartree-Fock density functionals HSE and B3LYP. We find that PBE-based hybrid functionals (specifically HSE) yield, with the exception of Pt, the correct site order on all considered metals, but they also considerably overestimate the adsorption energies compared to experiment. On the other hand, the semi-local BLYP functional and the corresponding hybrid functional B3LYP yield very satisfactory adsorption energies and the correct adsorption site for all surfaces. We are thus faced with a Procrustean problem: the B3LYP and BLYP functionals seem to be the overall best choice for describing adsorption on metal surfaces, but they simultaneously fail to account well for the properties of the metal, vastly overestimating the equilibrium volume and underestimating the atomization energies. Setting out from these observations, general conclusions are drawn on the relative merits and drawbacks of various semi-local and hybrid functionals. The discussion includes a revised version of the PBE functional specifically optimized for bulk properties and surface energies (PBEsol), a revised version of the PBE functional specifically optimized to predict accurate adsorption energies (rPBE), as well as the aforementioned BLYP functional. We conclude that no semi-local functional is capable of describing all aspects properly, and including non-local exchange also only improves some but worsens other properties.

  11. A Functional Near-Infrared Spectroscopy Study of Sustained Attention to Local and Global Target Features

    ERIC Educational Resources Information Center

    De Joux, Neil; Russell, Paul N.; Helton, William S.

    2013-01-01

    Despite a long history of vigilance research, the role of global and local feature discrimination in vigilance tasks has been relatively neglected. In this experiment participants performed a sustained attention task requiring either global or local shape stimuli discrimination. Reaction time to local feature discriminations was characterized by a…

  12. Constant-bandwidth constant-temperature hot-wire anemometer.

    PubMed

    Ligeza, P

    2007-07-01

    A constant-temperature anemometer (CTA) enables the measurement of fast-changing velocity fluctuations. In the classical solution of CTA, the transmission band is a function of flow velocity. This is a minor drawback when the mean flow velocity does not significantly change, though it might lead to dynamic errors when flow velocity varies over a considerable range. A modification is outlined, whereby an adaptive controller is incorporated in the CTA system such that the anemometer's transmission band remains constant in the function of flow velocity. For that purpose, a second feedback loop is provided, and the output signal from the anemometer will regulate the controller's parameters such that the transmission bandwidth remains constant. The mathematical model of a CTA that has been developed and model testing data allow a through evaluation of the proposed solution. A modified anemometer can be used in measurements of high-frequency variable flows in a wide range of velocities. The proposed modification allows the minimization of dynamic measurement errors.

  13. Functional characterization and localization of a gill-specific claudin isoform in Atlantic salmon

    PubMed Central

    Yu, A. S. L.; Li, J.; Madsen, S. S.; Færgeman, N. J.

    2012-01-01

    Claudins are the major determinants of paracellular epithelial permeability in multicellular organisms. In Atlantic salmon (Salmo salar L.), we previously found that mRNA expression of the abundant gill-specific claudin 30 decreases during seawater (SW) acclimation, suggesting that this claudin is associated with remodeling of the epithelium during salinity change. This study investigated localization, protein expression, and function of claudin 30. Confocal microscopy showed that claudin 30 protein was located at cell-cell interfaces in the gill filament in SW- and fresh water (FW)-acclimated salmon, with the same distribution, overall, as the tight junction protein ZO-1. Claudin 30 was located at the apical tight junction interface and in cell membranes deeper in the epithelia. Colocalization with the α-subunit of the Na+-K+-ATPase was negligible, suggesting limited association with mitochondria-rich cells. Immunoblotting of gill samples showed lower claudin 30 protein expression in SW than FW fish. Retroviral transduction of claudin 30 into Madin-Darby canine kidney cells resulted in a decreased conductance of 19%. The decreased conductance correlated with a decreased permeability of the cell monolayer to monovalent cations, whereas permeability to chloride was unaffected. Confocal microscopy revealed that claudin 30 was expressed in the lateral membrane, as well as in tight junctions of Madin-Darby canine kidney cells, thereby paralleling the findings in the native gill. This study suggests that claudin 30 functions as a cation barrier between pavement cells in the gill and also has a general role in cell-cell adhesion in deeper layers of the epithelium. PMID:21975646

  14. Patterns of Spontaneous Local Network Activity in Developing Cerebral Cortex: Relationship to Adult Cognitive Function.

    PubMed

    Peinado, Alejandro; Abrams, Charles K

    2015-01-01

    Detecting neurodevelopμental disorders of cognition at the earliest possible stages could assist in understanding them mechanistically and ultimately in treating them. Finding early physiological predictors that could be visualized with functional neuroimaging would represent an important advance in this regard. We hypothesized that one potential source of physiological predictors is the spontaneous local network activity prominent during specific periods in development. To test this we used calcium imaging in brain slices and analyzed variations in the frequency and intensity of this early activity in one area, the entorhinal cortex (EC), in order to correlate early activity with level of cognitive function later in life. We focused on EC because of its known role in different types of cognitive processes and because it is an area where spontaneous activity is prominent during early postnatal development in rodent models of cortical development. Using rat strains (Long-Evans, Wistar, Sprague-Dawley and Brattleboro) known to differ in cognitive performance in adulthood we asked whether neonatal animals exhibit corresponding strain-related differences in EC spontaneous activity. Our results show significant differences in this activity between strains: compared to a high cognitive-performing strain, we consistently found an increase in frequency and decrease in intensity in neonates from three lower performing strains. Activity was most different in one strain considered a model of schizophrenia-like psychopathology. While we cannot necessarily infer a causal relationship between early activity and adult cognition our findings suggest that the pattern of spontaneous activity in development could be an early predictor of a developmental trajectory advancing toward sub-optimal cognitive performance in adulthood. Our results further suggest that the strength of dopaminergic signaling, by setting the balance between excitation and inhibition, is a potential underlying

  15. Elastic constants of calcite

    USGS Publications Warehouse

    Peselnick, L.; Robie, R.A.

    1962-01-01

    The recent measurements of the elastic constants of calcite by Reddy and Subrahmanyam (1960) disagree with the values obtained independently by Voigt (1910) and Bhimasenachar (1945). The present authors, using an ultrasonic pulse technique at 3 Mc and 25??C, determined the elastic constants of calcite using the exact equations governing the wave velocities in the single crystal. The results are C11=13.7, C33=8.11, C44=3.50, C12=4.82, C13=5.68, and C14=-2.00, in units of 1011 dyncm2. Independent checks of several of the elastic constants were made employing other directions and polarizations of the wave velocities. With the exception of C13, these values substantially agree with the data of Voigt and Bhimasenachar. ?? 1962 The American Institute of Physics.

  16. Local administration of AAV-BDNF to subventricular zone induces functional recovery in stroke rats.

    PubMed

    Yu, Seong-Jin; Tseng, Kuan-Yin; Shen, Hui; Harvey, Brandon K; Airavaara, Mikko; Wang, Yun

    2013-01-01

    Migration of new neuroprogenitor cells (NPCs) from the subventricular zone (SVZ) plays an important role in neurorepair after injury. Previous studies have shown that brain derived neurotrophic factor (BDNF) enhances the migration of NPCs from SVZ explants in neonatal mice in vitro. The purpose of this study was to identify the role of BDNF in SVZ cells using AAV-BDNF in an animal model of stroke. BDNF protein production after AAV-BDNF infection was verified in primary neuronal culture. AAV-BDNF or AAV-RFP was injected into the left SVZ region of adult rats at 14 days prior to right middle cerebral artery occlusion (MCAo). SVZ tissues were collected from the brain and placed in Metrigel cultures 1 day after MCAo. Treatment with AAV-BDNF significantly increased the migration of SVZ cells in the stroke brain in vitro. In another set of animals, AAV-GFP was co-injected with AAV-BDNF or AAV-RFP to label cells in left SVZ prior to right MCAo. Local administration of AAV-BDNF significantly enhanced recovery of locomotor function and migration of GFP-positive cells from the SVZ toward the lesioned hemisphere in stroke rats. Our data suggest that focal administration of AAV-BDNF to the SVZ increases behavioral recovery post stroke, possibly through the enhancement of migration of cells from SVZ in stroke animals. Regional manipulation of BDNF expression through AAV may be a novel approach for neurorepair in stroke brains.

  17. Intrapulmonary receptors in the Tegu lizard: II. Functional characteristics and localization;.

    PubMed

    Scheid, P; Kuhlmann, W D; Fedde, M R

    1977-02-01

    Intrapulmonary receptors identified in the Tegu lizard by single-unit vagal recording (Fedde et al., 1977) were subjected to a number of stimuli and localized within the lung. Some carbon dioxide receptors could follow periodic changes in intrapulmonary CO2 concentrations as rapidly as 1.3 Hz; No oxygen sensitivity was observed with this receptor type, and halothane markedly depressed the discharge frequency. In response to intravenously injected acetazolamide they increased their discharge frequency and became almost totally insensitive to CO2, suggesting molecular per se is not the direct controller of receptor discharge; These receptors show many of the functional characteristics described for those in the avian lung. Afferent activity from both CO2 and mechanoreceptors could be elicited by electrically stimulating the lung surface. The CO2 receptors appeared to be organized in a receptive field covering more than 1 cm2 of lung surface, multiple receptors being innervated by a single afferent fiber. Activity in afferent fibers from mechanoreceptors could be evoked from only one distinct spot on the lung surface. Conduction velocities of afferent fibers from CO2 receptors ranged from 1 to 3 m-sec-1; from mechanoreceptors, from 1.9 to 5.2 m-sec-1.

  18. Breast Cancer–Associated Abraxas Mutation Disrupts Nuclear Localization and DNA Damage Response Functions

    PubMed Central

    Solyom, Szilvia; Aressy, Bernadette; Pylkäs, Katri; Patterson-Fortin, Jeffrey; Hartikainen, Jaana M.; Kallioniemi, Anne; Kauppila, Saila; Nikkilä, Jenni; Kosma, Veli-Matti; Mannermaa, Arto; Greenberg, Roger A.; Winqvist, Robert

    2013-01-01

    Breast cancer is the most common cancer in women in developed countries and has a well-established genetic component. Germline mutations in a network of genes encoding BRCA1, BRCA2, and their interacting partners confer hereditary susceptibility to breast cancer. Abraxas directly interacts with the BRCA1 BRCT (BRCA1 carboxyl-terminal) repeats and contributes to BRCA1-dependent DNA damage responses, making Abraxas a candidate for yet unexplained disease susceptibility. Here, we have screened 125 Northern Finnish breast cancer families for coding region and splice-site Abraxas mutations and genotyped three tagging single-nucleotide polymorphisms within the gene from 991 unselected breast cancer cases and 868 female controls for common cancer-associated variants. A novel heterozygous alteration, c.1082G>A (Arg361Gln), that results in abrogated nuclear localization and DNA response activities was identified in three breast cancer families and in one additional familial case from an unselected breast cancer cohort, but not in healthy controls (P = 0.002). On the basis of its exclusive occurrence in familial cancers, disease cosegregation, evolutionary conservation, and disruption of critical BRCA1 functions, the recurrent Abraxas c.1082G>A mutation connects to cancer predisposition. These findings contribute to the concept of a BRCA-centered tumor suppressor network and provide the identity of Abraxas as a new breast cancer susceptibility gene. PMID:22357538

  19. Almost commuting matrices, localized Wannier functions, and the quantum Hall effect

    NASA Astrophysics Data System (ADS)

    Hastings, Matthew B.; Loring, Terry A.

    2010-01-01

    For models of noninteracting fermions moving within sites arranged on a surface in three-dimensional space, there can be obstructions to finding localized Wannier functions. We show that such obstructions are K-theoretic obstructions to approximating almost commuting, complex-valued matrices by commuting matrices, and we demonstrate numerically the presence of this obstruction for a lattice model of the quantum Hall effect in a spherical geometry. The numerical calculation of the obstruction is straightforward and does not require translational invariance or introduce a flux torus. We further show that there is a Z2 index obstruction to approximating almost commuting self-dual matrices by exactly commuting self-dual matrices and present additional conjectures regarding the approximation of almost commuting real and self-dual matrices by exactly commuting real and self-dual matrices. The motivation for considering this problem is the case of physical systems with additional antiunitary symmetries such as time-reversal or particle-hole conjugation. Finally, in the case of the sphere—mathematically speaking, three almost commuting Hermitians whose sum of square is near the identity—we give the first quantitative result, showing that this index is the only obstruction to finding commuting approximations. We review the known nonquantitative results for the torus.

  20. Regulation of Rnd3 Localization and Function By PKCα-Mediated Phosphorylation

    PubMed Central

    Madigan, James P.; Bodemann, Brian O.; Brady, Donita C.; Dewar, Brian J.; Keller, Patricia J.; Leitges, Michael; Philips, Mark R.; Ridley, Anne J.; Der, Channing J.; Cox, Adrienne D.

    2010-01-01

    The Rnd proteins (Rnd1, Rnd2 and Rnd3/RhoE) form a distinct branch of the Rho family of small GTPases. Altered Rnd3 expression causes changes in cytoskeletal organization and cell cycle progression. Rnd3 functions to decrease RhoA activity, but how Rnd3 itself is regulated to cause these changes is still under investigation. Unlike other Rho family proteins, Rnd3 is regulated not by GTP/GDP cycling, but at the level of expression and by posttranslational modifications such as prenylation and phosphorylation. We show here that, upon PKC agonist stimulation, Rnd3 undergoes an electrophoretic mobility shift and its subcellular localization becomes enriched at internal membranes. These changes are blocked by inhibition of conventional PKC isoforms and do not occur in PKCα-null cells or to a nonphosphorylatable mutant of Rnd3. We further show that PKCα directly phosphorylates Rnd3 in an in vitro kinase assay. Additionally, we provide evidence that the phosphorylation status of Rnd3 has a direct effect on its ability to block signaling from the Rho-ROCK pathway. These results identify an additional mechanism of regulation and provide clarification of how Rnd3 modulates Rho signaling to alter cytoskeletal organization. PMID:19723022

  1. Calculations with the quasirelativistic local-spin-density-functional theory for high-Z atoms

    SciTech Connect

    Guo, Y.; Whitehead, M.A.

    1988-10-01

    The generalized-exchange local-spin-density-functional theory (LSD-GX) with relativistic corrections of the mass velocity and Darwin terms has been used to calculate statistical total energies for the neutral atoms, the positive ions, and the negative ions for high-Z elements. The effect of the correlation and relaxation correction on the statistical total energy is discussed. Comparing the calculated results for the ionization potentials and electron affinities for the atoms (atomic number Z from 37 to 56 and 72 to 80) with experiment, shows that for the atoms rubidium to barium both the LSD-GX and the quasirelativistic LSD-GX, with self-interaction correction, Gopinathan, Whitehead, and Bogdanovic's Fermi-hole parameters (Phys. Rev. A 14, 1 (1976)), and Vosko, Wilk, and Nusair's correlation correction (Can. J. Phys. 58, 1200 (1980)), are very good methods for calculating ionization potentials and electron affinities. For the atoms hafnium to mercury the relativistic effect has to be considered.

  2. Enhanced gas adsorption on graphitic substrates via defects and local curvature: A density functional theory study

    SciTech Connect

    Dutta, Debosruti; Wood, Brandon C.; Bhide, Shreyas Y.; Ayappa, K. Ganapathy; Narasimhan, Shobhana

    2014-03-24

    Using van-der-Waals-corrected density functional theory calculations, we explore the possibility of engineering the local structure and morphology of high-surface-area graphene-derived materials to improve the uptake of methane and carbon dioxide for gas storage and sensing. We test the sensitivity of the gas adsorption energy to the introduction of native point defects, curvature, and the application of strain. The binding energy at topological point defect sites is inversely correlated with the number of missing carbon atoms, causing Stone–Wales defects to show the largest enhancement with respect to pristine graphene (~20%). Improvements of similar magnitude are observed at concavely curved surfaces in buckled graphene sheets under compressive strain, whereas tensile strain tends to weaken gas binding. Trends for CO2 and CH4 are similar, although CO2 binding is generally stronger by ~4 to 5 kJ mol–1. Furthermore, the differential between the adsorption of CO2 and CH4 is much higher on folded graphene sheets and at concave curvatures; this could possibly be leveraged for CH4/CO2 flow separation and gas-selective sensors.

  3. Interaction-induced local moments in parallel quantum dots within the functional renormalization group approach

    NASA Astrophysics Data System (ADS)

    Protsenko, V. S.; Katanin, A. A.

    2016-11-01

    We propose a version of the functional renormalization-group (fRG) approach, which is, due to including Litim-type cutoff and switching off (or reducing) the magnetic field during fRG flow, capable of describing a singular Fermi-liquid (SFL) phase, formed due to the presence of local moments in quantum dot structures. The proposed scheme allows one to describe the first-order quantum phase transition from the "singular" to the "regular" paramagnetic phase with applied gate voltage to parallel quantum dots, symmetrically coupled to leads, and shows sizable spin splitting of electronic states in the SFL phase in the limit of vanishing magnetic field H →0 ; the calculated conductance shows good agreement with the results of the numerical renormalization group. Using the proposed fRG approach with the counterterm, we also show that for asymmetric coupling of the leads to the dots the SFL behavior similar to that for the symmetric case persists, but with occupation numbers, effective energy levels, and conductance changing continuously through the quantum phase transition into the SFL phase.

  4. Discrete domains of MARCH1 mediate its localization, functional interactions, and posttranscriptional control of expression.

    PubMed

    Jabbour, Maurice; Campbell, Erin M; Fares, Hanna; Lybarger, Lonnie

    2009-11-15

    Within APCs, ubiquitination regulates the trafficking of immune modulators such as MHC class II and CD86 (B7.2) molecules. MARCH1 (membrane-associated RING-CH), a newly identified ubiquitin E3 ligase expressed in APCs, ubiquitinates MHC class II, thereby reducing its surface expression. Following LPS-induced maturation of dendritic cells, MARCH1 mRNA is down-regulated and MHC class II is redistributed to the cell surface from endosomal compartments. Here, we show that MARCH1 expression is also regulated at the posttranscriptional level. In primary dendritic cell and APC cell lines of murine origin, MARCH1 had a half-life of <30 min. MARCH1 degradation appears to occur partly in lysosomes, since inhibiting lysosomal activity stabilized MARCH1. Similar stabilization was observed when MARCH1-expressing cells were treated with cysteine protease inhibitors. Mutational analyses of MARCH1 defined discrete domains required for destabilization, proper localization, and functional interaction with substrates. Taken together, these data suggest that MARCH1 expression is regulated at a posttranscriptional level by trafficking within the endolysosomal pathway where MARCH1 is proteolyzed. The short half-life of MARCH1 permits very rapid changes in the levels of the protein in response to changes in the mRNA, resulting in efficient induction of Ag presentation once APCs receive maturational signals.

  5. Evidence of Presynaptic Localization and Function of the c-Jun N-Terminal Kinase

    PubMed Central

    Biggi, Silvia; Buccarello, Lucia; Sclip, Alessandra; Lippiello, Pellegrino; Rumio, Cristiano; Di Marino, Daniele

    2017-01-01

    The c-Jun N-terminal kinase (JNK) is part of a stress signalling pathway strongly activated by NMDA-stimulation and involved in synaptic plasticity. Many studies have been focused on the post-synaptic mechanism of JNK action, and less is known about JNK presynaptic localization and its physiological role at this site. Here we examined whether JNK is present at the presynaptic site and its activity after presynaptic NMDA receptors stimulation. By using N-SIM Structured Super Resolution Microscopy as well as biochemical approaches, we demonstrated that presynaptic fractions contained significant amount of JNK protein and its activated form. By means of modelling design, we found that JNK, via the JBD domain, acts as a physiological effector on T-SNARE proteins; then using biochemical approaches we demonstrated the interaction between Syntaxin-1-JNK, Syntaxin-2-JNK, and Snap25-JNK. In addition, taking advance of the specific JNK inhibitor peptide, D-JNKI1, we defined JNK action on the SNARE complex formation. Finally, electrophysiological recordings confirmed the role of JNK in the presynaptic modulation of vesicle release. These data suggest that JNK-dependent phosphorylation of T-SNARE proteins may have an important functional role in synaptic plasticity. PMID:28367336

  6. Enhanced gas adsorption on graphitic substrates via defects and local curvature: A density functional theory study

    DOE PAGES

    Dutta, Debosruti; Wood, Brandon C.; Bhide, Shreyas Y.; ...

    2014-03-24

    Using van-der-Waals-corrected density functional theory calculations, we explore the possibility of engineering the local structure and morphology of high-surface-area graphene-derived materials to improve the uptake of methane and carbon dioxide for gas storage and sensing. We test the sensitivity of the gas adsorption energy to the introduction of native point defects, curvature, and the application of strain. The binding energy at topological point defect sites is inversely correlated with the number of missing carbon atoms, causing Stone–Wales defects to show the largest enhancement with respect to pristine graphene (~20%). Improvements of similar magnitude are observed at concavely curved surfaces inmore » buckled graphene sheets under compressive strain, whereas tensile strain tends to weaken gas binding. Trends for CO2 and CH4 are similar, although CO2 binding is generally stronger by ~4 to 5 kJ mol–1. Furthermore, the differential between the adsorption of CO2 and CH4 is much higher on folded graphene sheets and at concave curvatures; this could possibly be leveraged for CH4/CO2 flow separation and gas-selective sensors.« less

  7. Localized basis functions and other computational improvements in variational nonorthogonal basis function methods for quantum mechanical scattering problems involving chemical reactions

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Truhlar, Donald G.

    1990-01-01

    The Generalized Newton Variational Principle for 3D quantum mechanical reactive scattering is briefly reviewed. Then three techniques are described which improve the efficiency of the computations. First, the fact that the Hamiltonian is Hermitian is used to reduce the number of integrals computed, and then the properties of localized basis functions are exploited in order to eliminate redundant work in the integral evaluation. A new type of localized basis function with desirable properties is suggested. It is shown how partitioned matrices can be used with localized basis functions to reduce the amount of work required to handle the complex boundary conditions. The new techniques do not introduce any approximations into the calculations, so they may be used to obtain converged solutions of the Schroedinger equation.

  8. Localizing movement-related primary sensorimotor cortices with multi-band EEG frequency changes and functional MRI.

    PubMed

    Kuo, Ching-Chang; Luu, Phan; Morgan, Kyle K; Dow, Mark; Davey, Colin; Song, Jasmine; Malony, Allen D; Tucker, Don M

    2014-01-01

    Electroencephalographic (EEG) oscillations in multiple frequency bands can be observed during functional activity of the cerebral cortex. An important question is whether activity of focal areas of cortex, such as during finger movements, is tracked by focal oscillatory EEG changes. Although a number of studies have compared EEG changes to functional MRI hemodynamic responses, we can find no previous research that relates the fMRI hemodynamic activity to localization of the multiple EEG frequency changes observed in motor tasks. In the present study, five participants performed similar thumb and finger movement tasks in parallel EEG and functional MRI studies. We examined changes in five frequency bands (from 5-120 Hz) and localized them using 256 dense-array EEG (dEEG) recordings and high-resolution individual head models. These localizations were compared with fMRI localizations in the same participants. Results showed that beta-band (14-30 Hz) desynchronizations (power decreases) were the most robust effects, appearing in all individuals, consistently localized to the hand region of the primary motor cortex, and consistently aligned with fMRI localizations.

  9. The nuclear localization signal of mitotic kinesin-like protein Mklp-1: effect on Mklp-1 function during cytokinesis.

    PubMed

    Liu, Xiaoqi; Erikson, Raymond L

    2007-02-23

    The mitotic kinesin-like protein (Mklp-1) localizes in the nucleus during interphase due to the presence of nuclear localization signal(s) [NLS(s)] within its sequence. Here, we mapped two NLSs to be 899SRKRRSST906 and 949KRKKP953 in the tail domain of Mklp-1, and showed that ectopic expression of a mutant Mklp-1 without the NLSs leads to cell cycle arrest at cytokinesis, indicating that the NLSs are necessary for Mklp-1 to execute its normal function during cell division. Furthermore, mutation of two serine residues in the first NLS to aspartic acid, which mimics phosphorylation, attenuated its nuclear localization function, suggesting that the function of this NLS might be regulated by phosphorylation.

  10. Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction

    PubMed Central

    Cheng, Xinxin; Zhang, Yao; Jónsson, Elvar; Jónsson, Hannes; Weber, Peter M.

    2016-01-01

    Density functional theory (DFT) is widely applied in calculations of molecules and materials. Yet, it suffers from a well-known over-emphasis on charge delocalization arising from self-interaction error that destabilizes localized states. Here, using the symmetric diamine N,N′-dimethylpiperazine as a model, we have experimentally determined the relative energy of a state with positive charge localized on one of the two nitrogen atoms, and a state with positive charge delocalized over both nitrogen atoms. The charge-localized state was found to be 0.33 (0.04) eV higher in energy than the charge-delocalized state. This provides an important test of theoretical approaches to electronic structure calculations. Calculations with all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state. However, the application of an explicit self-interaction correction to a semi-local functional identifies both states and gives relative energy in excellent agreement with both experiment and CCSD(T) calculations. PMID:26980327

  11. Beyond lensing by the cosmological constant

    NASA Astrophysics Data System (ADS)

    Faraoni, Valerio; Lapierre-Léonard, Marianne

    2017-01-01

    The long-standing problem of whether the cosmological constant affects directly the deflection of light caused by a gravitational lens is reconsidered. We use a new approach based on the Hawking quasilocal mass of a sphere grazed by light rays and on its splitting into local and cosmological parts. Previous literature restricted to the cosmological constant is extended to any form of dark energy accelerating the universe in which the gravitational lens is embedded.

  12. Global behaviour of a predator-prey like model with piecewise constant arguments.

    PubMed

    Kartal, Senol; Gurcan, Fuat

    2015-01-01

    The present study deals with the analysis of a predator-prey like model consisting of system of differential equations with piecewise constant arguments. A solution of the system with piecewise constant arguments leads to a system of difference equations which is examined to study boundedness, local and global asymptotic behaviour of the positive solutions. Using Schur-Cohn criterion and a Lyapunov function, we derive sufficient conditions under which the positive equilibrium point is local and global asymptotically stable. Moreover, we show numerically that periodic solutions arise as a consequence of Neimark-Sacker bifurcation of a limit cycle.

  13. Numerical calculation of listener-specific head-related transfer functions and sound localization: Microphone model and mesh discretization.

    PubMed

    Ziegelwanger, Harald; Majdak, Piotr; Kreuzer, Wolfgang

    2015-07-01

    Head-related transfer functions (HRTFs) can be numerically calculated by applying the boundary element method on the geometry of a listener's head and pinnae. The calculation results are defined by geometrical, numerical, and acoustical parameters like the microphone used in acoustic measurements. The scope of this study was to estimate requirements on the size and position of the microphone model and on the discretization of the boundary geometry as triangular polygon mesh for accurate sound localization. The evaluation involved the analysis of localization errors predicted by a sagittal-plane localization model, the comparison of equivalent head radii estimated by a time-of-arrival model, and the analysis of actual localization errors obtained in a sound-localization experiment. While the average edge length (AEL) of the mesh had a negligible effect on localization performance in the lateral dimension, the localization performance in sagittal planes, however, degraded for larger AELs with the geometrical error as dominant factor. A microphone position at an arbitrary position at the entrance of the ear canal, a microphone size of 1 mm radius, and a mesh with 1 mm AEL yielded a localization performance similar to or better than observed with acoustically measured HRTFs.

  14. Verification of the Usefulness of the Trimble Rtx Extended Satellite Technology with the Xfill Function in the Local Network Implementing Rtk Measurements

    NASA Astrophysics Data System (ADS)

    Siejka, Zbigniew

    2014-12-01

    The paper presents the method of satellite measurements, which gives users the ability of GNSS continuous precise positioning in real time, even in the case of short interruptions in receiving the correction of the local ground system of measurements support. The proposed method is a combination of two satellite positioning technologies RTN GNSS and RTX Extended. In technology RTX Extended the xFill function was used for precise positioning in real time and in the local reference system. This function provides the ability to perform measurement without the need for constant communication with the ground support satellite system. Test measurements were performed on a test basis located in Krakow, and RTN GNSS positioning was done based on the national network of reference stations of the ASGEUPOS. The solution allows for short (up to 5 minutes) interruptions in radio or internet communication. When the primary stream of RTN correction is not available, then the global corrections Trimble xFill broadcasted by satellite are used. The new technology uses in the real-time data from the global network of tracking stations and contributes significantly to improving the quality and efficiency of surveying works. At present according to the authors, technology Trimble CenterPoint RTX can guarantee repeatability of measurements not worse than 3.8 cm (Trimble Survey Division, 2012). In the paper the comparative analysis of measurement results between the two technologies was performed: RTN carried out in the classic way, which was based on the corrections of the terrestrial local network of the Polish system of active geodetic network (ASG-EUPOS) and RTK xFill technology. The results were related to the data of test network, established as error free. The research gave satisfactory results and confirmed the great potential of the use of the new technology in the geodetic work realization. By combining these two technologies of GNSS surveying the user can greatly improve the

  15. Validation of soil hydraulic pedotransfer functions at the local and catchment scale for an Indonesian basin

    NASA Astrophysics Data System (ADS)

    Booij, Martijn J.; Oldhoff, Ruben J. J.; Rustanto, Andry

    2016-04-01

    In order to accurately model the hydrological processes in a catchment, information on the soil hydraulic properties is of great importance. These data can be obtained by conducting field work, which is costly and time consuming, or by using pedotransfer functions (PTFs). A PTF is an empirical relationship between easily obtainable soil characteristics and a soil hydraulic parameter. In this study, PTFs for the saturated hydraulic conductivity (Ks) and the available water content (AWC) are investigated. PTFs are area-specific, since for instance tropical soils often have a different composition and hydraulic behaviour compared to temperate soils. Application of temperate soil PTFs on tropical soils might result in poor performance, which is a problem as few tropical soil PTFs are available. The objective of this study is to determine whether Ks and AWC can be accurately approximated using PTFs, by analysing their performance at both the local scale and the catchment scale. Four published PTFs for Ks and AWC are validated on a data set of 91 soil samples collected in the Upper Bengawan Solo catchment on Java, Indonesia. The AWC is predicted very poorly, with Nash-Sutcliffe Efficiency (NSE) values below zero for all selected PTFs. For Ks PTFs better results were found. The Wösten and Rosetta-3 PTFs predict the Ks moderately accurate, with NSE values of 0.28 and 0.39, respectively. New PTFs for both AWC and Ks were developed using multiple linear regression and NSE values of 0.37 (AWC) and 0.55 (Ks) were obtained. Although these values are not very high, they are significantly higher than for the published PTFs. The hydrological SWAT model was set up for the Keduang, a sub-catchment of the Upper Bengawan Solo River, to simulate monthly catchment streamflow. Eleven cases were defined to validate the PTFs at the catchment scale. For the Ks-PTF cases NSE values of around 0.84 were obtained for the validation period. The use of AWC PTFs resulted in slightly lower NSE

  16. Functional renormalization-group approaches, one-particle (irreducible) reducible with respect to local Green's functions, with dynamical mean-field theory as a starting point

    NASA Astrophysics Data System (ADS)

    Katanin, A. A.

    2015-06-01

    We consider formulations of the functional renormalization-group (fRG) flow for correlated electronic systems with the dynamical mean-field theory as a starting point. We classify the corresponding renormalization-group schemes into those neglecting one-particle irreducible six-point vertices (with respect to the local Green's functions) and neglecting one-particle reducible six-point vertices. The former class is represented by the recently introduced DMF2RG approach [31], but also by the scale-dependent generalization of the one-particle irreducible representation (with respect to local Green's functions, 1PI-LGF) of the generating functional [20]. The second class is represented by the fRG flow within the dual fermion approach [16, 32]. We compare formulations of the fRG approach in each of these cases and suggest their further application to study 2D systems within the Hubbard model.

  17. The Cosmological Constant in Quantum Cosmology

    SciTech Connect

    Wu Zhongchao

    2008-10-10

    Hawking proposed that the cosmological constant is probably zero in quantum cosmology in 1984. By using the right configuration for the wave function of the universe, a complete proof is found very recently.

  18. Discriminative local subspaces in gene expression data for effective gene function prediction

    PubMed Central

    Gutiérrez, Rodrigo A.; Soto, Alvaro

    2012-01-01

    Motivation: Massive amounts of genome-wide gene expression data have become available, motivating the development of computational approaches that leverage this information to predict gene function. Among successful approaches, supervised machine learning methods, such as Support Vector Machines (SVMs), have shown superior prediction accuracy. However, these methods lack the simple biological intuition provided by co-expression networks (CNs), limiting their practical usefulness. Results: In this work, we present Discriminative Local Subspaces (DLS), a novel method that combines supervised machine learning and co-expression techniques with the goal of systematically predict genes involved in specific biological processes of interest. Unlike traditional CNs, DLS uses the knowledge available in Gene Ontology (GO) to generate informative training sets that guide the discovery of expression signatures: expression patterns that are discriminative for genes involved in the biological process of interest. By linking genes co-expressed with these signatures, DLS is able to construct a discriminative CN that links both, known and previously uncharacterized genes, for the selected biological process. This article focuses on the algorithm behind DLS and shows its predictive power using an Arabidopsis thaliana dataset and a representative set of 101 GO terms from the Biological Process Ontology. Our results show that DLS has a superior average accuracy than both SVMs and CNs. Thus, DLS is able to provide the prediction accuracy of supervised learning methods while maintaining the intuitive understanding of CNs. Availability: A MATLAB® implementation of DLS is available at http://virtualplant.bio.puc.cl/cgi-bin/Lab/tools.cgi Contact: tfpuelma@uc.cl Supplementary Information: Supplementary data are available at http://bioinformatics.mpimp-golm.mpg.de/. PMID:22820203

  19. Li-Ion Localization and Energetics as a Function of Anode Structure.

    PubMed

    McNutt, Nicholas W; McDonnell, Marshall; Rios, Orlando; Keffer, David J

    2017-03-01

    In this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes. The edges of the crystalline and amorphous fragments of aromatic carbon that exist in these composites are terminated by hydrogen atoms, which play a crucial role in adsorption. In this work, we demonstrate how differences in composite structure due to changes in the processing conditions alter the type and extent of the interface between the amorphous and crystalline domains, thus impacting the nature of Li-ion storage. The effects of structural properties are evaluated using a suite of pair distribution functions as well as an original technique to extract archetypal structures, in the form of three-dimensional atomic density distributions, from highly disordered systems. The energetics of Li-ion binding are understood by relating changes in the energy and charge distributions to changes in structural properties. The distribution of Li-ion energies reveals that some structures lead to greater chemisorption, while others have greater physisorption. Carbon composites with a high volume fraction of small crystallites demonstrate the highest ion storage capacity because of the high interfacial area between the crystalline and amorphous domains. At these interfaces, stable H atoms, terminating the graphitic crystallites, provide favorable sites for reversible Li adsorption.

  20. Influence of local application of glaucoma medications-travoprost eye drops on patients' tear film function.

    PubMed

    Zhang, Chengpu

    2015-03-01

    This study discussed about the influence of local application of glaucoma medications -- travoprost eye drops to patients' tear film function. We selected 24 patients, 45 eyes with primary open-angle glaucoma or intraocular hypertension. All of the patients topically used the travoprost eye drops for one time every night. After and before the pharmacy, we proceeded 1, 2, 3 mo lines symptom score and Schirmer's test (St), corneal fluorescein staining (FL), breakup time of tear film (BUT). Average value of symptom score and FL of all the patients before pharmacy were 1.32 ± 1. 55, 0.42 ± 0.68, and 1, 2, 3mo after pharmacy were respectively 2.68 ± 1.59, 0.96 ± 0.81; 4.97 ± 1.62, 1.46 ± 0.62; 6.21 ± 1.33, 1.88 ± 0.44. Symptom score and FL of 1, 2, 3 mo patients after pharmacy were all prominent higher than it before pharmacy (P=0.00), and it gradually increased. The average value of patients symptom BUT and St before pharmacy were (7.71 ± 0.87s), (8.32 ± 2.63mm /5min) and 1, 2, 3 mo after pharmacy were respectively (6.93 ± 1.17s), (7.69 ± 3. 33mm /5min); (5.48 ± 1.29s), (6.79 ± 2.94mm /5min); (4.33 ± 1.83s), (5.98 ± 3.11mm/5min). BUT and St value after pharmacy were prominent all lower than the level before pharmacy (P=0.00). And it gradually reduced. Short-term use of travoprost eye drops would aggravate the corneal irritation of patients, and decrease the tear film stability and tear secretion.

  1. Multiple nuclear localization signals function in the nuclear import of the transcription factor Nrf2.

    PubMed

    Theodore, Melanie; Kawai, Yumiko; Yang, Jianqi; Kleshchenko, Yuliya; Reddy, Sekhar P; Villalta, Fernando; Arinze, Ifeanyi J

    2008-04-04

    Nuclear factor erythroid 2-related factor 2 (Nrf2) mediates the transcriptional response of cells to oxidative stress and is translocated into the nucleus following, or concomitant with, its activation by electrophiles or reactive oxygen species. The mechanism of its translocation into the nucleus is not entirely elucidated. Here we have identified two novel nuclear localization signal (NLS) motifs in murine Nrf2, one located near the N-terminal region (amino acid residues 42-53) and the other (residues 587-593) located near the C-terminal region. Imaging of green fluorescent protein (GFP)-tagged Nrf2 revealed that mutation(s) in any of these sequences resulted in decreased nuclear fluorescence intensity compared with the wild-type Nrf2 when Nrf2 activation was induced with the electrophile tert-butylhydroquinone. The mutations also impaired Nrf2-induced transactivation of antioxidant response element-driven reporter gene expression to the same extent as the Nrf2 construct bearing mutation in a previously identified bipartite NLS that maps at residues 494-511. When linked to GFP or to GFP-PEPCK-C each of the novel NLS motifs was sufficient to drive nuclear translocation of the fusion proteins. Co-immunoprecipitation assays demonstrated that importins alpha5 and beta1 associate with Nrf2, an interaction that was blocked by the nuclear import inhibitor SN50. SN50 also blocked tert-butylhydroquinone-induced nuclear fluorescence of GFP-Nrf2 in cells transfected with wild-type GFP-Nrf2. Overall these results reveal that multiple NLS motifs in Nrf2 function in its nuclear translocation in response to pro-oxidant stimuli and that the importin alpha-beta heterodimer nuclear import receptor system plays a critical role in the import process.

  2. Functional Effect of Pim1 Depends upon Intracellular Localization in Human Cardiac Progenitor Cells.

    PubMed

    Samse, Kaitlen; Emathinger, Jacqueline; Hariharan, Nirmala; Quijada, Pearl; Ilves, Kelli; Völkers, Mirko; Ormachea, Lucia; De La Torre, Andrea; Orogo, Amabel M; Alvarez, Roberto; Din, Shabana; Mohsin, Sadia; Monsanto, Megan; Fischer, Kimberlee M; Dembitsky, Walter P; Gustafsson, Åsa B; Sussman, Mark A

    2015-05-29

    Human cardiac progenitor cells (hCPC) improve heart function after autologous transfer in heart failure patients. Regenerative potential of hCPCs is severely limited with age, requiring genetic modification to enhance therapeutic potential. A legacy of work from our laboratory with Pim1 kinase reveals effects on proliferation, survival, metabolism, and rejuvenation of hCPCs in vitro and in vivo. We demonstrate that subcellular targeting of Pim1 bolsters the distinct cardioprotective effects of this kinase in hCPCs to increase proliferation and survival, and antagonize cellular senescence. Adult hCPCs isolated from patients undergoing left ventricular assist device implantation were engineered to overexpress Pim1 throughout the cell (PimWT) or targeted to either mitochondrial (Mito-Pim1) or nuclear (Nuc-Pim1) compartments. Nuc-Pim1 enhances stem cell youthfulness associated with decreased senescence-associated β-galactosidase activity, preserved telomere length, reduced expression of p16 and p53, and up-regulation of nucleostemin relative to PimWT hCPCs. Alternately, Mito-Pim1 enhances survival by increasing expression of Bcl-2 and Bcl-XL and decreasing cell death after H2O2 treatment, thereby preserving mitochondrial integrity superior to PimWT. Mito-Pim1 increases the proliferation rate by up-regulation of cell cycle modulators Cyclin D, CDK4, and phospho-Rb. Optimal stem cell traits such as proliferation, survival, and increased youthful properties of aged hCPCs are enhanced after targeted Pim1 localization to mitochondrial or nuclear compartments. Targeted Pim1 overexpression in hCPCs allows for selection of the desired phenotypic properties to overcome patient variability and improve specific stem cell characteristics.

  3. Long term motor function after neonatal stroke: Lesion localization above all.

    PubMed

    Dinomais, Mickael; Hertz-Pannier, Lucie; Groeschel, Samuel; Chabrier, Stéphane; Delion, Matthieu; Husson, Béatrice; Kossorotoff, Manoelle; Renaud, Cyrille; Nguyen The Tich, Sylvie

    2015-12-01

    Motor outcome is variable following neonatal arterial ischemic stroke (NAIS). We analyzed the relationship between lesion characteristics on brain MRI and motor function in children who had suffered from NAIS. Thirty eight full term born children with unilateral NAIS were investigated at the age of seven. 3D T1- and 3D FLAIR-weighted MR images were acquired on a 3T MRI scanner. Lesion characteristics were compared between patients with and without cerebral palsy (CP) using the following approaches: lesion localization either using a category-based analysis, lesion mapping as well as voxel-based lesion-symptom mapping (VLSM). Using diffusion-weighted imaging the microstructure of the cortico-spinal tract (CST) was related to the status of CP by measuring DTI parameters. Whereas children with lesions sparing the primary motor system did not develop CP, CP was always present when extensive lesions damaged at least two brain structures involving the motor system. The VLSM approach provided a statistical map that confirmed the cortical lesions in the primary motor system and revealed that CP was highly correlated with lesions in close proximity to the CST. In children with CP, diffusion parameters indicated microstructural changes in the CST at the level of internal capsule and the centrum semiovale. White matter damage of the CST in centrum semiovale was a highly reproducible marker of CP. This is the first description of the implication of this latter region in motor impairment after NAIS. In conclusion, CP in childhood was closely linked to the location of the infarct in the motor system.

  4. Nuclear localization and functional characteristics of voltage-gated potassium channel Kv1.3.

    PubMed

    Jang, Soo Hwa; Byun, Jun Kyu; Jeon, Won-Il; Choi, Seon Young; Park, Jin; Lee, Bo Hyung; Yang, Ji Eun; Park, Jin Bong; O'Grady, Scott M; Kim, Dae-Yong; Ryu, Pan Dong; Joo, Sang-Woo; Lee, So Yeong

    2015-05-15

    It is widely known that ion channels are expressed in the plasma membrane. However, a few studies have suggested that several ion channels including voltage-gated K(+) (Kv) channels also exist in intracellular organelles where they are involved in the biochemical events associated with cell signaling. In the present study, Western blot analysis using fractionated protein clearly indicates that Kv1.3 channels are expressed in the nuclei of MCF7, A549, and SNU-484 cancer cells and human brain tissues. In addition, Kv1.3 is located in the plasma membrane and the nucleus of Jurkat T cells. Nuclear membrane hyperpolarization after treatment with margatoxin (MgTX), a specific blocker of Kv1.3 channels, provides evidence for functional channels at the nuclear membrane of A549 cells. MgTX-induced hyperpolarization is abolished in the nuclei of Kv1.3 silenced cells, and the effects of MgTX are dependent on the magnitude of the K(+) gradient across the nuclear membrane. Selective Kv1.3 blockers induce the phosphorylation of cAMP response element-binding protein (CREB) and c-Fos activation. Moreover, Kv1.3 is shown to form a complex with the upstream binding factor 1 in the nucleus. Chromatin immunoprecipitation assay reveals that Sp1 transcription factor is directly bound to the promoter region of the Kv1.3 gene, and the Sp1 regulates Kv1.3 expression in the nucleus of A549 cells. These results demonstrate that Kv1.3 channels are primarily localized in the nucleus of several types of cancer cells and human brain tissues where they are capable of regulating nuclear membrane potential and activation of transcription factors, such as phosphorylated CREB and c-Fos.

  5. Localization and functional characterization of a novel adipokinetic hormone in the mollusk, Aplysia californica.

    PubMed

    Johnson, Joshua I; Kavanaugh, Scott I; Nguyen, Cindy; Tsai, Pei-San

    2014-01-01

    Increasing evidence suggests that gonadotropin-releasing hormone (GnRH), corazonin, adipokinetic hormone (AKH), and red pigment-concentrating hormone all share common ancestry to form a GnRH superfamily. Despite the wide presence of these peptides in protostomes, their biological effects remain poorly characterized in many taxa. This study had three goals. First, we cloned the full-length sequence of a novel AKH, termed Aplysia-AKH, and examined its distribution in an opisthobranch mollusk, Aplysia californica. Second, we investigated in vivo biological effects of Aplysia-AKH. Lastly, we compared the effects of Aplysia-AKH to a related A. californica peptide, Aplysia-GnRH. Results suggest that Aplysia-AKH mRNA and peptide are localized exclusively in central tissues, with abdominal, cerebral, and pleural ganglia being the primary sites of Aplysia-AKH production. However, Aplysia-AKH-positive fibers were found in all central ganglia, suggesting diverse neuromodulatory roles. Injections of A. californica with Aplysia-AKH significantly inhibited feeding, reduced body mass, increased excretion of feces, and reduced gonadal mass and oocyte diameter. The in vivo effects of Aplysia-AKH differed substantially from Aplysia-GnRH. Overall, the distribution and biological effects of Aplysia-AKH suggest it has diverged functionally from Aplysia-GnRH over the course of evolution. Further, that both Aplysia-AKH and Aplysia-GnRH failed to activate reproduction suggest the critical role of GnRH as a reproductive activator may be a phenomenon unique to vertebrates.

  6. Subcellular Localization and Functional Analysis of the Arabidopsis GTPase RabE1[W][OA

    PubMed Central

    Speth, Elena Bray; Imboden, Lori; Hauck, Paula; He, Sheng Yang

    2009-01-01

    Membrane trafficking plays a fundamental role in eukaryotic cell biology. Of the numerous known or predicted protein components of the plant cell trafficking system, only a relatively small subset have been characterized with respect to their biological roles in plant growth, development, and response to stresses. In this study, we investigated the subcellular localization and function of an Arabidopsis (Arabidopsis thaliana) small GTPase belonging to the RabE family. RabE proteins are phylogenetically related to well-characterized regulators of polarized vesicle transport from the Golgi apparatus to the plasma membrane in animal and yeast cells. The RabE family of GTPases has also been proposed to be a putative host target of AvrPto, an effector protein produced by the plant pathogen Pseudomonas syringae, based on yeast two-hybrid analysis. We generated transgenic Arabidopsis plants that constitutively expressed one of the five RabE proteins (RabE1d) fused to green fluorescent protein (GFP). GFP-RabE1d and endogenous RabE proteins were found to be associated with the Golgi apparatus and the plasma membrane in Arabidopsis leaf cells. RabE down-regulation, due to cosuppression in transgenic plants, resulted in drastically altered leaf morphology and reduced plant size, providing experimental evidence for an important role of RabE GTPases in regulating plant growth. RabE down-regulation did not affect plant susceptibility to pathogenic P. syringae bacteria; conversely, expression of the constitutively active RabE1d-Q74L enhanced plant defenses, conferring resistance to P. syringae infection. PMID:19233904

  7. Nuclear Localization and Functional Characteristics of Voltage-gated Potassium Channel Kv1.3*

    PubMed Central

    Jang, Soo Hwa; Byun, Jun Kyu; Jeon, Won-Il; Choi, Seon Young; Park, Jin; Lee, Bo Hyung; Yang, Ji Eun; Park, Jin Bong; O'Grady, Scott M.; Kim, Dae-Yong; Ryu, Pan Dong; Joo, Sang-Woo; Lee, So Yeong

    2015-01-01

    It is widely known that ion channels are expressed in the plasma membrane. However, a few studies have suggested that several ion channels including voltage-gated K+ (Kv) channels also exist in intracellular organelles where they are involved in the biochemical events associated with cell signaling. In the present study, Western blot analysis using fractionated protein clearly indicates that Kv1.3 channels are expressed in the nuclei of MCF7, A549, and SNU-484 cancer cells and human brain tissues. In addition, Kv1.3 is located in the plasma membrane and the nucleus of Jurkat T cells. Nuclear membrane hyperpolarization after treatment with margatoxin (MgTX), a specific blocker of Kv1.3 channels, provides evidence for functional channels at the nuclear membrane of A549 cells. MgTX-induced hyperpolarization is abolished in the nuclei of Kv1.3 silenced cells, and the effects of MgTX are dependent on the magnitude of the K+ gradient across the nuclear membrane. Selective Kv1.3 blockers induce the phosphorylation of cAMP response element-binding protein (CREB) and c-Fos activation. Moreover, Kv1.3 is shown to form a complex with the upstream binding factor 1 in the nucleus. Chromatin immunoprecipitation assay reveals that Sp1 transcription factor is directly bound to the promoter region of the Kv1.3 gene, and the Sp1 regulates Kv1.3 expression in the nucleus of A549 cells. These results demonstrate that Kv1.3 channels are primarily localized in the nucleus of several types of cancer cells and human brain tissues where they are capable of regulating nuclear membrane potential and activation of transcription factors, such as phosphorylated CREB and c-Fos. PMID:25829491

  8. Macular SD-OCT Outcome Measures: Comparison of Local Structure-Function Relationships and Dynamic Range

    PubMed Central

    Miraftabi, Arezoo; Amini, Navid; Morales, Esteban; Henry, Sharon; Yu, Fei; Afifi, Abdolmonem; Coleman, Anne L.; Caprioli, Joseph; Nouri-Mahdavi, Kouros

    2016-01-01

    Purpose We tested the hypothesis that the macular ganglion cell layer (GCL) thickness demonstrates a stronger structure-function (SF) relationship and extends the useful range of macular measurements compared with combined macular inner layer or full thickness. Methods Ninety-eight glaucomatous eyes and eight normal eyes with macular spectral domain optical coherence tomography (SD-OCT) volume scans and 10-2 visual fields were enrolled. Inner plexiform layer (IPL), GCL, macular retinal nerve fiber layer (mRNFL), ganglion cell-inner plexiform layer (GCIPL), ganglion cell complex (GCC), and full thickness (FT) measurements were calculated for 8 × 8 arrays of 3° superpixels. Main outcome measures were local structure-function relationships between macular superpixels and corresponding sensitivities on 10-2 fields after adjusting for ganglion cell displacement, dynamic range of measurements, and the change point (total deviation value where macular parameters reached measurement floor). Results Median (interquartile range [IQR]) mean deviation was −7.2 (−11.6 to −3.2) dB in glaucoma eyes. Strength of SF relationships was highest for GCIPL, GCL, GCC, and IPL (ρ = 0.635, 0.627, 0.621, and 0.577, respectively; P ≤ 0.046 for comparisons against GCIPL). Highest SF correlations coincided with the peak of GCL thickness, where the dynamic range was widest for FT (81.1 μm), followed by GCC (65.7 μm), GCIPL (54.9 μm), GCL (35.2 μm), mRNFL (27.5 μm), and IPL (20.9 μm). Change points were similar for all macular parameters (−7.8 to −8.9 dB). Conclusions GCIPL, GCL, and GCC demonstrated comparable SF relationships while FT, GCC, and GCIPL had the widest dynamic range. Measurement of GCL did not extend the range of useful structural measurements. Measuring GCL does not provide any advantage for detection of progression with current SD-OCT technology. PMID:27623336

  9. A functional nuclear localization sequence in the VP1 capsid protein of coxsackievirus B3

    SciTech Connect

    Wang, Tianying; Yu, Bohai; Lin, Lexun; Zhai, Xia; Han, Yelu; Qin, Ying; Guo, Zhiwei; Wu, Shuo; Zhong, Xiaoyan; Wang, Yan; Tong, Lei; Zhang, Fengmin; Si, Xiaoning; Zhao, Wenran; Zhong, Zhaohua

    2012-11-25

    The capsid proteins of some RNA viruses can translocate to the nucleus and interfere with cellular phenotypes. In this study we found that the VP1 capsid protein of coxsackievirus B3 (CVB3) was dominantly localized in the nucleus of the cells transfected with VP1-expressing plasmid. The VP1 nuclear localization also occurred in the cells infected with CVB3. Truncation analysis indicated that the VP1 nuclear localization sequence located near the C-terminal. The substitution of His220 with threonine completely abolished its translocation. The VP1 proteins of other CVB types might have the nuclear localization potential because this region was highly conserved. Moreover, the VP1 nuclear localization induced cell cycle deregulation, including a prolonged S phase and shortened G2-M phase. Besides these findings, we also found a domain between Ala72 and Phe106 that caused the VP1 truncates dotted distributed in the cytoplasm. Our results suggest a new pathogenic mechanism of CVB. - Highlights: Black-Right-Pointing-Pointer The VP1 protein of coxsackievirus B3 can specifically localize in the nucleus. Black-Right-Pointing-Pointer The nuclear localization signal of coxsackievirus B3 VP1 protein locates near its C-terminal. Black-Right-Pointing-Pointer The VP1 nuclear localization of coxsackievirus B3 can deregulate cell cycle. Black-Right-Pointing-Pointer There is a domain in the VP1 that determines it dotted distributed in the cytoplasm.

  10. Adjustment of interaural time difference in head related transfer functions based on listeners' anthropometry and its effect on sound localization

    NASA Astrophysics Data System (ADS)

    Suzuki, Yôiti; Watanabe, Kanji; Iwaya, Yukio; Gyoba, Jiro; Takane, Shouichi

    2005-04-01

    Because the transfer functions governing subjective sound localization (HRTFs) show strong individuality, sound localization systems based on synthesis of HRTFs require suitable HRTFs for individual listeners. However, it is impractical to obtain HRTFs for all listeners based on measurements. Improving sound localization by adjusting non-individualized HRTFs to a specific listener based on that listener's anthropometry might be a practical method. This study first developed a new method to estimate interaural time differences (ITDs) using HRTFs. Then correlations between ITDs and anthropometric parameters were analyzed using the canonical correlation method. Results indicated that parameters relating to head size, and shoulder and ear positions are significant. Consequently, it was attempted to express ITDs based on listener's anthropometric data. In this process, the change of ITDs as a function of azimuth angle was parameterized as a sum of sine functions. Then the parameters were analyzed using multiple regression analysis, in which the anthropometric parameters were used as explanatory variables. The predicted or individualized ITDs were installed in the nonindividualized HRTFs to evaluate sound localization performance. Results showed that individualization of ITDs improved horizontal sound localization.

  11. Percutaneous Image-Guided Cryoablation of Head & Neck Tumors for Local Control, Preservation of Functional Status, and Pain Relief

    PubMed Central

    Guenette, Jeffrey P.; Tuncali, Kemal; Himes, Nathan; Shyn, Paul B.; Lee, Thomas C.

    2016-01-01

    We report 9 consecutive percutaneous image-guided cryoablation procedures of head and neck tumors in 7 patients (4 males, 3 females; mean age 68 years, range 50-78). Entire tumor ablation for local control or regional ablation for pain relief or functional status preservation was achieved in 8 of 9 procedures. One patient experienced intraprocedural bradycardia while another developed a neopharyngeal abscess. There were no deaths, permanent neurological or functional deficits, vascular complications, or adverse cosmetic sequelae. PMID:27845860

  12. Redshift in Hubble's constant.

    NASA Astrophysics Data System (ADS)

    Temple-Raston, M.

    1997-01-01

    A topological field theory with Bogomol'nyi solitons is examined. The Bogomol'nyi solitons have much in common with the instanton in Yang-Mills theory; consequently the author called them 'topological instantons'. When periodic boundary conditions are imposed, the field theory comments indirectly on the speed of light within the theory. In this particular model the speed of light is not a universal constant. This may or may not be relevant to the current debate in astronomy and cosmology over the large values of the Hubble constant obtained by the latest generation of ground- and space-based telescopes. An experiment is proposed to detect spatial variation in the speed of light.

  13. Wall of fundamental constants

    SciTech Connect

    Olive, Keith A.; Peloso, Marco; Uzan, Jean-Philippe

    2011-02-15

    We consider the signatures of a domain wall produced in the spontaneous symmetry breaking involving a dilatonlike scalar field coupled to electromagnetism. Domains on either side of the wall exhibit slight differences in their respective values of the fine-structure constant, {alpha}. If such a wall is present within our Hubble volume, absorption spectra at large redshifts may or may not provide a variation in {alpha} relative to the terrestrial value, depending on our relative position with respect to the wall. This wall could resolve the contradiction between claims of a variation of {alpha} based on Keck/Hires data and of the constancy of {alpha} based on Very Large Telescope data. We derive the properties of the wall and the parameters of the underlying microscopic model required to reproduce the possible spatial variation of {alpha}. We discuss the constraints on the existence of the low-energy domain wall and describe its observational implications concerning the variation of the fundamental constants.

  14. Optimal head related transfer functions for hearing and monaural localization in elevation: a signal processing design perspective.

    PubMed

    Rao, K R; Ben-Arie, J

    1996-11-01

    Localization of sound sources by human listeners has been widely studied and theories and various models of the localization and hearing mechanism have been constructed. In the classical "duplex" theory, sound localization in azimuth is explained by interaural time or equivalently, phase differences at low frequencies, and by interaural amplitude differences at higher frequencies. Head related transfer functions (HRTF's) present a linear system approach to modeling localization by representing the direction-dependent transformation the sound undergoes at each ear. Localization in elevation is explained by directional differences in the HRTF's, which also explains monaural localization. We conjecture that the HRTF's evolved during the course of nature (due to the evolution of the shape and structure of the ear etc.) are optimal with respect to several physically realizable criteria. In this paper, we investigate the problem of defining the design constraints which when optimized yield a set of HRTF's for hearing and monaural vertical localization in an attempt to better understand, and if possible, duplicate nature's design. We pursue an engineer's design perspective and formulate a constrained optimization problem, where the desired set of HRTF's is optimized according to a cost function based on several criteria for localization, hearing and smoothness, and also by imposing physically realizable constraints on the HRTF's such as nonnegativity, energy etc. The value of the cost function for a candidate set of HRTF's is an indication of the similarity of that set of HRTF's with respect to the ideal solution (measured HRTF data). The final optimization results we present are similar to the actual HRTF's measured in human subjects, and the associated cost function values are found to be almost equal. This points to the fact that the optimization criteria defined are quite relevant. The significant outcome of this research is the identification of a relevant set of

  15. Constant-pressure Blowers

    NASA Technical Reports Server (NTRS)

    Sorensen, E

    1940-01-01

    The conventional axial blowers operate on the high-pressure principle. One drawback of this type of blower is the relatively low pressure head, which one attempts to overcome with axial blowers producing very high pressure at a given circumferential speed. The Schicht constant-pressure blower affords pressure ratios considerably higher than those of axial blowers of conventional design with approximately the same efficiency.

  16. Universe of constant

    NASA Astrophysics Data System (ADS)

    Yongquan, Han

    2016-10-01

    The ideal gas state equation is not applicable to ordinary gas, it should be applied to the Electromagnetic ``gas'' that is applied to the radiation, the radiation should be the ultimate state of matter changes or initial state, the universe is filled with radiation. That is, the ideal gas equation of state is suitable for the Singular point and the universe. Maybe someone consider that, there is no vessel can accommodate radiation, it is because the Ordinary container is too small to accommodate, if the radius of your container is the distance that Light through an hour, would you still think it can't accommodates radiation? Modern scientific determinate that the radius of the universe now is about 1027 m, assuming that the universe is a sphere whose volume is approximately: V = 4.19 × 1081 cubic meters, the temperature radiation of the universe (cosmic microwave background radiation temperature of the universe, should be the closest the average temperature of the universe) T = 3.15k, radiation pressure P = 5 × 10-6 N / m 2, according to the law of ideal gas state equation, PV / T = constant = 6 × 1075, the value of this constant is the universe, The singular point should also equal to the constant Author: hanyongquan

  17. The Hubble Constant.

    PubMed

    Jackson, Neal

    2015-01-01

    I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give H0 values of around 72-74 km s(-1) Mpc(-1), with typical errors of 2-3 km s(-1) Mpc(-1). This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68 km s(-1) Mpc(-1) and typical errors of 1-2 km s(-1) Mpc(-1). The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.

  18. Localized states in an unbounded neural field equation with smooth firing rate function: a multi-parameter analysis.

    PubMed

    Faye, Grégory; Rankin, James; Chossat, Pascal

    2013-05-01

    The existence of spatially localized solutions in neural networks is an important topic in neuroscience as these solutions are considered to characterize working (short-term) memory. We work with an unbounded neural network represented by the neural field equation with smooth firing rate function and a wizard hat spatial connectivity. Noting that stationary solutions of our neural field equation are equivalent to homoclinic orbits in a related fourth order ordinary differential equation, we apply normal form theory for a reversible Hopf bifurcation to prove the existence of localized solutions; further, we present results concerning their stability. Numerical continuation is used to compute branches of localized solution that exhibit snaking-type behaviour. We describe in terms of three parameters the exact regions for which localized solutions persist.

  19. Quantum Monte Carlo study of the itinerant-localized model of strongly correlated electrons: Spin-spin correlation functions

    NASA Astrophysics Data System (ADS)

    Ivantsov, Ilya; Ferraz, Alvaro; Kochetov, Evgenii

    2016-12-01

    We perform quantum Monte Carlo simulations of the itinerant-localized periodic Kondo-Heisenberg model for the underdoped cuprates to calculate the associated spin correlation functions. The strong electron correlations are shown to play a key role in the abrupt destruction of the quasi-long-range antiferromagnetic order in the lightly doped regime.

  20. 34 CFR 462.44 - Which educational functioning levels must States and local eligible providers use to measure and...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 3 2010-07-01 2010-07-01 false Which educational functioning levels must States and local eligible providers use to measure and report educational gain in the NRS? 462.44 Section 462.44... ADULT EDUCATION, DEPARTMENT OF EDUCATION MEASURING EDUCATIONAL GAIN IN THE NATIONAL REPORTING SYSTEM...

  1. Novel Functional Dissection of the Localization-Specific Roles of Budding Yeast Polo Kinase Cdc5p

    PubMed Central

    Park, Jung-Eun; Park, Chong J.; Sakchaisri, Krisada; Karpova, Tatiana; Asano, Satoshi; McNally, James; Sunwoo, Yangil; Leem, Sun-Hee; Lee, Kyung S.

    2004-01-01

    Budding yeast polo kinase Cdc5p localizes to the spindle pole body (SPB) and to the bud-neck and plays multiple roles during M-phase progression. To dissect localization-specific mitotic functions of Cdc5p, we tethered a localization-defective N-terminal kinase domain of Cdc5p (Cdc5pΔC) to the SPB or to the bud-neck with components specifically localizing to one of these sites and characterized these mutants in a cdc5Δ background. Characterization of a viable, SPB-localizing, CDC5ΔC-CNM67 mutant revealed that it is defective in timely degradation of Swe1p, a negative regulator of Cdc28p. Loss of BFA1, a negative regulator of mitotic exit, rescued the lethality of a neck-localizing CDC5ΔC-CDC12 or CDC5ΔC-CDC3 mutant but yielded severe defects in cytokinesis. These data suggest that the SPB-associated Cdc5p activity is critical for both mitotic exit and cytokinesis, whereas the bud neck-localized Cdc5p is required for proper Swe1p regulation. Interestingly, a cdc5Δ bfa1Δ swe1Δ triple mutant is viable but grows slowly, whereas cdc5Δ cells bearing both CDC5ΔC-CNM67 and CDC5ΔC-CDC12 grow well with only a mild cell cycle delay. Thus, SPB- and the bud-neck-localized Cdc5p control most of the critical Cdc5p functions and downregulation of Bfa1p and Swe1p at the respective locations are two critical factors that require Cdc5p. PMID:15509790

  2. Localization of strain in the RNA backbone and its functional implication

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Rabitz, Herschel

    1992-07-01

    It is known that an RNA molecule capable of self-splicing shares a common pattern of Watson-Crick base paris with other RNA species endowed with the same capability. The aim of this work is to introduce a minimal model Hamiltonian which determines a localized strain in the RNA backbone as the search for the molecular conformation is subject to the constraint imposed by the concensus secondary structure. The site where the strain is localized is shown to coincide with the splicing site of the molecule. As justified posteriori, the level of structural complexity of the model is sufficient to account for energy localization in a nontrivial fashion.

  3. Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3).

    PubMed

    Liu, Wenbin; Wood, Robert H; Doren, Douglas J

    2008-06-19

    The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented.

  4. The relations among Shannon information entropy, quantum discord, concurrence and localization properties of one-dimensional single-electron wave functions

    NASA Astrophysics Data System (ADS)

    Gong, Longyan; Zheng, Yongcui; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2014-09-01

    Shannon information entropy (SE), concurrence (CC), quantum discord (QD) and localization properties for various one-dimensional one-electron wave functions are intensively studied, respectively. They include Gaussian functions, power-law functions, and functions in the Anderson model and the Harper ones. For all these wave functions, we find that SE, CC and QD increase as the localization length of a wave function increases, respectively. There are linear or quadratic relationships between two of them. Therefore, we can confirm for the analyzed models that SE, CC and QD are statistically equivalent quantities to reflect the localization properties of wave functions though they are different measures of quantum information.

  5. Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element

    PubMed Central

    Gilligan, Patrick C.; Kumari, Pooja; Lim, Shimin; Cheong, Albert; Chang, Alex; Sampath, Karuna

    2011-01-01

    RNA localization is emerging as a general principle of sub-cellular protein localization and cellular organization. However, the sequence and structural requirements in many RNA localization elements remain poorly understood. Whereas transcription factor-binding sites in DNA can be recognized as short degenerate motifs, and consensus binding sites readily inferred, protein-binding sites in RNA often contain structural features, and can be difficult to infer. We previously showed that zebrafish squint/nodal-related 1 (sqt/ndr1) RNA localizes to the future dorsal side of the embryo. Interestingly, mammalian nodal RNA can also localize to dorsal when injected into zebrafish embryos, suggesting that the sequence motif(s) may be conserved, even though the fish and mammal UTRs cannot be aligned. To define potential sequence and structural features, we obtained ndr1 3′-UTR sequences from approximately 50 fishes that are closely, or distantly, related to zebrafish, for high-resolution phylogenetic footprinting. We identify conserved sequence and structural motifs within the zebrafish/carp family and catfish. We find that two novel motifs, a single-stranded AGCAC motif and a small stem-loop, are required for efficient sqt RNA localization. These findings show that comparative sequencing in the zebrafish/carp family is an efficient approach for identifying weak consensus binding sites for RNA regulatory proteins. PMID:21149265

  6. The Hubble Constant

    NASA Astrophysics Data System (ADS)

    Freedman, Wendy; Madore, Barry; Mager, Violet; Persson, Eric; Rigby, Jane; Sturch, Laura

    2008-12-01

    We present a plan to measure a value of the Hubble constant having a final systematic uncertainty of only 3% by taking advantage of Spitzer's unique mid-infrared capabilities. This involves using IRAC to undertake a fundamental recalibration of the Cepheid distance scale and progressively moving it out to pure Hubble flow by an application of a revised mid-IR Tully-Fisher relation. The calibration and application, in one coherent and self-consistent program, will go continuously from distances of parsecs to several hundred megaparsecs. It will provide a first-ever mid-IR calibration of Cepheids in the Milky Way, LMC and Key Project spiral galaxies and a first-ever measurement and calibration of the TF relation at mid-infrared wavelengths, and finally a calibration of Type Ia SNe. Most importantly this program will be undertaken with a single instrument, on a single telescope, working exclusively at mid-infrared wavelengths that are far removed from the obscuring effects of dust extinction. Using Spitzer in this focused way will effectively eliminate all of the major systematics in the Cepheid and TF distance scales that have been the limiting factors in all previous applications, including the HST Key Project. By executing this program, based exclusively on Spitzer data, we will deliver a value of the Hubble constant, having a statistical precision better than 11%, with all currently known systematics quantified and constrained to a level of less than 3%. A value of Ho determined to this level of systematic accuracy is required for up-coming cosmology experiments, including Planck. A more accurate value of the Hubble constant will directly result in other contingently measured cosmological parameters (e.g., Omega_m, Omega_L, & w) having their covariant uncertainties reduced significantly now. Any further improvements using this route will have to await JWST, for which this study is designed to provide a lasting and solid foundation, and ultimately a value of Ho

  7. The Local Black Hole Mass Function Derived from the MBH-Pitch Angle and the MBH-Sersic Index Relations

    NASA Astrophysics Data System (ADS)

    Mutlu Pakdil, Burcin; Seigar, Marc S.; Davis, Benjamin L.

    2016-01-01

    We determined the local supermassive black hole mass function (BHMF) for all galaxy types with complementing the local BHMF for spiral galaxies derived by Davis et al. (2014). We used the empirical relation between supermassive black hole mass and the Sersic index for early type (E/S0) galaxies from the same parent sample with Davis et al. (2014), which is selected from galaxies in the Carnegie-Irvine Galaxy Survey (CGS) which is a very complete sample of the nearby galaxies.The observational simplicity of our approach and direct measurements from the statistically tightest correlations with black hole mass, which are the Sersic index for E/S0 galaxies and pitch angle for spiral galaxies, make it straightforward to estimate an accurate local BHMF. Integrating over the best-fitting mass function, the local mass density of SMBHs from early- and late-type galaxies combined is ρ=3.61+3.80-1.75 x105 M⊙ Mpc-3. The errors are estimated from Monte Carlo simulations which include uncertainities in the emprical relations and measurement errors in both Sersic index and Pitch angle. Assuming supermassive black holes form via baryonic accretion, we find that 0.013+0.013-0.006 per cent of baryons are contained in SMBHs at the centers of galaxies in the local universe.

  8. Evidence for intact local connectivity but disrupted regional function in the occipital lobe in children and adolescents with schizophrenia.

    PubMed

    White, Tonya; Moeller, Steen; Schmidt, Marcus; Pardo, Jose V; Olman, Cheryl

    2012-08-01

    It has long been known that specific visual frequencies result in greater blood flow to the striate cortex. These peaks are thought to reflect synchrony of local neuronal firing that is reflective of local cortical networks. Since disrupted neural connectivity is a possible etiology for schizophrenia, our goal was to investigate whether localized connectivity, as measured by aberrant synchrony, is abnormal in children and adolescents with schizophrenia. Subjects included 25 children and adolescents with schizophrenia and 39 controls matched for age and gender. Subjects were scanned on a Siemens 3 Tesla Trio scanner while observing flashing checkerboard presented at either 1, 4, 8, or 12 Hz. Image processing included both a standard GLM model and a Fourier transform analysis. Patients had significantly smaller volume of activation in the occipital lobe compared to controls. There were no differences in the integral or percent signal change of the hemodynamic response function for each of the four frequencies. Occipital activation was stable during development between childhood and late adolescence. Finally, both patients and controls demonstrated an increased response between 4 and 8 Hz consistent with synchrony or entrainment in the neuronal response. Children and adolescents with schizophrenia had a significantly lower volume of activation in the occipital lobe in response to the flashing checkerboard task. However, features of intact local connectivity in patients, such as the hemodynamic response function and maximal response at 8 Hz, were normal. These results are consistent with abnormalities in regional connectivity with preserved local connectivity in early-onset schizophrenia.

  9. Isoform-specific subcellular localization and function of protein kinase A identified by mosaic imaging of mouse brain

    PubMed Central

    Ilouz, Ronit; Lev-Ram, Varda; Bushong, Eric A; Stiles, Travis L; Friedmann-Morvinski, Dinorah; Douglas, Christopher; Goldberg, Geoffrey; Ellisman, Mark H; Taylor, Susan S

    2017-01-01

    Protein kinase A (PKA) plays critical roles in neuronal function that are mediated by different regulatory (R) subunits. Deficiency in either the RIβ or the RIIβ subunit results in distinct neuronal phenotypes. Although RIβ contributes to synaptic plasticity, it is the least studied isoform. Using isoform-specific antibodies, we generated high-resolution large-scale immunohistochemical mosaic images of mouse brain that provided global views of several brain regions, including the hippocampus and cerebellum. The isoforms concentrate in discrete brain regions, and we were able to zoom-in to show distinct patterns of subcellular localization. RIβ is enriched in dendrites and co-localizes with MAP2, whereas RIIβ is concentrated in axons. Using correlated light and electron microscopy, we confirmed the mitochondrial and nuclear localization of RIβ in cultured neurons. To show the functional significance of nuclear localization, we demonstrated that downregulation of RIβ, but not of RIIβ, decreased CREB phosphorylation. Our study reveals how PKA isoform specificity is defined by precise localization. DOI: http://dx.doi.org/10.7554/eLife.17681.001 PMID:28079521

  10. Change is a Constant.

    PubMed

    Lubowitz, James H; Provencher, Matthew T; Brand, Jefferson C; Rossi, Michael J; Poehling, Gary G

    2015-06-01

    In 2015, Henry P. Hackett, Managing Editor, Arthroscopy, retires, and Edward A. Goss, Executive Director, Arthroscopy Association of North America (AANA), retires. Association is a positive constant, in a time of change. With change comes a need for continuing education, research, and sharing of ideas. While the quality of education at AANA and ISAKOS is superior and most relevant, the unique reason to travel and meet is the opportunity to interact with innovative colleagues. Personal interaction best stimulates new ideas to improve patient care, research, and teaching. Through our network, we best create innovation.

  11. Cosmology with varying constants.

    PubMed

    Martins, Carlos J A P

    2002-12-15

    The idea of possible time or space variations of the 'fundamental' constants of nature, although not new, is only now beginning to be actively considered by large numbers of researchers in the particle physics, cosmology and astrophysics communities. This revival is mostly due to the claims of possible detection of such variations, in various different contexts and by several groups. I present the current theoretical motivations and expectations for such variations, review the current observational status and discuss the impact of a possible confirmation of these results in our views of cosmology and physics as a whole.

  12. New Quasar Studies Keep Fundamental Physical Constant Constant

    NASA Astrophysics Data System (ADS)

    2004-03-01

    certain spectral lines with present-day values. Quasars are here only used as a beacon - the flame - in the very distant Universe. Interstellar clouds of gas in galaxies, located between the quasars and us on the same line of sight and at distances varying from six to eleven thousand of million light years, absorb parts of the light emitted by the quasars. The resulting spectrum consequently presents dark "valleys" that can be attributed to well-known elements. If the fine-structure constant happens to change over the duration of the light's journey, the energy levels in the atoms would be affected and the wavelengths of the absorption lines would be shifted by different amounts. By comparing the relative gaps between the valleys with the laboratory values, it is possible to calculate alpha as a function of distance from us, that is, as a function of the age of the Universe. These measures are however extremely delicate and require a very good modelling of the absorption lines. They also put exceedingly strong requirements on the quality of the astronomical spectra. They must have enough resolution to allow very precise measurement of minuscule shifts in the spectra. And a sufficient number of photons must be captured in order to provide a statistically unambiguous result. For this, astronomers have to turn to the most advanced spectral instruments on the largest telescopes. This is where the Ultra-violet and Visible Echelle Spectrograph (UVES) and ESO's Kueyen 8.2-m telescope at the Paranal Observatory is unbeatable, thanks to the unequalled spectral quality and large collecting mirror area of this combination. Constant or not? ESO PR Photo 07/04 ESO PR Photo 07/04 Relative Changes with Redshift of the Fine Structure Constant [Preview - JPEG: 496 x 400 pix - 36k] [Normal - JPEG: 991 x 800 pix - 320k] Captions: ESO PR Photo 07/04 shows measured values of the relative change of alpha from the sample of absorption systems studied by Hum Chand and his colleagues, plotted as

  13. GENIUS: web server to predict local gene networks and key genes for biological functions.

    PubMed

    Puelma, Tomas; Araus, Viviana; Canales, Javier; Vidal, Elena A; Cabello, Juan M; Soto, Alvaro; Gutiérrez, Rodrigo A

    2016-12-19

    GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve several interacting processes. GENIUS also enriches the network with new genes related to the biological function of interest, with accuracies comparable to highly discriminative Support Vector Machine methods.

  14. Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

    SciTech Connect

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-14

    The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

  15. Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

    NASA Astrophysics Data System (ADS)

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-01

    The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

  16. Non Lyapunov stability of the constant spatially developing 1-D gas flow in presence of solutions having strictly positive exponential growth rate

    NASA Astrophysics Data System (ADS)

    Balint, Stefan; Balint, Agneta M.

    2017-01-01

    Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 1-D gas flow are analyzed in the phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the real axis. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].

  17. Probability Density Functions of Floating Potential Fluctuations Due to Local Electron Flux Intermittency in a Linear ECR Plasma

    NASA Astrophysics Data System (ADS)

    Yoshimura, Shinji; Terasaka, Kenichiro; Tanaka, Eiki; Aramaki, Mitsutoshi; Tanaka, Masayoshi Y.

    An intermittent behavior of local electron flux in a laboratory ECR plasma is statistically analyzed by means of probability density functions (PDFs). The PDF constructed from a time series of the floating potential signal on a Langmuir probe has a fat tail in the negative value side, which reflects the intermittency of the local electron flux. The PDF of the waiting time, which is defined by the time interval between two successive events, is found to exhibit an exponential distribution, suggesting that the phenomenon is characterized by a stationary Poisson process. The underlying Poisson process is also confirmed by the number of events in given time intervals that is Poisson distributed.

  18. Contaminant point source localization error estimates as functions of data quantity and model quality

    NASA Astrophysics Data System (ADS)

    Hansen, Scott K.; Vesselinov, Velimir V.

    2016-10-01

    We develop empirically-grounded error envelopes for localization of a point contamination release event in the saturated zone of a previously uncharacterized heterogeneous aquifer into which a number of plume-intercepting wells have been drilled. We assume that flow direction in the aquifer is known exactly and velocity is known to within a factor of two of our best guess from well observations prior to source identification. Other aquifer and source parameters must be estimated by interpretation of well breakthrough data via the advection-dispersion equation. We employ high performance computing to generate numerous random realizations of aquifer parameters and well locations, simulate well breakthrough data, and then employ unsupervised machine optimization techniques to estimate the most likely spatial (or space-time) location of the source. Tabulating the accuracy of these estimates from the multiple realizations, we relate the size of 90% and 95% confidence envelopes to the data quantity (number of wells) and model quality (fidelity of ADE interpretation model to actual concentrations in a heterogeneous aquifer with channelized flow). We find that for purely spatial localization of the contaminant source, increased data quantities can make up for reduced model quality. For space-time localization, we find similar qualitative behavior, but significantly degraded spatial localization reliability and less improvement from extra data collection. Since the space-time source localization problem is much more challenging, we also tried a multiple-initial-guess optimization strategy. This greatly enhanced performance, but gains from additional data collection remained limited.

  19. Contaminant point source localization error estimates as functions of data quantity and model quality

    SciTech Connect

    Hansen, Scott K.; Vesselinov, Velimir Valentinov

    2016-10-01

    We develop empirically-grounded error envelopes for localization of a point contamination release event in the saturated zone of a previously uncharacterized heterogeneous aquifer into which a number of plume-intercepting wells have been drilled. We assume that flow direction in the aquifer is known exactly and velocity is known to within a factor of two of our best guess from well observations prior to source identification. Other aquifer and source parameters must be estimated by interpretation of well breakthrough data via the advection-dispersion equation. We employ high performance computing to generate numerous random realizations of aquifer parameters and well locations, simulate well breakthrough data, and then employ unsupervised machine optimization techniques to estimate the most likely spatial (or space-time) location of the source. Tabulating the accuracy of these estimates from the multiple realizations, we relate the size of 90% and 95% confidence envelopes to the data quantity (number of wells) and model quality (fidelity of ADE interpretation model to actual concentrations in a heterogeneous aquifer with channelized flow). We find that for purely spatial localization of the contaminant source, increased data quantities can make up for reduced model quality. For space-time localization, we find similar qualitative behavior, but significantly degraded spatial localization reliability and less improvement from extra data collection. Since the space-time source localization problem is much more challenging, we also tried a multiple-initial-guess optimization strategy. Furthermore, this greatly enhanced performance, but gains from additional data collection remained limited.

  20. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics.

    PubMed

    Keasar, Chen; Levitt, Michael

    2003-05-23

    We suggest a new approach to the generation of candidate structures (decoys) for ab initio prediction of protein structures. Our method is based on random sampling of conformation space and subsequent local energy minimization. At the core of this approach lies the design of a novel type of energy function. This energy function has local minima with native structure characteristics and wide basins of attraction. The current work presents our motivation for deriving such an energy function and also tests the derived energy function. Our approach is novel in that it takes advantage of the inherently rough energy landscape of proteins, which is generally c