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Sample records for truncated plurigaussian simulation

  1. Conditional truncated plurigaussian simulation; Simulacao plurigaussiana truncada com condicionamento

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Vitor Hugo

    1997-12-01

    The goal of this work was a development of an algorithm for the Truncated Plurigaussian Stochastic Simulation and its validation in a complex geologic model. The reservoir data comes from Aux Vases Zone at Rural Hill Field in Illinois, USA, and from the 2D geological interpretation, described by WEIMER et al. (1982), three sets of samples, with different grid densities ware taken. These sets were used to condition the simulation and to refine the estimates of the non-stationary matrix of facies proportions, used to truncate the gaussian random functions (RF). The Truncated Plurigaussian Model is an extension of the Truncated Gaussian Model (TG). In this new model its possible to use several facies with different spatial structures, associated with the simplicity of TG. The geological interpretation, used as a validation model, was chosen because it shows a set of NW/SE elongated tidal channels cutting the NE/SW shoreline deposits interleaved by impermeable facies. These characteristics of spatial structures of sedimentary facies served to evaluate the simulation model. Two independent gaussian RF were used, as well as an 'erosive model' as the truncation strategy. Also, non-conditional simulations were proceeded, using linearly combined gaussian RF with varying correlation coefficients. It was analyzed the influence of some parameters like: number of gaussian RF,correlation coefficient, truncations strategy, in the outcome of simulation, and also the physical meaning of these parameters under a geological point of view. It was showed, step by step, using an example, the theoretical model, and how to construct an algorithm to simulate with the Truncated Plurigaussian Model. The conclusion of this work was that even with a plain algorithm of the Conditional Truncated Plurigaussian and a complex geological model it's possible to obtain a usefulness product. (author)

  2. Application of plurigaussian simulation to delineate the layout of alteration domains in Sungun copper deposit

    Science.gov (United States)

    Talebi, Hassan; Asghari, Omid; Emery, Xavier

    2013-12-01

    An accurate estimation of mineral grades in ore deposits with heterogeneous spatial variations requires defining geological domains that differentiate the types of mineralogy, alteration and lithology. Deterministic models define the layout of the domains based on the interpretation of the drill holes and do not take into account the uncertainty in areas with fewer data. Plurigaussian simulation (PGS) can be an alternative to generate multiple numerical models of the ore body, with the aim of assessing the uncertainty in the domain boundaries and improving the geological controls in the characterization of quantitative attributes. This study addresses the application of PGS to Sungun porphyry copper deposit (Iran), in order to simulate the layout of four hypogene alteration zones: potassic, phyllic, propylitic and argillic. The aim of this study is to construct numerical models in which the alteration structures reflect the evolution observed in the geology.

  3. Molecular dynamics simulations of lipid bilayers : major artifacts due to truncating electrostatic interactions

    NARCIS (Netherlands)

    Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Lindqvist, P.; Vattulainen, I.

    2003-01-01

    We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using

  4. Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation

    International Nuclear Information System (INIS)

    Wolf, D.; Keblinski, P.; Phillpot, S.R.; Eggebrecht, J.

    1999-01-01

    Based on a recent result showing that the net Coulomb potential in condensed ionic systems is rather short ranged, an exact and physically transparent method permitting the evaluation of the Coulomb potential by direct summation over the r -1 Coulomb pair potential is presented. The key observation is that the problems encountered in determining the Coulomb energy by pairwise, spherically truncated r -1 summation are a direct consequence of the fact that the system summed over is practically never neutral. A simple method is developed that achieves charge neutralization wherever the r -1 pair potential is truncated. This enables the extraction of the Coulomb energy, forces, and stresses from a spherically truncated, usually charged environment in a manner that is independent of the grouping of the pair terms. The close connection of our approach with the Ewald method is demonstrated and exploited, providing an efficient method for the simulation of even highly disordered ionic systems by direct, pairwise r -1 summation with spherical truncation at rather short range, i.e., a method which fully exploits the short-ranged nature of the interactions in ionic systems. The method is validated by simulations of crystals, liquids, and interfacial systems, such as free surfaces and grain boundaries. copyright 1999 American Institute of Physics

  5. Digestion proteomics: tracking lactoferrin truncation and peptide release during simulated gastric digestion.

    Science.gov (United States)

    Grosvenor, Anita J; Haigh, Brendan J; Dyer, Jolon M

    2014-11-01

    The extent to which nutritional and functional benefit is derived from proteins in food is related to its breakdown and digestion in the body after consumption. Further, detailed information about food protein truncation during digestion is critical to understanding and optimising the availability of bioactives, in controlling and limiting allergen release, and in minimising or monitoring the effects of processing and food preparation. However, tracking the complex array of products formed during the digestion of proteins is not easily accomplished using classical proteomics. We here present and develop a novel proteomic approach using isobaric labelling to mapping and tracking protein truncation and peptide release during simulated gastric digestion, using bovine lactoferrin as a model food protein. The relative abundance of related peptides was tracked throughout a digestion time course, and the effect of pasteurisation on peptide release assessed. The new approach to food digestion proteomics developed here therefore appears to be highly suitable not only for tracking the truncation and relative abundance of released peptides during gastric digestion, but also for determining the effects of protein modification on digestibility and potential bioavailability.

  6. Truncated Newton-Raphson Methods for Quasicontinuum Simulations

    National Research Council Canada - National Science Library

    Liang, Yu; Kanapady, Ramdev; Chung, Peter W

    2006-01-01

    .... In this research, we report the effectiveness of the truncated Newton-Raphson method and quasi-Newton method with low-rank Hessian update strategy that are evaluated against the full Newton-Raphson...

  7. Investigation of propagation dynamics of truncated vector vortex beams.

    Science.gov (United States)

    Srinivas, P; Perumangatt, C; Lal, Nijil; Singh, R P; Srinivasan, B

    2018-06-01

    In this Letter, we experimentally investigate the propagation dynamics of truncated vector vortex beams generated using a Sagnac interferometer. Upon focusing, the truncated vector vortex beam is found to regain its original intensity structure within the Rayleigh range. In order to explain such behavior, the propagation dynamics of a truncated vector vortex beam is simulated by decomposing it into the sum of integral charge beams with associated complex weights. We also show that the polarization of the truncated composite vector vortex beam is preserved all along the propagation axis. The experimental observations are consistent with theoretical predictions based on previous literature and are in good agreement with our simulation results. The results hold importance as vector vortex modes are eigenmodes of the optical fiber.

  8. Truncation correction for oblique filtering lines

    International Nuclear Information System (INIS)

    Hoppe, Stefan; Hornegger, Joachim; Lauritsch, Guenter; Dennerlein, Frank; Noo, Frederic

    2008-01-01

    State-of-the-art filtered backprojection (FBP) algorithms often define the filtering operation to be performed along oblique filtering lines in the detector. A limited scan field of view leads to the truncation of those filtering lines, which causes artifacts in the final reconstructed volume. In contrast to the case where filtering is performed solely along the detector rows, no methods are available for the case of oblique filtering lines. In this work, the authors present two novel truncation correction methods which effectively handle data truncation in this case. Method 1 (basic approach) handles data truncation in two successive preprocessing steps by applying a hybrid data extrapolation method, which is a combination of a water cylinder extrapolation and a Gaussian extrapolation. It is independent of any specific reconstruction algorithm. Method 2 (kink approach) uses similar concepts for data extrapolation as the basic approach but needs to be integrated into the reconstruction algorithm. Experiments are presented from simulated data of the FORBILD head phantom, acquired along a partial-circle-plus-arc trajectory. The theoretically exact M-line algorithm is used for reconstruction. Although the discussion is focused on theoretically exact algorithms, the proposed truncation correction methods can be applied to any FBP algorithm that exposes oblique filtering lines.

  9. Geostatistical Simulation of Hydrofacies Heterogeneity of the West Thessaly Aquifer Systems in Greece

    International Nuclear Information System (INIS)

    Modis, K.; Sideri, D.

    2013-01-01

    Integrating geological properties, such as relative positions and proportions of different hydrofacies, is of highest importance in order to render realistic geological patterns. Sequential indicator simulation (SIS) and Plurigaussian simulation (PS) are alternative methods for conceptual and deterministic modeling for the characterization of hydrofacies distribution. In this work, we studied the spatial differentiation of hydrofacies in the alluvial aquifer system of West Thessaly basin in Greece. For this, we applied both SIS and PS techniques to an extensive set of borehole data from that basin. Histograms of model versus experimental hydrofacies proportions and indicative cross sections were plotted in order to validate the results. The PS technique was shown to be more effective in reproducing the spatial characteristics of the different hydrofacies and their distribution across the study area. In addition, the permeability differentiations reflected in the PS model are in accordance to known heterogeneities of the aquifer capacity.

  10. Geostatistical Simulation of Hydrofacies Heterogeneity of the West Thessaly Aquifer Systems in Greece

    Energy Technology Data Exchange (ETDEWEB)

    Modis, K., E-mail: kmodis@mail.ntua.gr; Sideri, D. [National Technical University of Athens, School of Mining and Metallurgical Engineering (Greece)

    2013-06-15

    Integrating geological properties, such as relative positions and proportions of different hydrofacies, is of highest importance in order to render realistic geological patterns. Sequential indicator simulation (SIS) and Plurigaussian simulation (PS) are alternative methods for conceptual and deterministic modeling for the characterization of hydrofacies distribution. In this work, we studied the spatial differentiation of hydrofacies in the alluvial aquifer system of West Thessaly basin in Greece. For this, we applied both SIS and PS techniques to an extensive set of borehole data from that basin. Histograms of model versus experimental hydrofacies proportions and indicative cross sections were plotted in order to validate the results. The PS technique was shown to be more effective in reproducing the spatial characteristics of the different hydrofacies and their distribution across the study area. In addition, the permeability differentiations reflected in the PS model are in accordance to known heterogeneities of the aquifer capacity.

  11. A Post-Truncation Parameterization of Truncated Normal Technical Inefficiency

    OpenAIRE

    Christine Amsler; Peter Schmidt; Wen-Jen Tsay

    2013-01-01

    In this paper we consider a stochastic frontier model in which the distribution of technical inefficiency is truncated normal. In standard notation, technical inefficiency u is distributed as N^+ (μ,σ^2). This distribution is affected by some environmental variables z that may or may not affect the level of the frontier but that do affect the shortfall of output from the frontier. We will distinguish the pre-truncation mean (μ) and variance (σ^2) from the post-truncation mean μ_*=E(u) and var...

  12. Equivalence of truncated count mixture distributions and mixtures of truncated count distributions.

    Science.gov (United States)

    Böhning, Dankmar; Kuhnert, Ronny

    2006-12-01

    This article is about modeling count data with zero truncation. A parametric count density family is considered. The truncated mixture of densities from this family is different from the mixture of truncated densities from the same family. Whereas the former model is more natural to formulate and to interpret, the latter model is theoretically easier to treat. It is shown that for any mixing distribution leading to a truncated mixture, a (usually different) mixing distribution can be found so that the associated mixture of truncated densities equals the truncated mixture, and vice versa. This implies that the likelihood surfaces for both situations agree, and in this sense both models are equivalent. Zero-truncated count data models are used frequently in the capture-recapture setting to estimate population size, and it can be shown that the two Horvitz-Thompson estimators, associated with the two models, agree. In particular, it is possible to achieve strong results for mixtures of truncated Poisson densities, including reliable, global construction of the unique NPMLE (nonparametric maximum likelihood estimator) of the mixing distribution, implying a unique estimator for the population size. The benefit of these results lies in the fact that it is valid to work with the mixture of truncated count densities, which is less appealing for the practitioner but theoretically easier. Mixtures of truncated count densities form a convex linear model, for which a developed theory exists, including global maximum likelihood theory as well as algorithmic approaches. Once the problem has been solved in this class, it might readily be transformed back to the original problem by means of an explicitly given mapping. Applications of these ideas are given, particularly in the case of the truncated Poisson family.

  13. How Truncating Are 'Truncating Languages'? Evidence from Russian and German.

    Science.gov (United States)

    Rathcke, Tamara V

    Russian and German have pr eviously been described as 'truncating', or cutting off target frequencies of the phrase-final pitch trajectories when the time available for voicing is compromised. However, supporting evidence is rare and limited to only a few pitch categories. This paper reports a production study conducted to document pitch adjustments to linguistic materials, in which the amount of voicing available for the realization of a pitch pattern varies from relatively long to extremely short. Productions of nuclear H+L*, H* and L*+H pitch accents followed by a low boundary tone were investigated in the two languages. The results of the study show that speakers of both 'truncating languages' do not utilize truncation exclusively when accommodating to different segmental environments. On the contrary, they employ several strategies - among them is truncation but also compression and temporal re-alignment - to produce the target pitch categories under increasing time pressure. Given that speakers can systematically apply all three adjustment strategies to produce some pitch patterns (H* L% in German and Russian) while not using truncation in others (H+L* L% particularly in Russian), we question the effectiveness of the typological classification of these two languages as 'truncating'. Moreover, the phonetic detail of truncation varies considerably, both across and within the two languages, indicating that truncation cannot be easily modeled as a unified phenomenon. The results further suggest that the phrase-final pitch adjustments are sensitive to the phonological composition of the tonal string and the status of a particular tonal event (associated vs. boundary tone), and do not apply to falling vs. rising pitch contours across the board, as previously put forward for German. Implications for the intonational phonology and prosodic typology are addressed in the discussion. © 2017 S. Karger AG, Basel.

  14. The Dynamics of Truncated Black Hole Accretion Disks. I. Viscous Hydrodynamic Case

    Energy Technology Data Exchange (ETDEWEB)

    Hogg, J. Drew; Reynolds, Christopher S. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States)

    2017-07-10

    Truncated accretion disks are commonly invoked to explain the spectro-temporal variability in accreting black holes in both small systems, i.e., state transitions in galactic black hole binaries (GBHBs), and large systems, i.e., low-luminosity active galactic nuclei (LLAGNs). In the canonical truncated disk model of moderately low accretion rate systems, gas in the inner region of the accretion disk occupies a hot, radiatively inefficient phase, which leads to a geometrically thick disk, while the gas in the outer region occupies a cooler, radiatively efficient phase that resides in the standard geometrically thin disk. Observationally, there is strong empirical evidence to support this phenomenological model, but a detailed understanding of the dynamics of truncated disks is lacking. We present a well-resolved viscous, hydrodynamic simulation that uses an ad hoc cooling prescription to drive a thermal instability and, hence, produce the first sustained truncated accretion disk. With this simulation, we perform a study of the dynamics, angular momentum transport, and energetics of a truncated disk. We find that the time variability introduced by the quasi-periodic transition of gas from efficient cooling to inefficient cooling impacts the evolution of the simulated disk. A consequence of the thermal instability is that an outflow is launched from the hot/cold gas interface, which drives large, sub-Keplerian convective cells into the disk atmosphere. The convective cells introduce a viscous θ − ϕ stress that is less than the generic r − ϕ viscous stress component, but greatly influences the evolution of the disk. In the truncated disk, we find that the bulk of the accreted gas is in the hot phase.

  15. Stellar Disk Truncations: HI Density and Dynamics

    Science.gov (United States)

    Trujillo, Ignacio; Bakos, Judit

    2010-06-01

    Using HI Nearby Galaxy Survey (THINGS) 21-cm observations of a sample of nearby (nearly face-on) galaxies we explore whether the stellar disk truncation phenomenon produces any signature either in the HI gas density and/or in the gas dynamics. Recent cosmological simulations suggest that the origin of the break on the surface brightness distribution is produced by the appearance of a warp at the truncation position. This warp should produce a flaring on the gas distribution increasing the velocity dispersion of the HI component beyond the break. We do not find, however, any evidence of this increase in the gas velocity dispersion profile.

  16. Resonant Excitation of a Truncated Metamaterial Cylindrical Shell by a Thin Wire Monopole

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Erentok, Aycan; Breinbjerg, Olav

    2009-01-01

    A truncated metamaterial cylindrical shell excited by a thin wire monopole is investigated using the integral equation technique as well as the finite element method. Simulations reveal a strong field singularity at the edge of the truncated cylindrical shell, which critically affects the matching...

  17. Analytic reconstruction algorithms for triple-source CT with horizontal data truncation

    International Nuclear Information System (INIS)

    Chen, Ming; Yu, Hengyong

    2015-01-01

    Purpose: This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. Methods: The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and MATLAB. While the basic platform is constructed in MATLAB, the computationally intensive segments are coded in c + +, which are linked via a MEX interface. Results: A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle to cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. Conclusions: The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units

  18. R Programs for Truncated Distributions

    Directory of Open Access Journals (Sweden)

    Saralees Nadarajah

    2006-08-01

    Full Text Available Truncated distributions arise naturally in many practical situations. In this note, we provide programs for computing six quantities of interest (probability density function, mean, variance, cumulative distribution function, quantile function and random numbers for any truncated distribution: whether it is left truncated, right truncated or doubly truncated. The programs are written in R: a freely downloadable statistical software.

  19. Approximate truncation robust computed tomography—ATRACT

    International Nuclear Information System (INIS)

    Dennerlein, Frank; Maier, Andreas

    2013-01-01

    We present an approximate truncation robust algorithm to compute tomographic images (ATRACT). This algorithm targets at reconstructing volumetric images from cone-beam projections in scenarios where these projections are highly truncated in each dimension. It thus facilitates reconstructions of small subvolumes of interest, without involving prior knowledge about the object. Our method is readily applicable to medical C-arm imaging, where it may contribute to new clinical workflows together with a considerable reduction of x-ray dose. We give a detailed derivation of ATRACT that starts from the conventional Feldkamp filtered-backprojection algorithm and that involves, as one component, a novel original formula for the inversion of the two-dimensional Radon transform. Discretization and numerical implementation are discussed and reconstruction results from both, simulated projections and first clinical data sets are presented. (paper)

  20. Reduction of variable-truncation artifacts from beam occlusion during in situ x-ray tomography

    Science.gov (United States)

    Borg, Leise; Jørgensen, Jakob S.; Frikel, Jürgen; Sporring, Jon

    2017-12-01

    Many in situ x-ray tomography studies require experimental rigs which may partially occlude the beam and cause parts of the projection data to be missing. In a study of fluid flow in porous chalk using a percolation cell with four metal bars drastic streak artifacts arise in the filtered backprojection (FBP) reconstruction at certain orientations. Projections with non-trivial variable truncation caused by the metal bars are the source of these variable-truncation artifacts. To understand the artifacts a mathematical model of variable-truncation data as a function of metal bar radius and distance to sample is derived and verified numerically and with experimental data. The model accurately describes the arising variable-truncation artifacts across simulated variations of the experimental setup. Three variable-truncation artifact-reduction methods are proposed, all aimed at addressing sinogram discontinuities that are shown to be the source of the streaks. The ‘reduction to limited angle’ (RLA) method simply keeps only non-truncated projections; the ‘detector-directed smoothing’ (DDS) method smooths the discontinuities; while the ‘reflexive boundary condition’ (RBC) method enforces a zero derivative at the discontinuities. Experimental results using both simulated and real data show that the proposed methods effectively reduce variable-truncation artifacts. The RBC method is found to provide the best artifact reduction and preservation of image features using both visual and quantitative assessment. The analysis and artifact-reduction methods are designed in context of FBP reconstruction motivated by computational efficiency practical for large, real synchrotron data. While a specific variable-truncation case is considered, the proposed methods can be applied to general data cut-offs arising in different in situ x-ray tomography experiments.

  1. Zero-truncated negative binomial - Erlang distribution

    Science.gov (United States)

    Bodhisuwan, Winai; Pudprommarat, Chookait; Bodhisuwan, Rujira; Saothayanun, Luckhana

    2017-11-01

    The zero-truncated negative binomial-Erlang distribution is introduced. It is developed from negative binomial-Erlang distribution. In this work, the probability mass function is derived and some properties are included. The parameters of the zero-truncated negative binomial-Erlang distribution are estimated by using the maximum likelihood estimation. Finally, the proposed distribution is applied to real data, the number of methamphetamine in the Bangkok, Thailand. Based on the results, it shows that the zero-truncated negative binomial-Erlang distribution provided a better fit than the zero-truncated Poisson, zero-truncated negative binomial, zero-truncated generalized negative-binomial and zero-truncated Poisson-Lindley distributions for this data.

  2. Angular truncation errors in integrating nephelometry

    International Nuclear Information System (INIS)

    Moosmueller, Hans; Arnott, W. Patrick

    2003-01-01

    Ideal integrating nephelometers integrate light scattered by particles over all directions. However, real nephelometers truncate light scattered in near-forward and near-backward directions below a certain truncation angle (typically 7 deg. ). This results in truncation errors, with the forward truncation error becoming important for large particles. Truncation errors are commonly calculated using Mie theory, which offers little physical insight and no generalization to nonspherical particles. We show that large particle forward truncation errors can be calculated and understood using geometric optics and diffraction theory. For small truncation angles (i.e., <10 deg. ) as typical for modern nephelometers, diffraction theory by itself is sufficient. Forward truncation errors are, by nearly a factor of 2, larger for absorbing particles than for nonabsorbing particles because for large absorbing particles most of the scattered light is due to diffraction as transmission is suppressed. Nephelometers calibration procedures are also discussed as they influence the effective truncation error

  3. Impact of degree truncation on the spread of a contagious process on networks.

    Science.gov (United States)

    Harling, Guy; Onnela, Jukka-Pekka

    2018-03-01

    Understanding how person-to-person contagious processes spread through a population requires accurate information on connections between population members. However, such connectivity data, when collected via interview, is often incomplete due to partial recall, respondent fatigue or study design, e.g., fixed choice designs (FCD) truncate out-degree by limiting the number of contacts each respondent can report. Past research has shown how FCD truncation affects network properties, but its implications for predicted speed and size of spreading processes remain largely unexplored. To study the impact of degree truncation on predictions of spreading process outcomes, we generated collections of synthetic networks containing specific properties (degree distribution, degree-assortativity, clustering), and also used empirical social network data from 75 villages in Karnataka, India. We simulated FCD using various truncation thresholds and ran a susceptible-infectious-recovered (SIR) process on each network. We found that spreading processes propagated on truncated networks resulted in slower and smaller epidemics, with a sudden decrease in prediction accuracy at a level of truncation that varied by network type. Our results have implications beyond FCD to truncation due to any limited sampling from a larger network. We conclude that knowledge of network structure is important for understanding the accuracy of predictions of process spread on degree truncated networks.

  4. The effect of truncation on very small cardiac SPECT camera systems

    International Nuclear Information System (INIS)

    Rohmer, Damien; Eisner, Robert L.; Gullberg, Grant T.

    2006-01-01

    Background: The limited transaxial field-of-view (FOV) of a very small cardiac SPECT camera system causes view-dependent truncation of the projection of structures exterior to, but near the heart. Basic tomographic principles suggest that the reconstruction of non-attenuated truncated data gives a distortion-free image in the interior of the truncated region, but the DC term of the Fourier spectrum of the reconstructed image is incorrect, meaning that the intensity scale of the reconstruction is inaccurate. The purpose of this study was to characterize the reconstructed image artifacts from truncated data, and to quantify their effects on the measurement of tracer uptake in the myocardial. Particular attention was given to instances where the heart wall is close to hot structures (structures of high activity uptake).Methods: The MCAT phantom was used to simulate a 2D slice of the heart region. Truncated and non-truncated projections were formed both with and without attenuation. The reconstructions were analyzed for artifacts in the myocardium caused by truncation, and for the effect that attenuation has relative to increasing those artifacts. Results: The inaccuracy due to truncation is primarily caused by an incorrect DC component. For visualizing the left ventricular wall, this error is not worse than the effect of attenuation. The addition of a small hot bowel-like structure near the left ventricle causes few changes in counts on the wall. Larger artifacts due to the truncation are located at the boundary of the truncation and can be eliminated by sinogram interpolation. Finally,algebraic reconstruction methods are shown to give better reconstruction results than an analytical filtered back-projection reconstruction algorithm. Conclusion: Small inaccuracies in reconstructed images from small FOV camera systems should have little effect on clinical interpretation. However, changes in the degree of inaccuracy in counts from slice to slice are due to changes in

  5. The truncated Wigner method for Bose-condensed gases: limits of validity and applications

    International Nuclear Information System (INIS)

    Sinatra, Alice; Lobo, Carlos; Castin, Yvan

    2002-01-01

    We study the truncated Wigner method applied to a weakly interacting spinless Bose-condensed gas which is perturbed away from thermal equilibrium by a time-dependent external potential. The principle of the method is to generate an ensemble of classical fields ψ(r) which samples the Wigner quasi-distribution function of the initial thermal equilibrium density operator of the gas, and then to evolve each classical field with the Gross-Pitaevskii equation. In the first part of the paper we improve the sampling technique over our previous work (Sinatra et al 2000 J. Mod. Opt. 47 2629-44) and we test its accuracy against the exactly solvable model of the ideal Bose gas. In the second part of the paper we investigate the conditions of validity of the truncated Wigner method. For short evolution times it is known that the time-dependent Bogoliubov approximation is valid for almost pure condensates. The requirement that the truncated Wigner method reproduces the Bogoliubov prediction leads to the constraint that the number of field modes in the Wigner simulation must be smaller than the number of particles in the gas. For longer evolution times the nonlinear dynamics of the noncondensed modes of the field plays an important role. To demonstrate this we analyse the case of a three-dimensional spatially homogeneous Bose-condensed gas and we test the ability of the truncated Wigner method to correctly reproduce the Beliaev-Landau damping of an excitation of the condensate. We have identified the mechanism which limits the validity of the truncated Wigner method: the initial ensemble of classical fields, driven by the time-dependent Gross-Pitaevskii equation, thermalizes to a classical field distribution at a temperature T class which is larger than the initial temperature T of the quantum gas. When T class significantly exceeds T a spurious damping is observed in the Wigner simulation. This leads to the second validity condition for the truncated Wigner method, T class - T

  6. Truncated Groebner fans and lattice ideals

    OpenAIRE

    Lauritzen, Niels

    2005-01-01

    We outline a generalization of the Groebner fan of a homogeneous ideal with maximal cells parametrizing truncated Groebner bases. This "truncated" Groebner fan is usually much smaller than the full Groebner fan and offers the natural framework for conversion between truncated Groebner bases. The generic Groebner walk generalizes naturally to this setting by using the Buchberger algorithm with truncation on facets. We specialize to the setting of lattice ideals. Here facets along the generic w...

  7. Closed-form kinetic parameter estimation solution to the truncated data problem

    International Nuclear Information System (INIS)

    Zeng, Gengsheng L; Kadrmas, Dan J; Gullberg, Grant T

    2010-01-01

    In a dedicated cardiac single photon emission computed tomography (SPECT) system, the detectors are focused on the heart and the background is truncated in the projections. Reconstruction using truncated data results in biased images, leading to inaccurate kinetic parameter estimates. This paper has developed a closed-form kinetic parameter estimation solution to the dynamic emission imaging problem. This solution is insensitive to the bias in the reconstructed images that is caused by the projection data truncation. This paper introduces two new ideas: (1) it includes background bias as an additional parameter to estimate, and (2) it presents a closed-form solution for compartment models. The method is based on the following two assumptions: (i) the amount of the bias is directly proportional to the truncated activities in the projection data, and (ii) the background concentration is directly proportional to the concentration in the myocardium. In other words, the method assumes that the image slice contains only the heart and the background, without other organs, that the heart is not truncated, and that the background radioactivity is directly proportional to the radioactivity in the blood pool. As long as the background activity can be modeled, the proposed method is applicable regardless of the number of compartments in the model. For simplicity, the proposed method is presented and verified using a single compartment model with computer simulations using both noiseless and noisy projections.

  8. Statistical estimation for truncated exponential families

    CERN Document Server

    Akahira, Masafumi

    2017-01-01

    This book presents new findings on nonregular statistical estimation. Unlike other books on this topic, its major emphasis is on helping readers understand the meaning and implications of both regularity and irregularity through a certain family of distributions. In particular, it focuses on a truncated exponential family of distributions with a natural parameter and truncation parameter as a typical nonregular family. This focus includes the (truncated) Pareto distribution, which is widely used in various fields such as finance, physics, hydrology, geology, astronomy, and other disciplines. The family is essential in that it links both regular and nonregular distributions, as it becomes a regular exponential family if the truncation parameter is known. The emphasis is on presenting new results on the maximum likelihood estimation of a natural parameter or truncation parameter if one of them is a nuisance parameter. In order to obtain more information on the truncation, the Bayesian approach is also considere...

  9. NLO renormalization in the Hamiltonian truncation

    Science.gov (United States)

    Elias-Miró, Joan; Rychkov, Slava; Vitale, Lorenzo G.

    2017-09-01

    Hamiltonian truncation (also known as "truncated spectrum approach") is a numerical technique for solving strongly coupled quantum field theories, in which the full Hilbert space is truncated to a finite-dimensional low-energy subspace. The accuracy of the method is limited only by the available computational resources. The renormalization program improves the accuracy by carefully integrating out the high-energy states, instead of truncating them away. In this paper, we develop the most accurate ever variant of Hamiltonian Truncation, which implements renormalization at the cubic order in the interaction strength. The novel idea is to interpret the renormalization procedure as a result of integrating out exactly a certain class of high-energy "tail states." We demonstrate the power of the method with high-accuracy computations in the strongly coupled two-dimensional quartic scalar theory and benchmark it against other existing approaches. Our work will also be useful for the future goal of extending Hamiltonian truncation to higher spacetime dimensions.

  10. Cross-layer combining of power control and adaptive modulation with truncated ARQ for cognitive radios

    Institute of Scientific and Technical Information of China (English)

    CHENG Shi-lun; YANG Zhen

    2008-01-01

    To maximize throughput and to satisfy users' requirements in cognitive radios, a cross-layer optimization problem combining adaptive modulation and power control at the physical layer and truncated automatic repeat request at the medium access control layer is proposed. Simulation results show the combination of power control, adaptive modulation, and truncated automatic repeat request can regulate transmitter powers and increase the total throughput effectively.

  11. Stability of Slopes Reinforced with Truncated Piles

    Directory of Open Access Journals (Sweden)

    Shu-Wei Sun

    2016-01-01

    Full Text Available Piles are extensively used as a means of slope stabilization. A novel engineering technique of truncated piles that are unlike traditional piles is introduced in this paper. A simplified numerical method is proposed to analyze the stability of slopes stabilized with truncated piles based on the shear strength reduction method. The influential factors, which include pile diameter, pile spacing, depth of truncation, and existence of a weak layer, are systematically investigated from a practical point of view. The results show that an optimum ratio exists between the depth of truncation and the pile length above a slip surface, below which truncating behavior has no influence on the piled slope stability. This optimum ratio is bigger for slopes stabilized with more flexible piles and piles with larger spacing. Besides, truncated piles are more suitable for slopes with a thin weak layer than homogenous slopes. In practical engineering, the piles could be truncated reasonably while ensuring the reinforcement effect. The truncated part of piles can be filled with the surrounding soil and compacted to reduce costs by using fewer materials.

  12. Adaptation of the delta-m and δ-fit truncation methods to vector radiative transfer: Effect of truncation on radiative transfer accuracy

    International Nuclear Information System (INIS)

    Sanghavi, Suniti; Stephens, Graeme

    2015-01-01

    In the presence of aerosol and/or clouds, the use of appropriate truncation methods becomes indispensable for accurate but cost-efficient radiative transfer computations. Truncation methods allow the reduction of the large number (usually several hundreds) of Fourier components associated with particulate scattering functions to a more manageable number, thereby making it possible to carry out radiative transfer computations with a modest number of streams. While several truncation methods have been discussed for scalar radiative transfer, few rigorous studies have been made of truncation methods for the vector case. Here, we formally derive the vector form of Wiscombe's delta-m truncation method. Two main sources of error associated with delta-m truncation are identified as the delta-separation error (DSE) and the phase-truncation error (PTE). The view angles most affected by truncation error occur in the vicinity of the direction of exact backscatter. This view geometry occurs commonly in satellite based remote sensing applications, and is hence of considerable importance. In order to deal with these errors, we adapt the δ-fit approach of Hu et al. (2000) [17] to vector radiative transfer. The resulting δBGE-fit is compared with the vectorized delta-m method. For truncation at l=25 of an original phase matrix consisting of over 300 Fourier components, the use of the δBGE-fit minimizes the error due to truncation at these view angles, while practically eliminating error at other angles. We also show how truncation errors have a distorting effect on hyperspectral absorption line shapes. The choice of the δBGE-fit method over delta-m truncation minimizes errors in absorption line depths, thus affording greater accuracy for sensitive retrievals such as those of XCO 2 from OCO-2 or GOSAT measurements. - Highlights: • Derives vector form for delta-m truncation method. • Adapts δ-fit truncation approach to vector RTE as δBGE-fit. • Compares truncation

  13. Varying coefficient subdistribution regression for left-truncated semi-competing risks data.

    Science.gov (United States)

    Li, Ruosha; Peng, Limin

    2014-10-01

    Semi-competing risks data frequently arise in biomedical studies when time to a disease landmark event is subject to dependent censoring by death, the observation of which however is not precluded by the occurrence of the landmark event. In observational studies, the analysis of such data can be further complicated by left truncation. In this work, we study a varying co-efficient subdistribution regression model for left-truncated semi-competing risks data. Our method appropriately accounts for the specifical truncation and censoring features of the data, and moreover has the flexibility to accommodate potentially varying covariate effects. The proposed method can be easily implemented and the resulting estimators are shown to have nice asymptotic properties. We also present inference, such as Kolmogorov-Smirnov type and Cramér Von-Mises type hypothesis testing procedures for the covariate effects. Simulation studies and an application to the Denmark diabetes registry demonstrate good finite-sample performance and practical utility of the proposed method.

  14. Computing correct truncated excited state wavefunctions

    Science.gov (United States)

    Bacalis, N. C.; Xiong, Z.; Zang, J.; Karaoulanis, D.

    2016-12-01

    We demonstrate that, if a wave function's truncated expansion is small, then the standard excited states computational method, of optimizing one "root" of a secular equation, may lead to an incorrect wave function - despite the correct energy according to the theorem of Hylleraas, Undheim and McDonald - whereas our proposed method [J. Comput. Meth. Sci. Eng. 8, 277 (2008)] (independent of orthogonality to lower lying approximants) leads to correct reliable small truncated wave functions. The demonstration is done in He excited states, using truncated series expansions in Hylleraas coordinates, as well as standard configuration-interaction truncated expansions.

  15. Mixtures of truncated basis functions

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

    2012-01-01

    In this paper we propose a framework, called mixtures of truncated basis functions (MoTBFs), for representing general hybrid Bayesian networks. The proposed framework generalizes both the mixture of truncated exponentials (MTEs) framework and the mixture of polynomials (MoPs) framework. Similar t...

  16. Applications of Fast Truncated Multiplication in Cryptography

    Directory of Open Access Journals (Sweden)

    Laszlo Hars

    2006-12-01

    Full Text Available Truncated multiplications compute truncated products, contiguous subsequences of the digits of integer products. For an n-digit multiplication algorithm of time complexity O(nα, with 1<α≤2, there is a truncated multiplication algorithm, which is constant times faster when computing a short enough truncated product. Applying these fast truncated multiplications, several cryptographic long integer arithmetic algorithms are improved, including integer reciprocals, divisions, Barrett and Montgomery multiplications, 2n-digit modular multiplication on hardware for n-digit half products. For example, Montgomery multiplication is performed in 2.6 Karatsuba multiplication time.

  17. Properties of truncated multiplicity distributions

    International Nuclear Information System (INIS)

    Lupia, S.

    1995-01-01

    Truncation effects on multiplicity distributions are discussed. Observables sensitive to the tail, like factorial moments, factorial cumulants and their ratio, are shown to be strongly affected by truncation. A possible way to overcome this problem by looking at the head of the distribution is suggested. (author)

  18. Properties of truncated multiplicity distributions

    Energy Technology Data Exchange (ETDEWEB)

    Lupia, S. [Turin Univ. (Italy). Dipt. di Fisica

    1995-12-31

    Truncation effects on multiplicity distributions are discussed. Observables sensitive to the tail, like factorial moments, factorial cumulants and their ratio, are shown to be strongly affected by truncation. A possible way to overcome this problem by looking at the head of the distribution is suggested. (author)

  19. Analysis of truncation limit in probabilistic safety assessment

    International Nuclear Information System (INIS)

    Cepin, Marko

    2005-01-01

    A truncation limit defines the boundaries of what is considered in the probabilistic safety assessment and what is neglected. The truncation limit that is the focus here is the truncation limit on the size of the minimal cut set contribution at which to cut off. A new method was developed, which defines truncation limit in probabilistic safety assessment. The method specifies truncation limits with more stringency than presenting existing documents dealing with truncation criteria in probabilistic safety assessment do. The results of this paper indicate that the truncation limits for more complex probabilistic safety assessments, which consist of larger number of basic events, should be more severe than presently recommended in existing documents if more accuracy is desired. The truncation limits defined by the new method reduce the relative errors of importance measures and produce more accurate results for probabilistic safety assessment applications. The reduced relative errors of importance measures can prevent situations, where the acceptability of change of equipment under investigation according to RG 1.174 would be shifted from region, where changes can be accepted, to region, where changes cannot be accepted, if the results would be calculated with smaller truncation limit

  20. Truncated Calogero-Sutherland models

    Science.gov (United States)

    Pittman, S. M.; Beau, M.; Olshanii, M.; del Campo, A.

    2017-05-01

    A one-dimensional quantum many-body system consisting of particles confined in a harmonic potential and subject to finite-range two-body and three-body inverse-square interactions is introduced. The range of the interactions is set by truncation beyond a number of neighbors and can be tuned to interpolate between the Calogero-Sutherland model and a system with nearest and next-nearest neighbors interactions discussed by Jain and Khare. The model also includes the Tonks-Girardeau gas describing impenetrable bosons as well as an extension with truncated interactions. While the ground state wave function takes a truncated Bijl-Jastrow form, collective modes of the system are found in terms of multivariable symmetric polynomials. We numerically compute the density profile, one-body reduced density matrix, and momentum distribution of the ground state as a function of the range r and the interaction strength.

  1. Evidence for Truncated Exponential Probability Distribution of Earthquake Slip

    KAUST Repository

    Thingbaijam, Kiran Kumar; Mai, Paul Martin

    2016-01-01

    Earthquake ruptures comprise spatially varying slip on the fault surface, where slip represents the displacement discontinuity between the two sides of the rupture plane. In this study, we analyze the probability distribution of coseismic slip, which provides important information to better understand earthquake source physics. Although the probability distribution of slip is crucial for generating realistic rupture scenarios for simulation-based seismic and tsunami-hazard analysis, the statistical properties of earthquake slip have received limited attention so far. Here, we use the online database of earthquake source models (SRCMOD) to show that the probability distribution of slip follows the truncated exponential law. This law agrees with rupture-specific physical constraints limiting the maximum possible slip on the fault, similar to physical constraints on maximum earthquake magnitudes.We show the parameters of the best-fitting truncated exponential distribution scale with average coseismic slip. This scaling property reflects the control of the underlying stress distribution and fault strength on the rupture dimensions, which determines the average slip. Thus, the scale-dependent behavior of slip heterogeneity is captured by the probability distribution of slip. We conclude that the truncated exponential law accurately quantifies coseismic slip distribution and therefore allows for more realistic modeling of rupture scenarios. © 2016, Seismological Society of America. All rights reserverd.

  2. Evidence for Truncated Exponential Probability Distribution of Earthquake Slip

    KAUST Repository

    Thingbaijam, Kiran K. S.

    2016-07-13

    Earthquake ruptures comprise spatially varying slip on the fault surface, where slip represents the displacement discontinuity between the two sides of the rupture plane. In this study, we analyze the probability distribution of coseismic slip, which provides important information to better understand earthquake source physics. Although the probability distribution of slip is crucial for generating realistic rupture scenarios for simulation-based seismic and tsunami-hazard analysis, the statistical properties of earthquake slip have received limited attention so far. Here, we use the online database of earthquake source models (SRCMOD) to show that the probability distribution of slip follows the truncated exponential law. This law agrees with rupture-specific physical constraints limiting the maximum possible slip on the fault, similar to physical constraints on maximum earthquake magnitudes.We show the parameters of the best-fitting truncated exponential distribution scale with average coseismic slip. This scaling property reflects the control of the underlying stress distribution and fault strength on the rupture dimensions, which determines the average slip. Thus, the scale-dependent behavior of slip heterogeneity is captured by the probability distribution of slip. We conclude that the truncated exponential law accurately quantifies coseismic slip distribution and therefore allows for more realistic modeling of rupture scenarios. © 2016, Seismological Society of America. All rights reserverd.

  3. Lamp with a truncated reflector cup

    Science.gov (United States)

    Li, Ming; Allen, Steven C.; Bazydola, Sarah; Ghiu, Camil-Daniel

    2013-10-15

    A lamp assembly, and method for making same. The lamp assembly includes first and second truncated reflector cups. The lamp assembly also includes at least one base plate disposed between the first and second truncated reflector cups, and a light engine disposed on a top surface of the at least one base plate. The light engine is configured to emit light to be reflected by one of the first and second truncated reflector cups.

  4. Formal truncations of connected kernel equations

    International Nuclear Information System (INIS)

    Dixon, R.M.

    1977-01-01

    The Connected Kernel Equations (CKE) of Alt, Grassberger and Sandhas (AGS); Kouri, Levin and Tobocman (KLT); and Bencze, Redish and Sloan (BRS) are compared against reaction theory criteria after formal channel space and/or operator truncations have been introduced. The Channel Coupling Class concept is used to study the structure of these CKE's. The related wave function formalism of Sandhas, of L'Huillier, Redish and Tandy and of Kouri, Krueger and Levin are also presented. New N-body connected kernel equations which are generalizations of the Lovelace three-body equations are derived. A method for systematically constructing fewer body models from the N-body BRS and generalized Lovelace (GL) equations is developed. The formally truncated AGS, BRS, KLT and GL equations are analyzed by employing the criteria of reciprocity and two-cluster unitarity. Reciprocity considerations suggest that formal truncations of BRS, KLT and GL equations can lead to reciprocity-violating results. This study suggests that atomic problems should employ three-cluster connected truncations and that the two-cluster connected truncations should be a useful starting point for nuclear systems

  5. Perspective on rainbow-ladder truncation

    International Nuclear Information System (INIS)

    Eichmann, G.; Alkofer, R.; Krassnigg, A.; Cloeet, I. C.; Roberts, C. D.

    2008-01-01

    Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light

  6. Electro-optical study of nanoscale Al-Si-truncated conical photodetector with subwavelength aperture

    Science.gov (United States)

    Karelits, Matityahu; Mandelbaum, Yaakov; Chelly, Avraham; Karsenty, Avi

    2017-10-01

    A type of silicon photodiode has been designed and simulated to probe the optical near field and detect evanescent waves. These waves convey subwavelength resolution. This photodiode consists of a truncated conical shaped, silicon Schottky diode having a subwavelength aperture of 150 nm. Electrical and electro-optical simulations have been conducted. These results are promising toward the fabrication of a new generation of photodetector devices.

  7. Minimum decoding trellis length and truncation depth of wrap-around Viterbi algorithm for TBCC in mobile WiMAX

    Directory of Open Access Journals (Sweden)

    Liu Yu-Sun

    2011-01-01

    Full Text Available Abstract The performance of the wrap-around Viterbi decoding algorithm with finite truncation depth and fixed decoding trellis length is investigated for tail-biting convolutional codes in the mobile WiMAX standard. Upper bounds on the error probabilities induced by finite truncation depth and the uncertainty of the initial state are derived for the AWGN channel. The truncation depth and the decoding trellis length that yield negligible performance loss are obtained for all transmission rates over the Rayleigh channel using computer simulations. The results show that the circular decoding algorithm with an appropriately chosen truncation depth and a decoding trellis just a fraction longer than the original received code words can achieve almost the same performance as the optimal maximum likelihood decoding algorithm in mobile WiMAX. A rule of thumb for the values of the truncation depth and the trellis tail length is also proposed.

  8. Clustered survival data with left-truncation

    DEFF Research Database (Denmark)

    Eriksson, Frank; Martinussen, Torben; Scheike, Thomas H.

    2015-01-01

    Left-truncation occurs frequently in survival studies, and it is well known how to deal with this for univariate survival times. However, there are few results on how to estimate dependence parameters and regression effects in semiparametric models for clustered survival data with delayed entry....... Surprisingly, existing methods only deal with special cases. In this paper, we clarify different kinds of left-truncation and suggest estimators for semiparametric survival models under specific truncation schemes. The large-sample properties of the estimators are established. Small-sample properties...

  9. Optical asymmetric cryptography based on elliptical polarized light linear truncation and a numerical reconstruction technique.

    Science.gov (United States)

    Lin, Chao; Shen, Xueju; Wang, Zhisong; Zhao, Cheng

    2014-06-20

    We demonstrate a novel optical asymmetric cryptosystem based on the principle of elliptical polarized light linear truncation and a numerical reconstruction technique. The device of an array of linear polarizers is introduced to achieve linear truncation on the spatially resolved elliptical polarization distribution during image encryption. This encoding process can be characterized as confusion-based optical cryptography that involves no Fourier lens and diffusion operation. Based on the Jones matrix formalism, the intensity transmittance for this truncation is deduced to perform elliptical polarized light reconstruction based on two intensity measurements. Use of a quick response code makes the proposed cryptosystem practical, with versatile key sensitivity and fault tolerance. Both simulation and preliminary experimental results that support theoretical analysis are presented. An analysis of the resistance of the proposed method on a known public key attack is also provided.

  10. Phase retrieval via incremental truncated amplitude flow algorithm

    Science.gov (United States)

    Zhang, Quanbing; Wang, Zhifa; Wang, Linjie; Cheng, Shichao

    2017-10-01

    This paper considers the phase retrieval problem of recovering the unknown signal from the given quadratic measurements. A phase retrieval algorithm based on Incremental Truncated Amplitude Flow (ITAF) which combines the ITWF algorithm and the TAF algorithm is proposed. The proposed ITAF algorithm enhances the initialization by performing both of the truncation methods used in ITWF and TAF respectively, and improves the performance in the gradient stage by applying the incremental method proposed in ITWF to the loop stage of TAF. Moreover, the original sampling vector and measurements are preprocessed before initialization according to the variance of the sensing matrix. Simulation experiments verified the feasibility and validity of the proposed ITAF algorithm. The experimental results show that it can obtain higher success rate and faster convergence speed compared with other algorithms. Especially, for the noiseless random Gaussian signals, ITAF can recover any real-valued signal accurately from the magnitude measurements whose number is about 2.5 times of the signal length, which is close to the theoretic limit (about 2 times of the signal length). And it usually converges to the optimal solution within 20 iterations which is much less than the state-of-the-art algorithms.

  11. Analysis of the upper-truncated Weibull distribution for wind speed

    International Nuclear Information System (INIS)

    Kantar, Yeliz Mert; Usta, Ilhan

    2015-01-01

    Highlights: • Upper-truncated Weibull distribution is proposed to model wind speed. • Upper-truncated Weibull distribution nests Weibull distribution as special case. • Maximum likelihood is the best method for upper-truncated Weibull distribution. • Fitting accuracy of upper-truncated Weibull is analyzed on wind speed data. - Abstract: Accurately modeling wind speed is critical in estimating the wind energy potential of a certain region. In order to model wind speed data smoothly, several statistical distributions have been studied. Truncated distributions are defined as a conditional distribution that results from restricting the domain of statistical distribution and they also cover base distribution. This paper proposes, for the first time, the use of upper-truncated Weibull distribution, in modeling wind speed data and also in estimating wind power density. In addition, a comparison is made between upper-truncated Weibull distribution and well known Weibull distribution using wind speed data measured in various regions of Turkey. The obtained results indicate that upper-truncated Weibull distribution shows better performance than Weibull distribution in estimating wind speed distribution and wind power. Therefore, upper-truncated Weibull distribution can be an alternative for use in the assessment of wind energy potential

  12. Different truncation methods of AUC between Japan and the EU for bioequivalence assessment: influence on the regulatory judgment.

    Science.gov (United States)

    Oishi, Masayo; Chiba, Koji; Fukushima, Takashi; Tomono, Yoshiro; Suwa, Toshio

    2012-01-01

    In regulatory guidelines for bioequivalence (BE) assessment, the definitions of AUC for primary assessment are different in ICH countries, i.e., AUC from zero to the last sampling point (AUCall) in Japan, AUC from zero to infinity (AUCinf) or AUC from zero to the last measurable point (AUClast) in the US, and AUClast in the EU. To assure sufficient accuracy of truncated AUC for BE assessment, the ratio of truncated AUC (AUCall or AUClast) to AUCinf should be more than 80% both in Japanese and EU guidelines. We investigated how the difference in the definition of truncated AUC affects BE assessment of sustained release (SR) formulation. Our simulation result demonstrated that AUCall/AUCinf could be ≥80% despite AUClast/AUCinf being AUC affected the judgment of validity of truncated AUC for BE assessment, and AUCall could fail to detect the substantially different in vivo dissolution profile of generic drugs with SR formulation from the original drug.

  13. New Schemes for Positive Real Truncation

    Directory of Open Access Journals (Sweden)

    Kari Unneland

    2007-07-01

    Full Text Available Model reduction, based on balanced truncation, of stable and of positive real systems are considered. An overview over some of the already existing techniques are given: Lyapunov balancing and stochastic balancing, which includes Riccati balancing. A novel scheme for positive real balanced truncation is then proposed, which is a combination of the already existing Lyapunov balancing and Riccati balancing. Using Riccati balancing, the solution of two Riccati equations are needed to obtain positive real reduced order systems. For the suggested method, only one Lyapunov equation and one Riccati equation are solved in order to obtain positive real reduced order systems, which is less computationally demanding. Further it is shown, that in order to get positive real reduced order systems, only one Riccati equation needs to be solved. Finally, this is used to obtain positive real frequency weighted balanced truncation.

  14. Measuring a Truncated Disk in Aquila X-1

    Science.gov (United States)

    King, Ashley L.; Tomsick, John A.; Miller, Jon M.; Chenevez, Jerome; Barret, Didier; Boggs, Steven E.; Chakrabarty, Deepto; Christensen, Finn E.; Craig, William W.; Feurst, Felix; hide

    2016-01-01

    We present NuSTAR and Swift observations of the neutron star Aquila X-1 during the peak of its 2014 July outburst. The spectrum is soft with strong evidence for a broad Fe K(alpha) line. Modeled with a relativistically broadened reflection model, we find that the inner disk is truncated with an inner radius of 15 +/- 3RG. The disk is likely truncated by either the boundary layer and/or a magnetic field. Associating the truncated inner disk with pressure from a magnetic field gives an upper limit of B < 5+/- 2x10(exp 8) G. Although the radius is truncated far from the stellar surface, material is still reaching the neutron star surface as evidenced by the X-ray burst present in the NuSTAR observation.

  15. Evolution of truncated moments of singlet parton distributions

    International Nuclear Information System (INIS)

    Forte, S.; Magnea, L.; Piccione, A.; Ridolfi, G.

    2001-01-01

    We define truncated Mellin moments of parton distributions by restricting the integration range over the Bjorken variable to the experimentally accessible subset x 0 ≤x≤1 of the allowed kinematic range 0≤x≤1. We derive the evolution equations satisfied by truncated moments in the general (singlet) case in terms of an infinite triangular matrix of anomalous dimensions which couple each truncated moment to all higher moments with orders differing by integers. We show that the evolution of any moment can be determined to arbitrarily good accuracy by truncating the system of coupled moments to a sufficiently large but finite size, and show how the equations can be solved in a way suitable for numerical applications. We discuss in detail the accuracy of the method in view of applications to precision phenomenology

  16. Data and performance profiles applying an adaptive truncation criterion, within linesearch-based truncated Newton methods, in large scale nonconvex optimization

    Directory of Open Access Journals (Sweden)

    Andrea Caliciotti

    2018-04-01

    Full Text Available In this paper, we report data and experiments related to the research article entitled “An adaptive truncation criterion, for linesearch-based truncated Newton methods in large scale nonconvex optimization” by Caliciotti et al. [1]. In particular, in Caliciotti et al. [1], large scale unconstrained optimization problems are considered by applying linesearch-based truncated Newton methods. In this framework, a key point is the reduction of the number of inner iterations needed, at each outer iteration, to approximately solving the Newton equation. A novel adaptive truncation criterion is introduced in Caliciotti et al. [1] to this aim. Here, we report the details concerning numerical experiences over a commonly used test set, namely CUTEst (Gould et al., 2015 [2]. Moreover, comparisons are reported in terms of performance profiles (Dolan and Moré, 2002 [3], adopting different parameters settings. Finally, our linesearch-based scheme is compared with a renowned trust region method, namely TRON (Lin and Moré, 1999 [4].

  17. Exact fan-beam image reconstruction algorithm for truncated projection data acquired from an asymmetric half-size detector

    International Nuclear Information System (INIS)

    Leng Shuai; Zhuang Tingliang; Nett, Brian E; Chen Guanghong

    2005-01-01

    In this paper, we present a new algorithm designed for a specific data truncation problem in fan-beam CT. We consider a scanning configuration in which the fan-beam projection data are acquired from an asymmetrically positioned half-sized detector. Namely, the asymmetric detector only covers one half of the scanning field of view. Thus, the acquired fan-beam projection data are truncated at every view angle. If an explicit data rebinning process is not invoked, this data acquisition configuration will reek havoc on many known fan-beam image reconstruction schemes including the standard filtered backprojection (FBP) algorithm and the super-short-scan FBP reconstruction algorithms. However, we demonstrate that a recently developed fan-beam image reconstruction algorithm which reconstructs an image via filtering a backprojection image of differentiated projection data (FBPD) survives the above fan-beam data truncation problem. Namely, we may exactly reconstruct the whole image object using the truncated data acquired in a full scan mode (2π angular range). We may also exactly reconstruct a small region of interest (ROI) using the truncated projection data acquired in a short-scan mode (less than 2π angular range). The most important characteristic of the proposed reconstruction scheme is that an explicit data rebinning process is not introduced. Numerical simulations were conducted to validate the new reconstruction algorithm

  18. Truncated Levy flights and agenda-based mobility are useful for the assessment of personal human exposure

    International Nuclear Information System (INIS)

    Schlink, Uwe; Ragas, Ad M.J.

    2011-01-01

    Receptor-oriented approaches can assess the individual-specific exposure to air pollution. In such an individual-based model we analyse the impact of human mobility to the personal exposure that is perceived by individuals simulated in an exemplified urban area. The mobility models comprise random walk (reference point mobility, RPM), truncated Levy flights (TLF), and agenda-based walk (RPMA). We describe and review the general concepts and provide an inter-comparison of these concepts. Stationary and ergodic behaviour are explained and applied as well as performance criteria for a comparative evaluation of the investigated algorithms. We find that none of the studied algorithm results in purely random trajectories. TLF and RPMA prove to be suitable for human mobility modelling, because they provide conditions for very individual-specific trajectories and exposure. Suggesting these models we demonstrate the plausibility of their results for exposure to air-borne benzene and the combined exposure to benzene and nonane. - Highlights: → Human exposure to air pollutants is influenced by a person's movement in the urban area. → We provide a simulation study of approaches to modelling personal exposure. → Agenda-based models and truncated Levy flights are recommended for exposure assessment. → The procedure is demonstrated for benzene exposure in an urban region. - Truncated Levy flights and agenda-based mobility are useful for the assessment of personal human exposure.

  19. Truncation in diffraction pattern analysis. Pt. 1

    International Nuclear Information System (INIS)

    Delhez, R.; Keijser, T.H. de; Mittemeijer, E.J.; Langford, J.I.

    1986-01-01

    An evaluation of the concept of a line profile is provoked by truncation of the range of intensity measurement in practice. The measured truncated line profile can be considered either as part of the total intensity distribution which peaks at or near the reciprocal-lattice points (approach 1), or as part of a component line profile which is confined to a single reciprocal-lattice point (approach 2). Some false conceptions in line-profile analysis can then be avoided and recipes can be developed for the extrapolation of the tails of the truncated line profile. Fourier analysis of line profiles, according to the first approach, implies a Fourier series development of the total intensity distribution defined within [l - 1/2, l + 1/2] (l indicates the node considered in reciprocal space); the second approach implies a Fourier transformation of the component line profile defined within [ - ∞, + ∞]. Exact descriptions of size broadening are provided by both approaches, whereas combined size and strain broadening can only be evaluated adequately within the first approach. Straightforward methods are given for obtaining truncation-corrected values for the average crystallite size. (orig.)

  20. Left truncation results in substantial bias of the relation between time-dependent exposures and adverse events

    NARCIS (Netherlands)

    Hazelbag, Christijan M; Klungel, Olaf H; van Staa, Tjeerd P; de Boer, Anthonius; Groenwold, Rolf H H

    PURPOSE: To assess the impact of random left truncation of data on the estimation of time-dependent exposure effects. METHODS: A simulation study was conducted in which the relation between exposure and outcome was based on an immediate exposure effect, a first-time exposure effect, or a cumulative

  1. Left truncation results in substantial bias of the relation between time-dependent exposures and adverse events

    NARCIS (Netherlands)

    Hazelbag, Christijan M.; Klungel, Olaf H.; van Staa, Tjeerd P.; de Boer, Anthonius; Groenwold, Rolf H H

    2015-01-01

    PURPOSE: To assess the impact of random left truncation of data on the estimation of time-dependent exposure effects. METHODS: A simulation study was conducted in which the relation between exposure and outcome was based on an immediate exposure effect, a first-time exposure effect, or a cumulative

  2. Detecting and correcting for publication bias in meta-analysis - A truncated normal distribution approach.

    Science.gov (United States)

    Zhu, Qiaohao; Carriere, K C

    2016-01-01

    Publication bias can significantly limit the validity of meta-analysis when trying to draw conclusion about a research question from independent studies. Most research on detection and correction for publication bias in meta-analysis focus mainly on funnel plot-based methodologies or selection models. In this paper, we formulate publication bias as a truncated distribution problem, and propose new parametric solutions. We develop methodologies of estimating the underlying overall effect size and the severity of publication bias. We distinguish the two major situations, in which publication bias may be induced by: (1) small effect size or (2) large p-value. We consider both fixed and random effects models, and derive estimators for the overall mean and the truncation proportion. These estimators will be obtained using maximum likelihood estimation and method of moments under fixed- and random-effects models, respectively. We carried out extensive simulation studies to evaluate the performance of our methodology, and to compare with the non-parametric Trim and Fill method based on funnel plot. We find that our methods based on truncated normal distribution perform consistently well, both in detecting and correcting publication bias under various situations.

  3. Truncation Depth Rule-of-Thumb for Convolutional Codes

    Science.gov (United States)

    Moision, Bruce

    2009-01-01

    In this innovation, it is shown that a commonly used rule of thumb (that the truncation depth of a convolutional code should be five times the memory length, m, of the code) is accurate only for rate 1/2 codes. In fact, the truncation depth should be 2.5 m/(1 - r), where r is the code rate. The accuracy of this new rule is demonstrated by tabulating the distance properties of a large set of known codes. This new rule was derived by bounding the losses due to truncation as a function of the code rate. With regard to particular codes, a good indicator of the required truncation depth is the path length at which all paths that diverge from a particular path have accumulated the minimum distance of the code. It is shown that the new rule of thumb provides an accurate prediction of this depth for codes of varying rates.

  4. Wigner distribution function of circularly truncated light beams

    NARCIS (Netherlands)

    Bastiaans, M.J.; Nijhawan, O.P.; Gupta, A.K.; Musla, A.K.; Singh, Kehar

    1998-01-01

    Truncating a light beam is expressed as a convolution of its Wigner distribution function and the WDF of the truncating aperture. The WDF of a circular aperture is derived and an approximate expression - which is exact in the space and the spatial-frequency origin and whose integral over the spatial

  5. Flexible scheme to truncate the hierarchy of pure states.

    Science.gov (United States)

    Zhang, P-P; Bentley, C D B; Eisfeld, A

    2018-04-07

    The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

  6. Flexible scheme to truncate the hierarchy of pure states

    Science.gov (United States)

    Zhang, P.-P.; Bentley, C. D. B.; Eisfeld, A.

    2018-04-01

    The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

  7. Truncated predictor feedback for time-delay systems

    CERN Document Server

    Zhou, Bin

    2014-01-01

    This book provides a systematic approach to the design of predictor based controllers for (time-varying) linear systems with either (time-varying) input or state delays. Differently from those traditional predictor based controllers, which are infinite-dimensional static feedback laws and may cause difficulties in their practical implementation, this book develops a truncated predictor feedback (TPF) which involves only finite dimensional static state feedback. Features and topics: A novel approach referred to as truncated predictor feedback for the stabilization of (time-varying) time-delay systems in both the continuous-time setting and the discrete-time setting is built systematically Semi-global and global stabilization problems of linear time-delay systems subject to either magnitude saturation or energy constraints are solved in a systematic manner Both stabilization of a single system and consensus of a group of systems (multi-agent systems) are treated in a unified manner by applying the truncated pre...

  8. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    Science.gov (United States)

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

  9. New results to BDD truncation method for efficient top event probability calculation

    International Nuclear Information System (INIS)

    Mo, Yuchang; Zhong, Farong; Zhao, Xiangfu; Yang, Quansheng; Cui, Gang

    2012-01-01

    A Binary Decision Diagram (BDD) is a graph-based data structure that calculates an exact top event probability (TEP). It has been a very difficult task to develop an efficient BDD algorithm that can solve a large problem since its memory consumption is very high. Recently, in order to solve a large reliability problem within limited computational resources, Jung presented an efficient method to maintain a small BDD size by a BDD truncation during a BDD calculation. In this paper, it is first identified that Jung's BDD truncation algorithm can be improved for a more practical use. Then, a more efficient truncation algorithm is proposed in this paper, which can generate truncated BDD with smaller size and approximate TEP with smaller truncation error. Empirical results showed this new algorithm uses slightly less running time and slightly more storage usage than Jung's algorithm. It was also found, that designing a truncation algorithm with ideal features for every possible fault tree is very difficult, if not impossible. The so-called ideal features of this paper would be that with the decrease of truncation limits, the size of truncated BDD converges to the size of exact BDD, but should never be larger than exact BDD.

  10. Maximum nondiffracting propagation distance of aperture-truncated Airy beams

    Science.gov (United States)

    Chu, Xingchun; Zhao, Shanghong; Fang, Yingwu

    2018-05-01

    Airy beams have called attention of many researchers due to their non-diffracting, self-healing and transverse accelerating properties. A key issue in research of Airy beams and its applications is how to evaluate their nondiffracting propagation distance. In this paper, the critical transverse extent of physically realizable Airy beams is analyzed under the local spatial frequency methodology. The maximum nondiffracting propagation distance of aperture-truncated Airy beams is formulated and analyzed based on their local spatial frequency. The validity of the formula is verified by comparing the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam, aperture-truncated exponentially decaying Airy beam and exponentially decaying Airy beam. Results show that the formula can be used to evaluate accurately the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam. Therefore, it can guide us to select appropriate parameters to generate Airy beams with long nondiffracting propagation distance that have potential application in the fields of laser weapons or optical communications.

  11. An iterative reconstruction from truncated projection data

    International Nuclear Information System (INIS)

    Anon.

    1985-01-01

    Various methods have been proposed for tomographic reconstruction from truncated projection data. In this paper, a reconstructive method is discussed which consists of iterations of filtered back-projection, reprojection and some nonlinear processings. First, the method is so constructed that it converges to a fixed point. Then, to examine its effectiveness, comparisons are made by computer experiments with two existing reconstructive methods for truncated projection data, that is, the method of extrapolation based on the smooth assumption followed by filtered back-projection, and modified additive ART

  12. Truncated Wigner dynamics and conservation laws

    Science.gov (United States)

    Drummond, Peter D.; Opanchuk, Bogdan

    2017-10-01

    Ultracold Bose gases can be used to experimentally test many-body theory predictions. Here we point out that both exact conservation laws and dynamical invariants exist in the topical case of the one-dimensional Bose gas, and these provide an important validation of methods. We show that the first four quantum conservation laws are exactly conserved in the approximate truncated Wigner approach to many-body quantum dynamics. Center-of-mass position variance is also exactly calculable. This is nearly exact in the truncated Wigner approximation, apart from small terms that vanish as N-3 /2 as N →∞ with fixed momentum cutoff. Examples of this are calculated in experimentally relevant, mesoscopic cases.

  13. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

    Science.gov (United States)

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  14. Inference for shared-frailty survival models with left-truncated data

    NARCIS (Netherlands)

    van den Berg, G.J.; Drepper, B.

    2016-01-01

    Shared-frailty survival models specify that systematic unobserved determinants of duration outcomes are identical within groups of individuals. We consider random-effects likelihood-based statistical inference if the duration data are subject to left-truncation. Such inference with left-truncated

  15. Immature truncated O-glycophenotype of cancer directly induces oncogenic features

    DEFF Research Database (Denmark)

    Radhakrishnan, Prakash; Dabelsteen, Sally; Madsen, Frey Brus

    2014-01-01

    Aberrant expression of immature truncated O-glycans is a characteristic feature observed on virtually all epithelial cancer cells, and a very high frequency is observed in early epithelial premalignant lesions that precede the development of adenocarcinomas. Expression of the truncated O-glycan s...

  16. Probability distributions with truncated, log and bivariate extensions

    CERN Document Server

    Thomopoulos, Nick T

    2018-01-01

    This volume presents a concise and practical overview of statistical methods and tables not readily available in other publications. It begins with a review of the commonly used continuous and discrete probability distributions. Several useful distributions that are not so common and less understood are described with examples and applications in full detail: discrete normal, left-partial, right-partial, left-truncated normal, right-truncated normal, lognormal, bivariate normal, and bivariate lognormal. Table values are provided with examples that enable researchers to easily apply the distributions to real applications and sample data. The left- and right-truncated normal distributions offer a wide variety of shapes in contrast to the symmetrically shaped normal distribution, and a newly developed spread ratio enables analysts to determine which of the three distributions best fits a particular set of sample data. The book will be highly useful to anyone who does statistical and probability analysis. This in...

  17. Application of a truncated normal failure distribution in reliability testing

    Science.gov (United States)

    Groves, C., Jr.

    1968-01-01

    Statistical truncated normal distribution function is applied as a time-to-failure distribution function in equipment reliability estimations. Age-dependent characteristics of the truncated function provide a basis for formulating a system of high-reliability testing that effectively merges statistical, engineering, and cost considerations.

  18. Truncation scheme of time-dependent density-matrix approach II

    Energy Technology Data Exchange (ETDEWEB)

    Tohyama, Mitsuru [Kyorin University School of Medicine, Mitaka, Tokyo (Japan); Schuck, Peter [Institut de Physique Nucleaire, IN2P3-CNRS, Universite Paris-Sud, Orsay (France); Laboratoire de Physique et de Modelisation des Milieux Condenses, CNRS et Universite Joseph Fourier, Grenoble (France)

    2017-09-15

    A truncation scheme of the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy for reduced density matrices, where a three-body density matrix is approximated by two-body density matrices, is improved to take into account a normalization effect. The truncation scheme is tested for the Lipkin model. It is shown that the obtained results are in good agreement with the exact solutions. (orig.)

  19. Multiple-scattering theory with a truncated basis set

    International Nuclear Information System (INIS)

    Zhang, X.; Butler, W.H.

    1992-01-01

    Multiple-scattering theory (MST) is an extremely efficient technique for calculating the electronic structure of an assembly of atoms. The wave function in MST is expanded in terms of spherical waves centered on each atom and indexed by their orbital and azimuthal quantum numbers, l and m. The secular equation which determines the characteristic energies can be truncated at a value of the orbital angular momentum l max , for which the higher angular momentum phase shifts, δ l (l>l max ), are sufficiently small. Generally, the wave-function coefficients which are calculated from the secular equation are also truncated at l max . Here we point out that this truncation of the wave function is not necessary and is in fact inconsistent with the truncation of the secular equation. A consistent procedure is described in which the states with higher orbital angular momenta are retained but with their phase shifts set to zero. We show that this treatment gives smooth, continuous, and correctly normalized wave functions and that the total charge density calculated from the corresponding Green function agrees with the Lloyd formula result. We also show that this augmented wave function can be written as a linear combination of Andersen's muffin-tin orbitals in the case of muffin-tin potentials, and can be used to generalize the muffin-tin orbital idea to full-cell potentals

  20. Hamiltonian truncation approach to quenches in the Ising field theory

    Directory of Open Access Journals (Sweden)

    T. Rakovszky

    2016-10-01

    Full Text Available In contrast to lattice systems where powerful numerical techniques such as matrix product state based methods are available to study the non-equilibrium dynamics, the non-equilibrium behaviour of continuum systems is much harder to simulate. We demonstrate here that Hamiltonian truncation methods can be efficiently applied to this problem, by studying the quantum quench dynamics of the 1+1 dimensional Ising field theory using a truncated free fermionic space approach. After benchmarking the method with integrable quenches corresponding to changing the mass in a free Majorana fermion field theory, we study the effect of an integrability breaking perturbation by the longitudinal magnetic field. In both the ferromagnetic and paramagnetic phases of the model we find persistent oscillations with frequencies set by the low-lying particle excitations not only for small, but even for moderate size quenches. In the ferromagnetic phase these particles are the various non-perturbative confined bound states of the domain wall excitations, while in the paramagnetic phase the single magnon excitation governs the dynamics, allowing us to capture the time evolution of the magnetisation using a combination of known results from perturbation theory and form factor based methods. We point out that the dominance of low lying excitations allows for the numerical or experimental determination of the mass spectra through the study of the quench dynamics.

  1. Importance-truncated shell model for multi-shell valence spaces

    Energy Technology Data Exchange (ETDEWEB)

    Stumpf, Christina; Vobig, Klaus; Roth, Robert [Institut fuer Kernphysik, TU Darmstadt (Germany)

    2016-07-01

    The valence-space shell model is one of the work horses in nuclear structure theory. In traditional applications, shell-model calculations are carried out using effective interactions constructed in a phenomenological framework for rather small valence spaces, typically spanned by one major shell. We improve on this traditional approach addressing two main aspects. First, we use new effective interactions derived in an ab initio approach and, thus, establish a connection to the underlying nuclear interaction providing access to single- and multi-shell valence spaces. Second, we extend the shell model to larger valence spaces by applying an importance-truncation scheme based on a perturbative importance measure. In this way, we reduce the model space to the relevant basis states for the description of a few target eigenstates and solve the eigenvalue problem in this physics-driven truncated model space. In particular multi-shell valence spaces are not tractable otherwise. We combine the importance-truncated shell model with refined extrapolation schemes to approximately recover the exact result. We present first results obtained in the importance-truncated shell model with the newly derived ab initio effective interactions for multi-shell valence spaces, e.g., the sdpf shell.

  2. Flow equation of quantum Einstein gravity in a higher-derivative truncation

    International Nuclear Information System (INIS)

    Lauscher, O.; Reuter, M.

    2002-01-01

    Motivated by recent evidence indicating that quantum Einstein gravity (QEG) might be nonperturbatively renormalizable, the exact renormalization group equation of QEG is evaluated in a truncation of theory space which generalizes the Einstein-Hilbert truncation by the inclusion of a higher-derivative term (R 2 ). The beta functions describing the renormalization group flow of the cosmological constant, Newton's constant, and the R 2 coupling are computed explicitly. The fixed point properties of the 3-dimensional flow are investigated, and they are confronted with those of the 2-dimensional Einstein-Hilbert flow. The non-Gaussian fixed point predicted by the latter is found to generalize to a fixed point on the enlarged theory space. In order to test the reliability of the R 2 truncation near this fixed point we analyze the residual scheme dependence of various universal quantities; it turns out to be very weak. The two truncations are compared in detail, and their numerical predictions are found to agree with a surprisingly high precision. Because of the consistency of the results it appears increasingly unlikely that the non-Gaussian fixed point is an artifact of the truncation. If it is present in the exact theory QEG is probably nonperturbatively renormalizable and ''asymptotically safe.'' We discuss how the conformal factor problem of Euclidean gravity manifests itself in the exact renormalization group approach and show that, in the R 2 truncation, the investigation of the fixed point is not afflicted with this problem. Also the Gaussian fixed point of the Einstein-Hilbert truncation is analyzed; it turns out that it does not generalize to a corresponding fixed point on the enlarged theory space

  3. Enhancing propagation characteristics of truncated localized waves in silica

    KAUST Repository

    Salem, Mohamed

    2011-07-01

    The spectral characteristics of truncated Localized Waves propagating in dispersive silica are analyzed. Numerical experiments show that the immunity of the truncated Localized Waves propagating in dispersive silica to decay and distortion is enhanced as the non-linearity of the relation between the transverse spatial spectral components and the wave vector gets stronger, in contrast to free-space propagating waves, which suffer from early decay and distortion. © 2011 IEEE.

  4. Truncation of CPC solar collectors and its effect on energy collection

    Science.gov (United States)

    Carvalho, M. J.; Collares-Pereira, M.; Gordon, J. M.; Rabl, A.

    1985-01-01

    Analytic expressions are derived for the angular acceptance function of two-dimensional compound parabolic concentrator solar collectors (CPC's) of arbitrary degree of truncation. Taking into account the effect of truncation on both optical and thermal losses in real collectors, the increase in monthly and yearly collectible energy is also evaluated. Prior analyses that have ignored the correct behavior of the angular acceptance function at large angles for truncated collectors are shown to be in error by 0-2 percent in calculations of yearly collectible energy for stationary collectors.

  5. Simulation of Different Truncated p16INK4a Forms and In Silico Study of Interaction with Cdk4

    Directory of Open Access Journals (Sweden)

    Najmeh Fahham

    2009-01-01

    Full Text Available Protein-protein interactions studies can greatly increase the amount of structural and functional information pertaining to biologically active molecules and processes. The information obtained from such studies can lead to design and application of new modification in order to obtain a desired bioactivity. Many application packages and servers performing docking, such as HEX, DOT, AUTODOCK, and ZDOCK are now available for predicting the lowest free energy state of a protein complex. In this study, we have focused on cyclin-dependent kinase 4 (Cdk4, a key molecule in the regulation of cell cycle progression at the G1-S phase restriction point and p16INK4a, a tumor suppressor which inhibits Cdk4 activity. Truncated structures were created to find the more critical regions of p16 for interaction. The tertiary structures were determined by ProSAL, GENO3D Web Server. We evaluated their interactions with Cdk4 using two docking systems, HEX 4.5 and DOT 1. Calculations were performed on a high-speed computer. Minimizations and visualizations were carried out by PdbViewer 3.7. Considering shape and shape/electrostatic total energy, structures containing ANK II, III and IV motifs that lack the N-terminal region of the full length p16 molecule showed the best fi t complexes among the p16 truncated forms. The free energies were compatible with that of p16 full length original form, the full length. It seems that the N-terminal of the molecule is not crucial for the interaction since the truncated structure containing only this region did not show a good total energy.

  6. Transiently truncated and differentially regulated expression of midkine during mouse embryogenesis

    International Nuclear Information System (INIS)

    Chen Qin; Yuan Yuanyang; Lin Shuibin; Chang Youde; Zhuo Xinming; Wei Wei; Tao Ping; Ruan Lingjuan; Li Qifu; Li Zhixing

    2005-01-01

    Midkine (MK) is a retinoic acid response cytokine, mostly expressed in embryonic tissues. Aberrant expression of MK was found in numerous cancers. In human, a truncated MK was expressed specifically in tumor/cancer tissues. Here we report the discovery of a novel truncated form of MK transiently expressed during normal mouse embryonic development. In addition, MK is concentrated at the interface between developing epithelium and mesenchyme as well as highly proliferating cells. Its expression, which is closely coordinated with angiogenesis and vasculogenesis, is spatiotemporally regulated with peaks in extensive organogenesis period and undifferentiated cells tailing off in maturing cells, implying its role in nascent blood vessel (endothelial) signaling of tissue differentiation and stem cell renewal/differentiation.. Cloning and sequencing analysis revealed that the embryonic truncated MK, in which the conserved domain is in-frame deleted, presumably producing a novel secreted small peptide, is different from the truncated form in human cancer tissues, whose deletion results in a frame-shift mutation. Our data suggest that MK may play a role in epithelium-mesenchyme interactions, blood vessel signaling, and the decision of proliferation vs differentiation. Detection of the transiently expressed truncated MK reveals its novel function in development and sheds light on its role in carcinogenesis

  7. Modifications of Geometric Truncation of the Scattering Phase Function

    Science.gov (United States)

    Radkevich, A.

    2017-12-01

    Phase function (PF) of light scattering on large atmospheric particles has very strong peak in forward direction constituting a challenge for accurate numerical calculations of radiance. Such accurate (and fast) evaluations are important in the problems of remote sensing of the atmosphere. Scaling transformation replaces original PF with a sum of the delta function and a new regular smooth PF. A number of methods to construct such a PF were suggested. Delta-M and delta-fit methods require evaluation of the PF moments which imposes a numerical problem if strongly anisotropic PF is given as a function of angle. Geometric truncation keeps the original PF unchanged outside the forward peak cone replacing it with a constant within the cone. This approach is designed to preserve the asymmetry parameter. It has two disadvantages: 1) PF has discontinuity at the cone; 2) the choice of the cone is subjective, no recommendations were provided on the choice of the truncation angle. This choice affects both truncation fraction and the value of the phase function within the forward cone. Both issues are addressed in this study. A simple functional form of the replacement PF is suggested. This functional form allows for a number of modifications. This study consider 3 versions providing continuous PF. The considered modifications also bear either of three properties: preserve asymmetry parameter, provide continuity of the 1st derivative of the PF, and preserve mean scattering angle. The second problem mentioned above is addressed with a heuristic approach providing unambiguous criterion of selection of the truncation angle. The approach showed good performance on liquid water and ice clouds with different particle size distributions. Suggested modifications were tested on different cloud PFs using both discrete ordinates and Monte Carlo methods. It was showed that the modifications provide better accuracy of the radiance computation compare to the original geometric truncation.

  8. A Support Vector Machine Approach for Truncated Fingerprint Image Detection from Sweeping Fingerprint Sensors

    Science.gov (United States)

    Chen, Chi-Jim; Pai, Tun-Wen; Cheng, Mox

    2015-01-01

    A sweeping fingerprint sensor converts fingerprints on a row by row basis through image reconstruction techniques. However, a built fingerprint image might appear to be truncated and distorted when the finger was swept across a fingerprint sensor at a non-linear speed. If the truncated fingerprint images were enrolled as reference targets and collected by any automated fingerprint identification system (AFIS), successful prediction rates for fingerprint matching applications would be decreased significantly. In this paper, a novel and effective methodology with low time computational complexity was developed for detecting truncated fingerprints in a real time manner. Several filtering rules were implemented to validate existences of truncated fingerprints. In addition, a machine learning method of supported vector machine (SVM), based on the principle of structural risk minimization, was applied to reject pseudo truncated fingerprints containing similar characteristics of truncated ones. The experimental result has shown that an accuracy rate of 90.7% was achieved by successfully identifying truncated fingerprint images from testing images before AFIS enrollment procedures. The proposed effective and efficient methodology can be extensively applied to all existing fingerprint matching systems as a preliminary quality control prior to construction of fingerprint templates. PMID:25835186

  9. A Support Vector Machine Approach for Truncated Fingerprint Image Detection from Sweeping Fingerprint Sensors

    Directory of Open Access Journals (Sweden)

    Chi-Jim Chen

    2015-03-01

    Full Text Available A sweeping fingerprint sensor converts fingerprints on a row by row basis through image reconstruction techniques. However, a built fingerprint image might appear to be truncated and distorted when the finger was swept across a fingerprint sensor at a non-linear speed. If the truncated fingerprint images were enrolled as reference targets and collected by any automated fingerprint identification system (AFIS, successful prediction rates for fingerprint matching applications would be decreased significantly. In this paper, a novel and effective methodology with low time computational complexity was developed for detecting truncated fingerprints in a real time manner. Several filtering rules were implemented to validate existences of truncated fingerprints. In addition, a machine learning method of supported vector machine (SVM, based on the principle of structural risk minimization, was applied to reject pseudo truncated fingerprints containing similar characteristics of truncated ones. The experimental result has shown that an accuracy rate of 90.7% was achieved by successfully identifying truncated fingerprint images from testing images before AFIS enrollment procedures. The proposed effective and efficient methodology can be extensively applied to all existing fingerprint matching systems as a preliminary quality control prior to construction of fingerprint templates.

  10. Propagation of truncated modified Laguerre-Gaussian beams

    Science.gov (United States)

    Deng, D.; Li, J.; Guo, Q.

    2010-01-01

    By expanding the circ function into a finite sum of complex Gaussian functions and applying the Collins formula, the propagation of hard-edge diffracted modified Laguerre-Gaussian beams (MLGBs) through a paraxial ABCD system is studied, and the approximate closed-form propagation expression of hard-edge diffracted MLGBs is obtained. The transverse intensity distribution of the MLGB carrying finite power can be characterized by a single bright and symmetric ring during propagation when the aperture radius is very large. Starting from the definition of the generalized truncated second-order moments, the beam quality factor of MLGBs through a hard-edged circular aperture is investigated in a cylindrical coordinate system, which turns out to be dependent on the truncated radius and the beam orders.

  11. Balanced truncation for linear switched systems

    DEFF Research Database (Denmark)

    Petreczky, Mihaly; Wisniewski, Rafal; Leth, John-Josef

    2013-01-01

    In this paper, we present a theoretical analysis of the model reduction algorithm for linear switched systems from Shaker and Wisniewski (2011, 2009) and . This algorithm is a reminiscence of the balanced truncation method for linear parameter varying systems (Wood et al., 1996) [3]. Specifically...

  12. The Stars and Gas in Outer Parts of Galaxy Disks : Extended or Truncated, Flat or Warped?

    NARCIS (Netherlands)

    van der Kruit, P. C.; Funes, JG; Corsini, EM

    2008-01-01

    I review observations of truncations of stellar disks and models for their origin, compare observations of truncations in moderately inclined galaxies to those in edge-on systems and discuss the relation between truncations and H I-warps and their systematics and origin. Truncations are a common

  13. On truncated Taylor series and the position of their spurious zeros

    DEFF Research Database (Denmark)

    Christiansen, Søren; Madsen, Per A.

    2006-01-01

    A truncated Taylor series, or a Taylor polynomial, which may appear when treating the motion of gravity water waves, is obtained by truncating an infinite Taylor series for a complex, analytical function. For such a polynomial the position of the complex zeros is considered in case the Taylor...

  14. A Line Search Multilevel Truncated Newton Algorithm for Computing the Optical Flow

    Directory of Open Access Journals (Sweden)

    Lluís Garrido

    2015-06-01

    Full Text Available We describe the implementation details and give the experimental results of three optimization algorithms for dense optical flow computation. In particular, using a line search strategy, we evaluate the performance of the unilevel truncated Newton method (LSTN, a multiresolution truncated Newton (MR/LSTN and a full multigrid truncated Newton (FMG/LSTN. We use three image sequences and four models of optical flow for performance evaluation. The FMG/LSTN algorithm is shown to lead to better optical flow estimation with less computational work than both the LSTN and MR/LSTN algorithms.

  15. Performance Analysis of Thermoelectric Modules Consisting of Square Truncated Pyramid Elements Under Constant Heat Flux

    Science.gov (United States)

    Oki, Sae; Natsui, Shungo; Suzuki, Ryosuke O.

    2018-06-01

    System design of a thermoelectric (TE) power generation module is pursued in order to improve the TE performance. Square truncated pyramid shaped P-N pairs of TE elements are connected electronically in series in the open space between two flat insulator boards. The performance of the TE module consisting of 2-paired elements is numerically simulated using commercial software and original TE programs. Assuming that the heat radiating into the hot surface is regulated, i.e., the amount of heat from the hot surface to the cold one is steadily constant, as it happens for solar radiation heating, the performance is significantly improved by changing the shape and the alignment pattern of the elements. When the angle θ between the edge and the base is smaller than 72°, and when the cold surface is kept at a constant temperature, two patterns in particular, amongst the 17 studied, show the largest TE power and efficiency. In comparison to other geometries, the smarter square truncated pyramid shape can provide higher performance using a large cold bath and constant heat transfer by heat radiation.

  16. Low-mode truncation methods in the sine-Gordon equation

    International Nuclear Information System (INIS)

    Xiong Chuyu.

    1991-01-01

    In this dissertation, the author studies the chaotic and coherent motions (i.e., low-dimensional chaotic attractor) in some near integrable partial differential equations, particularly the sine-Gordon equation and the nonlinear Schroedinger equation. In order to study the motions, he uses low mode truncation methods to reduce these partial differential equations to some truncated models (low-dimensional ordinary differential equations). By applying many methods available to low-dimensional ordinary differential equations, he can understand the low-dimensional chaotic attractor of PDE's much better. However, there are two important questions one needs to answer: (1) How many modes is good enough for the low mode truncated models to capture the dynamics uniformly? (2) Is the chaotic attractor in a low mode truncated model close to the chaotic attractor in the original PDE? And how close is? He has developed two groups of powerful methods to help to answer these two questions. They are the computation methods of continuation and local bifurcation, and local Lyapunov exponents and Lyapunov exponents. Using these methods, he concludes that the 2N-nls ODE is a good model for the sine-Gordon equation and the nonlinear Schroedinger equation provided one chooses a 'good' basis and uses 'enough' modes (where 'enough' depends on the parameters of the system but is small for the parameter studied here). Therefore, one can use 2N-nls ODE to study the chaos of PDE's in more depth

  17. N-terminally truncated POM121C inhibits HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Hideki Saito

    Full Text Available Recent studies have identified host cell factors that regulate early stages of HIV-1 infection including viral cDNA synthesis and orientation of the HIV-1 capsid (CA core toward the nuclear envelope, but it remains unclear how viral DNA is imported through the nuclear pore and guided to the host chromosomal DNA. Here, we demonstrate that N-terminally truncated POM121C, a component of the nuclear pore complex, blocks HIV-1 infection. This truncated protein is predominantly localized in the cytoplasm, does not bind to CA, does not affect viral cDNA synthesis, reduces the formation of 2-LTR and diminished the amount of integrated proviral DNA. Studies with an HIV-1-murine leukemia virus (MLV chimeric virus carrying the MLV-derived Gag revealed that Gag is a determinant of this inhibition. Intriguingly, mutational studies have revealed that the blockade by N-terminally-truncated POM121C is closely linked to its binding to importin-β/karyopherin subunit beta 1 (KPNB1. These results indicate that N-terminally-truncated POM121C inhibits HIV-1 infection after completion of reverse transcription and before integration, and suggest an important role for KPNB1 in HIV-1 replication.

  18. Estimation of Panel Data Regression Models with Two-Sided Censoring or Truncation

    DEFF Research Database (Denmark)

    Alan, Sule; Honore, Bo E.; Hu, Luojia

    2014-01-01

    This paper constructs estimators for panel data regression models with individual speci…fic heterogeneity and two–sided censoring and truncation. Following Powell (1986) the estimation strategy is based on moment conditions constructed from re–censored or re–truncated residuals. While these moment...

  19. A generalized right truncated bivariate Poisson regression model with applications to health data.

    Science.gov (United States)

    Islam, M Ataharul; Chowdhury, Rafiqul I

    2017-01-01

    A generalized right truncated bivariate Poisson regression model is proposed in this paper. Estimation and tests for goodness of fit and over or under dispersion are illustrated for both untruncated and right truncated bivariate Poisson regression models using marginal-conditional approach. Estimation and test procedures are illustrated for bivariate Poisson regression models with applications to Health and Retirement Study data on number of health conditions and the number of health care services utilized. The proposed test statistics are easy to compute and it is evident from the results that the models fit the data very well. A comparison between the right truncated and untruncated bivariate Poisson regression models using the test for nonnested models clearly shows that the truncated model performs significantly better than the untruncated model.

  20. Bounded real and positive real balanced truncation using Σ-normalised coprime factors

    NARCIS (Netherlands)

    Trentelman, H.L.

    2009-01-01

    In this article, we will extend the method of balanced truncation using normalised right coprime factors of the system transfer matrix to balanced truncation with preservation of half line dissipativity. Special cases are preservation of positive realness and bounded realness. We consider a half

  1. No chiral truncation of quantum log gravity?

    Science.gov (United States)

    Andrade, Tomás; Marolf, Donald

    2010-03-01

    At the classical level, chiral gravity may be constructed as a consistent truncation of a larger theory called log gravity by requiring that left-moving charges vanish. In turn, log gravity is the limit of topologically massive gravity (TMG) at a special value of the coupling (the chiral point). We study the situation at the level of linearized quantum fields, focussing on a unitary quantization. While the TMG Hilbert space is continuous at the chiral point, the left-moving Virasoro generators become ill-defined and cannot be used to define a chiral truncation. In a sense, the left-moving asymptotic symmetries are spontaneously broken at the chiral point. In contrast, in a non-unitary quantization of TMG, both the Hilbert space and charges are continuous at the chiral point and define a unitary theory of chiral gravity at the linearized level.

  2. Design of a numerical model of lung by means of a special boundary condition in the truncated branches.

    Science.gov (United States)

    Tena, Ana F; Fernández, Joaquín; Álvarez, Eduardo; Casan, Pere; Walters, D Keith

    2017-06-01

    The need for a better understanding of pulmonary diseases has led to increased interest in the development of realistic computational models of the human lung. To minimize computational cost, a reduced geometry model is used for a model lung airway geometry up to generation 16. Truncated airway branches require physiologically realistic boundary conditions to accurately represent the effect of the removed airway sections. A user-defined function has been developed, which applies velocities mapped from similar locations in fully resolved airway sections. The methodology can be applied in any general purpose computational fluid dynamics code, with the only limitation that the lung model must be symmetrical in each truncated branch. Unsteady simulations have been performed to verify the operation of the model. The test case simulates a spirometry because the lung is obliged to rapidly perform both inspiration and expiration. Once the simulation was completed, the obtained pressure in the lower level of the lung was used as a boundary condition. The output velocity, which is a numerical spirometry, was compared with the experimental spirometry for validation purposes. This model can be applied for a wide range of patient-specific resolution levels. If the upper airway generations have been constructed from a computed tomography scan, it would be possible to quickly obtain a complete reconstruction of the lung specific to a specific person, which would allow individualized therapies. Copyright © 2016 John Wiley & Sons, Ltd.

  3. Artificial Neural Networks for Reducing Computational Effort in Active Truncated Model Testing of Mooring Lines

    DEFF Research Database (Denmark)

    Christiansen, Niels Hørbye; Voie, Per Erlend Torbergsen; Høgsberg, Jan Becker

    2015-01-01

    simultaneously, this method is very demanding in terms of numerical efficiency and computational power. Therefore, this method has not yet proved to be feasible. It has recently been shown how a hybrid method combining classical numerical models and artificial neural networks (ANN) can provide a dramatic...... prior to the experiment and with a properly trained ANN it is no problem to obtain accurate simulations much faster than real time-without any need for large computational capacity. The present study demonstrates how this hybrid method can be applied to the active truncated experiments yielding a system...

  4. Amplitude reconstruction from complete photoproduction experiments and truncated partial-wave expansions

    International Nuclear Information System (INIS)

    Workman, R. L.; Tiator, L.; Wunderlich, Y.; Doring, M.; Haberzettl, H.

    2017-01-01

    Here, we compare the methods of amplitude reconstruction, for a complete experiment and a truncated partial-wave analysis, applied to the photoproduction of pseudoscalar mesons. The approach is pedagogical, showing in detail how the amplitude reconstruction (observables measured at a single energy and angle) is related to a truncated partial-wave analysis (observables measured at a single energy and a number of angles).

  5. Modified Truncated Multiplicity Analysis to Improve Verification of Uranium Fuel Cycle Materials

    International Nuclear Information System (INIS)

    LaFleur, A.; Miller, K.; Swinhoe, M.; Belian, A.; Croft, S.

    2015-01-01

    Accurate verification of 235U enrichment and mass in UF6 storage cylinders and the UO2F2 holdup contained in the process equipment is needed to improve international safeguards and nuclear material accountancy at uranium enrichment plants. Small UF6 cylinders (1.5'' and 5'' diameter) are used to store the full range of enrichments from depleted to highly-enriched UF6. For independent verification of these materials, it is essential that the 235U mass and enrichment measurements do not rely on facility operator declarations. Furthermore, in order to be deployed by IAEA inspectors to detect undeclared activities (e.g., during complementary access), it is also imperative that the measurement technique is quick, portable, and sensitive to a broad range of 235U masses. Truncated multiplicity analysis is a technique that reduces the variance in the measured count rates by only considering moments 1, 2, and 3 of the multiplicity distribution. This is especially important for reducing the uncertainty in the measured doubles and triples rates in environments with a high cosmic ray background relative to the uranium signal strength. However, we believe that the existing truncated multiplicity analysis throws away too much useful data by truncating the distribution after the third moment. This paper describes a modified truncated multiplicity analysis method that determines the optimal moment to truncate the multiplicity distribution based on the measured data. Experimental measurements of small UF6 cylinders and UO2F2 working reference materials were performed at Los Alamos National Laboratory (LANL). The data were analyzed using traditional and modified truncated multiplicity analysis to determine the optimal moment to truncate the multiplicity distribution to minimize the uncertainty in the measured count rates. The results from this analysis directly support nuclear safeguards at enrichment plants and provide a more accurate verification method for UF6

  6. Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells

    Science.gov (United States)

    Barua, Dipak; Hlavacek, William S.

    2013-01-01

    In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β—catenin, which is regulated by a multiprotein complex called the destruction complex. The destruction complex comprises APC, Axin, β—catenin, serine/threonine kinases, and other proteins. The kinases and , which are recruited by Axin, mediate phosphorylation of β—catenin, which initiates its ubiquitination and proteosomal degradation. The mechanism of regulation of β—catenin degradation by the destruction complex and the role of truncation of APC in colorectal cancer are not entirely understood. Through formulation and analysis of a rule-based computational model, we investigated the regulation of β—catenin phosphorylation and degradation by APC and the effect of APC truncation on function of the destruction complex. The model integrates available mechanistic knowledge about site-specific interactions and phosphorylation of destruction complex components and is consistent with an array of published data. We find that the phosphorylated truncated form of APC can outcompete Axin for binding to β—catenin, provided that Axin is limiting, and thereby sequester β—catenin away from Axin and the Axin-recruited kinases and . Full-length APC also competes with Axin for binding to β—catenin; however, full-length APC is able, through its SAMP repeats, which bind Axin and which are missing in truncated oncogenic forms of APC, to bring β—catenin into indirect association with Axin and Axin-recruited kinases. Because our model indicates that the positive effects of truncated APC on β—catenin levels depend on phosphorylation of APC, at the first 20-amino acid repeat, and because phosphorylation of this site is mediated by , we suggest that is a potential target for therapeutic intervention in colorectal cancer. Specific inhibition of is predicted to limit binding of β—catenin to truncated

  7. A Lynden-Bell integral estimator for the tail index of right-truncated ...

    African Journals Online (AJOL)

    By means of a Lynden-Bell integral with deterministic threshold, Worms and Worms [A Lynden-Bell integral estimator for extremes of randomly truncated data. Statist. Probab. Lett. 2016; 109: 106-117] recently introduced an asymptotically normal estimator of the tail index for randomly right-truncated Pareto-type data.

  8. Truncated States Obtained by Iteration

    International Nuclear Information System (INIS)

    Cardoso, W. B.; Almeida, N. G. de

    2008-01-01

    We introduce the concept of truncated states obtained via iterative processes (TSI) and study its statistical features, making an analogy with dynamical systems theory (DST). As a specific example, we have studied TSI for the doubling and the logistic functions, which are standard functions in studying chaos. TSI for both the doubling and logistic functions exhibit certain similar patterns when their statistical features are compared from the point of view of DST

  9. A Multistep Extending Truncation Method towards Model Construction of Infinite-State Markov Chains

    Directory of Open Access Journals (Sweden)

    Kemin Wang

    2014-01-01

    Full Text Available The model checking of Infinite-State Continuous Time Markov Chains will inevitably encounter the state explosion problem when constructing the CTMCs model; our method is to get a truncated model of the infinite one; to get a sufficient truncated model to meet the model checking of Continuous Stochastic Logic based system properties, we propose a multistep extending advanced truncation method towards model construction of CTMCs and implement it in the INFAMY model checker; the experiment results show that our method is effective.

  10. Family Therapy for the "Truncated" Nuclear Family.

    Science.gov (United States)

    Zuk, Gerald H.

    1980-01-01

    The truncated nuclear family consists of a two-generation group in which conflict has produced a polarization of values. The single-parent family is at special risk. Go-between process enables the therapist to depolarize sharply conflicted values and reduce pathogenic relating. (Author)

  11. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations.

    Science.gov (United States)

    Aviat, Félix; Levitt, Antoine; Stamm, Benjamin; Maday, Yvon; Ren, Pengyu; Ponder, Jay W; Lagardère, Louis; Piquemal, Jean-Philip

    2017-01-10

    We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration ("peek"), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production

  12. On the viability of the truncated Israel–Stewart theory in cosmology

    International Nuclear Information System (INIS)

    Shogin, Dmitry; Amundsen, Per Amund; Hervik, Sigbjørn

    2015-01-01

    We apply the causal Israel–Stewart theory of irreversible thermodynamics to model the matter content of the Universe as a dissipative fluid with bulk and shear viscosity. Along with the full transport equations we consider their widely used truncated version. By implementing a dynamical systems approach to Bianchi type IV and V cosmological models with and without cosmological constant, we determine the future asymptotic states of such Universes and show that the truncated Israel–Stewart theory leads to solutions essentially different from the full theory. The solutions of the truncated theory may also manifest unphysical properties. Finally, we find that in the full theory shear viscosity can give a substantial rise to dissipative fluxes, driving the fluid extremely far from equilibrium, where the linear Israel–Stewart theory ceases to be valid. (paper)

  13. Riesz Representation Theorem on Bilinear Spaces of Truncated Laurent Series

    Directory of Open Access Journals (Sweden)

    Sabarinsyah

    2017-06-01

    Full Text Available In this study a generalization of the Riesz representation theorem on non-degenerate bilinear spaces, particularly on spaces of truncated Laurent series, was developed. It was shown that any linear functional on a non-degenerate bilinear space is representable by a unique element of the space if and only if its kernel is closed. Moreover an explicit equivalent condition can be identified for the closedness property of the kernel when the bilinear space is a space of truncated Laurent series.

  14. Pressure-sensitive paint on a truncated cone in hypersonic flow at incidences

    International Nuclear Information System (INIS)

    Yang, L.; Erdem, E.; Zare-Behtash, H.; Kontis, K.; Saravanan, S.

    2012-01-01

    Highlights: ► Global pressure map over the truncated cone is obtained at various incidence angles in Mach 5 flow. ► Successful application of AA-PSP in hypersonic flow expands operation area of this technique. ► AA-PSP reveals complex three-dimensional pattern which is difficult for transducer to obtain. ► Quantitative data provides strong correlation with colour Schlieren and oil flow results. ► High spatial resolution pressure mappings identify small scale vortices and flow separation. - Abstract: The flow over a truncated cone is a classical and fundamental problem for aerodynamic research due to its three-dimensional and complicated characteristics. The flow is made more complex when examining high angles of incidence. Recently these types of flows have drawn more attention for the purposes of drag reduction in supersonic/hypersonic flows. In the present study the flow over a truncated cone at various incidences was experimentally investigated in a Mach 5 flow with a unit Reynolds number of 13.5 × 10 6 m −1 . The cone semi-apex angle is 15° and the truncation ratio (truncated length/cone length) is 0.5. The incidence of the model varied from −12° to 12° with 3° intervals relative to the freestream direction. The external flow around the truncated cone was visualised by colour Schlieren photography, while the surface flow pattern was revealed using the oil flow method. The surface pressure distribution was measured using the anodized aluminium pressure-sensitive paint (AA-PSP) technique. Both top and sideviews of the pressure distribution on the model surface were acquired at various incidences. AA-PSP showed high pressure sensitivity and captured the complicated flow structures which correlated well with the colour Schlieren and oil flow visualisation results.

  15. On truncations of the exact renormalization group

    CERN Document Server

    Morris, T R

    1994-01-01

    We investigate the Exact Renormalization Group (ERG) description of (Z_2 invariant) one-component scalar field theory, in the approximation in which all momentum dependence is discarded in the effective vertices. In this context we show how one can perform a systematic search for non-perturbative continuum limits without making any assumption about the form of the lagrangian. Concentrating on the non-perturbative three dimensional Wilson fixed point, we then show that the sequence of truncations n=2,3,\\dots, obtained by expanding about the field \\varphi=0 and discarding all powers \\varphi^{2n+2} and higher, yields solutions that at first converge to the answer obtained without truncation, but then cease to further converge beyond a certain point. No completely reliable method exists to reject the many spurious solutions that are also found. These properties are explained in terms of the analytic behaviour of the untruncated solutions -- which we describe in some detail.

  16. Squeezing in multi-mode nonlinear optical state truncation

    International Nuclear Information System (INIS)

    Said, R.S.; Wahiddin, M.R.B.; Umarov, B.A.

    2007-01-01

    In this Letter, we show that multi-mode qubit states produced via nonlinear optical state truncation driven by classical external pumpings exhibit squeezing condition. We restrict our discussions to the two- and three-mode cases

  17. truncSP: An R Package for Estimation of Semi-Parametric Truncated Linear Regression Models

    Directory of Open Access Journals (Sweden)

    Maria Karlsson

    2014-05-01

    Full Text Available Problems with truncated data occur in many areas, complicating estimation and inference. Regarding linear regression models, the ordinary least squares estimator is inconsistent and biased for these types of data and is therefore unsuitable for use. Alternative estimators, designed for the estimation of truncated regression models, have been developed. This paper presents the R package truncSP. The package contains functions for the estimation of semi-parametric truncated linear regression models using three different estimators: the symmetrically trimmed least squares, quadratic mode, and left truncated estimators, all of which have been shown to have good asymptotic and ?nite sample properties. The package also provides functions for the analysis of the estimated models. Data from the environmental sciences are used to illustrate the functions in the package.

  18. Motion of isolated open vortex filaments evolving under the truncated local induction approximation

    Science.gov (United States)

    Van Gorder, Robert A.

    2017-11-01

    The study of nonlinear waves along open vortex filaments continues to be an area of active research. While the local induction approximation (LIA) is attractive due to locality compared with the non-local Biot-Savart formulation, it has been argued that LIA appears too simple to model some relevant features of Kelvin wave dynamics, such as Kelvin wave energy transfer. Such transfer of energy is not feasible under the LIA due to integrability, so in order to obtain a non-integrable model, a truncated LIA, which breaks the integrability of the classical LIA, has been proposed as a candidate model with which to study such dynamics. Recently Laurie et al. ["Interaction of Kelvin waves and nonlocality of energy transfer in superfluids," Phys. Rev. B 81, 104526 (2010)] derived truncated LIA systematically from Biot-Savart dynamics. The focus of the present paper is to study the dynamics of a section of common open vortex filaments under the truncated LIA dynamics. We obtain the analog of helical, planar, and more general filaments which rotate without a change in form in the classical LIA, demonstrating that while quantitative differences do exist, qualitatively such solutions still exist under the truncated LIA. Conversely, solitons and breather solutions found under the LIA should not be expected under the truncated LIA, as the existence of such solutions relies on the existence of an infinite number of conservation laws which is violated due to loss of integrability. On the other hand, similarity solutions under the truncated LIA can be quite different to their counterparts found for the classical LIA, as they must obey a t1/3 type scaling rather than the t1/2 type scaling commonly found in the LIA and Biot-Savart dynamics. This change in similarity scaling means that Kelvin waves are radiated at a slower rate from vortex kinks formed after reconnection events. The loss of soliton solutions and the difference in similarity scaling indicate that dynamics emergent under

  19. The combination of i-leader truncation and gemcitabine improves oncolytic adenovirus efficacy in an immunocompetent model.

    Science.gov (United States)

    Puig-Saus, C; Laborda, E; Rodríguez-García, A; Cascalló, M; Moreno, R; Alemany, R

    2014-02-01

    Adenovirus (Ad) i-leader protein is a small protein of unknown function. The C-terminus truncation of the i-leader protein increases Ad release from infected cells and cytotoxicity. In the current study, we use the i-leader truncation to enhance the potency of an oncolytic Ad. In vitro, an i-leader truncated oncolytic Ad is released faster to the supernatant of infected cells, generates larger plaques, and is more cytotoxic in both human and Syrian hamster cell lines. In mice bearing human tumor xenografts, the i-leader truncation enhances oncolytic efficacy. However, in a Syrian hamster pancreatic tumor model, which is immunocompetent and less permissive to human Ad, antitumor efficacy is only observed when the i-leader truncated oncolytic Ad, but not the non-truncated version, is combined with gemcitabine. This synergistic effect observed in the Syrian hamster model was not seen in vitro or in immunodeficient mice bearing the same pancreatic hamster tumors, suggesting a role of the immune system in this synergism. These results highlight the interest of the i-leader C-terminus truncation because it enhances the antitumor potency of an oncolytic Ad and provides synergistic effects with gemcitabine in the presence of an immune competent system.

  20. Local and accumulated truncation errors in a class of perturbative numerical methods

    International Nuclear Information System (INIS)

    Adam, G.; Adam, S.; Corciovei, A.

    1980-01-01

    The approach to the solution of the radial Schroedinger equation using piecewise perturbative theory with a step function reference potential leads to a class of powerful numerical methods, conveniently abridged as SF-PNM(K), where K denotes the order at which the perturbation series was truncated. In the present paper rigorous results are given for the local truncation errors and bounds are derived for the accumulated truncated errors associated to SF-PNM(K), K = 0, 1, 2. They allow us to establish the smoothness conditions which have to be fulfilled by the potential in order to ensure a safe use of SF-PNM(K), and to understand the experimentally observed behaviour of the numerical results with the step size h. (author)

  1. Frequency interval balanced truncation of discrete-time bilinear systems

    DEFF Research Database (Denmark)

    Jazlan, Ahmad; Sreeram, Victor; Shaker, Hamid Reza

    2016-01-01

    This paper presents the development of a new model reduction method for discrete-time bilinear systems based on the balanced truncation framework. In many model reduction applications, it is advantageous to analyze the characteristics of the system with emphasis on particular frequency intervals...... are the solution to a pair of new generalized Lyapunov equations. The conditions for solvability of these new generalized Lyapunov equations are derived and a numerical solution method for solving these generalized Lyapunov equations is presented. Numerical examples which illustrate the usage of the new...... generalized frequency interval controllability and observability gramians as part of the balanced truncation framework are provided to demonstrate the performance of the proposed method....

  2. Adaptive bit plane quadtree-based block truncation coding for image compression

    Science.gov (United States)

    Li, Shenda; Wang, Jin; Zhu, Qing

    2018-04-01

    Block truncation coding (BTC) is a fast image compression technique applied in spatial domain. Traditional BTC and its variants mainly focus on reducing computational complexity for low bit rate compression, at the cost of lower quality of decoded images, especially for images with rich texture. To solve this problem, in this paper, a quadtree-based block truncation coding algorithm combined with adaptive bit plane transmission is proposed. First, the direction of edge in each block is detected using Sobel operator. For the block with minimal size, adaptive bit plane is utilized to optimize the BTC, which depends on its MSE loss encoded by absolute moment block truncation coding (AMBTC). Extensive experimental results show that our method gains 0.85 dB PSNR on average compare to some other state-of-the-art BTC variants. So it is desirable for real time image compression applications.

  3. High-yield water-based synthesis of truncated silver nanocubes

    International Nuclear Information System (INIS)

    Chang, Yun-Min; Lu, I-Te; Chen, Chih-Yuan; Hsieh, Yu-Chi; Wu, Pu-Wei

    2014-01-01

    Highlights: • Development of a water-based formula to fabricate truncated Ag nanocubes. • The sample exhibits (1 0 0), (1 1 0), and (1 1 1) on the facets, edges, and corners. • The sample shows three characteristic absorption peaks due to plasma resonance. -- Abstract: A high-yield water-based hydrothermal synthesis was developed using silver nitrate, ammonia, glucose, and cetyltrimethylammonium bromide (CTAB) as precursors to synthesize truncated silver nanocubes with uniform sizes and in large quantities. With a fixed CTAB concentration, truncated silver nanocubes with sizes of 49.3 ± 4.1 nm were produced when the molar ratio of glucose/silver cation was maintained at 0.1. The sample exhibited (1 0 0), (1 1 0), and (1 1 1) planes on the facets, edges, and corners, respectively. In contrast, with a slightly larger glucose/silver cation ratio of 0.35, well-defined nanocubes with sizes of 70.9 ± 3.8 nm sizes were observed with the (1 0 0) plane on six facets. When the ratio was further increased to 1.5, excess reduction of silver cations facilitated the simultaneous formation of nanoparticles with cubic, spherical, and irregular shapes. Consistent results were obtained from transmission electron microscopy, scanning electron microscopy, X-ray diffraction, and UV–visible absorption measurements

  4. High-yield water-based synthesis of truncated silver nanocubes

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Yun-Min; Lu, I-Te; Chen, Chih-Yuan; Hsieh, Yu-Chi; Wu, Pu-Wei, E-mail: ppwu@mail.nctu.edu.tw

    2014-02-15

    Highlights: • Development of a water-based formula to fabricate truncated Ag nanocubes. • The sample exhibits (1 0 0), (1 1 0), and (1 1 1) on the facets, edges, and corners. • The sample shows three characteristic absorption peaks due to plasma resonance. -- Abstract: A high-yield water-based hydrothermal synthesis was developed using silver nitrate, ammonia, glucose, and cetyltrimethylammonium bromide (CTAB) as precursors to synthesize truncated silver nanocubes with uniform sizes and in large quantities. With a fixed CTAB concentration, truncated silver nanocubes with sizes of 49.3 ± 4.1 nm were produced when the molar ratio of glucose/silver cation was maintained at 0.1. The sample exhibited (1 0 0), (1 1 0), and (1 1 1) planes on the facets, edges, and corners, respectively. In contrast, with a slightly larger glucose/silver cation ratio of 0.35, well-defined nanocubes with sizes of 70.9 ± 3.8 nm sizes were observed with the (1 0 0) plane on six facets. When the ratio was further increased to 1.5, excess reduction of silver cations facilitated the simultaneous formation of nanoparticles with cubic, spherical, and irregular shapes. Consistent results were obtained from transmission electron microscopy, scanning electron microscopy, X-ray diffraction, and UV–visible absorption measurements.

  5. Intersection spaces, spatial homology truncation, and string theory

    CERN Document Server

    Banagl, Markus

    2010-01-01

    Intersection cohomology assigns groups which satisfy a generalized form of Poincaré duality over the rationals to a stratified singular space. The present monograph introduces a method that assigns to certain classes of stratified spaces cell complexes, called intersection spaces, whose ordinary rational homology satisfies generalized Poincaré duality. The cornerstone of the method is a process of spatial homology truncation, whose functoriality properties are analyzed in detail. The material on truncation is autonomous and may be of independent interest to homotopy theorists. The cohomology of intersection spaces is not isomorphic to intersection cohomology and possesses algebraic features such as perversity-internal cup-products and cohomology operations that are not generally available for intersection cohomology. A mirror-symmetric interpretation, as well as applications to string theory concerning massless D-branes arising in type IIB theory during a Calabi-Yau conifold transition, are discussed.

  6. The Apparent Lack of Lorentz Invariance in Zero-Point Fields with Truncated Spectra

    Directory of Open Access Journals (Sweden)

    Daywitt W. C.

    2009-01-01

    Full Text Available The integrals that describe the expectation values of the zero-point quantum-field-theoretic vacuum state are semi-infinite, as are the integrals for the stochastic electrodynamic vacuum. The unbounded upper limit to these integrals leads in turn to infinite energy densities and renormalization masses. A number of models have been put forward to truncate the integrals so that these densities and masses are finite. Unfortunately the truncation apparently destroys the Lorentz invariance of the integrals. This note argues that the integrals are naturally truncated by the graininess of the negative-energy Planck vacuum state from which the zero-point vacuum arises, and are thus automatically Lorentz invariant.

  7. Reduction of variable-truncation artifacts from beam occlusion during in situ x-ray tomography

    DEFF Research Database (Denmark)

    Borg, Leise; Jørgensen, Jakob Sauer; Frikel, Jürgen

    2017-01-01

    Many in situ x-ray tomography studies require experimental rigs which may partially occlude the beam and cause parts of the projection data to be missing. In a study of fluid flow in porous chalk using a percolation cell with four metal bars drastic streak artifacts arise in the filtered...... and artifact-reduction methods are designed in context of FBP reconstruction motivated by computational efficiency practical for large, real synchrotron data. While a specific variable-truncation case is considered, the proposed methods can be applied to general data cut-offs arising in different in situ x-ray...... backprojection (FBP) reconstruction at certain orientations. Projections with non-trivial variable truncation caused by the metal bars are the source of these variable-truncation artifacts. To understand the artifacts a mathematical model of variable-truncation data as a function of metal bar radius and distance...

  8. Propagation of a general-type beam through a truncated fractional Fourier transform optical system.

    Science.gov (United States)

    Zhao, Chengliang; Cai, Yangjian

    2010-03-01

    Paraxial propagation of a general-type beam through a truncated fractional Fourier transform (FRT) optical system is investigated. Analytical formulas for the electric field and effective beam width of a general-type beam in the FRT plane are derived based on the Collins formula. Our formulas can be used to study the propagation of a variety of laser beams--such as Gaussian, cos-Gaussian, cosh-Gaussian, sine-Gaussian, sinh-Gaussian, flat-topped, Hermite-cosh-Gaussian, Hermite-sine-Gaussian, higher-order annular Gaussian, Hermite-sinh-Gaussian and Hermite-cos-Gaussian beams--through a FRT optical system with or without truncation. The propagation properties of a Hermite-cos-Gaussian beam passing through a rectangularly truncated FRT optical system are studied as a numerical example. Our results clearly show that the truncated FRT optical system provides a convenient way for laser beam shaping.

  9. On the effect of numerical errors in large eddy simulations of turbulent flows

    International Nuclear Information System (INIS)

    Kravchenko, A.G.; Moin, P.

    1997-01-01

    Aliased and dealiased numerical simulations of a turbulent channel flow are performed using spectral and finite difference methods. Analytical and numerical studies show that aliasing errors are more destructive for spectral and high-order finite-difference calculations than for low-order finite-difference simulations. Numerical errors have different effects for different forms of the nonlinear terms in the Navier-Stokes equations. For divergence and convective forms, spectral methods are energy-conserving only if dealiasing is performed. For skew-symmetric and rotational forms, both spectral and finite-difference methods are energy-conserving even in the presence of aliasing errors. It is shown that discrepancies between the results of dealiased spectral and standard nondialiased finite-difference methods are due to both aliasing and truncation errors with the latter being the leading source of differences. The relative importance of aliasing and truncation errors as compared to subgrid scale model terms in large eddy simulations is analyzed and discussed. For low-order finite-difference simulations, truncation errors can exceed the magnitude of the subgrid scale term. 25 refs., 17 figs., 1 tab

  10. Functional analysis of Rift Valley fever virus NSs encoding a partial truncation.

    Science.gov (United States)

    Head, Jennifer A; Kalveram, Birte; Ikegami, Tetsuro

    2012-01-01

    Rift Valley fever virus (RVFV), belongs to genus Phlebovirus of the family Bunyaviridae, causes high rates of abortion and fetal malformation in infected ruminants as well as causing neurological disorders, blindness, or lethal hemorrhagic fever in humans. RVFV is classified as a category A priority pathogen and a select agent in the U.S., and currently there are no therapeutics available for RVF patients. NSs protein, a major virulence factor of RVFV, inhibits host transcription including interferon (IFN)-β mRNA synthesis and promotes degradation of dsRNA-dependent protein kinase (PKR). NSs self-associates at the C-terminus 17 aa., while NSs at aa.210-230 binds to Sin3A-associated protein (SAP30) to inhibit the activation of IFN-β promoter. Thus, we hypothesize that NSs function(s) can be abolished by truncation of specific domains, and co-expression of nonfunctional NSs with intact NSs will result in the attenuation of NSs function by dominant-negative effect. Unexpectedly, we found that RVFV NSs truncated at aa. 6-30, 31-55, 56-80, 81-105, 106-130, 131-155, 156-180, 181-205, 206-230, 231-248 or 249-265 lack functions of IFN-β mRNA synthesis inhibition and degradation of PKR. Truncated NSs were less stable in infected cells, while nuclear localization was inhibited in NSs lacking either of aa.81-105, 106-130, 131-155, 156-180, 181-205, 206-230 or 231-248. Furthermore, none of truncated NSs had exhibited significant dominant-negative functions for NSs-mediated IFN-β suppression or PKR degradation upon co-expression in cells infected with RVFV. We also found that any of truncated NSs except for intact NSs does not interact with RVFV NSs even in the presence of intact C-terminus self-association domain. Our results suggest that conformational integrity of NSs is important for the stability, cellular localization and biological functions of RVFV NSs, and the co-expression of truncated NSs does not exhibit dominant-negative phenotype.

  11. Functional analysis of Rift Valley fever virus NSs encoding a partial truncation.

    Directory of Open Access Journals (Sweden)

    Jennifer A Head

    Full Text Available Rift Valley fever virus (RVFV, belongs to genus Phlebovirus of the family Bunyaviridae, causes high rates of abortion and fetal malformation in infected ruminants as well as causing neurological disorders, blindness, or lethal hemorrhagic fever in humans. RVFV is classified as a category A priority pathogen and a select agent in the U.S., and currently there are no therapeutics available for RVF patients. NSs protein, a major virulence factor of RVFV, inhibits host transcription including interferon (IFN-β mRNA synthesis and promotes degradation of dsRNA-dependent protein kinase (PKR. NSs self-associates at the C-terminus 17 aa., while NSs at aa.210-230 binds to Sin3A-associated protein (SAP30 to inhibit the activation of IFN-β promoter. Thus, we hypothesize that NSs function(s can be abolished by truncation of specific domains, and co-expression of nonfunctional NSs with intact NSs will result in the attenuation of NSs function by dominant-negative effect. Unexpectedly, we found that RVFV NSs truncated at aa. 6-30, 31-55, 56-80, 81-105, 106-130, 131-155, 156-180, 181-205, 206-230, 231-248 or 249-265 lack functions of IFN-β mRNA synthesis inhibition and degradation of PKR. Truncated NSs were less stable in infected cells, while nuclear localization was inhibited in NSs lacking either of aa.81-105, 106-130, 131-155, 156-180, 181-205, 206-230 or 231-248. Furthermore, none of truncated NSs had exhibited significant dominant-negative functions for NSs-mediated IFN-β suppression or PKR degradation upon co-expression in cells infected with RVFV. We also found that any of truncated NSs except for intact NSs does not interact with RVFV NSs even in the presence of intact C-terminus self-association domain. Our results suggest that conformational integrity of NSs is important for the stability, cellular localization and biological functions of RVFV NSs, and the co-expression of truncated NSs does not exhibit dominant-negative phenotype.

  12. Truncated Dual-Cap Nucleation Site Development

    Science.gov (United States)

    Matson, Douglas M.; Sander, Paul J.

    2012-01-01

    During heterogeneous nucleation within a metastable mushy-zone, several geometries for nucleation site development must be considered. Traditional spherical dual cap and crevice models are compared to a truncated dual cap to determine the activation energy and critical cluster growth kinetics in ternary Fe-Cr-Ni steel alloys. Results of activation energy results indicate that nucleation is more probable at grain boundaries within the solid than at the solid-liquid interface.

  13. Mixed Platoon Flow Dispersion Model Based on Speed-Truncated Gaussian Mixture Distribution

    Directory of Open Access Journals (Sweden)

    Weitiao Wu

    2013-01-01

    Full Text Available A mixed traffic flow feature is presented on urban arterials in China due to a large amount of buses. Based on field data, a macroscopic mixed platoon flow dispersion model (MPFDM was proposed to simulate the platoon dispersion process along the road section between two adjacent intersections from the flow view. More close to field observation, truncated Gaussian mixture distribution was adopted as the speed density distribution for mixed platoon. Expectation maximum (EM algorithm was used for parameters estimation. The relationship between the arriving flow distribution at downstream intersection and the departing flow distribution at upstream intersection was investigated using the proposed model. Comparison analysis using virtual flow data was performed between the Robertson model and the MPFDM. The results confirmed the validity of the proposed model.

  14. Symmetric truncations of the shallow-water equations

    International Nuclear Information System (INIS)

    Rouhi, A.; Abarbanel, H.D.I.

    1993-01-01

    Conservation of potential vorticity in Eulerian fluids reflects particle interchange symmetry in the Lagrangian fluid version of the same theory. The algebra associated with this symmetry in the shallow-water equations is studied here, and we give a method for truncating the degrees of freedom of the theory which preserves a maximal number of invariants associated with this algebra. The finite-dimensional symmetry associated with keeping only N modes of the shallow-water flow is SU(N). In the limit where the number of modes goes to infinity (N→∞) all the conservation laws connected with potential vorticity conservation are recovered. We also present a Hamiltonian which is invariant under this truncated symmetry and which reduces to the familiar shallow-water Hamiltonian when N→∞. All this provides a finite-dimensional framework for numerical work with the shallow-water equations which preserves not only energy and enstrophy but all other known conserved quantities consistent with the finite number of degrees of freedom. The extension of these ideas to other nearly two-dimensional flows is discussed

  15. Miniaturized printed K shaped monopole antenna with truncated ground plane for 2.4/5.2/5.5/5.8 wireless lan applications

    Science.gov (United States)

    Chandan, Bharti, Gagandeep; Srivastava, Toolika; Rai, B. S.

    2018-04-01

    A novel truncated ground plane monopole antenna is proposed for wide band wireless local area network (WLAN) applications. The antenna contains a rectangular patch with a rectangular ring, a circular slot and a truncated ground plane printed on opposite sides of a low cost substrate FR4. The operating frequency bands for the antenna are band1 (2.4-2.88 GHz) and band 2 (4.8-6.3 GHz) with ≤ - 10 dB return loss which covers 2.4/5.2/5.5/5.8 GHz WLAN bands. The antenna is compact with overall dimension 26×40×0.8 mmł and with the dimension of patch 16×16×0.8 mm3. The two bands of antenna is obtained by cutting a rectangular ring and a circular slot in the patch and return loss is improved by cutting two rectangular slot in the ground plane. Performance measures of the antenna are shown in terms of return loss, current distribution, radiation pattern and gain. To verify the simulated results, the antenna is also fabricated and tested. The simulated and fabricated results have been found in good agreement.

  16. Autocorrelation as a source of truncated Lévy flights in foreign exchange rates

    Science.gov (United States)

    Figueiredo, Annibal; Gleria, Iram; Matsushita, Raul; Da Silva, Sergio

    2003-05-01

    We suggest that the ultraslow speed of convergence associated with truncated Lévy flights (Phys. Rev. Lett. 73 (1994) 2946) may well be explained by autocorrelations in data. We show how a particular type of autocorrelation generates power laws consistent with a truncated Lévy flight. Stock exchanges have been suggested to be modeled by a truncated Lévy flight (Nature 376 (1995) 46; Physica A 297 (2001) 509; Econom. Bull. 7 (2002) 1). Here foreign exchange rate data are taken instead. Scaling power laws in the “probability of return to the origin” are shown to emerge for most currencies. A novel approach to measure how distant a process is from a Gaussian regime is presented.

  17. Genome mining and motif truncation of glycoside hydrolase family 5 endo-β-1,4-mannanase encoded by Aspergillus oryzae RIB40 for potential konjac flour hydrolysis or feed additive.

    Science.gov (United States)

    Tang, Cun-Duo; Shi, Hong-Ling; Tang, Qing-Hai; Zhou, Jun-Shi; Yao, Lun-Guang; Jiao, Zhu-Jin; Kan, Yun-Chao

    2016-11-01

    Two novel glycosyl hydrolase family 5 (GH5) β-mannanases (AoMan5A and AoMan5B) were identified from Aspergillus oryzae RIB40 by genome mining. The AoMan5A contains a predicted family 1 carbohydrate binding module (CBM-1), located at its N-terminal. The AoMan5A, AoMan5B and truncated mutant AoMan5AΔCL (truncating the N-terminal CBM and linker of AoMan5A) were expressed retaining the N-terminus of the native protein in Pichia pastoris GS115 by pPIC9K M . The specific enzyme activity of the purified reAoMan5A, reAoMan5B and reAoMan5AΔCL towards locust bean gum at pH 3.6 and 40°C for 10min, was 8.3, 104.2 and 15.8U/mg, respectively. The temperature properties of the reAoMan5AΔCL were improved by truncating CBM. They can degrade the pretreated konjac flour and produce prebiotics. In addition, they had excellent stability under simulative gastric fluid and simulative prilling process. All these properties make these recombinant β-mannanases potential additives for use in the food and feed industries. Copyright © 2016. Published by Elsevier Inc.

  18. Optical image-hiding method with false information disclosure based on the interference principle and partial-phase-truncation in the fractional Fourier domain

    International Nuclear Information System (INIS)

    Dai, Chaoqing; Wang, Xiaogang; Zhou, Guoquan; Chen, Junlang

    2014-01-01

    An image-hiding method based on the optical interference principle and partial-phase-truncation in the fractional Fourier domain is proposed. The primary image is converted into three phase-only masks (POMs) using an analytical algorithm involved partial-phase-truncation and a fast random pixel exchange process. A procedure of a fake silhouette for a decryption key is suggested to reinforce the encryption and give a hint of the position of the key. The fractional orders of FrFT effectively enhance the security of the system. In the decryption process, the POM with false information and the other two POMs are, respectively, placed in the input and fractional Fourier planes to recover the primary image. There are no unintended information disclosures and iterative computations involved in the proposed method. Simulation results are presented to verify the validity of the proposed approach. (letters)

  19. A Residual Approach for Balanced Truncation Model Reduction (BTMR of Compartmental Systems

    Directory of Open Access Journals (Sweden)

    William La Cruz

    2014-05-01

    Full Text Available This paper presents a residual approach of the square root balanced truncation algorithm for model order reduction of continuous, linear and time-invariante compartmental systems. Specifically, the new approach uses a residual method to approximate the controllability and observability gramians, whose resolution is an essential step of the square root balanced truncation algorithm, that requires a great computational cost. Numerical experiences are included to highlight the efficacy of the proposed approach.

  20. Rotating D0-branes and consistent truncations of supergravity

    International Nuclear Information System (INIS)

    Anabalón, Andrés; Ortiz, Thomas; Samtleben, Henning

    2013-01-01

    The fluctuations around the D0-brane near-horizon geometry are described by two-dimensional SO(9) gauged maximal supergravity. We work out the U(1) 4 truncation of this theory whose scalar sector consists of five dilaton and four axion fields. We construct the full non-linear Kaluza–Klein ansatz for the embedding of the dilaton sector into type IIA supergravity. This yields a consistent truncation around a geometry which is the warped product of a two-dimensional domain wall and the sphere S 8 . As an application, we consider the solutions corresponding to rotating D0-branes which in the near-horizon limit approach AdS 2 ×M 8 geometries, and discuss their thermodynamical properties. More generally, we study the appearance of such solutions in the presence of non-vanishing axion fields

  1. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

    NARCIS (Netherlands)

    Rivas, Manuel A.; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A. Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Soeren; Kurki, Mitja I.; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K.; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L. E.; Ananthakrishnan, Ashwin N.; Luo, Yang; Heap, Graham A.; Visschedijk, Marijn C.; MacArthur, Daniel G.; Neale, Benjamin M.; Ahmad, Tariq; Anderson, Carl A.; Brant, Steven R.; Duerr, Richard H.; Silverberg, Mark S.; Cho, Judy H.; Palotie, Aarno; Saavalainen, Paivi; Kontula, Kimmo; Farkkila, Martti; McGovern, Dermot P. B.; Franke, Andre; Stefansson, Kari; Rioux, John D.; Xavier, Ramnik J.; Daly, Mark J.

    Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants

  2. A min cut-set-wise truncation procedure for importance measures computation in probabilistic safety assessment

    Energy Technology Data Exchange (ETDEWEB)

    Duflot, Nicolas [Universite de technologie de Troyes, Institut Charles Delaunay/LM2S, FRE CNRS 2848, 12, rue Marie Curie, BP2060, F-10010 Troyes cedex (France)], E-mail: nicolas.duflot@areva.com; Berenguer, Christophe [Universite de technologie de Troyes, Institut Charles Delaunay/LM2S, FRE CNRS 2848, 12, rue Marie Curie, BP2060, F-10010 Troyes cedex (France)], E-mail: christophe.berenguer@utt.fr; Dieulle, Laurence [Universite de technologie de Troyes, Institut Charles Delaunay/LM2S, FRE CNRS 2848, 12, rue Marie Curie, BP2060, F-10010 Troyes cedex (France)], E-mail: laurence.dieulle@utt.fr; Vasseur, Dominique [EPSNA Group (Nuclear PSA and Application), EDF Research and Development, 1, avenue du Gal de Gaulle, 92141 Clamart cedex (France)], E-mail: dominique.vasseur@edf.fr

    2009-11-15

    A truncation process aims to determine among the set of minimal cut-sets (MCS) produced by a probabilistic safety assessment (PSA) model which of them are significant. Several truncation processes have been proposed for the evaluation of the probability of core damage ensuring a fixed accuracy level. However, the evaluation of new risk indicators as importance measures requires to re-examine the truncation process in order to ensure that the produced estimates will be accurate enough. In this paper a new truncation process is developed permitting to estimate from a single set of MCS the importance measure of any basic event with the desired accuracy level. The main contribution of this new method is to propose an MCS-wise truncation criterion involving two thresholds: an absolute threshold in addition to a new relative threshold concerning the potential probability of the MCS of interest. The method has been tested on a complete level 1 PSA model of a 900 MWe NPP developed by 'Electricite de France' (EDF) and the results presented in this paper indicate that to reach the same accuracy level the proposed method produces a set of MCS whose size is significantly reduced.

  3. A min cut-set-wise truncation procedure for importance measures computation in probabilistic safety assessment

    International Nuclear Information System (INIS)

    Duflot, Nicolas; Berenguer, Christophe; Dieulle, Laurence; Vasseur, Dominique

    2009-01-01

    A truncation process aims to determine among the set of minimal cut-sets (MCS) produced by a probabilistic safety assessment (PSA) model which of them are significant. Several truncation processes have been proposed for the evaluation of the probability of core damage ensuring a fixed accuracy level. However, the evaluation of new risk indicators as importance measures requires to re-examine the truncation process in order to ensure that the produced estimates will be accurate enough. In this paper a new truncation process is developed permitting to estimate from a single set of MCS the importance measure of any basic event with the desired accuracy level. The main contribution of this new method is to propose an MCS-wise truncation criterion involving two thresholds: an absolute threshold in addition to a new relative threshold concerning the potential probability of the MCS of interest. The method has been tested on a complete level 1 PSA model of a 900 MWe NPP developed by 'Electricite de France' (EDF) and the results presented in this paper indicate that to reach the same accuracy level the proposed method produces a set of MCS whose size is significantly reduced.

  4. Lymphoscintigraphy for sentinel lymph node detection in breast cancer: usefulness of image truncation

    International Nuclear Information System (INIS)

    Carrier, P.; Remp, H.J.; Chaborel, J.P.; Lallement, M.; Bussiere, F.; Darcourt, J.; Lallement, M.; Leblanc-Talent, P.; Machiavello, J.C.; Ettore, F.

    2004-01-01

    The sentinel lymph node (SNL) detection in breast cancer has been recently validated. It allows the reduction of the number of axillary dissections and their corresponding side effects. We tested a simple method of image truncation in order to improve the sensitivity of lymphoscintigraphy. This approach is justified by the magnitude of uptake difference between the injection site and the SNL. We prospectively investigated SNL detection using a triple method (lymphoscintigraphy, blue dye and surgical radio detection) in 130 patients. SNL was identified in 104 of the 132 patients (80%) using the standard images and in 126 of them (96, 9%) using the truncated images. Blue dye detection and surgical radio detection had a sensitivity of 76,9% and 98,5% respectively. The false negative rate was 10,3%. 288 SNL were dissected, 31 were metastatic. Among the 19 patients with metastatic SNL and more than one SNL detected, the metastatic SNL was not the hottest in 9 of them. 28 metastatic SNL were detected Y on truncated images versus only 19 on standard images. Truncation which dramatically increases the sensitivity of lymphoscintigraphy allows to increase the number of dissected SNL and probably reduces the false negative rate. (author)

  5. Compact circularly polarized truncated square ring slot antenna with suppressed higher resonances.

    Directory of Open Access Journals (Sweden)

    Mursyidul Idzam Sabran

    Full Text Available This paper presents a compact circularly polarized (CP antenna with an integrated higher order harmonic rejection filter. The proposed design operates within the ISM band of 2.32 GHz- 2.63 GHz and is suitable for example for wireless power transfer applications. Asymmetrical truncated edges on a square ring create a defected ground structure to excite the CP property, simultaneously realizing compactness. It offers a 50.5% reduced patch area compared to a conventional design. Novel stubs and slot shapes are integrated in the transmission line to reduce higher (up to the third order harmonics. The proposed prototype yields a -10 dB reflection coefficient (S11 impedance bandwidth of 12.53%, a 3 dB axial ratio bandwidth of 3.27%, and a gain of 5.64 dBi. Measurements also show good agreement with simulations.

  6. Truncated forms of viral VP2 proteins fused to EGFP assemble into fluorescent parvovirus-like particles

    Directory of Open Access Journals (Sweden)

    Vuento Matti

    2006-12-01

    Full Text Available Abstract Fluorescence correlation spectroscopy (FCS monitors random movements of fluorescent molecules in solution, giving information about the number and the size of for example nano-particles. The canine parvovirus VP2 structural protein as well as N-terminal deletion mutants of VP2 (-14, -23, and -40 amino acids were fused to the C-terminus of the enhanced green fluorescent protein (EGFP. The proteins were produced in insect cells, purified, and analyzed by western blotting, confocal and electron microscopy as well as FCS. The non-truncated form, EGFP-VP2, diffused with a hydrodynamic radius of 17 nm, whereas the fluorescent mutants truncated by 14, 23 and 40 amino acids showed hydrodynamic radii of 7, 20 and 14 nm, respectively. These results show that the non-truncated EGFP-VP2 fusion protein and the EGFP-VP2 constructs truncated by 23 and by as much as 40 amino acids were able to form virus-like particles (VLPs. The fluorescent VLP, harbouring VP2 truncated by 23 amino acids, showed a somewhat larger hydrodynamic radius compared to the non-truncated EGFP-VP2. In contrast, the construct containing EGFP-VP2 truncated by 14 amino acids was not able to assemble into VLP-resembling structures. Formation of capsid structures was confirmed by confocal and electron microscopy. The number of fluorescent fusion protein molecules present within the different VLPs was determined by FCS. In conclusion, FCS provides a novel strategy to analyze virus assembly and gives valuable structural information for strategic development of parvovirus-like particles.

  7. Fluorometric graphene oxide-based detection of Salmonella enteritis using a truncated DNA aptamer.

    Science.gov (United States)

    Chinnappan, Raja; AlAmer, Saleh; Eissa, Shimaa; Rahamn, Anas Abdel; Abu Salah, Khalid M; Zourob, Mohammed

    2017-12-18

    The work describes a fluorescence-based study for mapping the highest affinity truncated aptamer from the full length sequence and its integration in a graphene oxide platform for the detection of Salmonella enteriditis. To identify the best truncated sequence, molecular beacons and a displacement assay design are applied. In the fluorescence displacement assay, the truncated aptamer was hybridized with fluorescein and quencher-labeled complementary sequences to form a fluorescence/quencher pair. In the presence of S. enteritidis, the aptamer dissociates from the complementary labeled oligonucleotides and thus, the fluorescein/quencher pair becomes physically separated. This leads to an increase in fluorescence intensity. One of the truncated aptamers identified has a 2-fold lower dissociation constant (3.2 nM) compared to its full length aptamer (6.3 nM). The truncated aptamer selected in this process was used to develop a fluorometric graphene oxide (GO) based assay. If fluorescein-labeled aptamer is adsorbed on GO via π stacking interaction, fluorescence is quenched. However, in the presence of target (S. enteriditis), the labeled aptamers is released from surface to form a stable complex with the bacteria and fluorescence is restored, depending on the quantity of bacteria being present. The resulting assay has an unsurpassed detection limit of 25 cfu·mL -1 in the best case. The cross reactivity to Salmonella typhimurium, Staphylococcus aureus and Escherichia coli is negligible. The assay was applied to analyze doped milk samples for and gave good recovery. Thus, we believe that the truncated aptamer/graphene oxide platform is a potential tool for the detection of S. Enteritidis. Graphical abstract Fluorescently labelled aptamer against Salmonella enteritidis was adsorbed on the surface of graphene oxide by π-stacking interaction. This results in quenching of the fluorescence of the label. Addition of Salmonella enteritidis restores fluorescence, and this

  8. Error bounds for augmented truncations of discrete-time block-monotone Markov chains under subgeometric drift conditions

    OpenAIRE

    Masuyama, Hiroyuki

    2015-01-01

    This paper studies the last-column-block-augmented northwest-corner truncation (LC-block-augmented truncation, for short) of discrete-time block-monotone Markov chains under subgeometric drift conditions. The main result of this paper is to present an upper bound for the total variation distance between the stationary probability vectors of a block-monotone Markov chain and its LC-block-augmented truncation. The main result is extended to Markov chains that themselves may not be block monoton...

  9. Analytic Method for Pressure Recovery in Truncated Diffusers ...

    African Journals Online (AJOL)

    A prediction method is presented for the static pressure recovery in subsonic axisymmetric truncated conical diffusers. In the analysis, a turbulent boundary layer is assumed at the diffuser inlet and a potential core exists throughout the flow. When flow separation occurs, this approach cannot be used to predict the maximum ...

  10. Rotating D0-branes and consistent truncations of supergravity

    Energy Technology Data Exchange (ETDEWEB)

    Anabalón, Andrés [Departamento de Ciencias, Facultad de Artes Liberales, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Av. Padre Hurtado 750, Viña del Mar (Chile); Université de Lyon, Laboratoire de Physique, UMR 5672, CNRS École Normale Supérieure de Lyon 46, allée d' Italie, F-69364 Lyon cedex 07 (France); Ortiz, Thomas; Samtleben, Henning [Université de Lyon, Laboratoire de Physique, UMR 5672, CNRS École Normale Supérieure de Lyon 46, allée d' Italie, F-69364 Lyon cedex 07 (France)

    2013-12-18

    The fluctuations around the D0-brane near-horizon geometry are described by two-dimensional SO(9) gauged maximal supergravity. We work out the U(1){sup 4} truncation of this theory whose scalar sector consists of five dilaton and four axion fields. We construct the full non-linear Kaluza–Klein ansatz for the embedding of the dilaton sector into type IIA supergravity. This yields a consistent truncation around a geometry which is the warped product of a two-dimensional domain wall and the sphere S{sup 8}. As an application, we consider the solutions corresponding to rotating D0-branes which in the near-horizon limit approach AdS{sub 2}×M{sub 8} geometries, and discuss their thermodynamical properties. More generally, we study the appearance of such solutions in the presence of non-vanishing axion fields.

  11. Generation of truncated recombinant form of tumor necrosis factor ...

    African Journals Online (AJOL)

    7. Original Research Article. Generation of truncated recombinant form of tumor necrosis factor ... as 6×His tagged using E.coli BL21 (DE3) expression system. The protein was ... proapoptotic signaling cascade through TNFR1. [5] which is ...

  12. The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

    Science.gov (United States)

    Aviat, Félix; Lagardère, Louis; Piquemal, Jean-Philip

    2017-10-01

    In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

  13. Zlib: A numerical library for optimal design of truncated power series algebra and map parameterization routines

    International Nuclear Information System (INIS)

    Yan, Y.T.

    1996-11-01

    A brief review of the Zlib development is given. Emphasized is the Zlib nerve system which uses the One-Step Index Pointers (OSIPs) for efficient computation and flexible use of the Truncated Power Series Algebra (TPSA). Also emphasized is the treatment of parameterized maps with an object-oriented language (e.g. C++). A parameterized map can be a Vector Power Series (Vps) or a Lie generator represented by an exponent of a Truncated Power Series (Tps) of which each coefficient is an object of truncated power series

  14. Measuring a truncated disk in Aquila X-1

    DEFF Research Database (Denmark)

    King, Ashley L.; Tomsick, John A.; Miller, Jon M.

    2016-01-01

    We present NuSTAR and Swift observations of the neutron star Aquila X-1 during the peak of its 2014 July outburst. The spectrum is soft with strong evidence for a broad Fe Kα line. Modeled with a relativistically broadened reflection model, we find that the inner disk is truncated with an inner r...

  15. Causal analysis of ordinal treatments and binary outcomes under truncation by death.

    Science.gov (United States)

    Wang, Linbo; Richardson, Thomas S; Zhou, Xiao-Hua

    2017-06-01

    It is common that in multi-arm randomized trials, the outcome of interest is "truncated by death," meaning that it is only observed or well-defined conditioning on an intermediate outcome. In this case, in addition to pairwise contrasts, the joint inference for all treatment arms is also of interest. Under a monotonicity assumption we present methods for both pairwise and joint causal analyses of ordinal treatments and binary outcomes in presence of truncation by death. We illustrate via examples the appropriateness of our assumptions in different scientific contexts.

  16. Fusion events lead to truncation of FOS in epithelioid hemangioma of bone

    DEFF Research Database (Denmark)

    van IJzendoorn, David G P; de Jong, Danielle; Romagosa, Cleofe

    2015-01-01

    in exon 4 of the FOS gene and the fusion event led to the introduction of a stop codon. In all instances, the truncation of the FOS gene would result in the loss of the transactivation domain (TAD). Using FISH probes we found a break in the FOS gene in two additional cases, in none of these cases...... differential diagnosis of vascular tumors of bone. Our data suggest that the translocation causes truncation of the FOS protein, with loss of the TAD, which is thereby a novel mechanism involved in tumorigenesis....

  17. Truncatable bootstrap equations in algebraic form and critical surface exponents

    Energy Technology Data Exchange (ETDEWEB)

    Gliozzi, Ferdinando [Dipartimento di Fisica, Università di Torino andIstituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1, Torino, I-10125 (Italy)

    2016-10-10

    We describe examples of drastic truncations of conformal bootstrap equations encoding much more information than that obtained by a direct numerical approach. A three-term truncation of the four point function of a free scalar in any space dimensions provides algebraic identities among conformal block derivatives which generate the exact spectrum of the infinitely many primary operators contributing to it. In boundary conformal field theories, we point out that the appearance of free parameters in the solutions of bootstrap equations is not an artifact of truncations, rather it reflects a physical property of permeable conformal interfaces which are described by the same equations. Surface transitions correspond to isolated points in the parameter space. We are able to locate them in the case of 3d Ising model, thanks to a useful algebraic form of 3d boundary bootstrap equations. It turns out that the low-lying spectra of the surface operators in the ordinary and the special transitions of 3d Ising model form two different solutions of the same polynomial equation. Their interplay yields an estimate of the surface renormalization group exponents, y{sub h}=0.72558(18) for the ordinary universality class and y{sub h}=1.646(2) for the special universality class, which compare well with the most recent Monte Carlo calculations. Estimates of other surface exponents as well as OPE coefficients are also obtained.

  18. A SUZAKU OBSERVATION OF NGC 4593: ILLUMINATING THE TRUNCATED DISK

    International Nuclear Information System (INIS)

    Markowitz, A. G.; Reeves, J. N.

    2009-01-01

    We report results from a 2007 Suzaku observation of the Seyfert 1 AGN NGC 4593. The narrow Fe Kα emission line has a FWHM width ∼ 4000 km s -1 , indicating emission from ∼> 5000 R g . There is no evidence for a relativistically broadened Fe K line, consistent with the presence of a radiatively efficient outer disk which is truncated or transitions to an interior radiatively inefficient flow. The Suzaku observation caught the source in a low-flux state; comparison to a 2002 XMM-Newton observation indicates that the hard X-ray flux decreased by 3.6, while the Fe Kα line intensity and width σ each roughly halved. Two model-dependent explanations for the changes in Fe Kα line profile are explored. In one, the Fe Kα line width has decreased from ∼10,000 to ∼4000 km s -1 from 2002 to 2007, suggesting that the thin disk truncation/transition radius has increased from 1000-2000 to ∼>5000 R g . However, there are indications from other compact accreting systems that such truncation radii tend to be associated only with accretion rates relative to Eddington much lower than that of NGC 4593. In the second model, the line profile in the XMM-Newton observation consists of a time-invariant narrow component plus a broad component originating from the inner part of the truncated disk (∼300 R g ) which has responded to the drop in continuum flux. The Compton reflection component strength R is ∼ 1.1, consistent with the measured Fe Kα line total equivalent width with an Fe abundance 1.7 times the solar value. The modest soft excess, modeled well by either thermal bremsstrahlung emission or by Comptonization of soft seed photons in an optical thin plasma, has fallen by a factor of ∼20 from 2002 to 2007, ruling out emission from a region 5 lt-yr in size.

  19. Observation of the dispersion of wedge waves propagating along cylinder wedge with different truncations by laser ultrasound technique

    Science.gov (United States)

    Jia, Jing; Zhang, Yu; Han, Qingbang; Jing, Xueping

    2017-10-01

    The research focuses on study the influence of truncations on the dispersion of wedge waves propagating along cylinder wedge with different truncations by using the laser ultrasound technique. The wedge waveguide models with different truncations were built by using finite element method (FEM). The dispersion curves were obtained by using 2D Fourier transformation method. Multiple mode wedge waves were observed, which was well agreed with the results estimated from Lagasse's empirical formula. We established cylinder wedge with radius of 3mm, 20° and 60°angle, with 0μm, 5μm, 10μm, 20μm, 30μm, 40μm, and 50μm truncations, respectively. It was found that non-ideal wedge tip caused abnormal dispersion of the mode of cylinder wedge, the modes of 20° cylinder wedge presents the characteristics of guide waves which propagating along hollow cylinder as the truncation increasing. Meanwhile, the modes of 60° cylinder wedge with truncations appears the characteristics of guide waves propagating along hollow cylinder, and its mode are observed clearly. The study can be used to evaluate and detect wedge structure.

  20. Truncation artifact suppression in cone-beam radionuclide transmission CT using maximum likelihood techniques: evaluation with human subjects

    International Nuclear Information System (INIS)

    Manglos, S.H.

    1992-01-01

    Transverse image truncation can be a serious problem for human imaging using cone-beam transmission CT (CB-CT) implemented on a conventional rotating gamma camera. This paper presents a reconstruction method to reduce or eliminate the artifacts resulting from the truncation. The method uses a previously published transmission maximum likelihood EM algorithm, adapted to the cone-beam geometry. The reconstruction method is evaluated qualitatively using three human subjects of various dimensions and various degrees of truncation. (author)

  1. On the Truncated Pareto Distribution with applications

    OpenAIRE

    Zaninetti, Lorenzo; Ferraro, Mario

    2008-01-01

    The Pareto probability distribution is widely applied in different fields such us finance, physics, hydrology, geology and astronomy. This note deals with an application of the Pareto distribution to astrophysics and more precisely to the statistical analysis of mass of stars and of diameters of asteroids. In particular a comparison between the usual Pareto distribution and its truncated version is presented. Finally a possible physical mechanism that produces Pareto tails for the distributio...

  2. On the propagation of truncated localized waves in dispersive silica

    KAUST Repository

    Salem, Mohamed; Bagci, Hakan

    2010-01-01

    Propagation characteristics of truncated Localized Waves propagating in dispersive silica and free space are numerically analyzed. It is shown that those characteristics are affected by the changes in the relation between the transverse spatial

  3. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

    Science.gov (United States)

    Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter; Rüber, Lukas

    2018-01-01

    Abstract The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development. PMID:29684203

  4. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.

    Science.gov (United States)

    Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter; Rüber, Lukas

    2018-04-01

    The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

  5. Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans.

    Directory of Open Access Journals (Sweden)

    Ganesh Ambigapathy

    Full Text Available Brain-derived neurotrophic factor (BDNF has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.

  6. Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans.

    Science.gov (United States)

    Ambigapathy, Ganesh; Zheng, Zhaoqing; Li, Wei; Keifer, Joyce

    2013-01-01

    Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF) are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.

  7. Theoretical analysis of balanced truncation for linear switched systems

    DEFF Research Database (Denmark)

    Petreczky, Mihaly; Wisniewski, Rafal; Leth, John-Josef

    2012-01-01

    In this paper we present theoretical analysis of model reduction of linear switched systems based on balanced truncation, presented in [1,2]. More precisely, (1) we provide a bound on the estimation error using L2 gain, (2) we provide a system theoretic interpretation of grammians and their singu......In this paper we present theoretical analysis of model reduction of linear switched systems based on balanced truncation, presented in [1,2]. More precisely, (1) we provide a bound on the estimation error using L2 gain, (2) we provide a system theoretic interpretation of grammians...... for showing this independence is realization theory of linear switched systems. [1] H. R. Shaker and R. Wisniewski, "Generalized gramian framework for model/controller order reduction of switched systems", International Journal of Systems Science, Vol. 42, Issue 8, 2011, 1277-1291. [2] H. R. Shaker and R....... Wisniewski, "Switched Systems Reduction Framework Based on Convex Combination of Generalized Gramians", Journal of Control Science and Engineering, 2009....

  8. Propagation of coherently combined truncated laser beam arrays with beam distortions in non-Kolmogorov turbulence.

    Science.gov (United States)

    Tao, Rumao; Si, Lei; Ma, Yanxing; Zhou, Pu; Liu, Zejin

    2012-08-10

    The propagation properties of coherently combined truncated laser beam arrays with beam distortions through non-Kolmogorov turbulence are studied in detail both analytically and numerically. The analytical expressions for the average intensity and the beam width of coherently combined truncated laser beam arrays with beam distortions propagating through turbulence are derived based on the combination of statistical optics methods and the extended Huygens-Fresnel principle. The effect of beam distortions, such as amplitude modulation and phase fluctuation, is studied by numerical examples. The numerical results reveal that phase fluctuations have significant influence on the spreading of coherently combined truncated laser beam arrays in non-Kolmogorov turbulence, and the effects of the phase fluctuations can be negligible as long as the phase fluctuations are controlled under a certain level, i.e., a>0.05 for the situation considered in the paper. Furthermore, large phase fluctuations can convert the beam distribution rapidly to a Gaussian form, vary the spreading, weaken the optimum truncation effects, and suppress the dependence of spreading on the parameters of the non-Kolmogorov turbulence.

  9. Solving Schwinger-Dyson equations by truncation in zero-dimensional scalar quantum field theory

    International Nuclear Information System (INIS)

    Okopinska, A.

    1991-01-01

    Three sets of Schwinger-Dyson equations, for all Green's functions, for connected Green's functions, and for proper vertices, are considered in scalar quantum field theory. A truncation scheme applied to the three sets gives three different approximation series for Green's functions. For the theory in zero-dimensional space-time the results for respective two-point Green's functions are compared with the exact value calculated numerically. The best convergence of the truncation scheme is obtained for the case of proper vertices

  10. Fitting Social Network Models Using Varying Truncation Stochastic Approximation MCMC Algorithm

    KAUST Repository

    Jin, Ick Hoon

    2013-10-01

    The exponential random graph model (ERGM) plays a major role in social network analysis. However, parameter estimation for the ERGM is a hard problem due to the intractability of its normalizing constant and the model degeneracy. The existing algorithms, such as Monte Carlo maximum likelihood estimation (MCMLE) and stochastic approximation, often fail for this problem in the presence of model degeneracy. In this article, we introduce the varying truncation stochastic approximation Markov chain Monte Carlo (SAMCMC) algorithm to tackle this problem. The varying truncation mechanism enables the algorithm to choose an appropriate starting point and an appropriate gain factor sequence, and thus to produce a reasonable parameter estimate for the ERGM even in the presence of model degeneracy. The numerical results indicate that the varying truncation SAMCMC algorithm can significantly outperform the MCMLE and stochastic approximation algorithms: for degenerate ERGMs, MCMLE and stochastic approximation often fail to produce any reasonable parameter estimates, while SAMCMC can do; for nondegenerate ERGMs, SAMCMC can work as well as or better than MCMLE and stochastic approximation. The data and source codes used for this article are available online as supplementary materials. © 2013 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.

  11. Reduction of Truncation Errors in Planar Near-Field Aperture Antenna Measurements Using the Gerchberg-Papoulis Algorithm

    DEFF Research Database (Denmark)

    Martini, Enrica; Breinbjerg, Olav; Maci, Stefano

    2008-01-01

    A simple and effective procedure for the reduction of truncation errors in planar near-field measurements of aperture antennas is presented. The procedure relies on the consideration that, due to the scan plane truncation, the calculated plane wave spectrum of the field radiated by the antenna is...

  12. Surface self-diffusion of adatom on Pt cluster with truncated octahedron structure

    International Nuclear Information System (INIS)

    Yang Jianyu; Hu Wangyu; Chen Shuguang

    2010-01-01

    Surface diffusion of single Pt adatom on Pt cluster with truncated octahedron structure is investigated through a combination of molecular dynamics and nudged elastic band method. Using an embedded atom method to describe the atomic interactions, the minimum energy paths are determined and the energy barriers for adatom diffusion across and along step are evaluated. The diffusion of adatom crossing step edge between {111} and {100} facets has a surprisingly low barrier of 0.03 eV, which is 0.12 eV lower than the barrier for adatom diffusion from {111} to neighboring {111} facet. Owing to the small barrier of adatom diffusion across the step edge between {111} and {100} facets, the diffusion of adatom along the step edge cannot occur. The molecular dynamics simulations at low temperatures also support these results. Our results show that mass transport will prefer step with {100} microfacet and the Pt clusters can have only {111} facets in epitaxial growth.

  13. Optimal auxiliary Hamiltonians for truncated boson-space calculations by means of a maximal-decoupling variational principle

    International Nuclear Information System (INIS)

    Li, C.

    1991-01-01

    A new method based on a maximal-decoupling variational principle is proposed to treat the Pauli-principle constraints for calculations of nuclear collective motion in a truncated boson space. The viability of the method is demonstrated through an application to the multipole form of boson Hamiltonians for the single-j and nondegenerate multi-j pairing interactions. While these boson Hamiltonians are Hermitian and contain only one- and two-boson terms, they are also the worst case for truncated boson-space calculations because they are not amenable to any boson truncations at all. By using auxiliary Hamiltonians optimally determined by the maximal-decoupling variational principle, however, truncations in the boson space become feasible and even yield reasonably accurate results. The method proposed here may thus be useful for doing realistic calculations of nuclear collective motion as well as for obtaining a viable interacting-boson-model type of boson Hamiltonian from the shell model

  14. Learning Mixtures of Truncated Basis Functions from Data

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre; Pérez-Bernabé, Inmaculada

    2014-01-01

    In this paper we investigate methods for learning hybrid Bayesian networks from data. First we utilize a kernel density estimate of the data in order to translate the data into a mixture of truncated basis functions (MoTBF) representation using a convex optimization technique. When utilizing a ke...... propose an alternative learning method that relies on the cumulative distribution function of the data. Empirical results demonstrate the usefulness of the approaches: Even though the methods produce estimators that are slightly poorer than the state of the art (in terms of log......In this paper we investigate methods for learning hybrid Bayesian networks from data. First we utilize a kernel density estimate of the data in order to translate the data into a mixture of truncated basis functions (MoTBF) representation using a convex optimization technique. When utilizing......-likelihood), they are significantly faster, and therefore indicate that the MoTBF framework can be used for inference and learning in reasonably sized domains. Furthermore, we show how a particular sub- class of MoTBF potentials (learnable by the proposed methods) can be exploited to significantly reduce complexity during inference....

  15. Determination of αS from scaling violations of truncated moments of structure functions

    International Nuclear Information System (INIS)

    Forte, Stefano; Latorre, J.I.; Magnea, Lorenzo; Piccione, Andrea

    2002-01-01

    We determine the strong coupling α S (M Z ) from scaling violations of truncated moments of the nonsinglet deep inelastic structure function F 2 . Truncated moments are determined from BCDMS and NMC data using a neural network parametrization which retains the full experimental information on errors and correlations. Our method minimizes all sources of theoretical uncertainty and bias which characterize extractions of α S from scaling violations. We obtain α S (M Z )=0.124 +0.004 -0.007 (exp.) +0.003 -0.004 (th.)

  16. Scavenger receptor AI/II truncation, lung function and COPD

    DEFF Research Database (Denmark)

    Thomsen, M; Nordestgaard, B G; Tybjaerg-Hansen, A

    2011-01-01

    The scavenger receptor A-I/II (SRA-I/II) on alveolar macrophages is involved in recognition and clearance of modified lipids and inhaled particulates. A rare variant of the SRA-I/II gene, Arg293X, truncates the distal collagen-like domain, which is essential for ligand recognition. We tested whet...

  17. Truncated RAP-MUSIC (TRAP-MUSIC) for MEG and EEG source localization.

    Science.gov (United States)

    Mäkelä, Niko; Stenroos, Matti; Sarvas, Jukka; Ilmoniemi, Risto J

    2018-02-15

    Electrically active brain regions can be located applying MUltiple SIgnal Classification (MUSIC) on magneto- or electroencephalographic (MEG; EEG) data. We introduce a new MUSIC method, called truncated recursively-applied-and-projected MUSIC (TRAP-MUSIC). It corrects a hidden deficiency of the conventional RAP-MUSIC algorithm, which prevents estimation of the true number of brain-signal sources accurately. The correction is done by applying a sequential dimension reduction to the signal-subspace projection. We show that TRAP-MUSIC significantly improves the performance of MUSIC-type localization; in particular, it successfully and robustly locates active brain regions and estimates their number. We compare TRAP-MUSIC and RAP-MUSIC in simulations with varying key parameters, e.g., signal-to-noise ratio, correlation between source time-courses, and initial estimate for the dimension of the signal space. In addition, we validate TRAP-MUSIC with measured MEG data. We suggest that with the proposed TRAP-MUSIC method, MUSIC-type localization could become more reliable and suitable for various online and offline MEG and EEG applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Linear and Quadratic Interpolators Using Truncated-Matrix Multipliers and Squarers

    Directory of Open Access Journals (Sweden)

    E. George Walters III

    2015-11-01

    Full Text Available This paper presents a technique for designing linear and quadratic interpolators for function approximation using truncated multipliers and squarers. Initial coefficient values are found using a Chebyshev-series approximation and then adjusted through exhaustive simulation to minimize the maximum absolute error of the interpolator output. This technique is suitable for any function and any precision up to 24 bits (IEEE single precision. Designs for linear and quadratic interpolators that implement the 1/x, 1/ √ x, log2(1+2x, log2(x and 2x functions are presented and analyzed as examples. Results show that a proposed 24-bit interpolator computing 1/x with a design specification of ±1 unit in the last place of the product (ulp error uses 16.4% less area and 15.3% less power than a comparable standard interpolator with the same error specification. Sixteen-bit linear interpolators for other functions are shown to use up to 17.3% less area and 12.1% less power, and 16-bit quadratic interpolators are shown to use up to 25.8% less area and 24.7% less power.

  19. Performance Comparison of Assorted Color Spaces for Multilevel Block Truncation Coding based Face Recognition

    OpenAIRE

    H.B. Kekre; Sudeep Thepade; Karan Dhamejani; Sanchit Khandelwal; Adnan Azmi

    2012-01-01

    The paper presents a performance analysis of Multilevel Block Truncation Coding based Face Recognition among widely used color spaces. In [1], Multilevel Block Truncation Coding was applied on the RGB color space up to four levels for face recognition. Better results were obtained when the proposed technique was implemented using Kekre’s LUV (K’LUV) color space [25]. This was the motivation to test the proposed technique using assorted color spaces. For experimental analysis, two face databas...

  20. The evidence for synthesis of truncated triangular silver nanoplates in the presence of CTAB

    International Nuclear Information System (INIS)

    He Xin; Zhao Xiujian; Chen Yunxia; Feng Jinyang

    2008-01-01

    Truncated triangular silver nanoplates were prepared by a solution-phase approach, which involved the seed-mediated growth of silver nanoparticles in the presence of cetyltrimethylammonium bromide (CTAB) at 40 deg. C. The result of X-ray diffraction indicates that the as-prepared nanoparticles are made of pure face centered cubic silver. Transmission electron microscopy and atomic force microscopy studies show that the truncated triangular silver nanoplates, with edge lengths of 50 ± 5 nm and thicknesses of 27 ± 3 nm, are oriented differently on substrates of a copper grid and a fresh mica flake. The corners of these nanoplates are round. The selected area electron diffraction analysis reveals that the silver nanoplates are single crystals with an atomically flat surface. We determine the holistic morphology of truncated triangular silver nanoplates through the above measurements with the aid of computer-aided 3D perspective images

  1. Dual scan CT image recovery from truncated projections

    Science.gov (United States)

    Sarkar, Shubhabrata; Wahi, Pankaj; Munshi, Prabhat

    2017-12-01

    There are computerized tomography (CT) scanners available commercially for imaging small objects and they are often categorized as mini-CT X-ray machines. One major limitation of these machines is their inability to scan large objects with good image quality because of the truncation of projection data. An algorithm is proposed in this work which enables such machines to scan large objects while maintaining the quality of the recovered image.

  2. Tau truncation is a productive posttranslational modification of neurofibrillary degeneration in Alzheimer's disease.

    Science.gov (United States)

    Kovacech, B; Novak, M

    2010-12-01

    Deposits of the misfolded neuronal protein tau are major hallmarks of neurodegeneration in Alzheimer's disease (AD) and other tauopathies. The etiology of the transformation process of the intrinsically disordered soluble protein tau into the insoluble misordered aggregate has attracted much attention. Tau undergoes multiple modifications in AD, most notably hyperphosphorylation and truncation. Hyperphosphorylation is widely regarded as the hottest candidate for the inducer of the neurofibrillary pathology. However, the true nature of the impetus that initiates the whole process in the human brains remains unknown. In AD, several site-specific tau cleavages were identified and became connected to the progression of the disease. In addition, western blot analyses of tau species in AD brains reveal multitudes of various truncated forms. In this review we summarize evidence showing that tau truncation alone is sufficient to induce the complete cascade of neurofibrillary pathology, including hyperphosphorylation and accumulation of misfolded insoluble forms of tau. Therefore, proteolytical abnormalities in the stressed neurons and production of aberrant tau cleavage products deserve closer attention and should be considered as early therapeutic targets for Alzheimer's disease.

  3. An implicit turbulence model for low-Mach Roe scheme using truncated Navier-Stokes equations

    Science.gov (United States)

    Li, Chung-Gang; Tsubokura, Makoto

    2017-09-01

    The original Roe scheme is well-known to be unsuitable in simulations of turbulence because the dissipation that develops is unsatisfactory. Simulations of turbulent channel flow for Reτ = 180 show that, with the 'low-Mach-fix for Roe' (LMRoe) proposed by Rieper [J. Comput. Phys. 230 (2011) 5263-5287], the Roe dissipation term potentially equates the simulation to an implicit large eddy simulation (ILES) at low Mach number. Thus inspired, a new implicit turbulence model for low Mach numbers is proposed that controls the Roe dissipation term appropriately. Referred to as the automatic dissipation adjustment (ADA) model, the method of solution follows procedures developed previously for the truncated Navier-Stokes (TNS) equations and, without tuning of parameters, uses the energy ratio as a criterion to automatically adjust the upwind dissipation. Turbulent channel flow at two different Reynold numbers and the Taylor-Green vortex were performed to validate the ADA model. In simulations of turbulent channel flow for Reτ = 180 at Mach number of 0.05 using the ADA model, the mean velocity and turbulence intensities are in excellent agreement with DNS results. With Reτ = 950 at Mach number of 0.1, the result is also consistent with DNS results, indicating that the ADA model is also reliable at higher Reynolds numbers. In simulations of the Taylor-Green vortex at Re = 3000, the kinetic energy is consistent with the power law of decaying turbulence with -1.2 exponents for both LMRoe with and without the ADA model. However, with the ADA model, the dissipation rate can be significantly improved near the dissipation peak region and the peak duration can be also more accurately captured. With a firm basis in TNS theory, applicability at higher Reynolds number, and ease in implementation as no extra terms are needed, the ADA model offers to become a promising tool for turbulence modeling.

  4. Parameter Estimation and Model Selection for Mixtures of Truncated Exponentials

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

    2010-01-01

    Bayesian networks with mixtures of truncated exponentials (MTEs) support efficient inference algorithms and provide a flexible way of modeling hybrid domains (domains containing both discrete and continuous variables). On the other hand, estimating an MTE from data has turned out to be a difficul...

  5. Amplitude of Light Scattering by a Truncated Pyramid and Cone in the Rayleigh-Gans-Debye Approximation

    Directory of Open Access Journals (Sweden)

    Konstantin A. Shapovalov

    2013-01-01

    Full Text Available The article considers general approach to structured particle and particle system form factor calculation in the Rayleigh-Gans-Debye (RGD approximation. Using this approach, amplitude of light scattering by a truncated pyramid and cone formulas in RGD approximation are obtained. Light scattering indicator by a truncated pyramid and cone in the RGD approximation are calculated.

  6. Protoplanetary disc truncation mechanisms in stellar clusters: comparing external photoevaporation and tidal encounters

    Science.gov (United States)

    Winter, A. J.; Clarke, C. J.; Rosotti, G.; Ih, J.; Facchini, S.; Haworth, T. J.

    2018-04-01

    Most stars form and spend their early life in regions of enhanced stellar density. Therefore the evolution of protoplanetary discs (PPDs) hosted by such stars are subject to the influence of other members of the cluster. Physically, PPDs might be truncated either by photoevaporation due to ultraviolet flux from massive stars, or tidal truncation due to close stellar encounters. Here we aim to compare the two effects in real cluster environments. In this vein we first review the properties of well studied stellar clusters with a focus on stellar number density, which largely dictates the degree of tidal truncation, and far ultraviolet (FUV) flux, which is indicative of the rate of external photoevaporation. We then review the theoretical PPD truncation radius due to an arbitrary encounter, additionally taking into account the role of eccentric encounters that play a role in hot clusters with a 1D velocity dispersion σv ≳ 2 km/s. Our treatment is then applied statistically to varying local environments to establish a canonical threshold for the local stellar density (nc ≳ 104 pc-3) for which encounters can play a significant role in shaping the distribution of PPD radii over a timescale ˜3 Myr. By combining theoretical mass loss rates due to FUV flux with viscous spreading in a PPD we establish a similar threshold for which a massive disc is completely destroyed by external photoevaporation. Comparing these thresholds in local clusters we find that if either mechanism has a significant impact on the PPD population then photoevaporation is always the dominating influence.

  7. Five-dimensional truncation of the plane incompressible navier-stokes equations

    Energy Technology Data Exchange (ETDEWEB)

    Boldrighini, C [Camerino Univ. (Italy). Istituto di Matematica; Franceschini, V [Modena Univ. (Italy). Istituto Matematico

    1979-01-01

    A five-modes truncation of the Navier-Stokes equations for a two dimensional incompressible fluid on a torus is considered. A computer analysis shows that for a certain range of the Reynolds number the system exhibits a stochastic behaviour, approached through an involved sequence of bifurcations.

  8. Hyperbolic Cross Truncations for Stochastic Fourier Cosine Series

    Science.gov (United States)

    Zhang, Zhihua

    2014-01-01

    Based on our decomposition of stochastic processes and our asymptotic representations of Fourier cosine coefficients, we deduce an asymptotic formula of approximation errors of hyperbolic cross truncations for bivariate stochastic Fourier cosine series. Moreover we propose a kind of Fourier cosine expansions with polynomials factors such that the corresponding Fourier cosine coefficients decay very fast. Although our research is in the setting of stochastic processes, our results are also new for deterministic functions. PMID:25147842

  9. Trapping of low-mass planets outside the truncated inner edges of protoplanetary discs

    Science.gov (United States)

    Miranda, Ryan; Lai, Dong

    2018-02-01

    We investigate the migration of a low-mass (≲10 M⊕) planet near the inner edge of a protoplanetary disc using two-dimensional viscous hydrodynamics simulations. We employ an inner boundary condition representing the truncation of the disc at the stellar corotation radius. As described by Tsang, wave reflection at the inner disc boundary modifies the Type I migration torque on the planet, allowing migration to be halted before the planet reaches the inner edge of the disc. For low-viscosity discs (α ≲ 10-3), planets may be trapped with semi-major axes as large as three to five times the inner disc radius. In general, planets are trapped closer to the inner edge as either the planet mass or the disc viscosity parameter α increases, and farther from the inner edge as the disc thickness is increased. This planet trapping mechanism may impact the formation and migration history of close-in compact multiplanet systems.

  10. The Truncated Lognormal Distribution as a Luminosity Function for SWIFT-BAT Gamma-Ray Bursts

    Directory of Open Access Journals (Sweden)

    Lorenzo Zaninetti

    2016-11-01

    Full Text Available The determination of the luminosity function (LF in Gamma ray bursts (GRBs depends on the adopted cosmology, each one characterized by its corresponding luminosity distance. Here, we analyze three cosmologies: the standard cosmology, the plasma cosmology and the pseudo-Euclidean universe. The LF of the GRBs is firstly modeled by the lognormal distribution and the four broken power law and, secondly, by a truncated lognormal distribution. The truncated lognormal distribution fits acceptably the range in luminosity of GRBs as a function of the redshift.

  11. Coupled high fidelity thermal hydraulics and neutronics for reactor safety simulations

    International Nuclear Information System (INIS)

    Vincent A. Mousseau; Hongbin Zhang; Haihua Zhao

    2008-01-01

    This work is a continuation of previous work on the importance of accuracy in the simulation of nuclear reactor safety transients. This work is qualitative in nature and future work will be more quantitative. The focus of this work will be on a simplified single phase nuclear reactor primary. The transient of interest investigates the importance of accuracy related to passive (inherent) safety systems. The transient run here will be an Unprotected Loss of Flow (ULOF) transient. Here the coolant pump is turned off and the un-SCRAM-ed reactor transitions from forced to free convection (Natural circulation). Results will be presented that show the difference that the first order in time truncation physics makes on the transient. The purpose of this document is to illuminate a possible problem in traditional reactor simulation approaches. Detailed studies need to be done on each simulation code for each transient analyzed to determine if the first order truncation physics plays an important role

  12. Generation of truncated recombinant form of tumor necrosis factor ...

    African Journals Online (AJOL)

    Purpose: To produce truncated recombinant form of tumor necrosis factor receptor 1 (TNFR1), cysteine-rich domain 2 (CRD2) and CRD3 regions of the receptor were generated using pET28a and E. coli/BL21. Methods: DNA coding sequence of CRD2 and CRD3 was cloned into pET28a vector and the corresponding ...

  13. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  14. The Extended Erlang-Truncated Exponential distribution: Properties and application to rainfall data.

    Science.gov (United States)

    Okorie, I E; Akpanta, A C; Ohakwe, J; Chikezie, D C

    2017-06-01

    The Erlang-Truncated Exponential ETE distribution is modified and the new lifetime distribution is called the Extended Erlang-Truncated Exponential EETE distribution. Some statistical and reliability properties of the new distribution are given and the method of maximum likelihood estimate was proposed for estimating the model parameters. The usefulness and flexibility of the EETE distribution was illustrated with an uncensored data set and its fit was compared with that of the ETE and three other three-parameter distributions. Results based on the minimized log-likelihood ([Formula: see text]), Akaike information criterion (AIC), Bayesian information criterion (BIC) and the generalized Cramér-von Mises [Formula: see text] statistics shows that the EETE distribution provides a more reasonable fit than the one based on the other competing distributions.

  15. Truncation effects in the functional renormalization group study of spontaneous symmetry breaking

    International Nuclear Information System (INIS)

    Defenu, N.; Mati, P.; Márián, I.G.; Nándori, I.; Trombettoni, A.

    2015-01-01

    We study the occurrence of spontaneous symmetry breaking (SSB) for O(N) models using functional renormalization group techniques. We show that even the local potential approximation (LPA) when treated exactly is sufficient to give qualitatively correct results for systems with continuous symmetry, in agreement with the Mermin-Wagner theorem and its extension to systems with fractional dimensions. For general N (including the Ising model N=1) we study the solutions of the LPA equations for various truncations around the zero field using a finite number of terms (and different regulators), showing that SSB always occurs even where it should not. The SSB is signalled by Wilson-Fisher fixed points which for any truncation are shown to stay on the line defined by vanishing mass beta functions.

  16. Firewalls as artefacts of inconsistent truncations of quantum geometries

    Science.gov (United States)

    Germani, Cristiano; Sarkar, Debajyoti

    2016-01-01

    In this paper we argue that a firewall is simply a manifestation of an inconsistent truncation of non-perturbative effects that unitarize the semiclassical black hole. Namely, we show that a naive truncation of quantum corrections to the Hawking spectrum at order ${\\cal O}(e^{-S})$, inexorably leads to a "localised'' divergent energy density near the black hole horizon. Nevertheless, in the same approximation, a distant observer only sees a discretised spectrum and concludes that unitarity is achieved by ${\\cal O}(e^{-S})$ effects. This is due to the fact that instead, the correct quantum corrections to the Hawking spectrum go like ${\\cal O}( g^{tt} e^{-S})$. Therefore, while at a distance far away from the horizon, where $g^{tt}\\approx 1$, quantum corrections {\\it are} perturbative, they {\\it do} diverge close to the horizon, where $g^{tt}\\rightarrow \\infty$. Nevertheless, these "corrections" nicely re-sum so that correlations functions are smooth at the would-be black hole horizon. Thus, we conclude that the appearance of firewalls is just a signal of the breaking of the semiclassical approximation at the Page time, even for large black holes.

  17. A Novel SCCA Approach via Truncated ℓ1-norm and Truncated Group Lasso for Brain Imaging Genetics.

    Science.gov (United States)

    Du, Lei; Liu, Kefei; Zhang, Tuo; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Han, Junwei; Guo, Lei; Saykin, Andrew J; Shen, Li

    2017-09-18

    Brain imaging genetics, which studies the linkage between genetic variations and structural or functional measures of the human brain, has become increasingly important in recent years. Discovering the bi-multivariate relationship between genetic markers such as single-nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is one major task in imaging genetics. Sparse Canonical Correlation Analysis (SCCA) has been a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ 1 -norm or its variants to induce sparsity. The ℓ 0 -norm penalty is a perfect sparsity-inducing tool which, however, is an NP-hard problem. In this paper, we propose the truncated ℓ 1 -norm penalized SCCA to improve the performance and effectiveness of the ℓ 1 -norm based SCCA methods. Besides, we propose an efficient optimization algorithms to solve this novel SCCA problem. The proposed method is an adaptive shrinkage method via tuning τ . It can avoid the time intensive parameter tuning if given a reasonable small τ . Furthermore, we extend it to the truncated group-lasso (TGL), and propose TGL-SCCA model to improve the group-lasso-based SCCA methods. The experimental results, compared with four benchmark methods, show that our SCCA methods identify better or similar correlation coefficients, and better canonical loading profiles than the competing methods. This demonstrates the effectiveness and efficiency of our methods in discovering interesting imaging genetic associations. The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/tlpscca/ . © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. Sparse Canonical Correlation Analysis via Truncated ℓ1-norm with Application to Brain Imaging Genetics.

    Science.gov (United States)

    Du, Lei; Zhang, Tuo; Liu, Kefei; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Guo, Lei; Saykin, Andrew J; Shen, Li

    2016-01-01

    Discovering bi-multivariate associations between genetic markers and neuroimaging quantitative traits is a major task in brain imaging genetics. Sparse Canonical Correlation Analysis (SCCA) is a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ 1 -norm or its variants. The ℓ 0 -norm is more desirable, which however remains unexplored since the ℓ 0 -norm minimization is NP-hard. In this paper, we impose the truncated ℓ 1 -norm to improve the performance of the ℓ 1 -norm based SCCA methods. Besides, we propose two efficient optimization algorithms and prove their convergence. The experimental results, compared with two benchmark methods, show that our method identifies better and meaningful canonical loading patterns in both simulated and real imaging genetic analyse.

  19. SimulaTE: simulating complex landscapes of transposable elements of populations.

    Science.gov (United States)

    Kofler, Robert

    2018-04-15

    Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation. robert.kofler@vetmeduni.ac.at.

  20. Efficient linear precoding for massive MIMO systems using truncated polynomial expansion

    KAUST Repository

    Müller, Axel

    2014-06-01

    Massive multiple-input multiple-output (MIMO) techniques have been proposed as a solution to satisfy many requirements of next generation cellular systems. One downside of massive MIMO is the increased complexity of computing the precoding, especially since the relatively \\'antenna-efficient\\' regularized zero-forcing (RZF) is preferred to simple maximum ratio transmission. We develop in this paper a new class of precoders for single-cell massive MIMO systems. It is based on truncated polynomial expansion (TPE) and mimics the advantages of RZF, while offering reduced and scalable computational complexity that can be implemented in a convenient parallel fashion. Using random matrix theory we provide a closed-form expression of the signal-to-interference-and-noise ratio under TPE precoding and compare it to previous works on RZF. Furthermore, the sum rate maximizing polynomial coefficients in TPE precoding are calculated. By simulation, we find that to maintain a fixed peruser rate loss as compared to RZF, the polynomial degree does not need to scale with the system, but it should be increased with the quality of the channel knowledge and signal-to-noise ratio. © 2014 IEEE.

  1. SIM-DSP: A DSP-Enhanced CAD Platform for Signal Integrity Macromodeling and Simulation

    Directory of Open Access Journals (Sweden)

    Chi-Un Lei

    2014-12-01

    Full Text Available Macromodeling-Simulation process for signal integrity verifications has become necessary for the high speed circuit system design. This paper aims to introduce a “VLSI Signal Integrity Macromodeling and Simulation via Digital Signal Processing Techniques” framework (known as SIM-DSP framework, which applies digital signal processing techniques to facilitate the SI verification process in the pre-layout design phase. Core identification modules and peripheral (pre-/post-processing modules have been developed and assembled to form a verification flow. In particular, a single-step discrete cosine transform truncation (DCTT module has been developed for modeling-simulation process. In DCTT, the response modeling problem is classified as a signal compression problem, wherein the system response can be represented by a truncated set of non-pole based DCT bases, and error can be analyzed through Parseval’s theorem. Practical examples are given to show the applicability of our proposed framework.

  2. Reduction of truncation errors in planar near-field aperture antenna measurements using the method of alternating orthogonal projections

    DEFF Research Database (Denmark)

    Martini, Enrica; Breinbjerg, Olav; Maci, Stefano

    2006-01-01

    A simple and effective procedure for the reduction of truncation error in planar near-field to far-field transformations is presented. The starting point is the consideration that the actual scan plane truncation implies a reliability of the reconstructed plane wave spectrum of the field radiated...

  3. The Extended Erlang-Truncated Exponential distribution: Properties and application to rainfall data

    Directory of Open Access Journals (Sweden)

    I.E. Okorie

    2017-06-01

    Full Text Available The Erlang-Truncated Exponential ETE distribution is modified and the new lifetime distribution is called the Extended Erlang-Truncated Exponential EETE distribution. Some statistical and reliability properties of the new distribution are given and the method of maximum likelihood estimate was proposed for estimating the model parameters. The usefulness and flexibility of the EETE distribution was illustrated with an uncensored data set and its fit was compared with that of the ETE and three other three-parameter distributions. Results based on the minimized log-likelihood (−ℓˆ, Akaike information criterion (AIC, Bayesian information criterion (BIC and the generalized Cramér–von Mises W⋆ statistics shows that the EETE distribution provides a more reasonable fit than the one based on the other competing distributions. Keywords: Mathematics, Applied mathematics

  4. Classification With Truncated Distance Kernel.

    Science.gov (United States)

    Huang, Xiaolin; Suykens, Johan A K; Wang, Shuning; Hornegger, Joachim; Maier, Andreas

    2018-05-01

    This brief proposes a truncated distance (TL1) kernel, which results in a classifier that is nonlinear in the global region but is linear in each subregion. With this kernel, the subregion structure can be trained using all the training data and local linear classifiers can be established simultaneously. The TL1 kernel has good adaptiveness to nonlinearity and is suitable for problems which require different nonlinearities in different areas. Though the TL1 kernel is not positive semidefinite, some classical kernel learning methods are still applicable which means that the TL1 kernel can be directly used in standard toolboxes by replacing the kernel evaluation. In numerical experiments, the TL1 kernel with a pregiven parameter achieves similar or better performance than the radial basis function kernel with the parameter tuned by cross validation, implying the TL1 kernel a promising nonlinear kernel for classification tasks.

  5. Fracture size and transmissivity correlations: Implications for transport simulations in sparse three-dimensional discrete fracture networks following a truncated power law distribution of fracture size

    Science.gov (United States)

    Hyman, J.; Aldrich, G. A.; Viswanathan, H. S.; Makedonska, N.; Karra, S.

    2016-12-01

    We characterize how different fracture size-transmissivity relationships influence flow and transport simulations through sparse three-dimensional discrete fracture networks. Although it is generally accepted that there is a positive correlation between a fracture's size and its transmissivity/aperture, the functional form of that relationship remains a matter of debate. Relationships that assume perfect correlation, semi-correlation, and non-correlation between the two have been proposed. To study the impact that adopting one of these relationships has on transport properties, we generate multiple sparse fracture networks composed of circular fractures whose radii follow a truncated power law distribution. The distribution of transmissivities are selected so that the mean transmissivity of the fracture networks are the same and the distributions of aperture and transmissivity in models that include a stochastic term are also the same.We observe that adopting a correlation between a fracture size and its transmissivity leads to earlier breakthrough times and higher effective permeability when compared to networks where no correlation is used. While fracture network geometry plays the principal role in determining where transport occurs within the network, the relationship between size and transmissivity controls the flow speed. These observations indicate DFN modelers should be aware that breakthrough times and effective permeabilities can be strongly influenced by such a relationship in addition to fracture and network statistics.

  6. Filter Factors of Truncated TLS Regularization with Multiple Observations

    Czech Academy of Sciences Publication Activity Database

    Hnětynková, I.; Plešinger, Martin; Žáková, J.

    2017-01-01

    Roč. 62, č. 2 (2017), s. 105-120 ISSN 0862-7940 R&D Projects: GA ČR GA13-06684S Institutional support: RVO:67985807 Keywords : truncated total least squares * multiple right-hand sides * eigenvalues of rank-d update * ill-posed problem * regularization * filter factors Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 0.618, year: 2016 http://hdl.handle.net/10338.dmlcz/146698

  7. Identification of target genes for wild type and truncated HMGA2 in mesenchymal stem-like cells

    DEFF Research Database (Denmark)

    Henriksen, Jørn Mølgaard; Stabell, Marianne; Meza-Zepeda, Leonardo A

    2010-01-01

    The HMGA2 gene, coding for an architectural transcription factor involved in mesenchymal embryogenesis, is frequently deranged by translocation and/or amplification in mesenchymal tumours, generally leading to over-expression of shortened transcripts and a truncated protein.......The HMGA2 gene, coding for an architectural transcription factor involved in mesenchymal embryogenesis, is frequently deranged by translocation and/or amplification in mesenchymal tumours, generally leading to over-expression of shortened transcripts and a truncated protein....

  8. Error Bounds for Augmented Truncations of Discrete-Time Block-Monotone Markov Chains under Geometric Drift Conditions

    OpenAIRE

    Masuyama, Hiroyuki

    2014-01-01

    In this paper we study the augmented truncation of discrete-time block-monotone Markov chains under geometric drift conditions. We first present a bound for the total variation distance between the stationary distributions of an original Markov chain and its augmented truncation. We also obtain such error bounds for more general cases, where an original Markov chain itself is not necessarily block monotone but is blockwise dominated by a block-monotone Markov chain. Finally,...

  9. Free vibration of symmetric angle ply truncated conical shells under different boundary conditions using spline method

    Energy Technology Data Exchange (ETDEWEB)

    Viswanathan, K. K.; Aziz, Z. A.; Javed, Saira; Yaacob, Y. [Universiti Teknologi Malaysia, Johor Bahru (Malaysia); Pullepu, Babuji [S R M University, Chennai (India)

    2015-05-15

    Free vibration of symmetric angle-ply laminated truncated conical shell is analyzed to determine the effects of frequency parameter and angular frequencies under different boundary condition, ply angles, different material properties and other parameters. The governing equations of motion for truncated conical shell are obtained in terms of displacement functions. The displacement functions are approximated by cubic and quintic splines resulting into a generalized eigenvalue problem. The parametric studies have been made and discussed.

  10. Free vibration of symmetric angle ply truncated conical shells under different boundary conditions using spline method

    International Nuclear Information System (INIS)

    Viswanathan, K. K.; Aziz, Z. A.; Javed, Saira; Yaacob, Y.; Pullepu, Babuji

    2015-01-01

    Free vibration of symmetric angle-ply laminated truncated conical shell is analyzed to determine the effects of frequency parameter and angular frequencies under different boundary condition, ply angles, different material properties and other parameters. The governing equations of motion for truncated conical shell are obtained in terms of displacement functions. The displacement functions are approximated by cubic and quintic splines resulting into a generalized eigenvalue problem. The parametric studies have been made and discussed.

  11. Increased infectivity in human cells and resistance to antibody-mediated neutralization by truncation of the SIV gp41 cytoplasmic tail

    Directory of Open Access Journals (Sweden)

    Takeo eKuwata

    2013-05-01

    Full Text Available The role of antibodies in protecting the host from human immunodeficiency virus type 1 (HIV-1 infection is of considerable interest, particularly because the RV144 trial results suggest that antibodies contribute to protection. Although infection of nonhuman primates with simian immunodeficiency virus (SIV is commonly used as an animal model of HIV-1 infection, the viral epitopes that elicit potent and broad neutralizing antibodies to SIV have not been identified. We isolated a monoclonal antibody (MAb B404 that potently and broadly neutralizes various SIV strains. B404 targets a conformational epitope comprising the V3 and V4 loops of Env that intensely exposed when Env binds CD4. B404-resistant variants were obtained by passaging viruses in the presence of increasing concentration of B404 in PM1/CCR5 cells. Genetic analysis revealed that the Q733stop mutation, which truncates the cytoplasmic tail of gp41, was the first major substitution in Env during passage. The maximal inhibition by B404 and other MAbs were significantly decreased against a recombinant virus with a gp41 truncation compared with the parental SIVmac316. This indicates that the gp41 truncation was associated with resistance to antibody-mediated neutralization. The infectivities of the recombinant virus with the gp41 truncation were 7900-fold, 1000-fold, and 140-fold higher than those of SIVmac316 in PM1, PM1/CCR5, and TZM-bl cells, respectively. Immunoblotting analysis revealed that the gp41 truncation enhanced the incorporation of Env into virions. The effect of the gp41 truncation on infectivity was not obvious in the HSC-F macaque cell line, although the resistance of viruses harboring the gp41 truncation to neutralization was maintained. These results suggest that viruses with a truncated gp41 cytoplasmic tail were selected by increased infectivity in human cells and by acquiring resistance to neutralizing antibody.

  12. The lamppost model: effects of photon trapping, the bottom lamp and disc truncation

    Science.gov (United States)

    Niedźwiecki, Andrzej; Zdziarski, Andrzej A.

    2018-04-01

    We study the lamppost model, in which the primary X-ray sources in accreting black-hole systems are located symmetrically on the rotation axis on both sides of the black hole surrounded by an accretion disc. We show the importance of the emission of the source on the opposite side to the observer. Due to gravitational light bending, its emission can increase the direct (i.e., not re-emitted by the disc) flux by as much as an order of magnitude. This happens for near to face-on observers when the disc is even moderately truncated. For truncated discs, we also consider effects of emission of the top source gravitationally bent around the black hole. We also present results for the attenuation of the observed radiation with respect to that emitted by the lamppost as functions of the lamppost height, black-hole spin and the degree of disc truncation. This attenuation, which is due to the time dilation, gravitational redshift and the loss of photons crossing the black-hole horizon, can be as severe as by several orders of magnitude for low lamppost heights. We also consider the contribution to the observed flux due to re-emission by optically-thick matter within the innermost stable circular orbit.

  13. Spectroscopic characterization of a truncated hemoglobin from the nitrogen-fixing bacterium Herbaspirillum seropedicae.

    Science.gov (United States)

    Razzera, Guilherme; Vernal, Javier; Baruh, Debora; Serpa, Viviane I; Tavares, Carolina; Lara, Flávio; Souza, Emanuel M; Pedrosa, Fábio O; Almeida, Fábio C L; Terenzi, Hernán; Valente, Ana Paula

    2008-09-01

    The Herbaspirillum seropedicae genome sequence encodes a truncated hemoglobin typical of group II (Hs-trHb1) members of this family. We show that His-tagged recombinant Hs-trHb1 is monomeric in solution, and its optical spectrum resembles those of previously reported globins. NMR analysis allowed us to assign heme substituents. All data suggest that Hs-trHb1 undergoes a transition from an aquomet form in the ferric state to a hexacoordinate low-spin form in the ferrous state. The close positions of Ser-E7, Lys-E10, Tyr-B10, and His-CD1 in the distal pocket place them as candidates for heme coordination and ligand regulation. Peroxide degradation kinetics suggests an easy access to the heme pocket, as the protein offered no protection against peroxide degradation when compared with free heme. The high solvent exposure of the heme may be due to the presence of a flexible loop in the access pocket, as suggested by a structural model obtained by using homologous globins as templates. The truncated hemoglobin described here has unique features among truncated hemoglobins and may function in the facilitation of O(2) transfer and scavenging, playing an important role in the nitrogen-fixation mechanism.

  14. Truncation of a mannanase from Trichoderma harzianum improves its enzymatic properties and expression efficiency in Trichoderma reesei.

    Science.gov (United States)

    Wang, Juan; Zeng, Desheng; Liu, Gang; Wang, Shaowen; Yu, Shaowen

    2014-01-01

    To obtain high expression efficiency of a mannanase gene, ThMan5A, cloned from Trichoderma harzianum MGQ2, both the full-length gene and a truncated gene (ThMan5AΔCBM) that contains only the catalytic domain, were expressed in Trichoderma reesei QM9414 using the strong constitutive promoter of the gene encoding pyruvate decarboxylase (pdc), and purified to homogeneity, respectively. We found that truncation of the gene improved its expression efficiency as well as the enzymatic properties of the encoded protein. The recombinant strain expressing ThMan5AΔCBM produced 2,460 ± 45.1 U/ml of mannanase activity in the culture supernatant; 2.3-fold higher than when expressing the full-length ThMan5A gene. In addition, the truncated mannanase had superior thermostability compared with the full-length enzyme and retained 100 % of its activity after incubation at 60 °C for 48 h. Our results clearly show that the truncated ThMan5A enzyme exhibited improved characteristics both in expression efficiency and in its thermal stability. These characteristics suggest that ThMan5AΔCBM has potential applications in the food, feed, paper, and pulp industries.

  15. Blunt traumatic axillary artery truncation, in the absence of associated fracture.

    Science.gov (United States)

    Bokser, Emily; Caputo, William; Hahn, Barry; Greenstein, Josh

    2018-02-01

    Axillary artery injuries can be associated with both proximal humeral fractures (Naouli et al., 2016; Ng et al., 2016) [1,2] as well as shoulder dislocations (Leclerc et al., 2017; Karnes et al., 2016) [3,4]. We report a rare case of an isolated axillary artery truncation following blunt trauma without any associated fracture or dislocation. A 58-year-old male presented to the emergency department for evaluation after falling on his outstretched right arm. The patient was found to have an absent right radial pulse with decreased sensation to the right arm. Point of care ultrasound showed findings suspicious for traumatic axillary artery injury, and X-rays did not demonstrate any fracture. Computed tomography with angiography confirmed axillary artery truncation with active extravasation. The patient underwent successful vascular repair with an axillary artery bypass. Although extremity injuries are common in emergency departments, emergency physicians need to recognize the risk for vascular injuries, even without associated fracture or dislocation. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Firewalls as artefacts of inconsistent truncations of quantum geometries

    Energy Technology Data Exchange (ETDEWEB)

    Germani, Cristiano [Max-Planck-Institut fuer Physik, Muenchen (Germany); Arnold Sommerfeld Center, Ludwig-Maximilians-University, Muenchen (Germany); Institut de Ciencies del Cosmos, Universitat de Barcelona (Spain); Sarkar, Debajyoti [Max-Planck-Institut fuer Physik, Muenchen (Germany); Arnold Sommerfeld Center, Ludwig-Maximilians-University, Muenchen (Germany)

    2016-01-15

    In this paper we argue that a firewall is simply a manifestation of an inconsistent truncation of non-perturbative effects that unitarize the semiclassical black hole. Namely, we show that a naive truncation of quantum corrections to the Hawking spectrum at order O(e{sup -S}), inexorably leads to a ''localised'' divergent energy density near the black hole horizon. Nevertheless, in the same approximation, a distant observer only sees a discretised spectrum and concludes that unitarity is achieved by (e{sup -S}) effects. This is due to the fact that instead, the correct quantum corrections to the Hawking spectrum go like (g{sup tt}e{sup -S}). Therefore, while at a distance far away from the horizon, where g{sup tt} ∼ 1, quantum corrections are perturbative, they do diverge close to the horizon, where g{sup tt} → ∞. Nevertheless, these ''corrections'' nicely re-sum so that correlations functions are smooth at the would-be black hole horizon. Thus, we conclude that the appearance of firewalls is just a signal of the breaking of the semiclassical approximation at the Page time, even for large black holes. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Firewalls as artefacts of inconsistent truncations of quantum geometries

    International Nuclear Information System (INIS)

    Germani, Cristiano; Sarkar, Debajyoti

    2016-01-01

    In this paper we argue that a firewall is simply a manifestation of an inconsistent truncation of non-perturbative effects that unitarize the semiclassical black hole. Namely, we show that a naive truncation of quantum corrections to the Hawking spectrum at order O(e -S ), inexorably leads to a ''localised'' divergent energy density near the black hole horizon. Nevertheless, in the same approximation, a distant observer only sees a discretised spectrum and concludes that unitarity is achieved by (e -S ) effects. This is due to the fact that instead, the correct quantum corrections to the Hawking spectrum go like (g tt e -S ). Therefore, while at a distance far away from the horizon, where g tt ∼ 1, quantum corrections are perturbative, they do diverge close to the horizon, where g tt → ∞. Nevertheless, these ''corrections'' nicely re-sum so that correlations functions are smooth at the would-be black hole horizon. Thus, we conclude that the appearance of firewalls is just a signal of the breaking of the semiclassical approximation at the Page time, even for large black holes. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Maltose binding protein-fusion enhances the bioactivity of truncated forms of pig myostatin propeptide produced in E. coli.

    Directory of Open Access Journals (Sweden)

    Sang Beum Lee

    Full Text Available Myostatin (MSTN is a potent negative regulator of skeletal muscle growth. MSTN propeptide (MSTNpro inhibits MSTN binding to its receptor through complex formation with MSTN, implying that MSTNpro can be a useful agent to improve skeletal muscle growth in meat-producing animals. Four different truncated forms of pig MSTNpro containing N-terminal maltose binding protein (MBP as a fusion partner were expressed in E. coli, and purified by the combination of affinity chromatography and gel filtration. The MSTN-inhibitory capacities of these proteins were examined in an in vitro gene reporter assay. A MBP-fused, truncated MSTNpro containing residues 42-175 (MBP-Pro42-175 exhibited the same MSTN-inhibitory potency as the full sequence MSTNpro. Truncated MSTNpro proteins containing either residues 42-115 (MBP-Pro42-115 or 42-98 (MBP-Pro42-98 also exhibited MSTN-inhibitory capacity even though the potencies were significantly lower than that of full sequence MSTNpro. In pull-down assays, MBP-Pro42-175, MBP-Pro42-115, and MBP-Pro42-98 demonstrated their binding to MSTN. MBP was removed from the truncated MSTNpro proteins by incubation with factor Xa to examine the potential role of MBP on MSTN-inhibitory capacity of those proteins. Removal of MBP from MBP-Pro42-175 and MBP-Pro42-98 resulted in 20-fold decrease in MSTN-inhibitory capacity of Pro42-175 and abolition of MSTN-inhibitory capacity of Pro42-98, indicating that MBP as fusion partner enhanced the MSTN-inhibitory capacity of those truncated MSTNpro proteins. In summary, this study shows that MBP is a very useful fusion partner in enhancing MSTN-inhibitory potency of truncated forms of MSTNpro proteins, and MBP-fused pig MSTNpro consisting of amino acid residues 42-175 is sufficient to maintain the full MSTN-inhibitory capacity.

  19. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

    Directory of Open Access Journals (Sweden)

    C.Y. Nishikawa

    2012-02-01

    Full Text Available Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ54 co-factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL. A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH4Cl but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

  20. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

    Energy Technology Data Exchange (ETDEWEB)

    Nishikawa, C.Y.; Araújo, L.M.; Kadowaki, M.A.S.; Monteiro, R.A.; Steffens, M.B.R.; Pedrosa, F.O.; Souza, E.M.; Chubatsu, L.S. [Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR (Brazil)

    2012-01-27

    Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ{sup 54} factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH{sub 4}Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

  1. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense.

    Science.gov (United States)

    Nishikawa, C Y; Araújo, L M; Kadowaki, M A S; Monteiro, R A; Steffens, M B R; Pedrosa, F O; Souza, E M; Chubatsu, L S

    2012-02-01

    Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ(54) co-factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH(4)Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

  2. Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

    International Nuclear Information System (INIS)

    Nishikawa, C.Y.; Araújo, L.M.; Kadowaki, M.A.S.; Monteiro, R.A.; Steffens, M.B.R.; Pedrosa, F.O.; Souza, E.M.; Chubatsu, L.S.

    2012-01-01

    Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ 54 factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH 4 Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription

  3. Organisation and melting of solution grown truncated lozenge polyethylene single crystals

    NARCIS (Netherlands)

    Loos, J.; Tian, M.

    2003-01-01

    Morphological features and the melting behaviour of truncated lozenge crystals have been studied. For the crystals investigated, the heights of the (110) and the (200) sectors were measured to be 14.5 and 12.7 nm, respectively, using atomic force microscopy (AFM) in contact and non-contact mode.

  4. Truncated SALL1 Impedes Primary Cilia Function in Townes-Brocks Syndrome

    DEFF Research Database (Denmark)

    Bozal-Basterra, Laura; Martín-Ruíz, Itziar; Pirone, Lucia

    2018-01-01

    by mutations in the gene encoding the transcriptional repressor SALL1 and is associated with the presence of a truncated protein that localizes to the cytoplasm. Here, we provide evidence that SALL1 mutations might cause TBS by means beyond its transcriptional capacity. By using proximity proteomics, we show...

  5. Efficient Tridiagonal Preconditioner for the Matrix-Free Truncated Newton Method

    Czech Academy of Sciences Publication Activity Database

    Lukšan, Ladislav; Vlček, Jan

    2014-01-01

    Roč. 235, 25 May (2014), s. 394-407 ISSN 0096-3003 R&D Projects: GA ČR GA13-06684S Institutional support: RVO:67985807 Keywords : unconstrained optimization * large scale optimization * matrix-free truncated Newton method * preconditioned conjugate gradient method * preconditioners obtained by the directional differentiation * numerical algorithms Subject RIV: BA - General Mathematics Impact factor: 1.551, year: 2014

  6. Surface self-diffusion of adatom on Pt cluster with truncated octahedron structure

    Energy Technology Data Exchange (ETDEWEB)

    Yang Jianyu, E-mail: wuliyangjianyu@yahoo.com.c [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Hu Wangyu, E-mail: wangyuhu2001@yahoo.com.c [Department of Applied Physics, Hunan University, Changsha 410082 (China); Chen Shuguang [Department of Applied Physics, Hunan University, Changsha 410082 (China)

    2010-05-03

    Surface diffusion of single Pt adatom on Pt cluster with truncated octahedron structure is investigated through a combination of molecular dynamics and nudged elastic band method. Using an embedded atom method to describe the atomic interactions, the minimum energy paths are determined and the energy barriers for adatom diffusion across and along step are evaluated. The diffusion of adatom crossing step edge between {l_brace}111{r_brace} and {l_brace}100{r_brace} facets has a surprisingly low barrier of 0.03 eV, which is 0.12 eV lower than the barrier for adatom diffusion from {l_brace}111{r_brace} to neighboring {l_brace}111{r_brace} facet. Owing to the small barrier of adatom diffusion across the step edge between {l_brace}111{r_brace} and {l_brace}100{r_brace} facets, the diffusion of adatom along the step edge cannot occur. The molecular dynamics simulations at low temperatures also support these results. Our results show that mass transport will prefer step with {l_brace}100{r_brace} microfacet and the Pt clusters can have only {l_brace}111{r_brace} facets in epitaxial growth.

  7. Family losses following truncation selection in populations of half-sib families

    Science.gov (United States)

    J. H. Roberds; G. Namkoong; H. Kang

    1980-01-01

    Family losses during truncation selection may be sizable in populations of half-sib families. Substantial losses may occur even in populations containing little or no variation among families. Heavier losses will occur, however, under conditions of high heritability where there is considerable family variation. Standard deviations and therefore variances of family loss...

  8. Transient Dynamics Simulation of Airflow in a CT-Scanned Human Airway Tree: More or Fewer Terminal Bronchi?

    Directory of Open Access Journals (Sweden)

    Shouliang Qi

    2017-01-01

    Full Text Available Using computational fluid dynamics (CFD method, the feasibility of simulating transient airflow in a CT-based airway tree with more than 100 outlets for a whole respiratory period is studied, and the influence of truncations of terminal bronchi on CFD characteristics is investigated. After an airway model with 122 outlets is extracted from CT images, the transient airflow is simulated. Spatial and temporal variations of flow velocity, wall pressure, and wall shear stress are presented; the flow pattern and lobar distribution of air are gotten as well. All results are compared with those of a truncated model with 22 outlets. It is found that the flow pattern shows lobar heterogeneity that the near-wall air in the trachea is inhaled into the upper lobe while the center flow enters the other lobes, and the lobar distribution of air is significantly correlated with the outlet area ratio. The truncation decreases airflow to right and left upper lobes and increases the deviation of airflow distributions between inspiration and expiration. Simulating the transient airflow in an airway tree model with 122 bronchi using CFD is feasible. The model with more terminal bronchi decreases the difference between the lobar distributions at inspiration and at expiration.

  9. LGI2 truncation causes a remitting focal epilepsy in dogs.

    Directory of Open Access Journals (Sweden)

    Eija H Seppälä

    2011-07-01

    Full Text Available One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2-10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years, and remits by four months (human eight years, versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission.

  10. A Novel Truncated Form of Serum Amyloid A in Kawasaki Disease.

    Directory of Open Access Journals (Sweden)

    John C Whitin

    Full Text Available Kawasaki disease (KD is an acute vasculitis in children that can cause coronary artery abnormalities. Its diagnosis is challenging, and many cytokines, chemokines, acute phase reactants, and growth factors have failed evaluation as specific biomarkers to distinguish KD from other febrile illnesses. We performed protein profiling, comparing plasma from children with KD with febrile control (FC subjects to determine if there were specific proteins or peptides that could distinguish the two clinical states.Plasma from three independent cohorts from the blood of 68 KD and 61 FC subjects was fractionated by anion exchange chromatography, followed by surface-enhanced laser desorption ionization (SELDI mass spectrometry of the fractions. The mass spectra of KD and FC plasma samples were analyzed for peaks that were statistically significantly different.A mass spectrometry peak with a mass of 7,860 Da had high intensity in acute KD subjects compared to subacute KD (p = 0.0003 and FC (p = 7.9 x 10-10 subjects. We identified this peak as a novel truncated form of serum amyloid A with N-terminal at Lys-34 of the circulating form and validated its identity using a hybrid mass spectrum immunoassay technique. The truncated form of serum amyloid A was present in plasma of KD subjects when blood was collected in tubes containing protease inhibitors. This peak disappeared when the patients were examined after their symptoms resolved. Intensities of this peptide did not correlate with KD-associated laboratory values or with other mass spectrum peaks from the plasma of these KD subjects.Using SELDI mass spectrometry, we have discovered a novel truncated form of serum amyloid A that is elevated in the plasma of KD when compared with FC subjects. Future studies will evaluate its relevance as a diagnostic biomarker and its potential role in the pathophysiology of KD.

  11. A computational approach for fluid queues driven by truncated birth-death processes.

    NARCIS (Netherlands)

    Lenin, R.B.; Parthasarathy, P.R.

    2000-01-01

    In this paper, we analyze fluid queues driven by truncated birth-death processes with general birth and death rates. We compute the equilibrium distribution of the content of the fluid buffer by providing efficient numerical procedures to compute the eigenvalues and the eigenvectors of the

  12. A truncated Kv1.1 protein in the brain of the megencephaly mouse: expression and interaction

    Directory of Open Access Journals (Sweden)

    Århem Peter

    2005-11-01

    Full Text Available Abstract Background The megencephaly mouse, mceph/mceph, is epileptic and displays a dramatically increased brain volume and neuronal count. The responsible mutation was recently revealed to be an eleven base pair deletion, leading to a frame shift, in the gene encoding the potassium channel Kv1.1. The predicted MCEPH protein is truncated at amino acid 230 out of 495. Truncated proteins are usually not expressed since nonsense mRNAs are most often degraded. However, high Kv1.1 mRNA levels in mceph/mceph brain indicated that it escaped this control mechanism. Therefore, we hypothesized that the truncated Kv1.1 would be expressed and dysregulate other Kv1 subunits in the mceph/mceph mice. Results We found that the MCEPH protein is expressed in the brain of mceph/mceph mice. MCEPH was found to lack mature (Golgi glycosylation, but to be core glycosylated and trapped in the endoplasmic reticulum (ER. Interactions between MCEPH and other Kv1 subunits were studied in cell culture, Xenopus oocytes and the brain. MCEPH can form tetramers with Kv1.1 in cell culture and has a dominant negative effect on Kv1.2 and Kv1.3 currents in oocytes. However, it does not retain Kv1.2 in the ER of neurons. Conclusion The megencephaly mice express a truncated Kv1.1 in the brain, and constitute a unique tool to study Kv1.1 trafficking relevant for understanding epilepsy, ataxia and pathologic brain overgrowth.

  13. Non-linear buckling of an FGM truncated conical shell surrounded by an elastic medium

    International Nuclear Information System (INIS)

    Sofiyev, A.H.; Kuruoglu, N.

    2013-01-01

    In this paper, the non-linear buckling of the truncated conical shell made of functionally graded materials (FGMs) surrounded by an elastic medium has been studied using the large deformation theory with von Karman–Donnell-type of kinematic non-linearity. A two-parameter foundation model (Pasternak-type) is used to describe the shell–foundation interaction. The FGM properties are assumed to vary continuously through the thickness direction. The fundamental relations, the modified Donnell type non-linear stability and compatibility equations of the FGM truncated conical shell resting on the Pasternak-type elastic foundation are derived. By using the Superposition and Galerkin methods, the non-linear stability equations for the FGM truncated conical shell is solved. Finally, influences of variations of Winkler foundation stiffness and shear subgrade modulus of the foundation, compositional profiles and shell characteristics on the dimensionless critical non-linear axial load are investigated. The present results are compared with the available data for a special case. -- Highlights: • Nonlinear buckling of FGM conical shell surrounded by elastic medium is studied. • Pasternak foundation model is used to describe the shell–foundation interaction. • Nonlinear basic equations are derived. • Problem is solved by using Superposition and Galerkin methods. • Influences of various parameters on the nonlinear critical load are investigated

  14. Selective translational repression of truncated proteins from frameshift mutation-derived mRNAs in tumors.

    Directory of Open Access Journals (Sweden)

    Kwon Tae You

    2007-05-01

    Full Text Available Frameshift and nonsense mutations are common in tumors with microsatellite instability, and mRNAs from these mutated genes have premature termination codons (PTCs. Abnormal mRNAs containing PTCs are normally degraded by the nonsense-mediated mRNA decay (NMD system. However, PTCs located within 50-55 nucleotides of the last exon-exon junction are not recognized by NMD (NMD-irrelevant, and some PTC-containing mRNAs can escape from the NMD system (NMD-escape. We investigated protein expression from NMD-irrelevant and NMD-escape PTC-containing mRNAs by Western blotting and transfection assays. We demonstrated that transfection of NMD-irrelevant PTC-containing genomic DNA of MARCKS generates truncated protein. In contrast, NMD-escape PTC-containing versions of hMSH3 and TGFBR2 generate normal levels of mRNA, but do not generate detectable levels of protein. Transfection of NMD-escape mutant TGFBR2 genomic DNA failed to generate expression of truncated proteins, whereas transfection of wild-type TGFBR2 genomic DNA or mutant PTC-containing TGFBR2 cDNA generated expression of wild-type protein and truncated protein, respectively. Our findings suggest a novel mechanism of gene expression regulation for PTC-containing mRNAs in which the deleterious transcripts are regulated either by NMD or translational repression.

  15. Chaos and noise in a truncated Toda potential

    International Nuclear Information System (INIS)

    Habib, S.; Kandrup, H.E.; Mahon, M.E.

    1996-01-01

    Results are reported from a numerical investigation of orbits in a truncated Toda potential that is perturbed by weak friction and noise. Aside from the perturbations displaying a simple scaling in the amplitude of the friction and noise, it is found that even very weak friction and noise can induce an extrinsic diffusion through cantori on a time scale that is much shorter than that associated with intrinsic diffusion in the unperturbed system. The results have applications in galactic dynamics and in the formation of a beam halo in charged particle beams. copyright 1996 The American Physical Society

  16. On the truncation of the azimuthal mode spectrum of high-order probes in probe-corrected spherical near-field antenna measurements

    DEFF Research Database (Denmark)

    Pivnenko, Sergey; Laitinen, Tommi

    2011-01-01

    Azimuthal mode (m mode) truncation of a high-order probe pattern in probe-corrected spherical near-field antenna measurements is studied in this paper. The results of this paper provide rules for appropriate and sufficient m-mode truncation for non-ideal first-order probes and odd-order probes wi...

  17. Modified truncated randomized singular value decomposition (MTRSVD) algorithms for large scale discrete ill-posed problems with general-form regularization

    Science.gov (United States)

    Jia, Zhongxiao; Yang, Yanfei

    2018-05-01

    In this paper, we propose new randomization based algorithms for large scale linear discrete ill-posed problems with general-form regularization: subject to , where L is a regularization matrix. Our algorithms are inspired by the modified truncated singular value decomposition (MTSVD) method, which suits only for small to medium scale problems, and randomized SVD (RSVD) algorithms that generate good low rank approximations to A. We use rank-k truncated randomized SVD (TRSVD) approximations to A by truncating the rank- RSVD approximations to A, where q is an oversampling parameter. The resulting algorithms are called modified TRSVD (MTRSVD) methods. At every step, we use the LSQR algorithm to solve the resulting inner least squares problem, which is proved to become better conditioned as k increases so that LSQR converges faster. We present sharp bounds for the approximation accuracy of the RSVDs and TRSVDs for severely, moderately and mildly ill-posed problems, and substantially improve a known basic bound for TRSVD approximations. We prove how to choose the stopping tolerance for LSQR in order to guarantee that the computed and exact best regularized solutions have the same accuracy. Numerical experiments illustrate that the best regularized solutions by MTRSVD are as accurate as the ones by the truncated generalized singular value decomposition (TGSVD) algorithm, and at least as accurate as those by some existing truncated randomized generalized singular value decomposition (TRGSVD) algorithms. This work was supported in part by the National Science Foundation of China (Nos. 11771249 and 11371219).

  18. Virtues and limitations of the truncated Holstein–Primakoff description of quantum rotors

    International Nuclear Information System (INIS)

    Hirsch, Jorge G; Castaños, Octavio; López-Peña, Ramón; Nahmad-Achar, Eduardo

    2013-01-01

    A Hamiltonian describing the collective behaviour of N interacting spins can be mapped to a bosonic one employing the Holstein–Primakoff realization, at the expense of having an infinite series in powers of the boson creation and annihilation operators. Truncating this series up to quadratic terms allows obtaining analytic solutions through a Bogoliubov transformation, which becomes exact in the limit N → ∞. The Hamiltonian exhibits a phase transition from single-spin excitations to a collective mode. In the vicinity of this phase transition, the truncated solutions predict the existence of singularities for a finite number of spins, which have no counterpart in the exact diagonalization. Renormalization allows to extract from these divergences the exact behaviour of relevant observables with the number of spins around the phase transition, and to relate it with the class of universality to which the model belongs. In this work a detailed analysis of these aspects is presented for the Lipkin model. (comment)

  19. Heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance.

    Science.gov (United States)

    Patel, Kashyap A; Kettunen, Jarno; Laakso, Markku; Stančáková, Alena; Laver, Thomas W; Colclough, Kevin; Johnson, Matthew B; Abramowicz, Marc; Groop, Leif; Miettinen, Päivi J; Shepherd, Maggie H; Flanagan, Sarah E; Ellard, Sian; Inagaki, Nobuya; Hattersley, Andrew T; Tuomi, Tiinamaija; Cnop, Miriam; Weedon, Michael N

    2017-10-12

    Finding new causes of monogenic diabetes helps understand glycaemic regulation in humans. To find novel genetic causes of maturity-onset diabetes of the young (MODY), we sequenced MODY cases with unknown aetiology and compared variant frequencies to large public databases. From 36 European patients, we identify two probands with novel RFX6 heterozygous nonsense variants. RFX6 protein truncating variants are enriched in the MODY discovery cohort compared to the European control population within ExAC (odds ratio = 131, P = 1 × 10 -4 ). We find similar results in non-Finnish European (n = 348, odds ratio = 43, P = 5 × 10 -5 ) and Finnish (n = 80, odds ratio = 22, P = 1 × 10 -6 ) replication cohorts. RFX6 heterozygotes have reduced penetrance of diabetes compared to common HNF1A and HNF4A-MODY mutations (27, 70 and 55% at 25 years of age, respectively). The hyperglycaemia results from beta-cell dysfunction and is associated with lower fasting and stimulated gastric inhibitory polypeptide (GIP) levels. Our study demonstrates that heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance.Maturity-onset diabetes of the young (MODY) is the most common subtype of familial diabetes. Here, Patel et al. use targeted DNA sequencing of MODY patients and large-scale publically available data to show that RFX6 heterozygous protein truncating variants cause reduced penetrance MODY.

  20. A truncated conical beam model for analysis of the vibration of rat whiskers.

    Science.gov (United States)

    Yan, Wenyi; Kan, Qianhua; Kergrene, Kenan; Kang, Guozheng; Feng, Xi-Qiao; Rajan, Ramesh

    2013-08-09

    A truncated conical beam model is developed to study the vibration behaviour of a rat whisker. Translational and rotational springs are introduced to better represent the constraint conditions at the base of the whiskers in a living rat. Dimensional analysis shows that the natural frequency of a truncated conical beam with generic spring constraints at its ends is inversely proportional to the square root of the mass density. Under all the combinations of the classical free, pinned, sliding or fixed boundary conditions of a truncated conical beam, it is proved that the natural frequency can be expressed as f = α(rb/L(2))E/ρ and the frequency coefficient α only depends on the ratio of the radii at the two ends of the beam. The natural frequencies of a representative rat whisker are predicted for two typical situations: freely whisking in air and the tip touching an object. Our numerical results show that there exists a window where the natural frequencies of a rat whisker are very sensitive to the change of the rotational constraint at the base. This finding is also confirmed by the numerical results of 18 whiskers with their data available from literature. It can be concluded that the natural frequencies of a rat whisker can be adjusted within a wide range through manipulating the constraints of the follicle on the rat base by a behaving animal. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Expression and characterization of a novel truncated rotavirus VP4 for the development of a recombinant rotavirus vaccine.

    Science.gov (United States)

    Li, Yijian; Xue, Miaoge; Yu, Linqi; Luo, Guoxing; Yang, Han; Jia, Lianzhi; Zeng, Yuanjun; Li, Tingdong; Ge, Shengxiang; Xia, Ningshao

    2018-04-12

    The outer capsid protein VP4 is an important target for the development of a recombinant rotavirus vaccine because it mediates the attachment and penetration of rotavirus. Due to the poor solubility of full-length VP4, VP8 was explored as candidate rotavirus vaccines in the past years. In previous studies, it has been found that the N-terminal truncated VP8 protein, VP8-1 (aa26-231), could be expressed in soluble form with improved immunogenicity compared to the core of VP8 (aa65-223). However, this protein stimulated only a weak immune response when aluminum hydroxide was used as an adjuvant. In addition, it should be noted that the protective efficacy of VP4 was higher than that of VP8 and VP5. In this study, it was found that when the N-terminal 25 amino acids were deleted, the truncated VP4 ∗ (aa26-476) containing VP8 and the stalk domain of VP5 could be expressed in soluble form in E. coli and purified to homogeneous trimers. Furthermore, the truncated VP4 could induce high titers of neutralizing antibodies when aluminum adjuvant was used and conferred high protective efficacy in reducing the severity of diarrhea and rotavirus shedding in stools in animal models. The immunogenicity of the truncated VP4 was significantly higher than that of VP8 ∗ and VP5 ∗ alone. Taken together, the truncated VP4 ∗ (aa26-476), with enhanced immunogenicity and immunoprotectivity, could be considered as a viable candidate for further development and has the potential to become a parenterally administered rotavirus vaccine. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Identification and purification of truncated insulin-like growth factor I from porcine uterus. Evidence for high biological potency

    International Nuclear Information System (INIS)

    Ogasawara, M.; Karey, K.P.; Marquardt, H.; Sirbasku, D.A.

    1989-01-01

    The authors report the completion of the purification of uterine-derived growth factors (UDGF) described previously by this laboratory. During isolation, the mitogenic activity was monitored by using the human MCF-7 breast cancer cells in serum-free Ham's F12 and Dulbecco's modified Eagle's medium (1:1, v/v) containing 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 200 μg/mL bovine serum albumin, and 10 μg/mL human transferrin. This medium sustained growth for several days in response to a single addition of growth factor. The mitogens were shown by protein microsequencing to be DES 1 → 3 to DES 1 → 6 forms of insulin-like growth factor I (truncated IGF-I). An M r estimated by 125 I labeling, urea-sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and autoradiography was consistent with a DES 1 → 3(4) N α truncation. Immunoadsorption and radioimmunoassay confirmed immunological properties equivalent to IGF-I. Radioreceptor assays showed truncated IGF-I was functionally equivalent to recombinant IGF-I. They conclude that the major acid-stable low-M r mitogenic activities isolated from uterus are very potent forms of truncated IGF-I capable of stimulating growth of epithelial and mesenchymal cells

  3. Alternative Hamiltonian for molecular dynamics simulations in the grand canonical ensemble

    International Nuclear Information System (INIS)

    Lo, C.; Palmer, B.

    1995-01-01

    An alternative to the Hamiltonian of Cagin and Pettitt for performing molecular dynamics simulations in the grand canonical ensemble is presented and used as the basis for a new algorithm. The algorithm is tested on the ideal gas and the truncated and shifted Lennard-Jones fluid. Simulations are used to calculate the vapor--liquid coexistence points for the Lennard-Jones system and are found to be in agreement with previous calculations using Gibbs ensemble calculations and with the Nicolas equation of state. Simulations are also performed on the Lennard-Jones solid

  4. Use of the negative binomial-truncated Poisson distribution in thunderstorm prediction

    Science.gov (United States)

    Cohen, A. C.

    1971-01-01

    A probability model is presented for the distribution of thunderstorms over a small area given that thunderstorm events (1 or more thunderstorms) are occurring over a larger area. The model incorporates the negative binomial and truncated Poisson distributions. Probability tables for Cape Kennedy for spring, summer, and fall months and seasons are presented. The computer program used to compute these probabilities is appended.

  5. Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

    International Nuclear Information System (INIS)

    Tang, Yanan; Li, Liang

    2013-01-01

    Graphical abstract: -- Highlights: •LC–MS was developed for quantifying protein mixtures containing both intact and N-terminal truncated proteins. • 12 C 2 -Dansylation of the N-terminal amino acid of proteins was done first, followed by microwave-assisted acid hydrolysis. •The released 12 C 2 -dansyl labeled N-terminal amino acid was quantified using 13 C 2 -dansyl labeled amino acid standards. •The method provided accurate and precise results for quantifying intact and N-terminal truncated proteins within 8 h. -- Abstract: The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards

  6. Field of view extension and truncation correction for MR-based human attenuation correction in simultaneous MR/PET imaging

    International Nuclear Information System (INIS)

    Blumhagen, Jan O.; Ladebeck, Ralf; Fenchel, Matthias; Braun, Harald; Quick, Harald H.; Faul, David; Scheffler, Klaus

    2014-01-01

    Purpose: In quantitative PET imaging, it is critical to accurately measure and compensate for the attenuation of the photons absorbed in the tissue. While in PET/CT the linear attenuation coefficients can be easily determined from a low-dose CT-based transmission scan, in whole-body MR/PET the computation of the linear attenuation coefficients is based on the MR data. However, a constraint of the MR-based attenuation correction (AC) is the MR-inherent field-of-view (FoV) limitation due to static magnetic field (B 0 ) inhomogeneities and gradient nonlinearities. Therefore, the MR-based human AC map may be truncated or geometrically distorted toward the edges of the FoV and, consequently, the PET reconstruction with MR-based AC may be biased. This is especially of impact laterally where the patient arms rest beside the body and are not fully considered. Methods: A method is proposed to extend the MR FoV by determining an optimal readout gradient field which locally compensates B 0 inhomogeneities and gradient nonlinearities. This technique was used to reduce truncation in AC maps of 12 patients, and the impact on the PET quantification was analyzed and compared to truncated data without applying the FoV extension and additionally to an established approach of PET-based FoV extension. Results: The truncation artifacts in the MR-based AC maps were successfully reduced in all patients, and the mean body volume was thereby increased by 5.4%. In some cases large patient-dependent changes in SUV of up to 30% were observed in individual lesions when compared to the standard truncated attenuation map. Conclusions: The proposed technique successfully extends the MR FoV in MR-based attenuation correction and shows an improvement of PET quantification in whole-body MR/PET hybrid imaging. In comparison to the PET-based completion of the truncated body contour, the proposed method is also applicable to specialized PET tracers with little uptake in the arms and might reduce the

  7. Quark-gluon vertex dressing and meson masses beyond ladder-rainbow truncation

    International Nuclear Information System (INIS)

    Matevosyan, Hrayr H.; Thomas, Anthony W.; Tandy, Peter C.

    2007-01-01

    We include a generalized infinite class of quark-gluon vertex dressing diagrams in a study of how dynamics beyond the ladder-rainbow truncation influences the Bethe-Salpeter description of light-quark pseudoscalar and vector mesons. The diagrammatic specification of the vertex is mapped into a corresponding specification of the Bethe-Salpeter kernel, which preserves chiral symmetry. This study adopts the algebraic format afforded by the simple interaction kernel used in previous work on this topic. The new feature of the present work is that in every diagram summed for the vertex and the corresponding Bethe-Salpeter kernel, each quark-gluon vertex is required to be the self-consistent vertex solution. We also adopt from previous work the effective accounting for the role of the explicitly non-Abelian three-gluon coupling in a global manner through one parameter determined from recent lattice-QCD data for the vertex. Within the current model, the more consistent dressed vertex limits the ladder-rainbow truncation error for vector mesons to be never more than 10% as the current quark mass is varied from the u/d region to the b region

  8. Truncated exponential-rigid-rotor model for strong electron and ion rings

    International Nuclear Information System (INIS)

    Larrabee, D.A.; Lovelace, R.V.; Fleischmann, H.H.

    1979-01-01

    A comprehensive study of exponential-rigid-rotor equilibria for strong electron and ion rings indicates the presence of a sizeable percentage of untrapped particles in all equilibria with aspect-ratios R/a approximately <4. Such aspect-ratios are required in fusion-relevant rings. Significant changes in the equilibria are observed when untrapped particles are excluded by the use of a truncated exponential-rigid-rotor distribution function. (author)

  9. Integral equation solution for truncated slab structures by using a fringe current formulation

    DEFF Research Database (Denmark)

    Jørgensen, Erik; Toccafondi, A.; Maci, S.

    1999-01-01

    Full-wave solutions of truncated dielectric slab problems are interesting for a variety of engineering applications, in particular patch antennas on finite ground planes. For this application a canonical reference solution is that of a semi-infinite slab illuminated by a line source. Standard int...

  10. The renormalized Hamiltonian truncation method in the large E{sub T} expansion

    Energy Technology Data Exchange (ETDEWEB)

    Elias-Miró, J. [SISSA and INFN, I-34136 Trieste (Italy); Montull, M. [Institut de Física d’Altes Energies (IFAE), Barcelona Institute of Science and Technology (BIST), Campus UAB, E-08193 Bellaterra (Spain); Riembau, M. [Institut de Física d’Altes Energies (IFAE), Barcelona Institute of Science and Technology (BIST), Campus UAB, E-08193 Bellaterra (Spain); DESY, Notkestrasse 85, 22607 Hamburg (Germany)

    2016-04-22

    Hamiltonian Truncation Methods are a useful numerical tool to study strongly coupled QFTs. In this work we present a new method to compute the exact corrections, at any order, in the Hamiltonian Truncation approach presented by Rychkov et al. in refs. http://dx.doi.org/10.1103/PhysRevD.91.085011; http://dx.doi.org/10.1103/PhysRevD.93.065014; http://dx.doi.org/10.1103/PhysRevD.91.025005. The method is general but as an example we calculate the exact g{sup 2} and some of the g{sup 3} contributions for the ϕ{sup 4} theory in two dimensions. The coefficients of the local expansion calculated in ref. http://dx.doi.org/10.1103/PhysRevD.91.085011 are shown to be given by phase space integrals. In addition we find new approximations to speed up the numerical calculations and implement them to compute the lowest energy levels at strong coupling. A simple diagrammatic representation of the corrections and various tests are also introduced.

  11. PLK1 has tumor-suppressive potential in APC-truncated colon cancer cells.

    Science.gov (United States)

    Raab, Monika; Sanhaji, Mourad; Matthess, Yves; Hörlin, Albrecht; Lorenz, Ioana; Dötsch, Christina; Habbe, Nils; Waidmann, Oliver; Kurunci-Csacsko, Elisabeth; Firestein, Ron; Becker, Sven; Strebhardt, Klaus

    2018-03-16

    The spindle assembly checkpoint (SAC) acts as a molecular safeguard in ensuring faithful chromosome transmission during mitosis, which is regulated by a complex interplay between phosphatases and kinases including PLK1. Adenomatous polyposis coli (APC) germline mutations cause aneuploidy and are responsible for familial adenomatous polyposis (FAP). Here we study the role of PLK1 in colon cancer cells with chromosomal instability promoted by APC truncation (APC-ΔC). The expression of APC-ΔC in colon cells reduces the accumulation of mitotic cells upon PLK1 inhibition, accelerates mitotic exit and increases the survival of cells with enhanced chromosomal abnormalities. The inhibition of PLK1 in mitotic, APC-∆C-expressing cells reduces the kinetochore levels of Aurora B and hampers the recruitment of SAC component suggesting a compromised mitotic checkpoint. Furthermore, Plk1 inhibition (RNAi, pharmacological compounds) promotes the development of adenomatous polyps in two independent Apc Min/+ mouse models. High PLK1 expression increases the survival of colon cancer patients expressing a truncated APC significantly.

  12. Design Optimization for a Truncated Catenary Mooring System for Scale Model Test

    Directory of Open Access Journals (Sweden)

    Climent Molins

    2015-11-01

    Full Text Available One of the main aspects when testing floating offshore platforms is the scaled mooring system, particularly with the increased depths where such platforms are intended. The paper proposes the use of truncated mooring systems to emulate the real mooring system by solving an optimization problem. This approach could be an interesting option when the existing testing facilities do not have enough available space. As part of the development of a new spar platform made of concrete for Floating Offshore Wind Turbines (FOWTs, called Windcrete, a station keeping system with catenary shaped lines was selected. The test facility available for the planned experiments had an important width constraint. Then, an algorithm to optimize the design of the scaled truncated mooring system using different weights of lines was developed. The optimization process adjusts the quasi-static behavior of the scaled mooring system as much as possible to the real mooring system within its expected maximum displacement range, where the catenary line provides the restoring forces by its suspended line length.

  13. Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yanan; Li, Liang, E-mail: Liang.Li@ualberta.ca

    2013-08-20

    Graphical abstract: -- Highlights: •LC–MS was developed for quantifying protein mixtures containing both intact and N-terminal truncated proteins. •{sup 12}C{sub 2}-Dansylation of the N-terminal amino acid of proteins was done first, followed by microwave-assisted acid hydrolysis. •The released {sup 12}C{sub 2}-dansyl labeled N-terminal amino acid was quantified using {sup 13}C{sub 2}-dansyl labeled amino acid standards. •The method provided accurate and precise results for quantifying intact and N-terminal truncated proteins within 8 h. -- Abstract: The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards.

  14. Increased frequency of FBN1 truncating and splicing variants in Marfan syndrome patients with aortic events.

    Science.gov (United States)

    Baudhuin, Linnea M; Kotzer, Katrina E; Lagerstedt, Susan A

    2015-03-01

    Marfan syndrome is a systemic disorder that typically involves FBN1 mutations and cardiovascular manifestations. We investigated FBN1 genotype-phenotype correlations with aortic events (aortic dissection and prophylactic aortic surgery) in patients with Marfan syndrome. Genotype and phenotype information from probands (n = 179) with an FBN1 pathogenic or likely pathogenic variant were assessed. A higher frequency of truncating or splicing FBN1 variants was observed in Ghent criteria-positive patients with an aortic event (n = 34) as compared with all other probands (n = 145) without a reported aortic event (79 vs. 39%; P Marfan syndrome patients with FBN1 truncating and splicing variants.Genet Med 17 3, 177-187.

  15. Three-dimensional free vibration of functionally graded truncated conical shells subjected to thermal environment

    Energy Technology Data Exchange (ETDEWEB)

    Malekzadeh, P., E-mail: p_malekz@yahoo.com [Department of Mechanical Engineering, Persian Gulf University, Bushehr 75168 (Iran, Islamic Republic of); Fiouz, A.R.; Sobhrouyan, M. [Department of Civil Engineering, Persian Gulf University, Bushehr 75168 (Iran, Islamic Republic of)

    2012-01-15

    A three-dimensional (3D) free vibration analysis of the functionally graded (FG) truncated conical shells subjected to thermal environment is presented. The material properties are assumed to be temperature-dependent and graded in the radius direction, which can vary according to a simple power law distribution. The initial thermal stresses are obtained accurately by solving the thermoelastic equilibrium equations and by considering the two-dimensional axisymmetric temperature distribution in the shell. The differential quadrature method (DQM) as an efficient and accurate numerical tool is adopted to solve the thermal and thermo-mechanical governing equations. For this purpose, a mapping technique is employed to transform the cross section of the shell into the computational domain of DQM. The convergence behavior of the method is numerically demonstrated and comparison studies with the available solutions in the literature are performed. The effects of temperature dependence of material properties, geometrical parameters, material graded index, thermal and mechanical boundary conditions on the frequency parameters of the FG truncated conical shells are carried out. - Highlights: Black-Right-Pointing-Pointer 3D free vibration analysis of the functionally graded truncated conical shells is presented. Black-Right-Pointing-Pointer Two-dimensional axisymmetric temperature distribution in the shell is assumed. Black-Right-Pointing-Pointer The material properties are assumed to be temperature-dependent. Black-Right-Pointing-Pointer Initial thermal stresses due to thermal environment are evaluated accurately and included. Black-Right-Pointing-Pointer Representing the effects of different parameters on the non-dimensional frequencies.

  16. Correlations between chaos in a perturbed sine-Gordon equation and a truncated model system

    International Nuclear Information System (INIS)

    Bishop, A.R.; Flesch, R.; Forests, M.G.; Overman, E.A.

    1990-01-01

    The purpose of this paper is to present a first step toward providing coordinates and associated dynamics for low-dimensional attractors in nearly integrable partial differential equations (pdes), in particular, where the truncated system reflects salient geometric properties of the pde. This is achieved by correlating: (1) numerical results on the bifurcations to temporal chaos with spatial coherence of the damped, periodically forced sine-Gordon equation with periodic boundary conditions; (2) an interpretation of the spatial and temporal bifurcation structures of this perturbed integrable system with regard to the exact structure of the sine-Gordon phase space; (3) a model dynamical systems problem, which is itself a perturbed integrable Hamiltonian system, derived from the perturbed sine-Gordon equation by a finite mode Fourier truncation in the nonlinear Schroedinger limit; and (4) the bifurcations to chaos in the truncated phase space. In particular, a potential source of chaos in both the pde and the model ordinary differential equation systems is focused on: the existence of homoclinic orbits in the unperturbed integrable phase space and their continuation in the perturbed problem. The evidence presented here supports the thesis that the chaotic attractors of the weakly perturbed periodic sine-Gordon system consists of low-dimensional metastable attacking states together with intermediate states that are O(1) unstable and correspond to homoclinic states in the integrable phase space. It is surmised that the chaotic dynamics on these attractors is due to the perturbation of these homocline integrable configurations

  17. Truncating SLC5A7 mutations underlie a spectrum of dominant hereditary motor neuropathies.

    Science.gov (United States)

    Salter, Claire G; Beijer, Danique; Hardy, Holly; Barwick, Katy E S; Bower, Matthew; Mademan, Ines; De Jonghe, Peter; Deconinck, Tine; Russell, Mark A; McEntagart, Meriel M; Chioza, Barry A; Blakely, Randy D; Chilton, John K; De Bleecker, Jan; Baets, Jonathan; Baple, Emma L; Walk, David; Crosby, Andrew H

    2018-04-01

    To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs). The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family. Variants were annotated and filtered, initially focusing on genes associated with neuropathy. Candidate variants were further investigated and confirmed by dideoxy sequence analysis and cosegregation studies. Thorough patient phenotyping was completed, comprising clinical history, examination, and neurologic investigation. dHMNs are a heterogeneous group of peripheral motor neuron disorders characterized by length-dependent neuropathy and progressive distal limb muscle weakness and wasting. We previously reported a dominant-negative frameshift mutation located in the concluding exon of the SLC5A7 gene encoding the choline transporter (CHT), leading to protein truncation, as the likely cause of dominantly-inherited dHMN-VII in an extended UK family. In this study, our genetic studies identified distinct heterozygous frameshift mutations located in the last coding exon of SLC5A7 , predicted to result in the truncation of the CHT C-terminus, as the likely cause of the condition in each family. This study corroborates C-terminal CHT truncation as a cause of autosomal dominant dHMN, confirming upper limb predominating over lower limb involvement, and broadening the clinical spectrum arising from CHT malfunction.

  18. Tailor-made dimensions of diblock copolymer truncated micelles on a solid by UV irradiation.

    Science.gov (United States)

    Liou, Jiun-You; Sun, Ya-Sen

    2015-09-28

    We investigated the structural evolution of truncated micelles in ultrathin films of polystyrene-block-poly(2-vinylpyridine), PS-b-P2VP, of monolayer thickness on bare silicon substrates (SiOx/Si) upon UV irradiation in air- (UVIA) and nitrogen-rich (UVIN) environments. The structural evolution of micelles upon UV irradiation was monitored using GISAXS measurements in situ, while the surface morphology was probed using atomic force microscopy ex situ and the chemical composition using X-ray photoelectron spectroscopy (XPS). This work provides clear evidence for the interpretation of the relationship between the structural evolution and photochemical reactions in PS-b-P2VP truncated micelles upon UVIA and UVIN. Under UVIA treatment, photolysis and cross-linking reactions coexisted within the micelles; photolysis occurred mainly at the top of the micelles, whereas cross-linking occurred preferentially at the bottom. The shape and size of UVIA-treated truncated micelles were controlled predominantly by oxidative photolysis reactions, which depended on the concentration gradient of free radicals and oxygen along the micelle height. Because of an interplay between photolysis and photo-crosslinking, the scattering length densities (SLD) of PS and P2VP remained constant. In contrast, UVIN treatments enhanced the contrast in SLD between the PS shell and the P2VP core as cross-linking dominated over photolysis in the presence of nitrogen. The enhancement of the SLD contrast was due to the various degrees of cross-linking under UVIN for the PS and P2VP blocks.

  19. Zero-truncated panel Poisson mixture models: Estimating the impact on tourism benefits in Fukushima Prefecture.

    Science.gov (United States)

    Narukawa, Masaki; Nohara, Katsuhito

    2018-04-01

    This study proposes an estimation approach to panel count data, truncated at zero, in order to apply a contingent behavior travel cost method to revealed and stated preference data collected via a web-based survey. We develop zero-truncated panel Poisson mixture models by focusing on respondents who visited a site. In addition, we introduce an inverse Gaussian distribution to unobserved individual heterogeneity as an alternative to a popular gamma distribution, making it possible to capture effectively the long tail typically observed in trip data. We apply the proposed method to estimate the impact on tourism benefits in Fukushima Prefecture as a result of the Fukushima Nuclear Power Plant No. 1 accident. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Non-perturbative methodologies for low-dimensional strongly-correlated systems: From non-Abelian bosonization to truncated spectrum methods.

    Science.gov (United States)

    James, Andrew J A; Konik, Robert M; Lecheminant, Philippe; Robinson, Neil J; Tsvelik, Alexei M

    2018-02-26

    We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an introduction to the basic elements of conformal field theory as applied to systems with a current algebra, and we orient the reader by presenting a number of applications of non-Abelian bosonization to models with large symmetries. We then tie this technique into recent advances in the ability of cold atomic systems to realize complex symmetries. Secondly, we discuss truncated spectrum methods for the numerical study of systems in one and two dimensions. For one-dimensional systems we provide the reader with considerable insight into the methodology by reviewing canonical applications of the technique to the Ising model (and its variants) and the sine-Gordon model. Following this we review recent work on the development of renormalization groups, both numerical and analytical, that alleviate the effects of truncating the spectrum. Using these technologies, we consider a number of applications to one-dimensional systems: properties of carbon nanotubes, quenches in the Lieb-Liniger model, 1  +  1D quantum chromodynamics, as well as Landau-Ginzburg theories. In the final part we move our attention to consider truncated spectrum methods applied to two-dimensional systems. This involves combining truncated spectrum methods with matrix product state algorithms. We describe applications of this method to two-dimensional systems of free fermions and the quantum Ising model, including their non-equilibrium dynamics.

  1. Non-perturbative methodologies for low-dimensional strongly-correlated systems: From non-Abelian bosonization to truncated spectrum methods

    Science.gov (United States)

    James, Andrew J. A.; Konik, Robert M.; Lecheminant, Philippe; Robinson, Neil J.; Tsvelik, Alexei M.

    2018-04-01

    We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an introduction to the basic elements of conformal field theory as applied to systems with a current algebra, and we orient the reader by presenting a number of applications of non-Abelian bosonization to models with large symmetries. We then tie this technique into recent advances in the ability of cold atomic systems to realize complex symmetries. Secondly, we discuss truncated spectrum methods for the numerical study of systems in one and two dimensions. For one-dimensional systems we provide the reader with considerable insight into the methodology by reviewing canonical applications of the technique to the Ising model (and its variants) and the sine-Gordon model. Following this we review recent work on the development of renormalization groups, both numerical and analytical, that alleviate the effects of truncating the spectrum. Using these technologies, we consider a number of applications to one-dimensional systems: properties of carbon nanotubes, quenches in the Lieb–Liniger model, 1  +  1D quantum chromodynamics, as well as Landau–Ginzburg theories. In the final part we move our attention to consider truncated spectrum methods applied to two-dimensional systems. This involves combining truncated spectrum methods with matrix product state algorithms. We describe applications of this method to two-dimensional systems of free fermions and the quantum Ising model, including their non-equilibrium dynamics.

  2. Characterization of mTOR-Responsive Truncated mRNAs in Cell Proliferation

    Science.gov (United States)

    2017-07-01

    These findings identify a previously uncharacterized role for mTOR in modulating 3’- UTR length of mRNAs by alternative polyadenylation ( APA ). Another...outcome of APA in the mTOR-activated transcriptome is an early termination of mRNA transcription to produce truncated mRNAs with polyadenylation in...for exhaustive analysis of Alternative cleavage and polyadenylation ( APA ) events (Figure 1). In IntMAP, first the position of multiple

  3. Truncated conformal space approach to scaling Lee-Yang model

    International Nuclear Information System (INIS)

    Yurov, V.P.; Zamolodchikov, Al.B.

    1989-01-01

    A numerical approach to 2D relativstic field theories is suggested. Considering a field theory model as an ultraviolet conformal field theory perturbed by suitable relevant scalar operator one studies it in finite volume (on a circle). The perturbed Hamiltonian acts in the conformal field theory space of states and its matrix elements can be extracted from the conformal field theory. Truncation of the space at reasonable level results in a finite dimensional problem for numerical analyses. The nonunitary field theory with the ultraviolet region controlled by the minimal conformal theory μ(2/5) is studied in detail. 9 refs.; 17 figs

  4. Phospholipid lateral diffusion in phosphatidylcholine-sphingomyelin-cholesterol monolayers; Effects of oxidatively truncated phosphatidylcholines

    Czech Academy of Sciences Publication Activity Database

    Parkkila, P.; Štefl, Martin; Olžyńska, Agnieszka; Hof, Martin; Kinnunen, P. K. J.

    2015-01-01

    Roč. 1848, č. 1 (2015), s. 167-173 ISSN 0005-2736 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388955 Keywords : Oxidatively truncated phosphatidylcholines * Lateral diffusion * Fluorescence correlation spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.687, year: 2015

  5. Expression of a truncated receptor protein tyrosine phosphatase kappa in the brain of an adult transgenic mouse

    DEFF Research Database (Denmark)

    Shen, P; Canoll, P D; Sap, J

    1999-01-01

    that goal, we have used this mouse model to map the distribution of the truncated RPTP-kappa/beta-geo fusion protein in the adult mouse brain using beta-galactosidase as a marker enzyme. Visualization of the beta-galactosidase activity revealed a non-random pattern of expression, and identified cells......-6596]. Nevertheless, since the transgene's expression is driven by the endogenous RPTP-kappa promoter, distribution of the truncated RPTP-kappa/beta-geo fusion protein should reflect the regional and cellular expression of wild-type RPTP-kappa, and thus may identify sites where RPTP-kappa is important. Towards...

  6. Entanglement entropy from the truncated conformal space

    Directory of Open Access Journals (Sweden)

    T. Palmai

    2016-08-01

    Full Text Available A new numerical approach to entanglement entropies of the Rényi type is proposed for one-dimensional quantum field theories. The method extends the truncated conformal spectrum approach and we will demonstrate that it is especially suited to study the crossover from massless to massive behavior when the subsystem size is comparable to the correlation length. We apply it to different deformations of massless free fermions, corresponding to the scaling limit of the Ising model in transverse and longitudinal fields. For massive free fermions the exactly known crossover function is reproduced already in very small system sizes. The new method treats ground states and excited states on the same footing, and the applicability for excited states is illustrated by reproducing Rényi entropies of low-lying states in the transverse field Ising model.

  7. Quasi-SU(3) truncation scheme for even-even sd-shell nuclei

    International Nuclear Information System (INIS)

    Vargas, C.E.; Hirsch, J.G.; Draayer, J.P.

    2001-01-01

    The quasi-SU(3) symmetry was uncovered in full pf and sdg shell-model calculations for both even-even and odd-even nuclei. It manifests itself through a dominance of single-particle and quadrupole-quadrupole terms in a Hamiltonian used to describe well-deformed nuclei. A practical consequence of the quasi-SU(3) symmetry is an efficient basis truncation scheme. In [C.E. Vargas et al., Phys. Rev. C 58 (1998) 1488] it is shown that when this type of Hamiltonian is diagonalized in an SU(3) basis, only a few irreducible representations (irreps) of SU(3) are needed to describe the yrast band, the leading S=0 irrep augmented with the leading S=1 irreps in the proton and neutron subspaces. In the present article the quasi-SU(3) truncation scheme is used, in conjunction with a 'realistic but schematic' Hamiltonian that includes the most important multipole terms, to describe the energy spectra and B(E2) transition strengths of 20,22 Ne, 24 Mg and 28 Si. The effect of the size of the Hilbert space on both sets of observables is discussed, as well as the structure of the yrast band and the importance of the various terms in the Hamiltonian. The limitations of the model are explicitly discussed

  8. On the propagation of truncated localized waves in dispersive silica

    KAUST Repository

    Salem, Mohamed

    2010-01-01

    Propagation characteristics of truncated Localized Waves propagating in dispersive silica and free space are numerically analyzed. It is shown that those characteristics are affected by the changes in the relation between the transverse spatial spectral components and the wave vector. Numerical experiments demonstrate that as the non-linearity of this relation gets stronger, the pulses propagating in silica become more immune to decay and distortion whereas the pulses propagating in free-space suffer from early decay and distortion. © 2010 Optical Society of America.

  9. Simulation of nuclear plant operation into a stochastic energy production model

    International Nuclear Information System (INIS)

    Pacheco, R.L.

    1983-04-01

    A simulation model of nuclear plant operation is developed to fit into a stochastic energy production model. In order to improve the stochastic model used, and also reduce its computational time burdened by the aggregation of the model of nuclear plant operation, a study of tail truncation of the unsupplied demand distribution function has been performed. (E.G.) [pt

  10. Selective apoptosis induction in MCF-7 cell line by truncated minimal functional region of Apoptin

    International Nuclear Information System (INIS)

    Shen Ni, Lim; Allaudin, Zeenathul Nazariah bt; Mohd Lila, Mohd Azmi b; Othman, Abas Mazni b; Othman, Fauziah bt

    2013-01-01

    Chicken Anemia Virus (CAV) VP3 protein (also known as Apoptin), a basic and proline-rich protein has a unique capability in inducing apoptosis in cancer cells but not in normal cells. Five truncated Apoptin proteins were analyzed to determine their selective ability to migrate into the nucleus of human breast adenocarcinoma MCF-7 cells for inducing apoptosis. For identification of the minimal selective domain for apoptosis, the wild-type Apoptin gene had been reconstructed by PCR to generate segmental deletions at the N’ terminal and linked with nuclear localization sites (NLS1 and NLS2). All the constructs were fused with maltose-binding protein gene and individually expressed by in vitro Rapid Translation System. Standardized dose of proteins were delivered into human breast adenocarcinoma MCF-7 cells and control human liver Chang cells by cytoplasmic microinjection, and subsequently observed for selective apoptosis effect. Three of the truncated Apoptin proteins with N-terminal deletions spanning amino acid 32–83 retained the cancer selective nature of wild-type Apoptin. The proteins were successfully translocated to the nucleus of MCF-7 cells initiating apoptosis, whereas non-toxic cytoplasmic retention was observed in normal Chang cells. Whilst these truncated proteins retained the tumour-specific death effector ability, the specificity for MCF-7 cells was lost in two other truncated proteins that harbor deletions at amino acid 1–31. The detection of apoptosing normal Chang cells and MCF-7 cells upon cytoplasmic microinjection of these proteins implicated a loss in Apoptin’s signature targeting activity. Therefore, the critical stretch spanning amino acid 1–31 at the upstream of a known hydrophobic leucine-rich stretch (LRS) was strongly suggested as one of the prerequisite region in Apoptin for cancer targeting. Identification of this selective domain provides a platform for developing small targets to facilitating carrier-mediated-transport across

  11. Ab Initio Study of 40Ca with an Importance Truncated No-Core Shell Model

    Energy Technology Data Exchange (ETDEWEB)

    Roth, R; Navratil, P

    2007-05-22

    We propose an importance truncation scheme for the no-core shell model, which enables converged calculations for nuclei well beyond the p-shell. It is based on an a priori measure for the importance of individual basis states constructed by means of many-body perturbation theory. Only the physically relevant states of the no-core model space are considered, which leads to a dramatic reduction of the basis dimension. We analyze the validity and efficiency of this truncation scheme using different realistic nucleon-nucleon interactions and compare to conventional no-core shell model calculations for {sup 4}He and {sup 16}O. Then, we present the first converged calculations for the ground state of {sup 40}Ca within no-core model spaces including up to 16{h_bar}{Omega}-excitations using realistic low-momentum interactions. The scheme is universal and can be easily applied to other quantum many-body problems.

  12. Solution of the Stieltjes truncated matrix moment problem

    Directory of Open Access Journals (Sweden)

    Vadim M. Adamyan

    2005-01-01

    Full Text Available The truncated Stieltjes matrix moment problem consisting in the description of all matrix distributions \\(\\boldsymbol{\\sigma}(t\\ on \\([0,\\infty\\ with given first \\(2n+1\\ power moments \\((\\mathbf{C}_j_{n=0}^j\\ is solved using known results on the corresponding Hamburger problem for which \\(\\boldsymbol{\\sigma}(t\\ are defined on \\((-\\infty,\\infty\\. The criterion of solvability of the Stieltjes problem is given and all its solutions in the non-degenerate case are described by selection of the appropriate solutions among those of the Hamburger problem for the same set of moments. The results on extensions of non-negative operators are used and a purely algebraic algorithm for the solution of both Hamburger and Stieltjes problems is proposed.

  13. Developmental regulation of human truncated nerve growth factor receptor

    Energy Technology Data Exchange (ETDEWEB)

    DiStefano, P.S.; Clagett-Dame, M.; Chelsea, D.M.; Loy, R. (Abbott Laboratories, Abbott Park, IL (USA))

    1991-01-01

    Monoclonal antibodies (designated XIF1 and IIIG5) recognizing distinct epitopes of the human truncated nerve growth factor receptor (NGF-Rt) were used in a two-site radiometric immunosorbent assay to monitor levels of NGF-Rt in human urine as a function of age. Urine samples were collected from 70 neurologically normal subjects ranging in age from 1 month to 68 years. By using this sensitive two-site radiometric immunosorbent assay, NGF-Rt levels were found to be highest in urine from 1-month old subjects. By 2.5 months, NGF-Rt values were half of those seen at 1 month and decreased more gradually between 0.5 and 15 years. Between 15 and 68 years, urine NGF-Rt levels were relatively constant at 5% of 1-month values. No evidence for diurnal variation of adult NGF-Rt was apparent. Pregnant women in their third trimester showed significantly elevated urine NGF-Rt values compared with age-matched normals. Affinity labeling of NGF-Rt with 125I-NGF followed by immunoprecipitation with ME20.4-IgG and gel autoradiography indicated that neonatal urine contained high amounts of truncated receptor (Mr = 50 kd); decreasingly lower amounts of NGF-Rt were observed on gel autoradiograms with development, indicating that the two-site radiometric immunosorbent assay correlated well with the affinity labeling technique for measuring NGF-Rt. NGF-Rt in urines from 1-month-old and 36-year-old subjects showed no differences in affinities for NGF or for the monoclonal antibody IIIG5. These data show that NGF-Rt is developmentally regulated in human urine, and are discussed in relation to the development and maturation of the peripheral nervous system.

  14. Developmental regulation of human truncated nerve growth factor receptor

    International Nuclear Information System (INIS)

    DiStefano, P.S.; Clagett-Dame, M.; Chelsea, D.M.; Loy, R.

    1991-01-01

    Monoclonal antibodies (designated XIF1 and IIIG5) recognizing distinct epitopes of the human truncated nerve growth factor receptor (NGF-Rt) were used in a two-site radiometric immunosorbent assay to monitor levels of NGF-Rt in human urine as a function of age. Urine samples were collected from 70 neurologically normal subjects ranging in age from 1 month to 68 years. By using this sensitive two-site radiometric immunosorbent assay, NGF-Rt levels were found to be highest in urine from 1-month old subjects. By 2.5 months, NGF-Rt values were half of those seen at 1 month and decreased more gradually between 0.5 and 15 years. Between 15 and 68 years, urine NGF-Rt levels were relatively constant at 5% of 1-month values. No evidence for diurnal variation of adult NGF-Rt was apparent. Pregnant women in their third trimester showed significantly elevated urine NGF-Rt values compared with age-matched normals. Affinity labeling of NGF-Rt with 125I-NGF followed by immunoprecipitation with ME20.4-IgG and gel autoradiography indicated that neonatal urine contained high amounts of truncated receptor (Mr = 50 kd); decreasingly lower amounts of NGF-Rt were observed on gel autoradiograms with development, indicating that the two-site radiometric immunosorbent assay correlated well with the affinity labeling technique for measuring NGF-Rt. NGF-Rt in urines from 1-month-old and 36-year-old subjects showed no differences in affinities for NGF or for the monoclonal antibody IIIG5. These data show that NGF-Rt is developmentally regulated in human urine, and are discussed in relation to the development and maturation of the peripheral nervous system

  15. Effect of Truncating AUC at 12, 24 and 48 hr When Evaluating the Bioequivalence of Drugs with a Long Half-Life.

    Science.gov (United States)

    Moreno, Isabel; Ochoa, Dolores; Román, Manuel; Cabaleiro, Teresa; Abad-Santos, Francisco

    2016-01-01

    Bioequivalence studies of drugs with a long half-life require long periods of time for pharmacokinetic sampling. The latest update of the European guideline allows the area under the curve (AUC) truncated at 72 hr to be used as an alternative to AUC0-t as the primary parameter. The objective of this study was to evaluate the effect of truncating the AUC at 48, 24 and 12 hr on the acceptance of the bioequivalence criterion as compared with truncation at 72 hr in bioequivalence trials. The effect of truncated AUC on the within-individual coefficient of variation (CVw) and on the ratio of the formulations was also analysed. Twenty-eight drugs were selected from bioequivalence trials. Pharmacokinetic data were analysed using WinNonLin 2.0 based on the trapezoidal method. Analysis of variance (ANOVA) was performed to obtain the ratios and 90% confidence intervals for AUC at different time-points. The degree of agreement of AUC0-72 in relation to AUC0-48 and AUC0-24, according to the Landis and Koch classification, was 'almost perfect'. Statistically significant differences were observed when the CVw of AUC truncated at 72, 48 and 24 hr was compared with the CVw of AUC0-12. There were no statistically significant differences in the AUC ratio at any time-point. Compared to AUC0-72, Pearson's correlation coefficient for mean AUC, AUC ratio and AUC CVw was worse for AUC0-12 than AUC0-24 or AUC0-48. These preliminary results could suggest that AUC truncation at 24 or 48 hr is adequate to determine whether two formulations are bioequivalent. © 2015 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

  16. Truncation effects in connected arrays: Analytical models to describe the edge-induced wave phenomena

    NARCIS (Netherlands)

    Neto, A.; Cavallo, D.; Gerini, G.

    2011-01-01

    This paper presents a Green's function based procedure to assess edge effects in finite wideband connected arrays. Truncation effects are more severe in broadband arrays, since the inter-element mutual coupling facilitates the propagation of edge-born waves that can become dominant over large

  17. Electron transfer reactions, cyanide and O2 binding of truncated hemoglobin from Bacillus subtilis

    DEFF Research Database (Denmark)

    Fernandez, Esther; Larsson, Jonas T.; McLean, Kirsty J.

    2013-01-01

    The truncated hemoglobin from Bacillus subtilis (trHb-Bs) possesses a surprisingly high affinity for oxygen and resistance to (auto)oxidation; its physiological role in the bacterium is not understood and may be connected with its very special redox and ligand binding reactions. Electron transfer...

  18. One-step green synthesis of cuprous oxide crystals with truncated octahedra shapes via a high pressure flux approach

    International Nuclear Information System (INIS)

    Li Benxian; Wang Xiaofeng; Xia Dandan; Chu Qingxin; Liu Xiaoyang; Lu Fengguo; Zhao Xudong

    2011-01-01

    Cuprous oxide (Cu 2 O) was synthesized via reactions between cupric oxide (CuO) and copper metal (Cu) at a low temperature of 300 deg. C. This progress is green, environmentally friendly and energy efficient. Cu 2 O crystals with truncated octahedra morphology were grown under high pressure using sodium hydroxide (NaOH) and potassium hydroxide (KOH) with a molar ratio of 1:1 as a flux. The growth mechanism of Cu 2 O polyhedral microcrystals are proposed and discussed. - Graphical Abstract: The Cu 2 O crystals with truncated octahedral shape were one-step synthesized in high yield via high pressure flux method for the first time, which is green and environmentally friendly. The mechanisms of synthesis and crystal growth were discussed in this paper. Highlights: → Cuprous oxide was one-step green synthesized by high pressure flux method. → The approach was based on the reverse dismutation reactions between cupric oxide and copper metal. → This progress is green, environmentally friendly and energy efficient. → The synthesized Cu2O crystals were of truncated octahedra morphology.

  19. Enhanced cell surface expression, immunogenicity and genetic stability resulting from a spontaneous truncation of HIV Env expressed by a recombinant MVA

    International Nuclear Information System (INIS)

    Wyatt, Linda S.; Belyakov, Igor M.; Earl, Patricia L.; Berzofsky, Jay A.; Moss, Bernard

    2008-01-01

    During propagation of modified vaccinia virus Ankara (MVA) encoding HIV 89.6 Env, a few viral foci stained very prominently. Virus cloned from such foci replicated to higher titers than the parent and displayed enhanced genetic stability on passage. Sequence analysis showed a single nucleotide deletion in the 89.6 env gene of the mutant that caused a frame shift and truncation of 115 amino acids from the cytoplasmic domain. The truncated Env was more highly expressed on the cell surface, induced higher antibody responses than the full-length Env, reacted with HIV neutralizing monoclonal antibodies and mediated CD4/co-receptor-dependent fusion. Intramuscular (IM), intradermal (ID) needleless, and intrarectal (IR) catheter inoculations gave comparable serum IgG responses. However, intraoral (IO) needleless injector route gave the highest IgA in lung washings and IR gave the highest IgA and IgG responses in fecal extracts. Induction of CTL responses in the spleens of individual mice as assayed by intracellular cytokine staining was similar with both the full-length and truncated Env constructs. Induction of acute and memory CTL in the spleens of mice immunized with the truncated Env construct by ID, IO, and IR routes was comparable and higher than by the IM route, but only the IR route induced CTL in the gut-associated lymphoid tissue. Thus, truncation of Env enhanced genetic stability as well as serum and mucosal antibody responses, suggesting the desirability of a similar modification in MVA-based candidate HIV vaccines

  20. Shell model truncation schemes for rotational nuclei

    International Nuclear Information System (INIS)

    Halse, P.; Jaqua, L.; Barrett, B.R.

    1990-01-01

    The suitability of the pair condensate approach for rotational states is studied in a single j = 17/2 shell of identical nucleons interacting through a quadrupole-quadrupole hamiltonian. The ground band and a K = 2 excited band are both studied in detail. A direct comparison of the exact states with those constituting the SD and SDG subspaces is used to identify the important degrees of freedom for these levels. The range of pairs necessary for a good description is found to be highly state dependent; S and D pairs are the major constituents of the low-spin ground band levels, while G pairs are needed for those in the γ-band. Energy spectra are obtained for each truncated subspace. SDG pairs allow accurate reproduction of the binding energy and K = 2 excitation energy, but still give a moment of inertia which is about 30% too small even for the lowest levels

  1. Joint survival probability via truncated invariant copula

    International Nuclear Information System (INIS)

    Kim, Jeong-Hoon; Ma, Yong-Ki; Park, Chan Yeol

    2016-01-01

    Highlights: • We have studied an issue of dependence structure between default intensities. • We use a multivariate shot noise intensity process, where jumps occur simultaneously and their sizes are correlated. • We obtain the joint survival probability of the integrated intensities by using a copula. • We apply our theoretical result to pricing basket default swap spread. - Abstract: Given an intensity-based credit risk model, this paper studies dependence structure between default intensities. To model this structure, we use a multivariate shot noise intensity process, where jumps occur simultaneously and their sizes are correlated. Through very lengthy algebra, we obtain explicitly the joint survival probability of the integrated intensities by using the truncated invariant Farlie–Gumbel–Morgenstern copula with exponential marginal distributions. We also apply our theoretical result to pricing basket default swap spreads. This result can provide a useful guide for credit risk management.

  2. N-terminally truncated forms of human cathepsin F accumulate in aggresome-like inclusions.

    Science.gov (United States)

    Jerič, Barbara; Dolenc, Iztok; Mihelič, Marko; Klarić, Martina; Zavašnik-Bergant, Tina; Gunčar, Gregor; Turk, Boris; Turk, Vito; Stoka, Veronika

    2013-10-01

    The contribution of individual cysteine cathepsins as positive mediators of programmed cell death is dependent on several factors, such as the type of stimuli, intensity and duration of the stimulus, and cell type involved. Of the eleven human cysteine cathepsins, cathepsin F is the only cathepsin that exhibits an extended N-terminal proregion, which contains a cystatin-like domain. We predicted that the wild-type human cathepsin F contains three natively disordered regions within the enzyme's propeptide and various amino acid stretches with high fibrillation propensity. Wild-type human cathepsin F and its N-terminally truncated forms, Ala(20)-Asp(484) (Δ(19)CatF), Pro(126)-Asp(484) (Δ(125)CatF), and Met(147)-Asp(484) (Δ(146)CatF) were cloned into the pcDNA3 vector and overexpressed in HEK 293T cells. Wild-type human cathepsin F displayed a clear vesicular labeling and colocalized with the LAMP2 protein, a lysosomal marker. However, all three N-terminally truncated forms of human cathepsin F were recovered as insoluble proteins, suggesting that the deletion of at least the signal peptides (Δ(19)CatF), results in protein aggregation. Noteworthy, they concentrated large perinuclear-juxtanuclear aggregates that accumulated within aggresome-like inclusions. These inclusions showed p62-positive immunoreactivity and were colocalized with the autophagy marker LC3B, but not with the LAMP2 protein. In addition, an approximately 2-3 fold increase in DEVDase activity was not sufficient to induce apoptotic cell death. These results suggested the clearance of the N-terminally truncated forms of human cathepsin F via the autophagy pathway, underlying its protective and prosurvival mechanisms. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Hardware Design and Implementation of Fixed-Width Standard and Truncated 4×4, 6×6, 8×8 and 12×12-BIT Multipliers Using Fpga

    Science.gov (United States)

    Rais, Muhammad H.

    2010-06-01

    This paper presents Field Programmable Gate Array (FPGA) implementation of standard and truncated multipliers using Very High Speed Integrated Circuit Hardware Description Language (VHDL). Truncated multiplier is a good candidate for digital signal processing (DSP) applications such as finite impulse response (FIR) and discrete cosine transform (DCT). Remarkable reduction in FPGA resources, delay, and power can be achieved using truncated multipliers instead of standard parallel multipliers when the full precision of the standard multiplier is not required. The truncated multipliers show significant improvement as compared to standard multipliers. Results show that the anomaly in Spartan-3 AN average connection and maximum pin delay have been efficiently reduced in Virtex-4 device.

  4. On the Minimax Value in the Scale Model with Truncated Data

    OpenAIRE

    Gajek, Leslaw

    1988-01-01

    Let $X$ be a positive random variable with Lebesgue density $f_\\theta(x)$, where $\\theta$ is the scale parameter, and let $Y$ be a positive random variable independent of $X$. We consider two models of truncation: the LHS model, where the data consist only of those observations of $X$ for which $X > Y$; and the RHS model, where the data consist of those observations of $X$ for which $X \\leq Y$. Consider the problem of estimating $\\theta^s, s \

  5. Algorithmic impediments filtration using the α-truncated mean method in resolver-to-digital converter

    Directory of Open Access Journals (Sweden)

    Gordiyenko V. I.

    2009-02-01

    Full Text Available A test diagram of the microcontroller-type resolver-to-digital converter and algorithms for impediments filtration therein are developed. Experimental verification of the α-truncated mean algorithm intended for the suppression of impulse and noise interference is conducted. The test results are given.

  6. An analysis of longitudinal data with nonignorable dropout using the truncated multivariate normal distribution

    NARCIS (Netherlands)

    Jolani, Shahab

    2014-01-01

    For a vector of multivariate normal when some elements, but not necessarily all, are truncated, we derive the moment generating function and obtain expressions for the first two moments involving the multivariate hazard gradient. To show one of many applications of these moments, we then extend the

  7. A truncated accretion disk in the galactic black hole candidate source H1743-322

    International Nuclear Information System (INIS)

    Sriram, Kandulapati; Agrawal, Vivek Kumar; Rao, Arikkala Raghurama

    2009-01-01

    To investigate the geometry of the accretion disk in the source H1743-322, we have carried out a detailed X-ray temporal and spectral study using RXTE pointed observations. We have selected all data pertaining to the Steep Power Law (SPL) state during the 2003 outburst of this source. We find anti-correlated hard X-ray lags in three of the observations and the changes in the spectral and timing parameters (like the QPO frequency) confirm the idea of a truncated accretion disk in this source. Compiling data from similar observations of other sources, we find a correlation between the fractional change in the QPO frequency and the observed delay. We suggest that these observations indicate a definite size scale in the inner accretion disk (the radius of the truncated disk) and we explain the observed correlation using various disk parameters like Compton cooling time scale, viscous time scale etc. (research papers)

  8. On the Computation of Optimal Monotone Mean-Variance Portfolios via Truncated Quadratic Utility

    OpenAIRE

    Ales Cerný; Fabio Maccheroni; Massimo Marinacci; Aldo Rustichini

    2008-01-01

    We report a surprising link between optimal portfolios generated by a special type of variational preferences called divergence preferences (cf. [8]) and optimal portfolios generated by classical expected utility. As a special case we connect optimization of truncated quadratic utility (cf. [2]) to the optimal monotone mean-variance portfolios (cf. [9]), thus simplifying the computation of the latter.

  9. A novel homozygous truncating GNAT1 mutation implicated in retinal degeneration.

    Science.gov (United States)

    Carrigan, Matthew; Duignan, Emma; Humphries, Pete; Palfi, Arpad; Kenna, Paul F; Farrar, G Jane

    2016-04-01

    The GNAT1 gene encodes the α subunit of the rod transducin protein, a key element in the rod phototransduction cascade. Variants in GNAT1 have been implicated in stationary night-blindness in the past, but unlike other proteins in the same pathway, it has not previously been implicated in retinitis pigmentosa. A panel of 182 retinopathy-associated genes was sequenced to locate disease-causing mutations in patients with inherited retinopathies. Sequencing revealed a novel homozygous truncating mutation in the GNAT1 gene in a patient with significant pigmentary disturbance and constriction of visual fields, a presentation consistent with retinitis pigmentosa. This is the first report of a patient homozygous for a complete loss-of-function GNAT1 mutation. The clinical data from this patient provide definitive evidence of retinitis pigmentosa with late onset in addition to the lifelong night-blindness that would be expected from a lack of transducin function. These data suggest that some truncating GNAT1 variants can indeed cause a recessive, mild, late-onset retinal degeneration in human beings rather than just stationary night-blindness as reported previously, with notable similarities to the phenotype of the Gnat1 knockout mouse. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  10. Quasi-SU(3) truncation scheme for even-even sd-shell nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Vargas, C.E. E-mail: cvargas@fis.cinvestav.mx; Hirsch, J.G. E-mail: hirsch@nuclecu.unam.mx; Draayer, J.P. E-mail: draayer@lsu.edu

    2001-07-30

    The quasi-SU(3) symmetry was uncovered in full pf and sdg shell-model calculations for both even-even and odd-even nuclei. It manifests itself through a dominance of single-particle and quadrupole-quadrupole terms in a Hamiltonian used to describe well-deformed nuclei. A practical consequence of the quasi-SU(3) symmetry is an efficient basis truncation scheme. In [C.E. Vargas et al., Phys. Rev. C 58 (1998) 1488] it is shown that when this type of Hamiltonian is diagonalized in an SU(3) basis, only a few irreducible representations (irreps) of SU(3) are needed to describe the yrast band, the leading S=0 irrep augmented with the leading S=1 irreps in the proton and neutron subspaces. In the present article the quasi-SU(3) truncation scheme is used, in conjunction with a 'realistic but schematic' Hamiltonian that includes the most important multipole terms, to describe the energy spectra and B(E2) transition strengths of {sup 20,22}Ne, {sup 24}Mg and {sup 28}Si. The effect of the size of the Hilbert space on both sets of observables is discussed, as well as the structure of the yrast band and the importance of the various terms in the Hamiltonian. The limitations of the model are explicitly discussed.

  11. Ascending-ramp biphasic waveform has a lower defibrillation threshold and releases less troponin I than a truncated exponential biphasic waveform.

    Science.gov (United States)

    Huang, Jian; Walcott, Gregory P; Ruse, Richard B; Bohanan, Scott J; Killingsworth, Cheryl R; Ideker, Raymond E

    2012-09-11

    We tested the hypothesis that the shape of the shock waveform affects not only the defibrillation threshold but also the amount of cardiac damage. Defibrillation thresholds were determined for 11 waveforms-3 ascending-ramp waveforms, 3 descending-ramp waveforms, 3 rectilinear first-phase biphasic waveforms, a Gurvich waveform, and a truncated exponential biphasic waveform-in 6 pigs with electrodes in the right ventricular apex and superior vena cava. The ascending, descending, and rectilinear waveforms had 4-, 8-, and 16-millisecond first phases and a 3.5-millisecond rectilinear second phase that was half the voltage of the first phase. The exponential biphasic waveform had a 60% first-phase and a 50% second-phase tilt. In a second study, we attempted to defibrillate after 10 seconds of ventricular fibrillation with a single ≈30-J shock (6 pigs successfully defibrillated with 8-millisecond ascending, 8-millisecond rectilinear, and truncated exponential biphasic waveforms). Troponin I blood levels were determined before and 2 to 10 hours after the shock. The lowest-energy defibrillation threshold was for the 8-milliseconds ascending ramp (14.6±7.3 J [mean±SD]), which was significantly less than for the truncated exponential (19.6±6.3 J). Six hours after shock, troponin I was significantly less for the ascending-ramp waveform (0.80±0.54 ng/mL) than for the truncated exponential (1.92±0.47 ng/mL) or the rectilinear waveform (1.17±0.45 ng/mL). The ascending ramp has a significantly lower defibrillation threshold and at ≈30 J causes 58% less troponin I release than the truncated exponential biphasic shock. Therefore, the shock waveform affects both the defibrillation threshold and the amount of cardiac damage.

  12. A computational approach for a fluid queue driven by a truncated birth-death process

    NARCIS (Netherlands)

    Lenin, R.B.; Parthasarathy, P.R.

    1999-01-01

    In this paper, we consider a fluid queue driven by a truncated birth-death process with general birth and death rates. We find the equilibrium distribution of the content of the fluid buffer by computing the eigenvalues and eigenvectors of an associated real tridiagonal matrix. We provide efficient

  13. Neurodegeneration caused by expression of human truncated tau leads to progressive neurobehavioural impairment in transgenic rats.

    Science.gov (United States)

    Hrnkova, Miroslava; Zilka, Norbert; Minichova, Zuzana; Koson, Peter; Novak, Michal

    2007-01-26

    Human truncated tau protein is an active constituent of the neurofibrillary degeneration in sporadic Alzheimer's disease. We have shown that modified tau protein, when expressed as a transgene in rats, induced AD characteristic tau cascade consisting of tau hyperphosphorylation, formation of argyrophilic tangles and sarcosyl-insoluble tau complexes. These pathological changes led to the functional impairment characterized by a variety of neurobehavioural symptoms. In the present study we have focused on the behavioural alterations induced by transgenic expression of human truncated tau. Transgenic rats underwent a battery of behavioural tests involving cognitive- and sensorimotor-dependent tasks accompanied with neurological assessment at the age of 4.5, 6 and 9 months. Behavioural examination of these rats showed altered spatial navigation in Morris water maze resulting in less time spent in target quadrant (popen field was not influenced by transgene expression. However beam walking test revealed that transgenic rats developed progressive sensorimotor disturbances related to the age of tested animals. The disturbances were most pronounced at the age of 9 months (p<0.01). Neurological alterations indicating impaired reflex responses were other added features of behavioural phenotype of this novel transgenic rat. These results allow us to suggest that neurodegeneration, caused by the non-mutated human truncated tau derived from sporadic human AD, result in the neuronal dysfunction consequently leading to the progressive neurobehavioural impairment.

  14. Seniority truncation in an equations-of-motion approach to the shell model

    International Nuclear Information System (INIS)

    Covello, A.; Andreozzi, F.; Gargano, A.; Porrino, A.

    1989-01-01

    This paper presents an equations-of-motion method for treating shell-model problems within the framework of the seniority scheme. This method can be applied at many levels of approximation and represents therefore a valuable tool to further reduce seniority truncated shell-model spaces. To show its practical value the authors report some results of an extensive study of the N = 82 isotones which is currently under way

  15. Loads experiments study on two-story RC box and truncated conical walls

    International Nuclear Information System (INIS)

    Asega, H.; Iizuka, S.; Kurihara, I.; Kubo, T.

    1987-01-01

    The failure modes of the two specimens were the sliding shear failure. The two specimens showed almost equal deformation at the maximum shear strength. The ratio of the flexural deformation in the deformation of the truncated conical was larger than that of the box wall. The ratio of the shear deformation in the deformation of the two-story RC box wall was larger than that of the flexural deformation. (orig./HP)

  16. An ABCA1 truncation shows no dominant negative effect in a familial hypoalphalipoproteinemia pedigree with three ABCA1 mutations

    Energy Technology Data Exchange (ETDEWEB)

    Sorrenson, Brie; Suetani, Rachel J. [Department of Biochemistry, University of Otago, Dunedin (New Zealand); Bickley, Vivienne M.; George, Peter M. [Clinical Biochemistry, Canterbury Health Laboratories, Christchurch (New Zealand); Williams, Michael J.A. [Department of Medicine, University of Otago, Dunedin (New Zealand); Scott, Russell S. [Lipid and Diabetes Research Group, Christchurch Hospital (New Zealand); McCormick, Sally P.A., E-mail: sally.mccormick@otago.ac.nz [Department of Biochemistry, University of Otago, Dunedin (New Zealand)

    2011-06-10

    Highlights: {yields} Characterisation of an ABCA1 truncation mutant, C978fsX988, in a pedigree with three ABCA1 mutations. {yields} Functional analysis of C978fsX988 in patient fibroblasts and HEK 293 cells shows no cholesterol efflux function. {yields} Allele-specific quantification shows C978fsX988 not expressed at mRNA level in fibroblasts. {yields} Unlike other ABCA1 truncations, C978fsX988 mutant shows no dominant negative effect at mRNA or protein level. -- Abstract: The ATP binding cassette transporter (ABCA1) A1 is a key determinant of circulating high density lipoprotein cholesterol (HDL-C) levels. Mutations in ABCA1 are a major genetic contributor to low HDL-C levels within the general population. Following the finding of three different ABCA1 mutations, p.C978fsX988, p.T1512M and p.N1800H in a subject with hypoalphalipoproteinemia, we aimed to establish whether the p.C978fsX988 truncation exerted a dominant negative effect on the full-length ABCA1 alleles within family members as has been reported for other ABCA1 truncations. Characterisation of the p.C978fsX988 mutant in transfected HEK 293 cells showed it to be expressed as a GFP fusion protein but lacking in cholesterol efflux function. This was in keeping with results from cholesterol efflux assays in the fibroblasts of p.C978fsX988 carriers which also showed impaired efflux. Allele- specific quantification of p.C978fsX988 mRNA and analysis of ABCA1 protein levels in the fibroblasts of p.C978fsX988 heterozygotes showed negligible levels of mRNA and protein expression. There was no evidence of a dominant negative effect on wildtype or p.N1800H protein levels. We conclude that in the case of the p.C978fsX988 truncated mutant a lack of expression precludes it from having a dominant negative effect.

  17. Vortex breakdown in a truncated conical bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Balci, Adnan; Brøns, Morten [DTU Compute, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark); Herrada, Miguel A [E.S.I, Universidad de Sevilla, Camino de los Descubrimientos s/n, E-41092 (Spain); Shtern, Vladimir N, E-mail: mobr@dtu.dk [Shtern Research and Consulting, Houston, TX 77096 (United States)

    2015-12-15

    This numerical study explains the eddy formation and disappearance in a slow steady axisymmetric air–water flow in a vertical truncated conical container, driven by the rotating top disk. Numerous topological metamorphoses occur as the water height, H{sub w}, and the bottom-sidewall angle, α, vary. It is found that the sidewall convergence (divergence) from the top to the bottom stimulates (suppresses) the development of vortex breakdown (VB) in both water and air. At α = 60°, the flow topology changes eighteen times as H{sub w} varies. The changes are due to (a) competing effects of AMF (the air meridional flow) and swirl, which drive meridional motions of opposite directions in water, and (b) feedback of water flow on AMF. For small H{sub w}, the AMF effect dominates. As H{sub w} increases, the swirl effect dominates and causes VB. The water flow feedback produces and modifies air eddies. The results are of fundamental interest and can be relevant for aerial bioreactors. (paper)

  18. Vortex breakdown in a truncated conical bioreactor

    International Nuclear Information System (INIS)

    Balci, Adnan; Brøns, Morten; Herrada, Miguel A; Shtern, Vladimir N

    2015-01-01

    This numerical study explains the eddy formation and disappearance in a slow steady axisymmetric air–water flow in a vertical truncated conical container, driven by the rotating top disk. Numerous topological metamorphoses occur as the water height, H w , and the bottom-sidewall angle, α, vary. It is found that the sidewall convergence (divergence) from the top to the bottom stimulates (suppresses) the development of vortex breakdown (VB) in both water and air. At α = 60°, the flow topology changes eighteen times as H w varies. The changes are due to (a) competing effects of AMF (the air meridional flow) and swirl, which drive meridional motions of opposite directions in water, and (b) feedback of water flow on AMF. For small H w , the AMF effect dominates. As H w increases, the swirl effect dominates and causes VB. The water flow feedback produces and modifies air eddies. The results are of fundamental interest and can be relevant for aerial bioreactors. (paper)

  19. Effect of truncated glucagon-like peptide-1 [proglucagon-(78-107) amide] on endocrine secretion from pig pancreas, antrum, and nonantral stomach

    DEFF Research Database (Denmark)

    Orskov, C; Holst, J J; Nielsen, O V

    1988-01-01

    We studied the effect of truncated glucagon-like peptide-1 [naturally occurring GLP-1; proglucagon-(78-107) amide], a potent insulinotropic peptide from the pig ileum, on endocrine and exocrine secretion of potential gastrointestinal target organs using isolated perfused preparations of the porcine...... pancreas, antrum, and nonantral part of the stomach. Truncated GLP-1 significantly increased somatostatin secretion from the pancreas at 10(-10) mol/liter and more than doubled the secretion at 10(-9) mol/liter, but had no effect on either somatostatin or gastrin secretion from the antrum...... or on somatostatin secretion from the nonantral stomach in concentrations up to 10(-8) mol/liter. Insulin secretion from the pancreas (with 7 mmol/liter glucose in the perfusate) increased 2-fold with truncated GLP-1 at 10(-10) mol/liter and almost 5-fold at 10(-9) mol/liter. Pancreatic glucagon secretion...

  20. CONVERGENCE OF THE FRACTIONAL PARTS OF THE RANDOM VARIABLES TO THE TRUNCATED EXPONENTIAL DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    Bogdan Gheorghe Munteanu

    2013-01-01

    Full Text Available Using the stochastic approximations, in this paper it was studiedthe convergence in distribution of the fractional parts of the sum of random variables to the truncated exponential distribution with parameter lambda. This fact is feasible by means of the Fourier-Stieltjes sequence (FSS of the random variable.

  1. General Relativistic Radiation MHD Simulations of Supercritical Accretion onto a Magnetized Neutron Star: Modeling of Ultraluminous X-Ray Pulsars

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Hiroyuki R. [Center for Computational Astrophysics, National Astronomical Observatory of Japan, National Institutes of Natural Sciences, Mitaka, Tokyo 181-8588 (Japan); Ohsuga, Ken, E-mail: takahashi@cfca.jp, E-mail: ken.ohsuga@nao.ac.jp [Division of Theoretical Astronomy, National Astronomical Observatory of Japan, National Institutes of Natural Sciences, Mitaka, Tokyo 181-8588 (Japan)

    2017-08-10

    By performing 2.5-dimensional general relativistic radiation magnetohydrodynamic simulations, we demonstrate supercritical accretion onto a non-rotating, magnetized neutron star, where the magnetic field strength of dipole fields is 10{sup 10} G on the star surface. We found the supercritical accretion flow consists of two parts: the accretion columns and the truncated accretion disk. The supercritical accretion disk, which appears far from the neutron star, is truncated at around ≃3 R {sub *} ( R {sub *} = 10{sup 6} cm is the neutron star radius), where the magnetic pressure via the dipole magnetic fields balances with the radiation pressure of the disks. The angular momentum of the disk around the truncation radius is effectively transported inward through magnetic torque by dipole fields, inducing the spin up of a neutron star. The evaluated spin-up rate, ∼−10{sup −11} s s{sup −1}, is consistent with the recent observations of the ultraluminous X-ray pulsars. Within the truncation radius, the gas falls onto a neutron star along the dipole fields, which results in a formation of accretion columns onto the northern and southern hemispheres. The net accretion rate and the luminosity of the column are ≃66 L {sub Edd}/ c {sup 2} and ≲10 L {sub Edd}, where L {sub Edd} is the Eddington luminosity and c is the light speed. Our simulations support a hypothesis whereby the ultraluminous X-ray pulsars are powered by the supercritical accretion onto the magnetized neutron stars.

  2. Computing the Moments of Order Statistics from Truncated Pareto Distributions Based on the Conditional Expectation

    Directory of Open Access Journals (Sweden)

    Gökhan Gökdere

    2014-05-01

    Full Text Available In this paper, closed form expressions for the moments of the truncated Pareto order statistics are obtained by using conditional distribution. We also derive some results for the moments which will be useful for moment computations based on ordered data.

  3. Effect of Synthetic Truncated Apolipoprotein C-I Peptide on Plasma Lipoprotein Cholesterol in Nonhuman Primates

    Directory of Open Access Journals (Sweden)

    Rampratap S. Kushwaha

    2004-01-01

    Full Text Available The present studies were conducted to determine whether a synthetic truncated apoC-I peptide that inhibits CETP activity in baboons would raise plasma HDL cholesterol levels in nonhuman primates with low HDL levels. We used 2 cynomolgus monkeys and 3 baboons fed a cholesterol- and fat-enriched diet. In cynomolgus monkeys, we injected synthetic truncated apoC-I inhibitor peptide at a dose of 20 mg/kg and, in baboons, at doses of 10, 15, and 20 mg/kg at weekly intervals. Blood samples were collected 3 times a week and VLDL + LDL and HDL cholesterol concentrations were measured. In cynomolgus monkeys, administration of the inhibitor peptide caused a rapid decrease in VLDL + LDL cholesterol concentrations (30%–60% and an increase in HDL cholesterol concentrations (10%–20%. VLDL + LDL cholesterol concentrations returned to baseline levels in approximately 15 days. In baboons, administration of the synthetic inhibitor peptide caused a decrease in VLDL + LDL cholesterol (20%–60% and an increase in HDL cholesterol (10%–20%. VLDL + LDL cholesterol returned to baseline levels by day 21, whereas HDL cholesterol concentrations remained elevated for up to 26 days. ApoA-I concentrations increased, whereas apoE and triglyceride concentrations decreased. Subcutaneous and intravenous administrations of the inhibitor peptide had similar effects on LDL and HDL cholesterol concentrations. There was no change in body weight, food consumption, or plasma IgG levels of any baboon during the study. These studies suggest that the truncated apoC-I peptide can be used to raise HDL in humans.

  4. Assembly of α-synuclein fibrils in nanoscale studied by peptide truncation and AFM

    International Nuclear Information System (INIS)

    Zhang Feng; Lin Xiaojing; Ji Lina; Du Haining; Tang Lin; He Jianhua; Hu Jun; Hu Hongyu

    2008-01-01

    α-Synuclein (α-Syn) fibrils are the major component of Lewy bodies that are closely associated with the pathogenesis of Parkinson's disease, but the mechanism for the fibril assembly remains poorly understood. Here we report using a combination of peptide truncation and atomic force microscopy (AFM) to elucidate the self-assembly and morphology of the α-Syn fibrils. The results show that protease K significantly slims the fibrils from the mean height of ∼6.6 to ∼4.7 nm, whereas chaotropic denaturant urea completely breaks down the fibrils into small particles. The in situ enzymatic digestion also results in thinning of the fibrils, giving rise to some nicks on the fibrils. Moreover, N- or C-terminally truncated α-Syn fragments assemble into thinner filaments with the heights depending on the peptide lengths. A nine-residue peptide corresponding to the homologous GAV-motif sequence can form very thin (∼2.2 nm) but long (>1 μm) filaments. Thus, the central sequence of α-Syn forms a fibrillar core by cross-β-structure that is flanked by two flexible termini, and the orientation of the fibril growth is perpendicular to the β-sheet structures

  5. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk

    DEFF Research Database (Denmark)

    Easton, Douglas F; Lesueur, Fabienne; Decker, Brennan

    2016-01-01

    BACKGROUND: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants...

  6. Acceptance Sampling Plans Based on Truncated Life Tests for Sushila Distribution

    Directory of Open Access Journals (Sweden)

    Amer Ibrahim Al-Omari

    2018-03-01

    Full Text Available An acceptance sampling plan problem based on truncated life tests when the lifetime following a Sushila distribution is considered in this paper. For various acceptance numbers, confidence levels and values of the ratio between fixed experiment time and particular mean lifetime, the minimum sample sizes required to ascertain a specified mean life were found. The operating characteristic function values of the suggested sampling plans and the producer’s risk are presented. Some tables are provided and the results are illustrated by an example of a real data set.

  7. Ideal versus real: simulated annealing of experimentally derived and geometric platinum nanoparticles

    Science.gov (United States)

    Ellaby, Tom; Aarons, Jolyon; Varambhia, Aakash; Jones, Lewys; Nellist, Peter; Ozkaya, Dogan; Sarwar, Misbah; Thompsett, David; Skylaris, Chris-Kriton

    2018-04-01

    Platinum nanoparticles find significant use as catalysts in industrial applications such as fuel cells. Research into their design has focussed heavily on nanoparticle size and shape as they greatly influence activity. Using high throughput, high precision electron microscopy, the structures of commercially available Pt catalysts have been determined, and we have used classical and quantum atomistic simulations to examine and compare them with geometric cuboctahedral and truncated octahedral structures. A simulated annealing procedure was used both to explore the potential energy surface at different temperatures, and also to assess the effect on catalytic activity that annealing would have on nanoparticles with different geometries and sizes. The differences in response to annealing between the real and geometric nanoparticles are discussed in terms of thermal stability, coordination number and the proportion of optimal binding sites on the surface of the nanoparticles. We find that annealing both experimental and geometric nanoparticles results in structures that appear similar in shape and predicted activity, using oxygen adsorption as a measure. Annealing is predicted to increase the catalytic activity in all cases except the truncated octahedra, where it has the opposite effect. As our simulations have been performed with a classical force field, we also assess its suitability to describe the potential energy of such nanoparticles by comparing with large scale density functional theory calculations.

  8. Cross-layer designed adaptive modulation algorithm with packet combining and truncated ARQ over MIMO Nakagami fading channels

    KAUST Repository

    Aniba, Ghassane

    2011-04-01

    This paper presents an optimal adaptive modulation (AM) algorithm designed using a cross-layer approach which combines truncated automatic repeat request (ARQ) protocol and packet combining. Transmissions are performed over multiple-input multiple-output (MIMO) Nakagami fading channels, and retransmitted packets are not necessarily modulated using the same modulation format as in the initial transmission. Compared to traditional approach, cross-layer design based on the coupling across the physical and link layers, has proven to yield better performance in wireless communications. However, there is a lack for the performance analysis and evaluation of such design when the ARQ protocol is used in conjunction with packet combining. Indeed, previous works addressed the link layer performance of AM with truncated ARQ but without packet combining. In addition, previously proposed AM algorithms are not optimal and can provide poor performance when packet combining is implemented. Herein, we first show that the packet loss rate (PLR) resulting from the combining of packets modulated with different constellations can be well approximated by an exponential function. This model is then used in the design of an optimal AM algorithm for systems employing packet combining, truncated ARQ and MIMO antenna configurations, considering transmission over Nakagami fading channels. Numerical results are provided for operation with or without packet combining, and show the enhanced performance and efficiency of the proposed algorithm in comparison with existing ones. © 2011 IEEE.

  9. Reducing C-terminal-truncated alpha-synuclein by immunotherapy attenuates neurodegeneration and propagation in Parkinson's disease-like models.

    Science.gov (United States)

    Games, Dora; Valera, Elvira; Spencer, Brian; Rockenstein, Edward; Mante, Michael; Adame, Anthony; Patrick, Christina; Ubhi, Kiren; Nuber, Silke; Sacayon, Patricia; Zago, Wagner; Seubert, Peter; Barbour, Robin; Schenk, Dale; Masliah, Eliezer

    2014-07-09

    Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are common neurodegenerative disorders of the aging population, characterized by progressive and abnormal accumulation of α-synuclein (α-syn). Recent studies have shown that C-terminus (CT) truncation and propagation of α-syn play a role in the pathogenesis of PD/DLB. Therefore, we explored the effect of passive immunization against the CT of α-syn in the mThy1-α-syn transgenic (tg) mouse model, which resembles the striato-nigral and motor deficits of PD. Mice were immunized with the new monoclonal antibodies 1H7, 5C1, or 5D12, all directed against the CT of α-syn. CT α-syn antibodies attenuated synaptic and axonal pathology, reduced the accumulation of CT-truncated α-syn (CT-α-syn) in axons, rescued the loss of tyrosine hydroxylase fibers in striatum, and improved motor and memory deficits. Among them, 1H7 and 5C1 were most effective at decreasing levels of CT-α-syn and higher-molecular-weight aggregates. Furthermore, in vitro studies showed that preincubation of recombinant α-syn with 1H7 and 5C1 prevented CT cleavage of α-syn. In a cell-based system, CT antibodies reduced cell-to-cell propagation of full-length α-syn, but not of the CT-α-syn that lacked the 118-126 aa recognition site needed for antibody binding. Furthermore, the results obtained after lentiviral expression of α-syn suggest that antibodies might be blocking the extracellular truncation of α-syn by calpain-1. Together, these results demonstrate that antibodies against the CT of α-syn reduce levels of CT-truncated fragments of the protein and its propagation, thus ameliorating PD-like pathology and improving behavioral and motor functions in a mouse model of this disease. Copyright © 2014 the authors 0270-6474/14/349441-14$15.00/0.

  10. Multivariate density estimation using dimension reducing information and tail flattening transformations for truncated or censored data

    DEFF Research Database (Denmark)

    Buch-Kromann, Tine; Nielsen, Jens

    2012-01-01

    This paper introduces a multivariate density estimator for truncated and censored data with special emphasis on extreme values based on survival analysis. A local constant density estimator is considered. We extend this estimator by means of tail flattening transformation, dimension reducing prior...

  11. Use of the truncated shifted Pareto distribution in assessing size distribution of oil and gas fields

    Science.gov (United States)

    Houghton, J.C.

    1988-01-01

    The truncated shifted Pareto (TSP) distribution, a variant of the two-parameter Pareto distribution, in which one parameter is added to shift the distribution right and left and the right-hand side is truncated, is used to model size distributions of oil and gas fields for resource assessment. Assumptions about limits to the left-hand and right-hand side reduce the number of parameters to two. The TSP distribution has advantages over the more customary lognormal distribution because it has a simple analytic expression, allowing exact computation of several statistics of interest, has a "J-shape," and has more flexibility in the thickness of the right-hand tail. Oil field sizes from the Minnelusa play in the Powder River Basin, Wyoming and Montana, are used as a case study. Probability plotting procedures allow easy visualization of the fit and help the assessment. ?? 1988 International Association for Mathematical Geology.

  12. The polyproline site in hinge 2 influences the functional capacity of truncated dystrophins.

    Directory of Open Access Journals (Sweden)

    Glen B Banks

    2010-05-01

    Full Text Available Mutations in dystrophin can lead to Duchenne muscular dystrophy or the more mild form of the disease, Becker muscular dystrophy. The hinge 3 region in the rod domain of dystrophin is particularly prone to deletion mutations. In-frame deletions of hinge 3 are predicted to lead to BMD, however the severity of disease can vary considerably. Here we performed extensive structure-function analyses of truncated dystrophins with modified hinges and spectrin-like repeats in mdx mice. We found that the polyproline site in hinge 2 profoundly influences the functional capacity of a microdystrophin(DeltaR4-R23/DeltaCT with a large deletion in the hinge 3 region. Inclusion of polyproline in microdystrophin(DeltaR4-R23/DeltaCT led to small myofibers (12% smaller than wild-type, Achilles myotendinous disruption, ringed fibers, and aberrant neuromuscular junctions in the mdx gastrocnemius muscles. Replacing hinge 2 of microdystrophin(DeltaR4-R23/DeltaCT with hinge 3 significantly improved the functional capacity to prevent muscle degeneration, increase muscle fiber area, and maintain the junctions. We conclude that the rigid alpha-helical structure of the polyproline site significantly impairs the functional capacity of truncated dystrophins to maintain appropriate connections between the cytoskeleton and extracellular matrix.

  13. Comment on the consistency of truncated nonlinear integral equation based theories of freezing

    International Nuclear Information System (INIS)

    Cerjan, C.; Bagchi, B.; Rice, S.A.

    1985-01-01

    We report the results of two studies of aspects of the consistency of truncated nonlinear integral equation based theories of freezing: (i) We show that the self-consistent solutions to these nonlinear equations are unfortunately sensitive to the level of truncation. For the hard sphere system, if the Wertheim--Thiele representation of the pair direct correlation function is used, the inclusion of part but not all of the triplet direct correlation function contribution, as has been common, worsens the predictions considerably. We also show that the convergence of the solutions found, with respect to number of reciprocal lattice vectors kept in the Fourier expansion of the crystal singlet density, is slow. These conclusions imply great sensitivity to the quality of the pair direct correlation function employed in the theory. (ii) We show the direct correlation function based and the pair correlation function based theories of freezing can be cast into a form which requires solution of isomorphous nonlinear integral equations. However, in the pair correlation function theory the usual neglect of the influence of inhomogeneity of the density distribution on the pair correlation function is shown to be inconsistent to the lowest order in the change of density on freezing, and to lead to erroneous predictions

  14. An effective absorbing layer for the boundary condition in acoustic seismic wave simulation

    Science.gov (United States)

    Yao, Gang; da Silva, Nuno V.; Wu, Di

    2018-04-01

    Efficient numerical simulation of seismic wavefields generally involves truncating the Earth model in order to keep computing time and memory requirements down. Absorbing boundary conditions, therefore, are applied to remove the boundary reflections caused by this truncation, thereby allowing for accurate modeling of wavefields. In this paper, we derive an effective absorbing boundary condition for both acoustic and elastic wave simulation, through the simplification of the damping term of the split perfectly matched layer (SPML) boundary condition. This new boundary condition is accurate, cost-effective, and easily implemented, especially for high-performance computing. Stability analysis shows that this boundary condition is effectively as stable as normal (non-absorbing) wave equations for explicit time-stepping finite differences. We found that for full-waveform inversion (FWI), the strengths of the effective absorbing layer—a reduction of the computational and memory cost coupled with a simplistic implementation—significantly outweighs the limitation of incomplete absorption of outgoing waves relative to the SPML. More importantly, we demonstrate that this limitation can easily be overcome through the use of two strategies in FWI, namely variable cell size and model extension thereby fully compensating for the imperfectness of the proposed absorbing boundary condition.

  15. On the Analytical and Numerical Properties of the Truncated Laplace Transform

    Science.gov (United States)

    2014-05-01

    classical study of the truncated Fourier trans- form. The resulting algorithms are applicable to all environments likely to be encountered in applications...other words, (((La,b)∗ ◦ La,b) (un)) (t) = ∫ b a 1 t+ s un(s)ds = α 2 nun (t). (2.69) Observation 2.22. Similarly, La,b ◦ (La,b)∗ of a function g ∈ L2(0...3.20)) are even and odd functions in the regular sense: Un(s) = (Cγ(un)) (s) = (−1) nUn (−s). (3.25) In particular, at the point s = 0, we have: U2j+1(0

  16. Analysis and design of optimized truncated scarfed nozzles subject to external flow effects

    Science.gov (United States)

    Shyne, Rickey J.; Keith, Theo G., Jr.

    1990-01-01

    Rao's method for computing optimum thrust nozzles is modified to study the effects of external flow on the performance of a class of exhaust nozzles. Members of this class are termed scarfed nozzles. These are two-dimensional, nonsymmetric nozzles with a flat lower wall. The lower wall (the cowl) is truncated in order to save weight. Results from a parametric investigation are presented to show the effects of the external flowfield on performance.

  17. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma

    KAUST Repository

    Lissanu Deribe, Yonathan

    2016-03-01

    PREX2 (phosphatidylinositol-3,4,5-triphosphate-dependent Rac-exchange factor 2) is a PTEN (phosphatase and tensin homolog deleted on chromosome 10) binding protein that is significantly mutated in cutaneous melanoma and pancreatic ductal adenocarcinoma. Here, genetic and biochemical analyses were conducted to elucidate the nature and mechanistic basis of PREX2 mutation in melanoma development. By generating an inducible transgenic mouse model we showed an oncogenic role for a truncating PREX2 mutation (PREX2E824*) in vivo in the context of mutant NRAS. Using integrative cross-species gene expression analysis, we identified deregulated cell cycle and cytoskeleton organization as significantly perturbed biological pathways in PREX2 mutant tumors. Mechanistically, truncation of PREX2 activated its Rac1 guanine nucleotide exchange factor activity, abolished binding to PTEN and activated the PI3K (phosphatidyl inositol 3 kinase)/Akt signaling pathway. We further showed that PREX2 truncating mutations or PTEN deletion induces down-regulation of the tumor suppressor and cell cycle regulator CDKN1C (also known as p57KIP2). This down-regulation occurs, at least partially, through DNA hypomethylation of a differentially methylated region in chromosome 11 that is a known regulatory region for expression of the CDKN1C gene. Together, these findings identify PREX2 as a mediator of NRAS-mutant melanoma development that acts through the PI3K/PTEN/Akt pathway to regulate gene expression of a cell cycle regulator.

  18. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma.

    Science.gov (United States)

    Lissanu Deribe, Yonathan; Shi, Yanxia; Rai, Kunal; Nezi, Luigi; Amin, Samir B; Wu, Chia-Chin; Akdemir, Kadir C; Mahdavi, Mozhdeh; Peng, Qian; Chang, Qing Edward; Hornigold, Kirsti; Arold, Stefan T; Welch, Heidi C E; Garraway, Levi A; Chin, Lynda

    2016-03-01

    PREX2 (phosphatidylinositol-3,4,5-triphosphate-dependent Rac-exchange factor 2) is a PTEN (phosphatase and tensin homolog deleted on chromosome 10) binding protein that is significantly mutated in cutaneous melanoma and pancreatic ductal adenocarcinoma. Here, genetic and biochemical analyses were conducted to elucidate the nature and mechanistic basis of PREX2 mutation in melanoma development. By generating an inducible transgenic mouse model we showed an oncogenic role for a truncating PREX2 mutation (PREX2(E824)*) in vivo in the context of mutant NRAS. Using integrative cross-species gene expression analysis, we identified deregulated cell cycle and cytoskeleton organization as significantly perturbed biological pathways in PREX2 mutant tumors. Mechanistically, truncation of PREX2 activated its Rac1 guanine nucleotide exchange factor activity, abolished binding to PTEN and activated the PI3K (phosphatidyl inositol 3 kinase)/Akt signaling pathway. We further showed that PREX2 truncating mutations or PTEN deletion induces down-regulation of the tumor suppressor and cell cycle regulator CDKN1C (also known as p57(KIP2)). This down-regulation occurs, at least partially, through DNA hypomethylation of a differentially methylated region in chromosome 11 that is a known regulatory region for expression of the CDKN1C gene. Together, these findings identify PREX2 as a mediator of NRAS-mutant melanoma development that acts through the PI3K/PTEN/Akt pathway to regulate gene expression of a cell cycle regulator.

  19. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma

    KAUST Repository

    Lissanu Deribe, Yonathan; Shi, Yanxia; Rai, Kunal; Nezi, Luigi; Amin, Samir B.; Wu, Chia-Chin; Akdemir, Kadir C.; Mahdavi, Mozhdeh; Peng, Qian; Chang, Qing Edward; Hornigold, Kirsti; Arold, Stefan T.; Welch, Heidi C. E.; Garraway, Levi A.; Chin, Lynda

    2016-01-01

    PREX2 (phosphatidylinositol-3,4,5-triphosphate-dependent Rac-exchange factor 2) is a PTEN (phosphatase and tensin homolog deleted on chromosome 10) binding protein that is significantly mutated in cutaneous melanoma and pancreatic ductal adenocarcinoma. Here, genetic and biochemical analyses were conducted to elucidate the nature and mechanistic basis of PREX2 mutation in melanoma development. By generating an inducible transgenic mouse model we showed an oncogenic role for a truncating PREX2 mutation (PREX2E824*) in vivo in the context of mutant NRAS. Using integrative cross-species gene expression analysis, we identified deregulated cell cycle and cytoskeleton organization as significantly perturbed biological pathways in PREX2 mutant tumors. Mechanistically, truncation of PREX2 activated its Rac1 guanine nucleotide exchange factor activity, abolished binding to PTEN and activated the PI3K (phosphatidyl inositol 3 kinase)/Akt signaling pathway. We further showed that PREX2 truncating mutations or PTEN deletion induces down-regulation of the tumor suppressor and cell cycle regulator CDKN1C (also known as p57KIP2). This down-regulation occurs, at least partially, through DNA hypomethylation of a differentially methylated region in chromosome 11 that is a known regulatory region for expression of the CDKN1C gene. Together, these findings identify PREX2 as a mediator of NRAS-mutant melanoma development that acts through the PI3K/PTEN/Akt pathway to regulate gene expression of a cell cycle regulator.

  20. Cross-layer designed adaptive modulation algorithm with packet combining and truncated ARQ over MIMO Nakagami fading channels

    KAUST Repository

    Aniba, Ghassane; Aissa, Sonia

    2011-01-01

    works addressed the link layer performance of AM with truncated ARQ but without packet combining. In addition, previously proposed AM algorithms are not optimal and can provide poor performance when packet combining is implemented. Herein, we first show

  1. Ptychographic x-ray imaging of surfaces on crystal truncation rod

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chenhui; Barbour, Andi; Liu, Yaohua; You, Hoydoo, E-mail: hyou@anl.gov [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Harder, Ross; Xu, Ruqing [Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Diaz, Ana; Menzel, Andreas [Paul Scherrer Institut, Villigen PSI 5232 (Switzerland); Komanicky, Vladimir [Faculty of Sciences, Safarik University, Kosice 04154 (Slovakia); Huang, Xiaojing [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973 (United States); Pierce, Michael S. [School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623 (United States)

    2015-03-09

    Ptychography is a high-resolution imaging technique, which does not require lenses for image magnification and which provides phase contrast with high sensitivity. Here, we propose to use x-ray ptychography for the imaging of surface structure in crystalline samples. We show that ptychography can be used to image atomic step structures using coherent diffraction patterns recorded along the crystal truncation rod of a crystal surface. In a proof-of-concept experiment on a Pt (111) sample, we present ptychographic reconstructions showing features consistent with surface steps. Due to the penetration power of x-rays, this method could find interesting applications for the study of surface structures under buried interfaces or in harsh environments.

  2. Ptychographic x-ray imaging of surfaces on crystal truncation rod

    International Nuclear Information System (INIS)

    Zhu, Chenhui; Barbour, Andi; Liu, Yaohua; You, Hoydoo; Harder, Ross; Xu, Ruqing; Diaz, Ana; Menzel, Andreas; Komanicky, Vladimir; Huang, Xiaojing; Pierce, Michael S.

    2015-01-01

    Ptychography is a high-resolution imaging technique, which does not require lenses for image magnification and which provides phase contrast with high sensitivity. Here, we propose to use x-ray ptychography for the imaging of surface structure in crystalline samples. We show that ptychography can be used to image atomic step structures using coherent diffraction patterns recorded along the crystal truncation rod of a crystal surface. In a proof-of-concept experiment on a Pt (111) sample, we present ptychographic reconstructions showing features consistent with surface steps. Due to the penetration power of x-rays, this method could find interesting applications for the study of surface structures under buried interfaces or in harsh environments

  3. Non-perturbative Calculation of the Scalar Yukawa Theory in Four-Body Truncation

    International Nuclear Information System (INIS)

    Li, Yang; Maris, P.; Vary, J. P.; Karmanov, V. A.

    2015-01-01

    The quenched scalar Yukawa theory is solved in the light-front Tamm–Dancoff approach including up to four constituents (one scalar nucleon, three scalar pions). The Fock sector dependent renormalization is implemented. By studying the Fock sector norms, we find that the lowest two Fock sectors dominate the state even in the large-coupling region. The one-body sector shows convergence with respect to the Fock sector truncation. However, the four-body norm exceeds the three-body norm at the coupling α≈1.7 . (author)

  4. Impact of improved attenuation correction featuring a bone atlas and truncation correction on PET quantification in whole-body PET/MR.

    Science.gov (United States)

    Oehmigen, Mark; Lindemann, Maike E; Gratz, Marcel; Kirchner, Julian; Ruhlmann, Verena; Umutlu, Lale; Blumhagen, Jan Ole; Fenchel, Matthias; Quick, Harald H

    2018-04-01

    Recent studies have shown an excellent correlation between PET/MR and PET/CT hybrid imaging in detecting lesions. However, a systematic underestimation of PET quantification in PET/MR has been observed. This is attributable to two methodological challenges of MR-based attenuation correction (AC): (1) lack of bone information, and (2) truncation of the MR-based AC maps (μmaps) along the patient arms. The aim of this study was to evaluate the impact of improved AC featuring a bone atlas and truncation correction on PET quantification in whole-body PET/MR. The MR-based Dixon method provides four-compartment μmaps (background air, lungs, fat, soft tissue) which served as a reference for PET/MR AC in this study. A model-based bone atlas provided bone tissue as a fifth compartment, while the HUGE method provided truncation correction. The study population comprised 51 patients with oncological diseases, all of whom underwent a whole-body PET/MR examination. Each whole-body PET dataset was reconstructed four times using standard four-compartment μmaps, five-compartment μmaps, four-compartment μmaps + HUGE, and five-compartment μmaps + HUGE. The SUV max for each lesion was measured to assess the impact of each μmap on PET quantification. All four μmaps in each patient provided robust results for reconstruction of the AC PET data. Overall, SUV max was quantified in 99 tumours and lesions. Compared to the reference four-compartment μmap, the mean SUV max of all 99 lesions increased by 1.4 ± 2.5% when bone was added, by 2.1 ± 3.5% when HUGE was added, and by 4.4 ± 5.7% when bone + HUGE was added. Larger quantification bias of up to 35% was found for single lesions when bone and truncation correction were added to the μmaps, depending on their individual location in the body. The novel AC method, featuring a bone model and truncation correction, improved PET quantification in whole-body PET/MR imaging. Short reconstruction times, straightforward

  5. Impact of improved attenuation correction featuring a bone atlas and truncation correction on PET quantification in whole-body PET/MR

    Energy Technology Data Exchange (ETDEWEB)

    Oehmigen, Mark; Lindemann, Maike E. [University Hospital Essen, High Field and Hybrid MR Imaging, Essen (Germany); Gratz, Marcel; Quick, Harald H. [University Hospital Essen, High Field and Hybrid MR Imaging, Essen (Germany); University Duisburg-Essen, Erwin L. Hahn Institute for MR Imaging, Essen (Germany); Kirchner, Julian [University Dusseldorf, Department of Diagnostic and Interventional Radiology, Medical Faculty, Dusseldorf (Germany); Ruhlmann, Verena [University Hospital Essen, Department of Nuclear Medicine, Essen (Germany); Umutlu, Lale [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Blumhagen, Jan Ole; Fenchel, Matthias [Siemens Healthcare GmbH, Erlangen (Germany)

    2018-04-15

    Recent studies have shown an excellent correlation between PET/MR and PET/CT hybrid imaging in detecting lesions. However, a systematic underestimation of PET quantification in PET/MR has been observed. This is attributable to two methodological challenges of MR-based attenuation correction (AC): (1) lack of bone information, and (2) truncation of the MR-based AC maps (μmaps) along the patient arms. The aim of this study was to evaluate the impact of improved AC featuring a bone atlas and truncation correction on PET quantification in whole-body PET/MR. The MR-based Dixon method provides four-compartment μmaps (background air, lungs, fat, soft tissue) which served as a reference for PET/MR AC in this study. A model-based bone atlas provided bone tissue as a fifth compartment, while the HUGE method provided truncation correction. The study population comprised 51 patients with oncological diseases, all of whom underwent a whole-body PET/MR examination. Each whole-body PET dataset was reconstructed four times using standard four-compartment μmaps, five-compartment μmaps, four-compartment μmaps + HUGE, and five-compartment μmaps + HUGE. The SUV{sub max} for each lesion was measured to assess the impact of each μmap on PET quantification. All four μmaps in each patient provided robust results for reconstruction of the AC PET data. Overall, SUV{sub max} was quantified in 99 tumours and lesions. Compared to the reference four-compartment μmap, the mean SUV{sub max} of all 99 lesions increased by 1.4 ± 2.5% when bone was added, by 2.1 ± 3.5% when HUGE was added, and by 4.4 ± 5.7% when bone + HUGE was added. Larger quantification bias of up to 35% was found for single lesions when bone and truncation correction were added to the μmaps, depending on their individual location in the body. The novel AC method, featuring a bone model and truncation correction, improved PET quantification in whole-body PET/MR imaging. Short reconstruction times, straightforward

  6. Progress and new advances in simulating electron microscopy datasets using MULTEM

    Energy Technology Data Exchange (ETDEWEB)

    Lobato, I., E-mail: Ivan.Lobato@uantwerpen.be; Van Aert, S.; Verbeeck, J.

    2016-09-15

    A new version of the open source program MULTEM is presented here. It includes a graphical user interface, tapering truncation of the atomic potential, CPU multithreading functionality, single/double precision calculations, scanning transmission electron microscopy (STEM) simulations using experimental detector sensitivities, imaging STEM (ISTEM) simulations, energy filtered transmission electron microscopy (EFTEM) simulations, STEM electron energy loss spectroscopy (EELS) simulations along with other improvements in the algorithms. We also present a mixed channeling approach for the calculation of inelastic excitations, which allows one to considerably speed up time consuming EFTEM/STEM-EELS calculations. - Highlights: • We present a new version of the CPU/GPU open source program MULTEM. • A cross-platform graphical user interface is developed. • We include inelastic excitations for EFTEM/STEM-EELS calculations. • We add CPU multithreading functionality and single/double precision calculations.

  7. Progress and new advances in simulating electron microscopy datasets using MULTEM

    International Nuclear Information System (INIS)

    Lobato, I.; Van Aert, S.; Verbeeck, J.

    2016-01-01

    A new version of the open source program MULTEM is presented here. It includes a graphical user interface, tapering truncation of the atomic potential, CPU multithreading functionality, single/double precision calculations, scanning transmission electron microscopy (STEM) simulations using experimental detector sensitivities, imaging STEM (ISTEM) simulations, energy filtered transmission electron microscopy (EFTEM) simulations, STEM electron energy loss spectroscopy (EELS) simulations along with other improvements in the algorithms. We also present a mixed channeling approach for the calculation of inelastic excitations, which allows one to considerably speed up time consuming EFTEM/STEM-EELS calculations. - Highlights: • We present a new version of the CPU/GPU open source program MULTEM. • A cross-platform graphical user interface is developed. • We include inelastic excitations for EFTEM/STEM-EELS calculations. • We add CPU multithreading functionality and single/double precision calculations.

  8. Prediction of the moments in advection-diffusion lattice Boltzmann method. I. Truncation dispersion, skewness, and kurtosis

    Science.gov (United States)

    Ginzburg, Irina

    2017-01-01

    The effect of the heterogeneity in the soil structure or the nonuniformity of the velocity field on the modeled resident time distribution (RTD) and breakthrough curves is quantified by their moments. While the first moment provides the effective velocity, the second moment is related to the longitudinal dispersion coefficient (kT) in the developed Taylor regime; the third and fourth moments are characterized by their normalized values skewness (Sk) and kurtosis (Ku), respectively. The purpose of this investigation is to examine the role of the truncation corrections of the numerical scheme in kT, Sk, and Ku because of their interference with the second moment, in the form of the numerical dispersion, and in the higher-order moments, by their definition. Our symbolic procedure is based on the recently proposed extended method of moments (EMM). Originally, the EMM restores any-order physical moments of the RTD or averaged distributions assuming that the solute concentration obeys the advection-diffusion equation in multidimensional steady-state velocity field, in streamwise-periodic heterogeneous structure. In our work, the EMM is generalized to the fourth-order-accurate apparent mass-conservation equation in two- and three-dimensional duct flows. The method looks for the solution of the transport equation as the product of a long harmonic wave and a spatially periodic oscillating component; the moments of the given numerical scheme are derived from a chain of the steady-state fourth-order equations at a single cell. This mathematical technique is exemplified for the truncation terms of the two-relaxation-time lattice Boltzmann scheme, using plug and parabolic flow in straight channel and cylindrical capillary with the d2Q9 and d3Q15 discrete velocity sets as simple but illustrative examples. The derived symbolic dependencies can be readily extended for advection by another, Newtonian or non-Newtonian, flow profile in any-shape open-tabular conduits. It is

  9. Truncating variants in the majority of the cytoplasmic domain of PCDH15 are unlikely to cause Usher syndrome 1F.

    Science.gov (United States)

    Perreault-Micale, Cynthia; Frieden, Alexander; Kennedy, Caleb J; Neitzel, Dana; Sullivan, Jessica; Faulkner, Nicole; Hallam, Stephanie; Greger, Valerie

    2014-11-01

    Loss of function variants in the PCDH15 gene can cause Usher syndrome type 1F, an autosomal recessive disease associated with profound congenital hearing loss, vestibular dysfunction, and retinitis pigmentosa. The Ashkenazi Jewish population has an increased incidence of Usher syndrome type 1F (founder variant p.Arg245X accounts for 75% of alleles), yet the variant spectrum in a panethnic population remains undetermined. We sequenced the coding region and intron-exon borders of PCDH15 using next-generation DNA sequencing technology in approximately 14,000 patients from fertility clinics. More than 600 unique PCDH15 variants (single nucleotide changes and small indels) were identified, including previously described pathogenic variants p.Arg3X, p.Arg245X (five patients), p.Arg643X, p.Arg929X, and p.Arg1106X. Novel truncating variants were also found, including one in the N-terminal extracellular domain (p.Leu877X), but all other novel truncating variants clustered in the exon 33 encoded C-terminal cytoplasmic domain (52 patients, 14 variants). One variant was observed predominantly in African Americans (carrier frequency of 2.3%). The high incidence of truncating exon 33 variants indicates that they are unlikely to cause Usher syndrome type 1F even though many remove a large portion of the gene. They may be tolerated because PCDH15 has several alternate cytoplasmic domain exons and differentially spliced isoforms may function redundantly. Effects of some PCDH15 truncating variants were addressed by deep sequencing of a panethnic population. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. Novel and recurrent non-truncating mutations of the MITF basic domain: genotypic and phenotypic variations in Waardenburg and Tietz syndromes

    Science.gov (United States)

    Léger, Sandy; Balguerie, Xavier; Goldenberg, Alice; Drouin-Garraud, Valérie; Cabot, Annick; Amstutz-Montadert, Isabelle; Young, Paul; Joly, Pascal; Bodereau, Virginie; Holder-Espinasse, Muriel; Jamieson, Robyn V; Krause, Amanda; Chen, Hongsheng; Baumann, Clarisse; Nunes, Luis; Dollfus, Hélène; Goossens, Michel; Pingault, Véronique

    2012-01-01

    The microphthalmia-associated transcription factor (MITF) is a basic helix-loop-helix leucine zipper transcription factor, which regulates melanocyte development and the biosynthetic melanin pathway. A notable relationship has been described between non-truncating mutations of its basic domain and Tietz syndrome, which is characterized by albinoid-like hypopigmentation of the skin and hair, rather than the patchy depigmentation seen in Waardenburg syndrome, and severe hearing loss. Twelve patients with new or recurrent non-truncating mutations of the MITF basic domain from six families were enrolled in this study. We observed a wide range of phenotypes and some unexpected features. All the patients had blue irides and pigmentation abnormalities that ranged from diffuse hypopigmentation to Waardenburg-like patches. In addition, they showed congenital complete hearing loss, diffuse hypopigmentation of the skin, freckling and ocular abnormalities, more frequently than patients with MITF mutations outside the basic domain. In conclusion, the non-truncating mutations of the basic domain do not always lead to Tietz syndrome but rather to a large range of phenotypes. Sun-exposed freckles are interestingly observed more frequently in Asian populations. This variability argues for the possible interaction with modifier loci. PMID:22258527

  11. Uniform physical theory of diffraction equivalent edge currents for truncated wedge strips

    DEFF Research Database (Denmark)

    Johansen, Peter Meincke

    1996-01-01

    New uniform closed-form expressions for physical theory of diffraction equivalent edge currents are derived for truncated incremental wedge strips. In contrast to previously reported expressions, the new expressions are well behaved for all directions of incidence and observation and take a finite...... value for zero strip length. This means that the expressions are well suited for implementation in general computer codes. The new expressions are expressed as the difference between two terms. The first term is obtained by integrating the exact fringe wave current on a wedge along an untruncated...

  12. Computation of Lie transformations from a power series: Bounds and optimum truncation

    International Nuclear Information System (INIS)

    Gjaja, I.

    1996-01-01

    The problem considered is the computation of an infinite product (composition) of Lie transformations generated by homogeneous polynomials of increasing order from a given asymptotic power series. Bounds are computed for the infinitesimal form of the Lie transformations and for the domain of analyticity of the first n of them. Even when the power series is convergent, the estimates exhibit a factorial-type growth, and thus do not guarantee convergence of the product. The optimum truncation is determined by minimizing the remainder after the first n Lie transformations have been applied

  13. Expression of a truncated receptor protein tyrosine phosphatase kappa in the brain of an adult transgenic mouse

    DEFF Research Database (Denmark)

    Shen, P; Canoll, P D; Sap, J

    1999-01-01

    processes such as axonal growth and target recognition, as has been demonstrated for certain Drosophila RPTPs. The brain distribution of RPTP-kappa-expressing cells has not been determined, however. In a gene-trap mouse model with a beta-gal+neo (beta-geo) insertion in the endogenous RPTP-kappa gene......-6596]. Nevertheless, since the transgene's expression is driven by the endogenous RPTP-kappa promoter, distribution of the truncated RPTP-kappa/beta-geo fusion protein should reflect the regional and cellular expression of wild-type RPTP-kappa, and thus may identify sites where RPTP-kappa is important. Towards...... that goal, we have used this mouse model to map the distribution of the truncated RPTP-kappa/beta-geo fusion protein in the adult mouse brain using beta-galactosidase as a marker enzyme. Visualization of the beta-galactosidase activity revealed a non-random pattern of expression, and identified cells...

  14. Generalized Truncated Methods for an Efficient Solution of Retrial Systems

    Directory of Open Access Journals (Sweden)

    Ma Jose Domenech-Benlloch

    2008-01-01

    Full Text Available We are concerned with the analytic solution of multiserver retrial queues including the impatience phenomenon. As there are not closed-form solutions to these systems, approximate methods are required. We propose two different generalized truncated methods to effectively solve this type of systems. The methods proposed are based on the homogenization of the state space beyond a given number of users in the retrial orbit. We compare the proposed methods with the most well-known methods appeared in the literature in a wide range of scenarios. We conclude that the proposed methods generally outperform previous proposals in terms of accuracy for the most common performance parameters used in retrial systems with a moderated growth in the computational cost.

  15. Cap integration in spectral gravity forward modelling: near- and far-zone gravity effects via Molodensky's truncation coefficients

    Science.gov (United States)

    Bucha, Blažej; Hirt, Christian; Kuhn, Michael

    2018-04-01

    Spectral gravity forward modelling is a technique that converts a band-limited topography into its implied gravitational field. This conversion implicitly relies on global integration of topographic masses. In this paper, a modification of the spectral technique is presented that provides gravity effects induced only by the masses located inside or outside a spherical cap centred at the evaluation point. This is achieved by altitude-dependent Molodensky's truncation coefficients, for which we provide infinite series expansions and recurrence relations with a fixed number of terms. Both representations are generalized for an arbitrary integer power of the topography and arbitrary radial derivative. Because of the altitude-dependency of the truncation coefficients, a straightforward synthesis of the near- and far-zone gravity effects at dense grids on irregular surfaces (e.g. the Earth's topography) is computationally extremely demanding. However, we show that this task can be efficiently performed using an analytical continuation based on the gradient approach, provided that formulae for radial derivatives of the truncation coefficients are available. To demonstrate the new cap-modified spectral technique, we forward model the Earth's degree-360 topography, obtaining near- and far-zone effects on gravity disturbances expanded up to degree 3600. The computation is carried out on the Earth's surface and the results are validated against an independent spatial-domain Newtonian integration (1 μGal RMS agreement). The new technique is expected to assist in mitigating the spectral filter problem of residual terrain modelling and in the efficient construction of full-scale global gravity maps of highest spatial resolution.

  16. ANN Synthesis Model of Single-Feed Corner-Truncated Circularly Polarized Microstrip Antenna with an Air Gap for Wideband Applications

    Directory of Open Access Journals (Sweden)

    Zhongbao Wang

    2014-01-01

    Full Text Available A computer-aided design model based on the artificial neural network (ANN is proposed to directly obtain patch physical dimensions of the single-feed corner-truncated circularly polarized microstrip antenna (CPMA with an air gap for wideband applications. To take account of the effect of the air gap, an equivalent relative permittivity is introduced and adopted to calculate the resonant frequency and Q-factor of square microstrip antennas for obtaining the training data sets. ANN architectures using multilayered perceptrons (MLPs and radial basis function networks (RBFNs are compared. Also, six learning algorithms are used to train the MLPs for comparison. It is found that MLPs trained with the Levenberg-Marquardt (LM algorithm are better than RBFNs for the synthesis of the CPMA. An accurate model is achieved by using an MLP with three hidden layers. The model is validated by the electromagnetic simulation and measurements. It is enormously useful to antenna engineers for facilitating the design of the single-feed CPMA with an air gap.

  17. First results from simulations of supersymmetric lattices

    Science.gov (United States)

    Catterall, Simon

    2009-01-01

    We conduct the first numerical simulations of lattice theories with exact supersymmetry arising from the orbifold constructions of \\cite{Cohen:2003xe,Cohen:2003qw,Kaplan:2005ta}. We consider the Script Q = 4 theory in D = 0,2 dimensions and the Script Q = 16 theory in D = 0,2,4 dimensions. We show that the U(N) theories do not possess vacua which are stable non-perturbatively, but that this problem can be circumvented after truncation to SU(N). We measure the distribution of scalar field eigenvalues, the spectrum of the fermion operator and the phase of the Pfaffian arising after integration over the fermions. We monitor supersymmetry breaking effects by measuring a simple Ward identity. Our results indicate that simulations of Script N = 4 super Yang-Mills may be achievable in the near future.

  18. Duality quantum algorithm efficiently simulates open quantum systems

    Science.gov (United States)

    Wei, Shi-Jie; Ruan, Dong; Long, Gui-Lu

    2016-01-01

    Because of inevitable coupling with the environment, nearly all practical quantum systems are open system, where the evolution is not necessarily unitary. In this paper, we propose a duality quantum algorithm for simulating Hamiltonian evolution of an open quantum system. In contrast to unitary evolution in a usual quantum computer, the evolution operator in a duality quantum computer is a linear combination of unitary operators. In this duality quantum algorithm, the time evolution of the open quantum system is realized by using Kraus operators which is naturally implemented in duality quantum computer. This duality quantum algorithm has two distinct advantages compared to existing quantum simulation algorithms with unitary evolution operations. Firstly, the query complexity of the algorithm is O(d3) in contrast to O(d4) in existing unitary simulation algorithm, where d is the dimension of the open quantum system. Secondly, By using a truncated Taylor series of the evolution operators, this duality quantum algorithm provides an exponential improvement in precision compared with previous unitary simulation algorithm. PMID:27464855

  19. Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations

    International Nuclear Information System (INIS)

    Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja

    2015-01-01

    Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor–liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields T c = 1.3128 ± 0.0016, ρ c = 0.316 ± 0.004, and p c = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρ t ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using r cut = 3.5σ yield T c and p c that are higher by 0.2% and 1.4% than simulations with r cut = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that r cut = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard-core square-well particles with various

  20. Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

    Directory of Open Access Journals (Sweden)

    Hayes Michael L

    2012-05-01

    Full Text Available Abstract Background Pentatricopeptide repeat (PPR proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82 and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. Results All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3’ UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. Conclusion PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative

  1. Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.

    Science.gov (United States)

    Hayes, Michael L; Giang, Karolyn; Mulligan, R Michael

    2012-05-14

    Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions. All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes. PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target

  2. Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain.

    Science.gov (United States)

    Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian

    2016-06-14

    The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s(-1) mM(-1). The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.

  3. Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin.

    Science.gov (United States)

    Salas, Remmer L; Garcia, Jan Kathryne D L; Miranda, Ana Carmela R; Rivera, Windell L; Nellas, Ricky B; Sabido, Portia Mahal G

    2018-06-01

    Anoplin (GLLKRIKTLL-NH 2 ) is of current interest due to its short sequence and specificity towards bacteria. Recent studies on anoplin have shown that truncation and acylation compromises its antimicrobial activity and specificity, respectively. In this study, truncated analogues (pal-ano-9 to pal-ano-5) of palmitoylated anoplin (pal-anoplin) were synthesized to determine the effects of C-truncation on its bioactivities. Moreover, secondary structure of each analogue using circular dichroism (CD) spectroscopy was determined to correlate with bioactivities. Interestingly, pal-anoplin, pal-ano-9 and pal-ano-6 were helical in water, unlike anoplin. In contrast, pal-ano-8, pal-ano-7 and pal-ano-5, with polar amino acid residues at the C-terminus, were random coil in water. Nevertheless, all the peptides folded into helical structures in 30% trifluoroethanol/water (TFE/H 2 O) except for the shortest analogue pal-ano-5. Hydrophobicity played a significant role in the enhancement of activity against bacteria E. coli and S. aureus as all lipopeptides including the random coil pal-ano-5 were more active than the parent anoplin. Meanwhile, the greatest improvement in activity against the fungus C. albicans was observed for pal-anoplin analogues (pal-ano-9 and pal-ano-6) that were helical in water. Although, hydrophobicity is a major factor in the secondary structure and antimicrobial activity, it appears that the nature of amino acids at the C-terminus also influence folding of lipopeptides in water and its antifungal activity. Moreover, the hemolytic activity of the analogues was found to correlate with hydrophobicity, except for the least hemolytic, pal-ano-5. Since most of the analogues are more potent and shorter than anoplin, they are promising drug candidates for further development. Copyright © 2018. Published by Elsevier Inc.

  4. Truncation of the many body hierarchy and relaxation times in the McKean model

    International Nuclear Information System (INIS)

    Schmitt, K.J.

    1987-01-01

    In the McKean model the BBGKY-hierarchy is equivalent to a simple hierarchy of coupled equations for the p-particle correlation functions. Truncation effects and the convergence of the one-particle distribution towards its exact shape have been studied. In the long time limit the equations can be solved in a closed form. It turns out that the p-particle correlation decays p-times faster than the non-equilibrium one-particle distribution

  5. Scavenger receptor AI/II truncation, lung function and COPD: a large population-based study

    DEFF Research Database (Denmark)

    Thomsen, M; Nordestgaard, B G; Tybjærg-Hansen, Anne

    2011-01-01

    The scavenger receptor A-I/II (SRA-I/II) on alveolar macrophages is involved in recognition and clearance of modified lipids and inhaled particulates. A rare variant of the SRA-I/II gene, Arg293X, truncates the distal collagen-like domain, which is essential for ligand recognition. We tested...... whether the Arg293X variant is associated with reduced lung function and risk of chronic obstructive pulmonary disease (COPD) in the general population....

  6. TRUNCATION OF THE MANY BODY HIERARCHY AND RELAXATION TIMES IN THE McKEAN MODEL

    OpenAIRE

    Schmitt , K.-J.

    1987-01-01

    In the McKean model the BBGKY-hierarchy is equivalent to a simple hierarchy of coupled equations for the p-particle correlation functions. Truncation effects and the convergence of the one-particle distribution towards its exact shape have been studied. In the long time limit the equations can be solved in a closed form. It turns out that the p-particle correlation decays p-times faster than the non-equilibrium one-particle distribution.

  7. Pair truncation for rotational nuclei: j=17/2 model

    International Nuclear Information System (INIS)

    Halse, P.; Jaqua, L.; Barrett, B.R.

    1989-01-01

    The suitability of the pair condensate approach for rotational states is studied in a single j=17/2 shell of identical nucleons interacting through a quadrupole-quadrupole Hamiltonian. The ground band and a K=2 excited band are both studied in detail. A direct comparison of the exact states with those constituting the SD and SDG subspaces is used to identify the important degrees of freedom for these levels. The range of pairs necessary for a good description is found to be highly state dependent; S and D pairs are the major constituents of the low-spin ground-band levels, while G pairs are needed for those in the γ band. Energy spectra are obtained for each truncated subspace. SDG pairs allow accurate reproduction of the binding energy and K=2 excitation energy, but still give a moment of inertia which is about 30% too small even for the lowest levels

  8. Expression of a truncated Hmga1b gene induces gigantism, lipomatosis and B-cell lymphomas in mice.

    Science.gov (United States)

    Fedele, Monica; Visone, Rosa; De Martino, Ivana; Palmieri, Dario; Valentino, Teresa; Esposito, Francesco; Klein-Szanto, Andres; Arra, Claudio; Ciarmiello, Andrea; Croce, Carlo M; Fusco, Alfredo

    2011-02-01

    HMGA1 gene rearrangements have been frequently described in human lipomas. In vitro studies suggest that HMGA1 proteins have a negative role in the control of adipocyte cell growth, and that HMGA1 gene truncation acts in a dominant-negative fashion. Therefore, to define better the role of the HMGA1 alterations in the generation of human lipomas, we generated mice carrying an Hmga1b truncated (Hmga1b/T) gene. These mice develop a giant phenotype together with a drastic expansion of the retroperitoneal and subcutaneous white adipose tissue. We show that the activation of the E2F pathway likely accounts, at least in part, for this phenotype. Interestingly, the Hmga1b/T mice also develop B-cell lymphomas similar to that occurring in Hmga1-knockout mice, supporting a dominant-negative role of the Hmga1b/T mutant also in vivo. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. N-terminal truncation enables crystallization of the receptor-binding domain of the FedF bacterial adhesin

    Energy Technology Data Exchange (ETDEWEB)

    De Kerpel, Maia; Van Molle, Inge [Department of Ultrastructure, Vrije Universiteit Brussel (VUB), Flanders Interuniversity Institute for Biotechnology (VIB), Pleinlaan 2, 1050 Brussels (Belgium); Brys, Lea [Department of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Flanders Interuniversity Institute for Biotechnology (VIB), Pleinlaan 2, 1050 Brussels (Belgium); Wyns, Lode; De Greve, Henri; Bouckaert, Julie, E-mail: bouckaej@vub.ac.be [Department of Ultrastructure, Vrije Universiteit Brussel (VUB), Flanders Interuniversity Institute for Biotechnology (VIB), Pleinlaan 2, 1050 Brussels (Belgium)

    2006-12-01

    The N-terminal receptor-binding domain of the FedF adhesin from enterotoxigenic E. coli has been crystallized. This required the deletion of its first 14 residues, which are also cleaved off naturally. FedF is the two-domain tip adhesin of F18 fimbriae from enterotoxigenic Escherichia coli. Bacterial adherence, mediated by the N-terminal receptor-binding domain of FedF to carbohydrate receptors on intestinal microvilli, causes diarrhoea and oedema disease in newly weaned piglets and induces the secretion of Shiga toxins. A truncate containing only the receptor-binding domain of FedF was found to be further cleaved at its N-terminus. Reconstruction of this N-terminal truncate rendered FedF amenable to crystallization, resulting in crystals with space group P2{sub 1}2{sub 1}2{sub 1} and unit-cell parameters a = 36.20, b = 74.64, c = 99.03 Å that diffracted to beyond 2 Å resolution. The binding specificity of FedF was screened for on a glycan array, exposing 264 glycoconjugates, to identify specific receptors for cocrystallization with FedF.

  10. Consistent Kaluza-Klein truncations via exceptional field theory

    Energy Technology Data Exchange (ETDEWEB)

    Hohm, Olaf [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States); Samtleben, Henning [Université de Lyon, Laboratoire de Physique, UMR 5672, CNRS,École Normale Supérieure de Lyon, 46, allée d’Italie, F-69364 Lyon cedex 07 (France)

    2015-01-26

    We present the generalized Scherk-Schwarz reduction ansatz for the full supersymmetric exceptional field theory in terms of group valued twist matrices subject to consistency equations. With this ansatz the field equations precisely reduce to those of lower-dimensional gauged supergravity parametrized by an embedding tensor. We explicitly construct a family of twist matrices as solutions of the consistency equations. They induce gauged supergravities with gauge groups SO(p,q) and CSO(p,q,r). Geometrically, they describe compactifications on internal spaces given by spheres and (warped) hyperboloides H{sup p,q}, thus extending the applicability of generalized Scherk-Schwarz reductions beyond homogeneous spaces. Together with the dictionary that relates exceptional field theory to D=11 and IIB supergravity, respectively, the construction defines an entire new family of consistent truncations of the original theories. These include not only compactifications on spheres of different dimensions (such as AdS{sub 5}×S{sup 5}), but also various hyperboloid compactifications giving rise to a higher-dimensional embedding of supergravities with non-compact and non-semisimple gauge groups.

  11. CRISPR/Cas9-induced transgene insertion and telomere-associated truncation of a single human chromosome for chromosome engineering in CHO and A9 cells.

    Science.gov (United States)

    Uno, Narumi; Hiramatsu, Kei; Uno, Katsuhiro; Komoto, Shinya; Kazuki, Yasuhiro; Oshimura, Mitsuo

    2017-10-06

    Chromosome engineering techniques including gene insertion, telomere-associated truncation and microcell-mediated chromosome transfer (MMCT) are powerful tools for generation of humanised model animal, containing megabase-sized genomic fragments. However, these techniques require two cell lines: homologous recombination (HR)-proficient DT40 cells for chromosome modification, and CHO cells for transfer to recipient cells. Here we show an improved technique using a combination of CRISPR/Cas9-induced HR in CHO and mouse A9 cells without DT40 cells following MMCT to recipient cells. Transgene insertion was performed in CHO cells with the insertion of enhanced green fluorescence protein (EGFP) using CRISPR/Cas9 and a circular targeting vector containing two 3 kb HR arms. Telomere-associated truncation was performed in CHO cells using CRISPR/Cas9 and a linearised truncation vector containing a single 7 kb HR arm at the 5' end, a 1 kb artificial telomere at the 3' end. At least 11% and 6% of the targeting efficiency were achieved for transgene insertion and telomere-associated truncation, respectively. The transgene insertion was also confirmed in A9 cells (29%). The modified chromosomes were transferrable to other cells. Thus, this CHO and A9 cell-mediated chromosome engineering using the CRISPR/Cas9 for direct transfer of the modified chromosome is a rapid technique that will facilitate chromosome manipulation.

  12. A numerical method for multigroup slab-geometry discrete ordinates problems with no spatial truncation error

    International Nuclear Information System (INIS)

    Barros, R.C. de; Larsen, E.W.

    1991-01-01

    A generalization of the one-group Spectral Green's Function (SGF) method is developed for multigroup, slab-geometry discrete ordinates (S N ) problems. The multigroup SGF method is free from spatial truncation errors; it generated numerical values for the cell-edge and cell-average angular fluxes that agree with the analytic solution of the multigroup S N equations. Numerical results are given to illustrate the method's accuracy

  13. Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

    Science.gov (United States)

    Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

    2015-07-14

    In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http

  14. Design and Synthesis of a Series of Truncated Neplanocin Fleximers

    Directory of Open Access Journals (Sweden)

    Sarah C. Zimmermann

    2014-12-01

    Full Text Available In an effort to study the effects of flexibility on enzyme recognition and activity, we have developed several different series of flexible nucleoside analogues in which the purine base is split into its respective imidazole and pyrimidine components. The focus of this particular study was to synthesize the truncated neplanocin A fleximers to investigate their potential anti-protozoan activities by inhibition of S-adenosylhomocysteine hydrolase (SAHase. The three fleximers tested displayed poor anti-trypanocidal activities, with EC50 values around 200 μM. Further studies of the corresponding ribose fleximers, most closely related to the natural nucleoside substrates, revealed low affinity for the known T. brucei nucleoside transporters P1 and P2, which may be the reason for the lack of trypanocidal activity observed.

  15. The robustness of truncated Airy beam in PT Gaussian potentials media

    Science.gov (United States)

    Wang, Xianni; Fu, Xiquan; Huang, Xianwei; Yang, Yijun; Bai, Yanfeng

    2018-03-01

    The robustness of truncated Airy beam in parity-time (PT) symmetric Gaussian potentials media is numerically investigated. A high-peak power beam sheds from the Airy beam due to the media modulation while the Airy wavefront still retain its self-bending and non-diffraction characteristics under the influence of modulation parameters. Increasing the modulation factor results in the smaller value of maximum power of the center beam, and the opposite trend occurs with the increment of the modulation depth. However, the parabolic trajectory of the Airy wavefront does not be influenced. By utilizing the unique features, the Airy beam can be used as a long distance transmission source under the PT symmetric Gaussian potentials medium.

  16. Pulse column hydrodynamics for liquid-liquid extraction with truncated-disc packing

    International Nuclear Information System (INIS)

    Bracou, H.; Hanssens, A.

    1993-01-01

    The experimental installation is composed of a stainless steel truncated disc packing with 25% of axial transparency, 25 mm of distance between the plates and 50 mm of diameter (DT 25/25/50 stainless steel). The phase system used during these tests is the hydrogenated tetra-propylene (HTP dispersed phase) /water (continuous phase) in continuous aqueous operating ''FAC'' method. The aim of this work is to gather the whole requisite data to the modelization stage based on the extrapolation of a mathematical tool, type population evaluation with a double object to supply the basis information useful for the model, and to establish an experimental data base for the model validation. 9 refs., 4 figs

  17. Glycoprotein gene truncation in avian metapneumovirus subtype C isolates from the United States.

    Science.gov (United States)

    Velayudhan, Binu T; Yu, Qingzhong; Estevez, Carlos N; Nagaraja, Kakambi V; Halvorson, David A

    2008-10-01

    The length of the published glycoprotein (G) gene sequences of avian metapneumovirus subtype-C (aMPV-C) isolated from domestic turkeys and wild birds in the United States (1996-2003) remains controversial. To explore the G gene size variation in aMPV-C by the year of isolation and cell culture passage levels, we examined 21 turkey isolates of aMPV-C at different cell culture passages. The early domestic turkey isolates of aMPV-C (aMPV/CO/1996, aMPV/MN/1a-b, and 2a-b/97) had a G gene of 1,798 nucleotides (nt) that coded for a predicted protein of 585 amino acids (aa) and showed >97% nt similarity with that of aMPV-C isolated from Canada geese. This large G gene got truncated upon serial passages in Vero cell cultures by deletion of 1,015 nt near the end of the open reading frame. The recent domestic turkey isolates of aMPV-C lacked the large G gene but instead had a small G gene of 783 nt, irrespective of cell culture passage levels. In some cultures, both large and small genes were detected, indicating the existence of a mixed population of the virus. Apparently, serial passage of aMPV-C in cell cultures and natural passage in turkeys in the field led to truncation of the G gene, which may be a mechanism of virus evolution for survival in a new host or environment.

  18. Error-measure for anisotropic grid-adaptation in turbulence-resolving simulations

    Science.gov (United States)

    Toosi, Siavash; Larsson, Johan

    2015-11-01

    Grid-adaptation requires an error-measure that identifies where the grid should be refined. In the case of turbulence-resolving simulations (DES, LES, DNS), a simple error-measure is the small-scale resolved energy, which scales with both the modeled subgrid-stresses and the numerical truncation errors in many situations. Since this is a scalar measure, it does not carry any information on the anisotropy of the optimal grid-refinement. The purpose of this work is to introduce a new error-measure for turbulence-resolving simulations that is capable of predicting nearly-optimal anisotropic grids. Turbulent channel flow at Reτ ~ 300 is used to assess the performance of the proposed error-measure. The formulation is geometrically general, applicable to any type of unstructured grid.

  19. An improved method for purification of recombinant truncated heme oxygenase-1 by expanded bed adsorption and gel filtration.

    Science.gov (United States)

    Hu, Hong-Bo; Wang, Wei; Han, Ling; Zhou, Wen-Pu; Zhang, Xue-Hong

    2007-03-01

    Recombinant truncated human heme oxygenase-1 (hHO-1) expressed in Escherichia coli was efficiently separated and purified from feedstock by DEAE-ion exchange expanded bed adsorption. Protocol optimization of hHO-1 on DEAE adsorbent resulted in adsorption in 0 M NaCl and elution in 150 mM NaCl at a pH of 8.5. The active enzyme fractions separated from the expanded bed column were further purified by a Superdex 75 gel filtration step. The specific hHO-1 activity increased from 0.82 +/- 0.05 to 24.8 +/- 1.8 U/mg during the whole purification steps. The recovery and purification factor of truncated hHO-1 of the whole purification were 72.7 +/- 4.7 and 30.2 +/- 2.3%, respectively. This purification process can decrease the demand on the preparation of feedstock and simplify the purification process.

  20. Human truncated thioredoxin (Trx80) as a novel mitogenic cytokine for white blood cells

    OpenAIRE

    Pekkari, Klas

    2001-01-01

    Thioredoxin (Trx) is a 12 kDa protein present in all species with a well-conserved active site sequence comprising -Cys-Gly-Pro-Cys-, which catalyzes oxido-reductase reactions. Trx regulates the activity of transcription factors and intracellular signalling pathways, and secreted Trx is a co-cytokine with several interleukins. In addition to full-length Trx a 10 kDa C-terminally truncated form of the protein is produced mainly by monocytes. This protein has unique eosinophil...

  1. Evaluation of the truncated perturbed chain-polar statistical associating fluid theory for complex mixture fluid phase equilibria

    DEFF Research Database (Denmark)

    Karakatsani, Eirini; Kontogeorgis, Georgios; Economou, Ioannis

    2006-01-01

    Perturbed chain-statistical associating fluid theory (PC-SAFT) was extended rigorously to polar fluids based on the theory of Stell and co-workers [Mol. Phys. 1977, 33, 987]. The new PC-PSAFT was simplified to truncated PC-PSAFT (tPC-PSAFT) so that it can be practical for real polar fluid...

  2. Weakly nonlinear sloshing in a truncated circular conical tank

    International Nuclear Information System (INIS)

    Gavrilyuk, I P; Hermann, M; Lukovsky, I A; Solodun, O V; Timokha, A N

    2013-01-01

    Sloshing of an ideal incompressible liquid in a rigid truncated (tapered) conical tank is considered when the tank performs small-magnitude oscillatory motions with the forcing frequency close to the lowest natural sloshing frequency. The multimodal method, the non-conformal mapping technique and the Moiseev type asymptotics are employed to derive a finite-dimensional system of weakly nonlinear ordinary differential (modal) equations. This modal system is a generalization of that by Gavrilyuk et al 2005 Fluid Dyn. Res. 37 399–429. Using the derived modal equations, we classify the resonant steady-state wave regimes occurring due to horizontal harmonic tank excitations. The frequency ranges are detected where the ‘planar’ and/or ‘swirling’ steady-state sloshing are stable as well as a range in which all steady-state wave regimes are not stable and irregular (chaotic) liquid motions occur is established. The results on the frequency ranges are qualitatively supported by experiments by Matta E 2002 PhD Thesis Politecnico di Torino, Torino. (paper)

  3. Administering truncated receive functions in a parallel messaging interface

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

    2014-12-09

    Administering truncated receive functions in a parallel messaging interface (`PMI`) of a parallel computer comprising a plurality of compute nodes coupled for data communications through the PMI and through a data communications network, including: sending, through the PMI on a source compute node, a quantity of data from the source compute node to a destination compute node; specifying, by an application on the destination compute node, a portion of the quantity of data to be received by the application on the destination compute node and a portion of the quantity of data to be discarded; receiving, by the PMI on the destination compute node, all of the quantity of data; providing, by the PMI on the destination compute node to the application on the destination compute node, only the portion of the quantity of data to be received by the application; and discarding, by the PMI on the destination compute node, the portion of the quantity of data to be discarded.

  4. Crystallization and preliminary X-ray analysis of a truncated mutant of yeast nuclear thiol peroxidase, a novel atypical 2-Cys peroxiredoxin

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jongkeun; Choi, Soonwoong [Department of Chemistry, Seoul National University, Seoul 151-742 (Korea, Republic of); Choi, Jungwon [Department of Chemistry, The University of Suwon, Suwon 445-743 (Korea, Republic of); Cha, Mee-Kyung; Kim, Il-Han [Department of Biochemistry, Paichai University, Taejon 302-735 (Korea, Republic of); Shin, Whanchul, E-mail: nswcshin@plaza.snu.ac.kr [Department of Chemistry, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2005-07-01

    A double mutant of yeast nuclear thiol peroxidase has been crystallized in a truncated form. The crystal belongs to space group P3{sub 2}, with unit-cell parameters a = b = 37.54, c = 83.26 Å. A diffraction data set has been collected to 1.8 Å resolution. Saccharomyces cerevisiae nTPx is a thioredoxin-dependent thiol peroxidase that is localized in the nucleus. nTPx belongs to the C-type atypical 2-Cys peroxiredoxin family members, which are frequently called BCPs or PrxQs. A double mutant (C107S/C112S) of nTPx overexpressed in Escherichia coli was spontaneously degraded upon freezing and thawing and its truncated form (residues 57–215; MW = 17837 Da) was crystallized with PEG 3350 and mercury(II) acetate as precipitants using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.8 Å resolution using X-ray synchrotron radiation. The crystals belong to the trigonal space group P3{sub 2}, with unit-cell parameters a = b = 37.54, c = 83.26 Å. The asymmetric unit contains one molecule of truncated mutant nTPx, with a corresponding V{sub M} of 1.91 Å{sup 3} Da{sup −1} and a solvent content of 35.5%.

  5. Crystallization and preliminary X-ray analysis of a truncated mutant of yeast nuclear thiol peroxidase, a novel atypical 2-Cys peroxiredoxin

    International Nuclear Information System (INIS)

    Choi, Jongkeun; Choi, Soonwoong; Choi, Jungwon; Cha, Mee-Kyung; Kim, Il-Han; Shin, Whanchul

    2005-01-01

    A double mutant of yeast nuclear thiol peroxidase has been crystallized in a truncated form. The crystal belongs to space group P3 2 , with unit-cell parameters a = b = 37.54, c = 83.26 Å. A diffraction data set has been collected to 1.8 Å resolution. Saccharomyces cerevisiae nTPx is a thioredoxin-dependent thiol peroxidase that is localized in the nucleus. nTPx belongs to the C-type atypical 2-Cys peroxiredoxin family members, which are frequently called BCPs or PrxQs. A double mutant (C107S/C112S) of nTPx overexpressed in Escherichia coli was spontaneously degraded upon freezing and thawing and its truncated form (residues 57–215; MW = 17837 Da) was crystallized with PEG 3350 and mercury(II) acetate as precipitants using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.8 Å resolution using X-ray synchrotron radiation. The crystals belong to the trigonal space group P3 2 , with unit-cell parameters a = b = 37.54, c = 83.26 Å. The asymmetric unit contains one molecule of truncated mutant nTPx, with a corresponding V M of 1.91 Å 3 Da −1 and a solvent content of 35.5%

  6. C-terminal truncations in human 3'-5' DNA exonuclease TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy

    NARCIS (Netherlands)

    Richards, Anna; van den Maagdenberg, Arn M. J. M.; Jen, Joanna C.; Kavanagh, David; Bertram, Paula; Spitzer, Dirk; Liszewski, M. Kathryn; Barilla-LaBarca, Maria-Louise; Terwindt, Gisela M.; Kasai, Yumi; McLellan, Mike; Grand, Mark Gilbert; Vanmolkot, Kaate R. J.; de Vries, Boukje; Wan, Jijun; Kane, Michael J.; Mamsa, Hafsa; Schäfer, Ruth; Stam, Anine H.; Haan, Joost; de Jong, Paulus T. V. M.; Storimans, Caroline W.; van Schooneveld, Mary J.; Oosterhuis, Jendo A.; Gschwendter, Andreas; Dichgans, Martin; Kotschet, Katya E.; Hodgkinson, Suzanne; Hardy, Todd A.; Delatycki, Martin B.; Hajj-Ali, Rula A.; Kothari, Parul H.; Nelson, Stanley F.; Frants, Rune R.; Baloh, Robert W.; Ferrari, Michel D.; Atkinson, John P.

    2007-01-01

    Autosomal dominant retinal vasculopathy with cerebral leukodystrophy is a microvascular endotheliopathy with middle-age onset. In nine families, we identified heterozygous C-terminal frameshift mutations in TREX1, which encodes a 3'-5' exonuclease. These truncated proteins retain exonuclease

  7. C-terminal truncations in human 3 '-5 ' DNA exonuclease TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy

    NARCIS (Netherlands)

    Richards, Anna; van den Maagdenberg, Arn M. J. M.; Jen, Joanna C.; Kavanagh, David; Bertram, Paula; Spitzer, Dirk; Liszewski, M. Kathryn; Barilla-LaBarca, Maria-Louise; Terwindt, Gisela M.; Kasai, Yumi; McLellan, Mike; Grand, Mark Gilbert; Vanmolkot, Kaate R. J.; de Vries, Boukje; Wan, Jijun; Kane, Michael J.; Mamsa, Hafsa; Schaefer, Ruth; Stam, Anine H.; Haan, Joost; Paulus, T. V. M. de Jong; Storimans, Caroline W.; van Schooneveld, Mary J.; Oosterhuis, Jendo A.; Gschwendter, Andreas; Dichgans, Martin; Kotschet, Katya E.; Hodgkinson, Suzanne; Hardy, Todd A.; Delatycki, Martin B.; Hajj-Ali, Rula A.; Kothari, Parul H.; Nelson, Stanley F.; Frants, Rune R.; Baloh, Robert W.; Ferrari, Michel D.; Atkinson, John P.

    Autosomal dominant retinal vasculopathy with cerebral leukodystrophy is a microvascular endotheliopathy with middle- age onset. In nine families, we identified heterozygous C- terminal frameshift mutations in TREX1, which encodes a 3'-5' exonuclease. These truncated proteins retain exonuclease

  8. Pressure Overload by Transverse Aortic Constriction Induces Maladaptive Hypertrophy in a Titin-Truncated Mouse Model

    Directory of Open Access Journals (Sweden)

    Qifeng Zhou

    2015-01-01

    Full Text Available Mutations in the giant sarcomeric protein titin (TTN are a major cause for inherited forms of dilated cardiomyopathy (DCM. We have previously developed a mouse model that imitates a TTN truncation mutation we found in a large pedigree with DCM. While heterozygous Ttn knock-in mice do not display signs of heart failure under sedentary conditions, they recapitulate the human phenotype when exposed to the pharmacological stressor angiotensin II or isoproterenol. In this study we investigated the effects of pressure overload by transverse aortic constriction (TAC in heterozygous (Het Ttn knock-in mice. Two weeks after TAC, Het mice developed marked impairment of left ventricular ejection fraction (p<0.05, while wild-type (WT TAC mice did not. Het mice also trended toward increased ventricular end diastolic pressure and volume compared to WT littermates. We found an increase in histologically diffuse cardiac fibrosis in Het compared to WT in TAC mice. This study shows that a pattern of DCM can be induced by TAC-mediated pressure overload in a TTN-truncated mouse model. This model enlarges our arsenal of cardiac disease models, adding a valuable tool to understand cardiac pathophysiological remodeling processes and to develop therapeutic approaches to combat heart failure.

  9. The combination of heteroduplex analysis and protein truncation test for exact detection of the APC gene mutations

    International Nuclear Information System (INIS)

    Tomka, M.; Kirchhoff, T.; Stefurkova, V.; Zajac, V.; Kulcsar, L.

    1998-01-01

    Familial adenomatous polyposis (FAP) is usually associated with mutation in the adenomatous polyposis coli (APC) gene. To examine the occurrence of these mutations in the number of FAP suspected families from the whole Slovakia effectively, we have applied heteroduplex analysis (HDA) and protein truncation test (PTT) for the analyses of 2-5 base pair deletions and point mutations of the APC gene. In the analyzed exon 15 of the APC gene determined by the primers 15Efor-15Grev for HDA and 15ET7-15J3 for PTT more than 70% of mutations should be deletions [3, 12], which are detectable by HDA. In our collection of 5 FAP families mutations in the APC gene were found in families 10, 27 and 41 using HDA. By PTT test the formation of truncated APC protein in FAP families 2, 10, 16 and 27 were revealed. The necessity of combination of at least HDA and PTT techniques for exact detection of APC mutations in analyzed APC region is discussed. (authors)

  10. A truncating mutation of HDAC2 in human cancers confers resistance to histone deacetylase inhibition

    DEFF Research Database (Denmark)

    Ropero, S; Fraga, MF; Ballestar, E

    2006-01-01

    Disruption of histone acetylation patterns is a common feature of cancer cells, but very little is known about its genetic basis. We have identified truncating mutations in one of the primary human histone deacetylases, HDAC2, in sporadic carcinomas with microsatellite instability and in tumors a...... deacetylase inhibitors. As such drugs may serve as therapeutic agents for cancer, our findings support the use of HDAC2 mutational status in future pharmacogenetic treatment of these individuals....

  11. Influence of miscut on crystal truncation rod scattering

    International Nuclear Information System (INIS)

    Munkholm, A.; Brennan, S.

    1999-01-01

    X-rays can be used to measure the roughness of a surface by the study of crystal truncation rod scattering. It is shown that for a simple cubic lattice the presence of a miscut surface with a regular step array has no effect on the scattered intensity of a single rod and that a distribution of terrace widths on the surface is shown to have the same effect as adding roughness to the surface. For a perfect crystal without miscut, the scattered intensity is the sum of the intensity from all the rods with the same in-plane momentum transfer. For all real crystals, the scattered intensity is better described as that from a single rod. It is shown that data-collection strategies must correctly account for the sample miscut or there is a potential for improperly measuring the rod intensity. This can result in an asymmetry in the rod intensity above and below the Bragg peak, which can be misinterpreted as being due to a relaxation of the surface. The calculations presented here are compared with data for silicon (001) wafers with 0.1 and 4 miscuts. (orig.)

  12. Truncated Newton-Raphson Methods for Quasicontinuum Simulations

    National Research Council Canada - National Science Library

    Liang, Yu; Kanapady, Ramdev; Chung, Peter W

    2006-01-01

    ... and preconditioned nonlinear conjugate gradient implementation. Results of illustrative examples mainly focus on the number of minimization iterations to converge and CPU time for the two-dimensional nanoindentation and shearing grain boundary problems.

  13. Simulations of hydrogen sorption in rht-MOF-1: identifying the binding sites through explicit polarization and quantum rotation calculations

    KAUST Repository

    Pham, Tony

    2014-01-01

    Grand canonical Monte Carlo (GCMC) simulations of hydrogen sorption were performed in rht-MOF-1, a metal-organic framework (MOF) that consists of isophthalate groups joined by copper paddlewheel clusters and Cu3O trimers through tetrazolate moeities. This is a charged rht-MOF that contains extra-framework nitrate counterions within the material. For the simulations performed herein, excellent agreement with experiment was achieved for the simulated hydrogen sorption isotherms and calculated isosteric heat of adsorption, Qst, values only when using a polarizable potential. Thermodynamic agreement is demonstrated via comparing to experimental isotherms and binding sites are revealed by combining simulation and inelastic neutron scattering (INS) data. Simulations involving explicit many-body polarization interactions assisted in the determination of the binding sites in rht-MOF-1 through the distribution of the induced dipoles that led to strong adsorbate interactions. Four distinct hydrogen sorption sites were determined from the polarization distribution: the nitrate ions located in the corners of the truncated tetrahedral cages, the Cu2+ ions of the paddlewheels that project into the truncated tetrahedral and truncated octahedral cages (Cu1 ions), the Cu2+ ions of the Cu3O trimers (Cu3 ions), and the sides of the paddlewheels in the cuboctahedral cage. The simulations revealed that the initial sorption sites for hydrogen in rht-MOF-1 are the nitrate ions; this site corresponds to the high initial Qst value for hydrogen (9.5 kJ mol-1) in the MOF. The radial distribution functions, g(r), about the Cu2+ ions at various loadings revealed that the Cu1 ions are the preferred open-metal sorption sites for hydrogen at low loading, while the Cu3 ions become occupied at higher loadings. The validation of the aforementioned sorption sites in rht-MOF-1 was confirmed by calculating the two-dimensional quantum rotational levels about each site and comparing the levels to the

  14. Autoantibodies to N-terminally truncated GAD improve clinical phenotyping of individuals with adult-onset diabetes: Action LADA 12.

    Science.gov (United States)

    Achenbach, Peter; Hawa, Mohammed I; Krause, Stephanie; Lampasona, Vito; Jerram, Samuel T; Williams, Alistair J K; Bonifacio, Ezio; Ziegler, Anette G; Leslie, R David

    2018-04-04

    Adult-onset type 1 diabetes, in which the 65 kDa isoform of GAD (GAD65) is a major autoantigen, has a broad clinical phenotype encompassing variable need for insulin therapy. This study aimed to evaluate whether autoantibodies against N-terminally truncated GAD65 more closely defined a type 1 diabetes phenotype associated with insulin therapy. Of 1114 participants with adult-onset diabetes from the Action LADA (latent autoimmune diabetes in adults) study with sufficient sera, we selected those designated type 1 (n = 511) or type 2 diabetes (n = 603) and retested the samples in radiobinding assays for human full-length GAD65 autoantibodies (f-GADA) and N-terminally truncated (amino acids 96-585) GAD65 autoantibodies (t-GADA). Individuals' clinical phenotypes were analysed according to antibody binding patterns. Overall, 478 individuals were f-GADA-positive, 431 were t-GADA-positive and 628 were negative in both assays. Risk of insulin treatment was augmented in t-GADA-positive individuals (OR 4.69 [95% CI 3.57, 6.17]) compared with f-GADA-positive individuals (OR 3.86 [95% CI 2.95, 5.06]), irrespective of diabetes duration. Of 55 individuals who were f-GADA-positive but t-GADA-negative, i.e. with antibody binding restricted to the N-terminus of GAD65, the phenotype was similar to type 2 diabetes with low risk of progression to insulin treatment. Compared with these individuals with N-terminal GAD65-restricted GADA, t-GADA-positive individuals were younger at diagnosis (p = 0.005), leaner (p N-terminally truncated GAD65 autoantibodies is associated with the clinical phenotype of autoimmune type 1 diabetes and predicts insulin therapy.

  15. Heterozygous truncation mutations of the SMC1A gene cause a severe early onset epilepsy with cluster seizures in females: Detailed phenotyping of 10 new cases.

    Science.gov (United States)

    Symonds, Joseph D; Joss, Shelagh; Metcalfe, Kay A; Somarathi, Suresh; Cruden, Jamie; Devlin, Anita M; Donaldson, Alan; DiDonato, Nataliya; Fitzpatrick, David; Kaiser, Frank J; Lampe, Anne K; Lees, Melissa M; McLellan, Ailsa; Montgomery, Tara; Mundada, Vivek; Nairn, Lesley; Sarkar, Ajoy; Schallner, Jens; Pozojevic, Jelena; Parenti, Ilaria; Tan, Jeen; Turnpenny, Peter; Whitehouse, William P; Zuberi, Sameer M

    2017-04-01

    The phenotype of seizure clustering with febrile illnesses in infancy/early childhood is well recognized. To date the only genetic epilepsy consistently associated with this phenotype is PCDH19, an X-linked disorder restricted to females, and males with mosaicism. The SMC1A gene, which encodes a structural component of the cohesin complex is also located on the X chromosome. Missense variants and small in-frame deletions of SMC1A cause approximately 5% of Cornelia de Lange Syndrome (CdLS). Recently, protein truncating mutations in SMC1A have been reported in five females, all of whom have been affected by a drug-resistant epilepsy, and severe developmental impairment. Our objective was to further delineate the phenotype of SMC1A truncation. Female cases with de novo truncation mutations in SMC1A were identified from the Deciphering Developmental Disorders (DDD) study (n = 8), from postmortem testing of an affected twin (n = 1), and from clinical testing with an epilepsy gene panel (n = 1). Detailed information on the phenotype in each case was obtained. Ten cases with heterozygous de novo mutations in the SMC1A gene are presented. All 10 mutations identified are predicted to result in premature truncation of the SMC1A protein. All cases are female, and none had a clinical diagnosis of CdLS. They presented with onset of epileptic seizures between <4 weeks and 28 months of age. In the majority of cases, a marked preponderance for seizures to occur in clusters was noted. Seizure clusters were associated with developmental regression. Moderate or severe developmental impairment was apparent in all cases. Truncation mutations in SMC1A cause a severe epilepsy phenotype with cluster seizures in females. These mutations are likely to be nonviable in males. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

  16. Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation

    Directory of Open Access Journals (Sweden)

    Chris S. Booker

    2014-09-01

    Full Text Available Interleukin-18 (IL-18 is a pro-inflammatory cytokine which stimulates activation of the nuclear factor kappa beta (NF-κB pathway via interaction with the IL-18 receptor. The receptor itself is formed from a dimer of two subunits, with the ligand-binding IL-18Rα subunit being encoded by the IL18R1 gene. A splice variant of murine IL18r1, which has been previously described, is formed by transcription of an unspliced intron (forming a ‘type II’ IL18r1 transcript and is predicted to encode a receptor with a truncated intracellular domain lacking the capacity to generate downstream signalling. In order to examine the relevance of this finding to human IL-18 function, we assessed the presence of a homologous transcript by reverse transcription-polymerase chain reaction (RT-PCR in the human and rat as another common laboratory animal. We present evidence for type II IL18R1 transcripts in both species. While the mouse and rat transcripts are predicted to encode a truncated receptor with a novel 5 amino acid C-terminal domain, the human sequence is predicted to encode a truncated protein with a novel 22 amino acid sequence bearing resemblance to the ‘Box 1’ motif of the Toll/interleukin-1 receptor (TIR domain, in a similar fashion to the inhibitory interleukin-1 receptor 2. Given that transcripts from these three species are all formed by inclusion of homologous unspliced intronic regions, an analysis of homologous introns across a wider array of 33 species with available IL18R1 gene records was performed, which suggests similar transcripts may encode truncated type II IL-18Rα subunits in other species. This splice variant may represent a conserved evolutionary mechanism for regulating IL-18 activity.

  17. Deteksi Dini Kasus Demam Berdarah Dengue Berdasarkan Faktor Cuaca di DKI Jakarta Menggunakan Metode Zero Truncated Negative Binomial

    Directory of Open Access Journals (Sweden)

    Robert Kurniawan

    2017-11-01

    Full Text Available AbstractThe incidence rates of DHF in Jakarta in 2010 to 2014 are always higher than that of the national rates. Therefore, this study aims to find the effect of weather parameter on DHF cases. Weather is chosen because it can be observed daily and can be predicted so that it can be used as earlydetection in estimating the number of DHF cases. Data use includes DHF cases which is collected daily and weather data including lowest and highest temperatures and rainfall. Data analysis used is zero-truncated negative binomial analysis at 10% significance level. Based on the periodic dataof selected variables from January 1st 2015 until May 31st 2015, the study revealed that weather factors consisting of highest temperature, lowest temperature, and rainfall rate were significant enough to predict the number of DHF patients in DKI Jakarta. The three variables had positiveeffects in influencing the number of DHF patients in the same period. However, the weather factors cannot be controlled by humans, so that appropriate preventions are required whenever weather’s predictions indicate the increasing number of DHF cases in DKI Jakarta.Keywords: Dengue Hemorrhagic Fever, zero truncated negative binomial, early warning.AbstrakAngka kesakitan DBD pada tahun 2010 hingga 2014 selalu lebih tinggi dibandingkan dengan angka kesakitan DBD nasional. Oleh karena itu, penelitian ini bertujuan untuk mencari pengaruh faktor cuaca terhadap kasus DBD. Faktor cuaca dipilih karena dapat diamati setiap harinya dan dapat diprediksi sehingga dapat dijadikan deteksi dini dalam perkiraan jumlah penderita DBD. Data yang digunakan dalam penelitian ini adalah data jumlah penderita DBD di DKI Jakarta per hari dan data cuaca yang meliputi suhu terendah, suhu tertinggi dan curah hujan. Untuk mengetahui pengaruh faktor cuaca tersebut terhadap jumlah penderita DBD di DKI Jakarta digunakan metode analisis zero-truncated negative binomial. Berdasarkan data periode 1 Januari 2015 hingga

  18. Distinct Ezrin Truncations Differentiate Metastases in Sentinel Lymph Nodes from Unaffected Lymph Node Tissues, from Primary Breast Tumors, and from Healthy Glandular Breast Tissues

    Directory of Open Access Journals (Sweden)

    Claudia Röwer

    2018-02-01

    Full Text Available BACKGROUND: Lymph node metastasis status is a prognostic factor for further lymph node involvement and for patient survival in breast cancer patients. Frozen section analysis of lymph nodes is a reliable method for detection of macro-metastases. However, this method is far less effective in detecting micro-metastases, requesting improved diagnostic procedures. METHODS: We investigated expression and truncation of ezrin in (i sentinel lymph node metastases, (ii unaffected axillary lymph nodes, (iii primary breast tumors, and (iv healthy glandular breast tissues using 2D gel electrophoresis, SDS-PAGE, and mass spectrometry in addition to Western blotting. RESULTS: Full-length ezrin (E1; amino acids 1–586 is present in all four investigated tissues. Two truncated ezrin forms, one missing about the first hundred amino acids (E2a and the other lacking about 150 C-terminal amino acids (E2b were detectable in primary tumor tissues and in sentinel lymph node metastases but not in glandular tissues. Strikingly, an ezrin truncation (E3 which consists approximately of amino acids 238–586 was found strongly expressed in all sentinel lymph node metastases. Moreover, an N-terminal ezrin fragment (E4 that consists approximately of amino acids 1–273 was identified in sentinel lymph node metastases as well. CONCLUSIONS: We show for the first time the existence of tissue-dependent specific ezrin truncations. The distinguished strong Western blot staining of ezrin E3 in sentinel lymph node metastases underlines its capability to substantiate the occurrence of lymph node (micrometastases in breast cancer patients.

  19. Effect of truncated cone roughness element density on hydrodynamic drag

    Science.gov (United States)

    Womack, Kristofer; Schultz, Michael; Meneveau, Charles

    2017-11-01

    An experimental study was conducted on rough-wall, turbulent boundary layer flow with roughness elements whose idealized shape model barnacles that cause hydrodynamic drag in many applications. Varying planform densities of truncated cone roughness elements were investigated. Element densities studied ranged from 10% to 79%. Detailed turbulent boundary layer velocity statistics were recorded with a two-component LDV system on a three-axis traverse. Hydrodynamic roughness length (z0) and skin-friction coefficient (Cf) were determined and compared with the estimates from existing roughness element drag prediction models including Macdonald et al. (1998) and other recent models. The roughness elements used in this work model idealized barnacles, so implications of this data set for ship powering are considered. This research was supported by the Office of Naval Research and by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

  20. Prion Protein on Astrocytes or in Extracellular Fluid Impedes Neurodegeneration Induced by Truncated Prion Protein

    OpenAIRE

    Race, Brent; Meade-White, Kimberly; Race, Richard; Baumann, Frank; Aguzzi, Adriano; Chesebro, Bruce

    2009-01-01

    Prion protein (PrP) is a host-encoded membrane-anchored glycoprotein which is required for susceptibility to prion disease. PrP may also be important for normal brain functions such as hippocampal spatial memory. Previously transgenic mice expressing amino terminally truncated mouse PrP (Δ32–134) spontaneously developed a fatal disease associated with degeneration of cerebellar granular neurons as well as vacuolar degeneration of deep cerebellar and brain stem white matter. This disease could...

  1. Exact and approximate Fourier rebinning algorithms for the solution of the data truncation problem in 3-D PET.

    Science.gov (United States)

    Bouallègue, Fayçal Ben; Crouzet, Jean-François; Comtat, Claude; Fourcade, Marjolaine; Mohammadi, Bijan; Mariano-Goulart, Denis

    2007-07-01

    This paper presents an extended 3-D exact rebinning formula in the Fourier space that leads to an iterative reprojection algorithm (iterative FOREPROJ), which enables the estimation of unmeasured oblique projection data on the basis of the whole set of measured data. In first approximation, this analytical formula also leads to an extended Fourier rebinning equation that is the basis for an approximate reprojection algorithm (extended FORE). These algorithms were evaluated on numerically simulated 3-D positron emission tomography (PET) data for the solution of the truncation problem, i.e., the estimation of the missing portions in the oblique projection data, before the application of algorithms that require complete projection data such as some rebinning methods (FOREX) or 3-D reconstruction algorithms (3DRP or direct Fourier methods). By taking advantage of all the 3-D data statistics, the iterative FOREPROJ reprojection provides a reliable alternative to the classical FOREPROJ method, which only exploits the low-statistics nonoblique data. It significantly improves the quality of the external reconstructed slices without loss of spatial resolution. As for the approximate extended FORE algorithm, it clearly exhibits limitations due to axial interpolations, but will require clinical studies with more realistic measured data in order to decide on its pertinence.

  2. Modelling noise in second generation sequencing forensic genetics STR data using a one-inflated (zero-truncated) negative binomial model

    DEFF Research Database (Denmark)

    Vilsen, Søren B.; Tvedebrink, Torben; Mogensen, Helle Smidt

    2015-01-01

    We present a model fitting the distribution of non-systematic errors in STR second generation sequencing, SGS, analysis. The model fits the distribution of non-systematic errors, i.e. the noise, using a one-inflated, zero-truncated, negative binomial model. The model is a two component model...

  3. [Anesthesia simulators and training devices].

    Science.gov (United States)

    Hartmannsgruber, M; Good, M; Carovano, R; Lampotang, S; Gravenstein, J S

    1993-07-01

    Simulators and training devices are used extensively by educators in 'high-tech' occupations, especially those requiring an understanding of complex systems and co-ordinated psychomotor skills. Because of advances in computer technology, anaesthetised patients can now be realistically simulated. This paper describes several training devices and a simulator currently being employed in the training of anaesthesia personnel at the University of Florida. This Gainesville Anesthesia Simulator (GAS) comprises a patient mannequin, anaesthesia gas machine, and a full set of normally operating monitoring instruments. The patient can spontaneously breathe, has audible heart and breath sounds, and palpable pulses. The mannequin contains a sophisticated lung model that consumes and eliminates gas according to physiological principles. Interconnected computers controlling the physical signs of the mannequin enable the presentation of a multitude of clinical signs. In addition, the anaesthesia machine, which is functionally intact, has hidden fault activators to challenge the user to correct equipment malfunctions. Concealed sensors monitor the users' actions and responses. A robust data acquisition and control system and a user-friendly scripting language for programming simulation scenarios are key features of GAS and make this system applicable for the training of both the beginning resident and the experienced practitioner. GAS enhances clinical education in anaesthesia by providing a non-threatening environment that fosters learning by doing. Exercises with the simulator are supported by sessions on a number of training devices. These present theoretical and practical interactive courses on the anaesthesia machine and on monitors. An extensive system, for example, introduces the student to the physics and clinical application of transoesophageal echocardiography.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Diagnostic efficiency of truncated area under the curve from 0 to 2 h (AUC₀₋₂) of mycophenolic acid in kidney transplant recipients receiving mycophenolate mofetil and concomitant tacrolimus.

    Science.gov (United States)

    Lampón, Natalia; Tutor-Crespo, María J; Romero, Rafael; Tutor, José C

    2011-07-01

    Recently, the use of the truncated area under the curve from 0 to 2 h (AUC(0-2)) of mycophenolic acid (MPA) has been proposed for therapeutic monitoring in liver transplant recipients. The aim of our study was the evaluation of the clinical usefulness of truncated AUC(0-2) in kidney transplant patients. Plasma MPA was measured in samples taken before the morning dose of mycophenolate mofetil, and one-half and 2 h post-dose, completing 63 MPA concentration-time profiles from 40 adult kidney transplant recipients. The AUC from 0 to 12 h (AUC(0-12)) was calculated using the validated algorithm of Pawinski et al. The truncated AUC(0-2) was calculated using the linear trapezoidal rule, and extrapolated to 0-12 h (trapezoidal extrapolated AUC(0-12)) as previously described. Algorithm calculated and trapezoidal extrapolated AUC(0-12) values showed high correlation (r=0.995) and acceptable dispersion (ma68=0.71 μg·h/mL), median prediction error (6.6%) and median absolute prediction error (12.6%). The truncated AUC(0-2) had acceptable diagnostic efficiency (87%) in the classification of subtherapeutic, therapeutic or supratherapeutic values with respect to AUC(0-12). However, due to the high inter-individual variation of the drug absorption-rate, the dispersion between both pharmacokinetic variables (ma68=6.9 μg·h/mL) was unacceptable. The substantial dispersion between truncated AUC(0-2) and AUC(0-12) values may be a serious objection for the routine use of MPA AUC(0-2) in clinical practice.

  5. Analytical Investigation of Elastic Thin-Walled Cylinder and Truncated Cone Shell Intersection Under Internal Pressure

    OpenAIRE

    Zamani, J.; Soltani, B.; Aghaei, M.

    2014-01-01

    An elastic solution of cylinder-truncated cone shell intersection under internal pressure is presented. The edge solution theory that has been used in this study takes bending moments and shearing forces into account in the thin-walled shell of revolution element. The general solution of the cone equations is based on power series method. The effect of cone apex angle on the stress distribution in conical and cylindrical parts of structure is investigated. In addition, the effect of the inter...

  6. Adaptive designs based on the truncated product method

    Directory of Open Access Journals (Sweden)

    Neuhäuser Markus

    2005-09-01

    Full Text Available Abstract Background Adaptive designs are becoming increasingly important in clinical research. One approach subdivides the study into several (two or more stages and combines the p-values of the different stages using Fisher's combination test. Methods Alternatively to Fisher's test, the recently proposed truncated product method (TPM can be applied to combine the p-values. The TPM uses the product of only those p-values that do not exceed some fixed cut-off value. Here, these two competing analyses are compared. Results When an early termination due to insufficient effects is not appropriate, such as in dose-response analyses, the probability to stop the trial early with the rejection of the null hypothesis is increased when the TPM is applied. Therefore, the expected total sample size is decreased. This decrease in the sample size is not connected with a loss in power. The TPM turns out to be less advantageous, when an early termination of the study due to insufficient effects is possible. This is due to a decrease of the probability to stop the trial early. Conclusion It is recommended to apply the TPM rather than Fisher's combination test whenever an early termination due to insufficient effects is not suitable within the adaptive design.

  7. Characterization and protective efficacy in an animal model of a novel truncated rotavirus VP8 subunit parenteral vaccine candidate.

    Science.gov (United States)

    Xue, Miaoge; Yu, Linqi; Che, Yaojian; Lin, Haijun; Zeng, Yuanjun; Fang, Mujin; Li, Tingdong; Ge, Shengxiang; Xia, Ningshao

    2015-05-21

    The cell-attachment protein VP8* of rotavirus is a potential candidate parenteral vaccine. However, the yield of full-length VP8 protein (VP8*, residues 1-231) expressed in Escherichia coli was low, and a truncated VP8 protein (ΔVP8*, residues 65-231) cannot elicit efficient protective immunity in a mouse model. In this study, tow novel truncated VP8 proteins, VP8-1 (residues 26-231) and VP8-2 (residues 51-231), were expressed in E. coli and evaluated for immunogenicity and protective efficacy, compared with VP8* and ΔVP8*. As well as ΔVP8*, the protein VP8-1 and VP8-2 were successfully expressed in high yield and purified in homogeneous dimeric forms, while the protein VP8* was expressed with lower yield and prone to aggregation and degradation in solution. Although the immunogenicity of the protein VP8*, VP8-1, VP8-2 and ΔVP8* was comparable, immunization of VP8* and VP8-1 elicited significantly higher neutralizing antibody titers than that of VP8-2 and ΔVP8* in mice. Furthermore, when assessed using a mouse maternal antibody model, the efficacy of VP8-1 to protect against rotavirus-induced diarrhea in pups was comparable to that of VP8*, both were dramatically higher than that of VP8-2 and ΔVP8*. Taken together, the novel truncated protein VP8-1, with increased yield, improved homogeneity and high protective efficacy, is a viable candidate for further development of a parenterally administrated prophylactic vaccine against rotavirus infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. The truncate mutation of Notch2 enhances cell proliferation through activating the NF-κB signal pathway in the diffuse large B-cell lymphomas.

    Directory of Open Access Journals (Sweden)

    Xinxia Zhang

    Full Text Available The Notch2 is a critical membrane receptor for B-cell functions, and also displays various biological roles in lymphoma pathogenesis. In this article, we reported that 3 of 69 (4.3% diffuse large B-cell lymphomas (DLBCLs exhibited a truncate NOTCH2 mutation at the nucleotide 7605 (G/A in the cDNA sequence, which led to partial deletion of the C-terminal of PEST (proline-, glutamic acid-, serine- and threonine-rich domain. The truncate Notch2 activated both the Notch2 and the NF-κB signals and promoted the proliferation of B-cell lymphoma cell lines, including DLBCL and Burkitt's lymphoma cell lines. Moreover, the ectopic proliferation was completely inhibited by ammonium pyrrolidinedithiocarbamate (PDTC, an NF-κB inhibitor. Simultaneously, PDTC also reduced the expression level of Notch2. Based on these results, we conclude that the Notch2 receptor with PEST domain truncation enhances cell proliferation which may be associated with the activation of the Notch2 and the NF-κB signaling. Our results are expected to provide a possible target for new DLBCL therapies by suppressing the Notch2 and the NF-κB signaling.

  9. Infection of human and non-human cells by a highly fusogenic primary CD4-independent HIV-1 isolate with a truncated envelope cytoplasmic tail

    International Nuclear Information System (INIS)

    Saha, Kunal; Yan Hui; Nelson, Julie A.E.; Zerhouni-Layachi, Bouchra

    2005-01-01

    Truncation of the envelope cytoplasmic tail has enabled FIV, SIV, and some laboratory HIV-1 strains to acquire broader cellular tropism and enhanced fusogenicity. Here we have characterized a primary CD4-independent HIV-1 isolate (92UG046-T8) with a truncated cytoplasmic tail that was able to infect and induce syncytia in primary lymphocytes from human, chimpanzee, and monkey, as well as CD4-negative cell lines from human and monkey. Increased syncytia were also noticeable with 293 cells expressing the cloned envelope from the 92UG046-T8 isolate suggesting envelope-mediated cellular fusion. Except pooled serum from HIV-1-infected individuals, monoclonal anti-envelope antibodies or antibodies/antagonists against CD4, CXCR4, and CCR5 were not able to prevent infection by the 92UG046-T8 isolate. This is the first report showing a primary HIV-1 variant with truncated cytoplasmic tail which is highly fusogenic and can infect a broad range of cells from human and non-human origins. In vivo evolution of similar HIV-1 mutants may have important implications in AIDS pathogenesis

  10. Functional analysis of truncated and site-directed mutagenesis dextransucrases to produce different type dextrans.

    Science.gov (United States)

    Wang, Chao; Zhang, Hong-Bin; Li, Meng-Qi; Hu, Xue-Qin; Li, Yao

    2017-07-01

    Dextrans with distinct molecular size and structure are increasingly being used in the food and pharmaceutical industries. Dextran is produced by dextransucrase (DSR, EC2.4.5.1), which is produced by Leuconostoc mesenteroides. DSR belongs to glycosyl hydrolase family (GH70) and synthesizes branched α-glucan (dextran) with both 5% α(1-3) and 95% α(1-6) glycosidic linkages. The DSR gene dex-YG (Genebank, Accession No. DQ345760) was cloned from the wild strain Leuconostoc mesenteroides 0326. This study generated a series of C-terminally truncated variants of dextransucrase and substituting the amino-acid residues in the active site of DSR. With shorter length of DSR, its polysaccharide-synthesizing capability was impaired heavily, whereas oligosaccharide (acting as prebiotics)-synthesizing capability increased significantly, efficiently producing special sizes of dextran. All truncated mutant enzymes were active. Results demonstrated that the catalytic domain dextransucrase was likely in 800 aa or less. Based on the three-dimensional structure model of dextransucrase built through homology modeling methods, the DSR and its mutants with the acceptor substrate of maltose and donor substrate of sucrose were studied by molecular-docking method. Substituting these amino-acid residues significantly affected enzyme activities. Compared with the wild-type dextran, mutant enzymes catalyzed the synthesis of a-glucan with 1-9% α(1-3) and 90-98% α(1-6) branching linkages. Some mutants introduced a small amount of α(1-4) linkages and α(1-2) linkages. This strategy can be effectively used for the rational protein design of dextransucrase. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. MEASUREMENT ERROR EFFECT ON THE POWER OF CONTROL CHART FOR ZERO-TRUNCATED POISSON DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    Ashit Chakraborty

    2013-09-01

    Full Text Available Measurement error is the difference between the true value and the measured value of a quantity that exists in practice and may considerably affect the performance of control charts in some cases. Measurement error variability has uncertainty which can be from several sources. In this paper, we have studied the effect of these sources of variability on the power characteristics of control chart and obtained the values of average run length (ARL for zero-truncated Poisson distribution (ZTPD. Expression of the power of control chart for variable sample size under standardized normal variate for ZTPD is also derived.

  12. Verifying and Validating Simulation Models

    Energy Technology Data Exchange (ETDEWEB)

    Hemez, Francois M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-02-23

    This presentation is a high-level discussion of the Verification and Validation (V&V) of computational models. Definitions of V&V are given to emphasize that “validation” is never performed in a vacuum; it accounts, instead, for the current state-of-knowledge in the discipline considered. In particular comparisons between physical measurements and numerical predictions should account for their respective sources of uncertainty. The differences between error (bias), aleatoric uncertainty (randomness) and epistemic uncertainty (ignorance, lack-of- knowledge) are briefly discussed. Four types of uncertainty in physics and engineering are discussed: 1) experimental variability, 2) variability and randomness, 3) numerical uncertainty and 4) model-form uncertainty. Statistical sampling methods are available to propagate, and analyze, variability and randomness. Numerical uncertainty originates from the truncation error introduced by the discretization of partial differential equations in time and space. Model-form uncertainty is introduced by assumptions often formulated to render a complex problem more tractable and amenable to modeling and simulation. The discussion concludes with high-level guidance to assess the “credibility” of numerical simulations, which stems from the level of rigor with which these various sources of uncertainty are assessed and quantified.

  13. Conflict Resolution: the Truncated Zoning Arrangement and the Buhari Political Tsunami in Nigeria

    Directory of Open Access Journals (Sweden)

    Isaac Terungwa Terwase

    2015-08-01

    Full Text Available The Nigerian Fourth Republic ushered in a demo-cratically elected government in 1999 that paved way for the civilians to take over government after a long period of military rule in Nigeria. This made the political parties to project their candidates for contest in occupying the political positions at the federal, states and local government levels. Thus, such projection through the ruling political party that won the election in 1999 known as the People’s Democratic Party (PDP, went into zoning arrange-ment that could give the country’s six geopolitical zones a place for participation in the administration of the country. This arrangement coordinated the highest positions such as the President, Vice-Presi-dent, President of the Senate, Speaker of the House of Representatives, Secretary to the Government of the Federation, and Chairman of the ruling party. However, such arrangements were only practiced from 1999 to 2011. The zoning arrangements were trun-cated in 2011, which led to conflict in the Northern part of the country. The objective of the study there-fore, is to examine the consequences of the trun-cated zoning arrangement and lessons from the Buhari Political tsunami in 2015 general elections in Nigeria, with interest on how to resolve such con-flicts that emanated. The study made use of qualita-tive research and the review of previous literature as sources of data collection. The findings revealed that, many people were killed during the years 2011-2015 under study; both private and public properties were also destroyed. This study recom-mends constitutional approach regarding the zoning formula to accom-modate all the six geopolitical zones in Nigeria in order to resolve the conflicts therein.

  14. Finite size effects in neutron star and nuclear matter simulations

    Energy Technology Data Exchange (ETDEWEB)

    Giménez Molinelli, P.A., E-mail: pagm@df.uba.ar; Dorso, C.O.

    2015-01-15

    In this work we study molecular dynamics simulations of symmetric nuclear and neutron star matter using a semi-classical nucleon interaction model. Our aim is to gain insight on the nature of the so-called “finite size effects”, unavoidable in this kind of simulations, and to understand what they actually affect. To do so, we explore different geometries for the periodic boundary conditions imposed on the simulation cell: cube, hexagonal prism and truncated octahedron. For nuclear matter simulations we show that, at sub-saturation densities and low temperatures, the solutions are non-homogeneous structures reminiscent of the “nuclear pasta” phases expected in neutron star matter simulations, but only one structure per cell and shaped by specific artificial aspects of the simulations—for the same physical conditions (i.e. number density and temperature) different cells yield different solutions. The particular shape of the solution at low enough temperature and a given density can be predicted analytically by surface minimization. We also show that even if this behavior is due to the imposition of periodic boundary conditions on finite systems, this does not mean that it vanishes for very large systems, and it is actually independent of the system size. We conclude that, for nuclear matter simulations, the cells' size sets the only characteristic length scale for the inhomogeneities, and the geometry of the periodic cell determines the shape of those inhomogeneities. To model neutron star matter we add a screened Coulomb interaction between protons, and perform simulations in the three cell geometries. Our simulations indeed produce the well known nuclear pasta, with (in most cases) several structures per cell. However, we find that for systems not too large results are affected by finite size in different ways depending on the geometry of the cell. In particular, at the same certain physical conditions and system size, the hexagonal prism yields a

  15. Unified theory of fermion pair to boson mappings in full and truncated spaces

    International Nuclear Information System (INIS)

    Ginocchio, J.N.; Johnson, C.W.

    1995-01-01

    After a brief review of various mappings of fermion pairs to bosons, we rigorously derive a general approach. Following the methods of Marumori and Otsuka, Arima, and Iachello, our approach begins with mapping states and constructs boson representations that preserve fermion matrix elements. In several cases these representations factor into finite, Hermitian boson images times a projection or norm operator that embodies the Pauli principle. We pay particular attention to truncated boson spaces, and describe general methods for constructing Hermitian and approximately finite boson image Hamiltonians. This method is akin to that of Otsuka, Arima, and Iachello introduced in connection with the interacting boson model, but is more rigorous, general, and systematic

  16. Truncating Mutations of MAGEL2, a Gene within the Prader-Willi Locus, Are Responsible for Severe Arthrogryposis

    Science.gov (United States)

    Mejlachowicz, Dan; Nolent, Flora; Maluenda, Jérome; Ranjatoelina-Randrianaivo, Hanitra; Giuliano, Fabienne; Gut, Ivo; Sternberg, Damien; Laquerrière, Annie; Melki, Judith

    2015-01-01

    Arthrogryposis multiplex congenita (AMC) is characterized by the presence of multiple joint contractures resulting from reduced or absent fetal movement. Here, we report two unrelated families affected by lethal AMC. By genetic mapping and whole-exome sequencing in a multiplex family, a heterozygous truncating MAGEL2 mutation leading to frameshift and a premature stop codon (c.1996delC, p.Gln666Serfs∗36) and inherited from the father was identified in the probands. In another family, a distinct heterozygous truncating mutation leading to frameshift (c.2118delT, p.Leu708Trpfs∗7) and occurring de novo on the paternal allele of MAGEL2 was identified in the affected individual. In both families, RNA analysis identified the mutated paternal MAGEL2 transcripts only in affected individuals. MAGEL2 is one of the paternally expressed genes within the Prader-Willi syndrome (PWS) locus. PWS is associated with, to varying extents, reduced fetal mobility, severe infantile hypotonia, childhood-onset obesity, hypogonadism, and intellectual disability. MAGEL2 mutations have been recently reported in affected individuals with features resembling PWS and called Schaaf-Yang syndrome. Here, we show that paternal MAGEL2 mutations are also responsible for lethal AMC, recapitulating the clinical spectrum of PWS and suggesting that MAGEL2 is a PWS-determining gene. PMID:26365340

  17. MULTISTAGE BITRATE REDUCTION IN ABSOLUTE MOMENT BLOCK TRUNCATION CODING FOR IMAGE COMPRESSION

    Directory of Open Access Journals (Sweden)

    S. Vimala

    2012-05-01

    Full Text Available Absolute Moment Block Truncation Coding (AMBTC is one of the lossy image compression techniques. The computational complexity involved is less and the quality of the reconstructed images is appreciable. The normal AMBTC method requires 2 bits per pixel (bpp. In this paper, two novel ideas have been incorporated as part of AMBTC method to improve the coding efficiency. Generally, the quality degrades with the reduction in the bit-rate. But in the proposed method, the quality of the reconstructed image increases with the decrease in the bit-rate. The proposed method has been tested with standard images like Lena, Barbara, Bridge, Boats and Cameraman. The results obtained are better than that of the existing AMBTC method in terms of bit-rate and the quality of the reconstructed images.

  18. Truncated power control for improving TCP/IP performance over CDMA wireless links

    DEFF Research Database (Denmark)

    Cianca, Ernestina; Prasad, Ramjee; De Sanctis, Mauro

    2005-01-01

    The issue of the performance degradation of transmission control protocol/Internet Protocol (TCP/IP) over wireless links due to the presence of noncongestion-related packet losses has been addressed with a physical layer approach. The effectiveness of automatic repeat request techniques...... in enhancing TCP/IP performance depends on the tradeoff between frame transmission delay and residual errors after retransmissions. The paper shows how a truncated power control can be effectively applied to improve that tradeoff so that a higher transmission reliability is provided without increasing...... the frame transmission delay through the radio link layer and without increasing the energy consumption. An analytical framework has been developed to show the feasibility and effectiveness of the proposed power control. The analytical results, which are carried out assuming a constant multiuser...

  19. Lethal mutants and truncated selection together solve a paradox of the origin of life.

    Directory of Open Access Journals (Sweden)

    David B Saakian

    Full Text Available BACKGROUND: Many attempts have been made to describe the origin of life, one of which is Eigen's cycle of autocatalytic reactions [Eigen M (1971 Naturwissenschaften 58, 465-523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor must be transmitted to the next generation with a minimal number of misprints. In Eigen's theory, the maximum chain length that could be maintained is restricted to 100-1000 nucleotides, while for the most primitive genome the length is around 7000-20,000. This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life. METHODOLOGY/PRINCIPAL FINDINGS: We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life. CONCLUSIONS/SIGNIFICANCE: We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.

  20. Mechanical properties of regular porous biomaterials made from truncated cube repeating unit cells: Analytical solutions and computational models.

    Science.gov (United States)

    Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

    2016-03-01

    Additive manufacturing (AM) has enabled fabrication of open-cell porous biomaterials based on repeating unit cells. The micro-architecture of the porous biomaterials and, thus, their physical properties could then be precisely controlled. Due to their many favorable properties, porous biomaterials manufactured using AM are considered as promising candidates for bone substitution as well as for several other applications in orthopedic surgery. The mechanical properties of such porous structures including static and fatigue properties are shown to be strongly dependent on the type of the repeating unit cell based on which the porous biomaterial is built. In this paper, we study the mechanical properties of porous biomaterials made from a relatively new unit cell, namely truncated cube. We present analytical solutions that relate the dimensions of the repeating unit cell to the elastic modulus, Poisson's ratio, yield stress, and buckling load of those porous structures. We also performed finite element modeling to predict the mechanical properties of the porous structures. The analytical solution and computational results were found to be in agreement with each other. The mechanical properties estimated using both the analytical and computational techniques were somewhat higher than the experimental data reported in one of our recent studies on selective laser melted Ti-6Al-4V porous biomaterials. In addition to porosity, the elastic modulus and Poisson's ratio of the porous structures were found to be strongly dependent on the ratio of the length of the inclined struts to that of the uninclined (i.e. vertical or horizontal) struts, α, in the truncated cube unit cell. The geometry of the truncated cube unit cell approaches the octahedral and cube unit cells when α respectively approaches zero and infinity. Consistent with those geometrical observations, the analytical solutions presented in this study approached those of the octahedral and cube unit cells when

  1. Carboxyl-terminal Truncations of ClC-Kb Abolish Channel Activation by Barttin Via Modified Common Gating and Trafficking.

    Science.gov (United States)

    Stölting, Gabriel; Bungert-Plümke, Stefanie; Franzen, Arne; Fahlke, Christoph

    2015-12-18

    ClC-K chloride channels are crucial for auditory transduction and urine concentration. Mutations in CLCNKB, the gene encoding the renal chloride channel hClC-Kb, cause Bartter syndrome type III, a human genetic condition characterized by polyuria, hypokalemia, and alkalosis. In recent years, several Bartter syndrome-associated mutations have been described that result in truncations of the intracellular carboxyl terminus of hClC-Kb. We here used a combination of whole-cell patch clamp, confocal imaging, co-immunoprecipitation, and surface biotinylation to study the functional consequences of a frequent CLCNKB mutation that creates a premature stop codon at Trp-610. We found that W610X leaves the association of hClC-Kb and the accessory subunit barttin unaffected, but impairs its regulation by barttin. W610X attenuates hClC-Kb surface membrane insertion. Moreover, W610X results in hClC-Kb channel opening in the absence of barttin and prevents further barttin-mediated activation. To describe how the carboxyl terminus modifies the regulation by barttin we used V166E rClC-K1. V166E rClC-K1 is active without barttin and exhibits prominent, barttin-regulated voltage-dependent gating. Electrophysiological characterization of truncated V166E rClC-K1 demonstrated that the distal carboxyl terminus is necessary for slow cooperative gating. Since barttin modifies this particular gating process, channels lacking the distal carboxyl-terminal domain are no longer regulated by the accessory subunit. Our results demonstrate that the carboxyl terminus of hClC-Kb is not part of the binding site for barttin, but functionally modifies the interplay with barttin. The loss-of-activation of truncated hClC-Kb channels in heterologous expression systems fully explains the reduced basolateral chloride conductance in affected kidneys and the clinical symptoms of Bartter syndrome patients. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Carboxyl-terminal Truncations of ClC-Kb Abolish Channel Activation by Barttin Via Modified Common Gating and Trafficking*

    Science.gov (United States)

    Stölting, Gabriel; Bungert-Plümke, Stefanie; Franzen, Arne; Fahlke, Christoph

    2015-01-01

    ClC-K chloride channels are crucial for auditory transduction and urine concentration. Mutations in CLCNKB, the gene encoding the renal chloride channel hClC-Kb, cause Bartter syndrome type III, a human genetic condition characterized by polyuria, hypokalemia, and alkalosis. In recent years, several Bartter syndrome-associated mutations have been described that result in truncations of the intracellular carboxyl terminus of hClC-Kb. We here used a combination of whole-cell patch clamp, confocal imaging, co-immunoprecipitation, and surface biotinylation to study the functional consequences of a frequent CLCNKB mutation that creates a premature stop codon at Trp-610. We found that W610X leaves the association of hClC-Kb and the accessory subunit barttin unaffected, but impairs its regulation by barttin. W610X attenuates hClC-Kb surface membrane insertion. Moreover, W610X results in hClC-Kb channel opening in the absence of barttin and prevents further barttin-mediated activation. To describe how the carboxyl terminus modifies the regulation by barttin we used V166E rClC-K1. V166E rClC-K1 is active without barttin and exhibits prominent, barttin-regulated voltage-dependent gating. Electrophysiological characterization of truncated V166E rClC-K1 demonstrated that the distal carboxyl terminus is necessary for slow cooperative gating. Since barttin modifies this particular gating process, channels lacking the distal carboxyl-terminal domain are no longer regulated by the accessory subunit. Our results demonstrate that the carboxyl terminus of hClC-Kb is not part of the binding site for barttin, but functionally modifies the interplay with barttin. The loss-of-activation of truncated hClC-Kb channels in heterologous expression systems fully explains the reduced basolateral chloride conductance in affected kidneys and the clinical symptoms of Bartter syndrome patients. PMID:26453302

  3. Supersymmetric deformations of 3D SCFTs from tri-Sasakian truncation

    Energy Technology Data Exchange (ETDEWEB)

    Karndumri, Parinya [Chulalongkorn University, String Theory and Supergravity Group, Department of Physics, Faculty of Science, Bangkok (Thailand)

    2017-02-15

    We holographically study supersymmetric deformations of N = 3 and N = 1 superconformal field theories in three dimensions using four-dimensional N = 4 gauged supergravity coupled to three-vector multiplets with non-semisimple SO(3) x (T{sup 3},T{sup 3}) gauge group. This gauged supergravity can be obtained from a truncation of 11-dimensional supergravity on a tri-Sasakian manifold and admits both N = 1,3 supersymmetric and stable non-supersymmetric AdS{sub 4} critical points. We analyze the BPS equations for SO(3) singlet scalars in detail and study possible supersymmetric solutions. A number of RG flows to non-conformal field theories and half-supersymmetric domain walls are found, and many of them can be given analytically. Apart from these ''flat'' domain walls, we also consider AdS{sub 3}-sliced domain wall solutions describing two-dimensional conformal defects with N = (1,0) supersymmetry within the dual N = 1 field theory while this type of solutions does not exist in the N = 3 case. (orig.)

  4. Proteolysis of truncated hemolysin A yields a stable dimerization interface

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Walter R.P.; Bhattacharyya, Basudeb; Grilley, Daniel P.; Weaver, Todd M. (Wabash); (UW)

    2017-02-21

    Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.

  5. Truncation of power law behavior in 'scale-free' network models due to information filtering

    International Nuclear Information System (INIS)

    Mossa, Stefano; Barthelemy, Marc; Eugene Stanley, H.; Nunes Amaral, Luis A.

    2002-01-01

    We formulate a general model for the growth of scale-free networks under filtering information conditions--that is, when the nodes can process information about only a subset of the existing nodes in the network. We find that the distribution of the number of incoming links to a node follows a universal scaling form, i.e., that it decays as a power law with an exponential truncation controlled not only by the system size but also by a feature not previously considered, the subset of the network 'accessible' to the node. We test our model with empirical data for the World Wide Web and find agreement

  6. Overexpression of the truncated version of ILV2 enhances glycerol production in Saccharomyces cerevisiae.

    Science.gov (United States)

    Murashchenko, Lidiia; Abbas, Charles; Dmytruk, Kostyantyn; Sibirny, Andriy

    2016-08-01

    Acetolactate synthase is a mitochondrial enzyme that catalyses the conversion of two pyruvate molecules to an acetolactate molecule with release of carbon dioxide. The overexpression of the truncated version of the corresponding gene, ILV2, that codes for presumably cytosolic acetolactate synthase in the yeast Saccharomyces cerevisiae, led to a decrease in intracellular pyruvate concentration. This recombinant strain was also characterized by a four-fold increase in glycerol production, with a concomitant 1.8-fold reduction in ethanol production, when compared to that of the wild-type strain under anaerobic conditions in a glucose alcoholic fermentation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  7. Production of biodiesel by transesterification of corn and soybean oils with ethanol or butanol using resin-bound truncated Candida antarctica lipase B

    Science.gov (United States)

    Enzymatic catalysts, such as lipases, have advantages over chemical catalysts for transesterification of triglycerides to produce biodiesel. A gene encoding a synthetic truncated Candida antarctica lipase B (CALB) was generated via automated PCR and expressed in Saccharomyces cerevisiae. Western b...

  8. GLP-1 (glucagon-like peptide 1) and truncated GLP-1, fragments of human proglucagon, inhibit gastric acid secretion in humans

    DEFF Research Database (Denmark)

    Schjoldager, B T; Mortensen, P E; Christiansen, J

    1989-01-01

    Glucagon-like peptide 1 amide (GLP-1 amide), a predicted product of the glucagon gene (proglucagon 72-107-amide), and truncated GLP-1 (proglucagon 78-107-amide), recently isolated from porcine small intestine, were infused in doses of 100 and 400 ng/kg/hr and 12.5 and 50 ng/kg/hr, respectively...

  9. Instabilities of the chiral-symmetry-breaking ground state in a truncation-free expansion

    International Nuclear Information System (INIS)

    Rembiesa, P.

    1988-01-01

    We use the composite-field effective-action method to examine the stability of the chiral-symmetry-breaking vacua in a QED-like model of interacting fermion fields. Unlike most of the existing approaches, ours does not rely on the truncated Baker-Johnson-Willey expansion. Instead, we break the hierarchy of the Dyson-Schwinger equations by the requirement that the vertex function is dominated by the contributions from the vicinity of the mass shell of the exchanged gluon and that it explicitly satisfies the Ward identity. The composite-field effective potential is then expanded in terms of the eigenfunctions of the Bethe-Salpeter equation. The signature of the second derivatives of the effective potential shows that the broken-symmetry vacua are unstable

  10. A Platoon Dispersion Model Based on a Truncated Normal Distribution of Speed

    Directory of Open Access Journals (Sweden)

    Ming Wei

    2012-01-01

    Full Text Available Understanding platoon dispersion is critical for the coordination of traffic signal control in an urban traffic network. Assuming that platoon speed follows a truncated normal distribution, ranging from minimum speed to maximum speed, this paper develops a piecewise density function that describes platoon dispersion characteristics as the platoon moves from an upstream to a downstream intersection. Based on this density function, the expected number of cars in the platoon that pass the downstream intersection, and the expected number of cars in the platoon that do not pass the downstream point are calculated. To facilitate coordination in a traffic signal control system, dispersion models for the front and the rear of the platoon are also derived. Finally, a numeric computation for the coordination of successive signals is presented to illustrate the validity of the proposed model.

  11. Analytical Investigation of Elastic Thin-Walled Cylinder and Truncated Cone Shell Intersection Under Internal Pressure.

    Science.gov (United States)

    Zamani, J; Soltani, B; Aghaei, M

    2014-10-01

    An elastic solution of cylinder-truncated cone shell intersection under internal pressure is presented. The edge solution theory that has been used in this study takes bending moments and shearing forces into account in the thin-walled shell of revolution element. The general solution of the cone equations is based on power series method. The effect of cone apex angle on the stress distribution in conical and cylindrical parts of structure is investigated. In addition, the effect of the intersection and boundary locations on the circumferential and longitudinal stresses is evaluated and it is shown that how quantitatively they are essential.

  12. SU-E-I-51: Use of Blade Sequences in Cervical Spine MR Imaging for Eliminating Motion, Truncation and Flow Artifacts

    Energy Technology Data Exchange (ETDEWEB)

    Mavroidis, P [University of Texas Health Science Center, UTHSCSA, San Antonio, TX (United States); Lavdas, E; Kostopoulos, S; Ninos, C; Strikou, A; Glotsos, D; Vlachopoulou, A; Oikonomou, G [Technological Education Institute of Athens, Athens, Athens (Greece); Economopoulos, N [General University Hospital ATTIKON, Athens, Athens (Greece); Roka, V [Health Center of Farkadona, Trikala (Greece); Sakkas, G [Center for Research and Technology of Thessaly, Trikala (Greece); Tsagkalis, A; Batsikas, G [IASO Thessalias Hospital, Larissa (Greece); Statkahis, S [Cancer Therapy and Research Center, San Antonio, TX (United States); Papanikolaou, N [University of Texas HSC SA, San Antonio, TX (United States)

    2014-06-01

    Purpose: To assess the efficacy of the BLADE technique to eliminate motion, truncation, flow and other artifacts in Cervical Spine MRI compared to the conventional technique. To study the ability of the examined sequences to reduce the indetention and wrap artifacts, which have been reported in BLADE sagittal sequences. Methods: Forty consecutive subjects, who had been routinely scanned for cervical spine examination using four different image acquisition techniques, were analyzed. More specifically, the following pairs of sequences were compared: a) T2 TSE SAG vs. T2 TSE SAG BLADE and b) T2 TIRM SAG vs. T2 TIRM SAG BLADE. A quantitative analysis was performed using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures. A qualitative analysis was also performed by two radiologists, who graded seven image characteristics on a 5-point scale (0:non-visualization; 1:poor; 2:average; 3:good; 4:excellent). The observers also evaluated the presence of image artifacts (motion, truncation, flow, indentation). Results: Based on the findings of the quantitative analysis, the ReCON values of the CSF (cerebrospinal fluid)/SC (spinal cord) between TIRM SAG and TIRM SAG BLADE were found to present statistical significant differences (p<0.001). Regarding motion and truncation artifacts, the T2 TSE SAG BLADE was superior compared to the T2 TSE SAG and the T2 TIRM SAG BLADE was superior compared to the T2 TIRM SAG. Regarding flow artifacts, T2 TIRM SAG BLADE eliminated more artifacts compared to the T2 TIRM SAG. Conclusion: The use of BLADE sequences in cervical spine MR examinations appears to be capable of potentially eliminating motion, pulsatile flow and trancation artifacts. Furthermore, BLADE sequences are proposed to be used in the standard examination protocols based on the fact that a significantly improved image quality could be achieved.

  13. SU-E-I-51: Use of Blade Sequences in Cervical Spine MR Imaging for Eliminating Motion, Truncation and Flow Artifacts

    International Nuclear Information System (INIS)

    Mavroidis, P; Lavdas, E; Kostopoulos, S; Ninos, C; Strikou, A; Glotsos, D; Vlachopoulou, A; Oikonomou, G; Economopoulos, N; Roka, V; Sakkas, G; Tsagkalis, A; Batsikas, G; Statkahis, S; Papanikolaou, N

    2014-01-01

    Purpose: To assess the efficacy of the BLADE technique to eliminate motion, truncation, flow and other artifacts in Cervical Spine MRI compared to the conventional technique. To study the ability of the examined sequences to reduce the indetention and wrap artifacts, which have been reported in BLADE sagittal sequences. Methods: Forty consecutive subjects, who had been routinely scanned for cervical spine examination using four different image acquisition techniques, were analyzed. More specifically, the following pairs of sequences were compared: a) T2 TSE SAG vs. T2 TSE SAG BLADE and b) T2 TIRM SAG vs. T2 TIRM SAG BLADE. A quantitative analysis was performed using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures. A qualitative analysis was also performed by two radiologists, who graded seven image characteristics on a 5-point scale (0:non-visualization; 1:poor; 2:average; 3:good; 4:excellent). The observers also evaluated the presence of image artifacts (motion, truncation, flow, indentation). Results: Based on the findings of the quantitative analysis, the ReCON values of the CSF (cerebrospinal fluid)/SC (spinal cord) between TIRM SAG and TIRM SAG BLADE were found to present statistical significant differences (p<0.001). Regarding motion and truncation artifacts, the T2 TSE SAG BLADE was superior compared to the T2 TSE SAG and the T2 TIRM SAG BLADE was superior compared to the T2 TIRM SAG. Regarding flow artifacts, T2 TIRM SAG BLADE eliminated more artifacts compared to the T2 TIRM SAG. Conclusion: The use of BLADE sequences in cervical spine MR examinations appears to be capable of potentially eliminating motion, pulsatile flow and trancation artifacts. Furthermore, BLADE sequences are proposed to be used in the standard examination protocols based on the fact that a significantly improved image quality could be achieved

  14. Truncation of the C-terminal region of Toscana Virus NSs protein is critical for interferon-β antagonism and protein stability.

    Science.gov (United States)

    Gori Savellini, Gianni; Gandolfo, Claudia; Cusi, Maria Grazia

    2015-12-01

    Toscana Virus (TOSV) is a Phlebovirus responsible for central nervous system (CNS) injury in humans. The TOSV non-structural protein (NSs), which interacting with RIG-I leads to its degradation, was analysed in the C terminus fragment in order to identify its functional domains. To this aim, two C-terminal truncated NSs proteins, Δ1C-NSs (aa 1-284) and Δ2C-NSs (aa 1-287) were tested. Only Δ1C-NSs did not present any inhibitory effect on RIG-I and it showed a greater stability than the whole NSs protein. Moreover, the deletion of the TLQ aa sequence interposed between the two ΔC constructs caused a greater accumulation of the protein with a weak inhibitory effect on RIG-I, indicating some involvement of these amino acids in the NSs activity. Nevertheless, all the truncated proteins were still able to interact with RIG-I, suggesting that the domains responsible for RIG-I signaling and RIG-I interaction are mapped on different regions of the protein. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Repair for scattering expansion truncation errors in transport calculations

    International Nuclear Information System (INIS)

    Emmett, M.B.; Childs, R.L.; Rhoades, W.A.

    1980-01-01

    Legendre expansion of angular scattering distributions is usually limited to P 3 in practical transport calculations. This truncation often results in non-trivial errors, especially alternating negative and positive lateral scattering peaks. The effect is especially prominent in forward-peaked situations such as the within-group component of the Compton Scattering of gammas. Increasing the expansion to P 7 often makes the peaks larger and narrower. Ward demonstrated an accurate repair, but his method requires special cross section sets and codes. The DOT IV code provides fully-compatible, but heuristic, repair of the erroneous scattering. An analytical Klein-Nishina estimator, newly available in the MORSE code, allows a test of this method. In the MORSE calculation, particle scattering histories are calculated in the usual way, with scoring by an estimator routine at each collision site. Results for both the conventional P 3 estimator and the analytical estimator were obtained. In the DOT calculation, the source moments are expanded into the directional representation at each iteration. Optionally a sorting procedure removes all negatives, and removes enough small positive values to restore particle conservation. The effect of this is to replace the alternating positive and negative values with positive values of plausible magnitude. The accuracy of those values is examined herein

  16. A truncated spherical shell model for nuclear collective excitations: Applications to the odd-mass systems, neutron-proton systems, and other topics

    International Nuclear Information System (INIS)

    Wu, Hua.

    1989-01-01

    One of the most elusive quantum system in nature is the nucleus, which is a strongly interacting many body system. In the hadronic (a la neutrons and protons) phase, the primary concern of this thesis, the nucleus' single particle excitations are intertwined with their various collective excitations. Although the underpinning of the nucleus is the spherical shell model, it is rendered powerless without a severe, but intelligent truncation of the infinite Hilbert space. The recently proposed Fermion Dynamical Symmetry Model (FDSM) is precisely such a truncation scheme and in which a symmetry-dictated truncation scheme is introduced in nuclear physics for the first time. In this thesis, extensions and explorations of the FDSM are made to specifically study the odd mass (where the most intricate mixing of the single particle and the collective excitations are observed) and the neutron-proton systems. In particular, the author finds that the previously successful phenomenological particle-rotor-model of the Copenhagen school can now be well understood microscopically via the FDSM. Furthermore, the well known Coriolis attenuation and variable moment of inertia effects are naturally understood from the model as well. A computer code FDUO was written by one of us to study, for the first time, the numerical implications of the FDSM. Several collective modes were found even when the system does not admit a group chain description. In addition, the code is most suitable to study the connection between level statistical behavior (a at Gaussian Orthogonal Ensemble) and dynamical symmetry. It is found that there exist critical region of the interaction parameter space were the system behaves chaotically. This information is certainly crucial to understanding quantum chaotic behavior

  17. Wave Simulation in Truncated Domains for Offshore Applications

    NARCIS (Netherlands)

    Wellens, P.R.

    2012-01-01

    There is a desire to assess extreme wave loads on offshore structures like Floating Production, Storage and Offloading (FPSO) vessels, either for design, or for evaluation when circumstances near the structure change. Design formulae for extreme wave loads are scarce and

  18. Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide.

    Science.gov (United States)

    Seim, Inge; Jeffery, Penny L; Thomas, Patrick B; Walpole, Carina M; Maugham, Michelle; Fung, Jenny N T; Yap, Pei-Yi; O'Keeffe, Angela J; Lai, John; Whiteside, Eliza J; Herington, Adrian C; Chopin, Lisa K

    2016-06-01

    The peptide hormone ghrelin is a potent orexigen produced predominantly in the stomach. It has a number of other biological actions, including roles in appetite stimulation, energy balance, the stimulation of growth hormone release and the regulation of cell proliferation. Recently, several ghrelin gene splice variants have been described. Here, we attempted to identify conserved alternative splicing of the ghrelin gene by cross-species sequence comparisons. We identified a novel human exon 2-deleted variant and provide preliminary evidence that this splice variant and in1-ghrelin encode a C-terminally truncated form of the ghrelin peptide, termed minighrelin. These variants are expressed in humans and mice, demonstrating conservation of alternative splicing spanning 90 million years. Minighrelin appears to have similar actions to full-length ghrelin, as treatment with exogenous minighrelin peptide stimulates appetite and feeding in mice. Forced expression of the exon 2-deleted preproghrelin variant mirrors the effect of the canonical preproghrelin, stimulating cell proliferation and migration in the PC3 prostate cancer cell line. This is the first study to characterise an exon 2-deleted preproghrelin variant and to demonstrate sequence conservation of ghrelin gene-derived splice variants that encode a truncated ghrelin peptide. This adds further impetus for studies into the alternative splicing of the ghrelin gene and the function of novel ghrelin peptides in vertebrates.

  19. Investigation of Numerical Dissipation in Classical and Implicit Large Eddy Simulations

    Directory of Open Access Journals (Sweden)

    Moutassem El Rafei

    2017-12-01

    Full Text Available The quantitative measure of dissipative properties of different numerical schemes is crucial to computational methods in the field of aerospace applications. Therefore, the objective of the present study is to examine the resolving power of Monotonic Upwind Scheme for Conservation Laws (MUSCL scheme with three different slope limiters: one second-order and two third-order used within the framework of Implicit Large Eddy Simulations (ILES. The performance of the dynamic Smagorinsky subgrid-scale model used in the classical Large Eddy Simulation (LES approach is examined. The assessment of these schemes is of significant importance to understand the numerical dissipation that could affect the accuracy of the numerical solution. A modified equation analysis has been employed to the convective term of the fully-compressible Navier–Stokes equations to formulate an analytical expression of truncation error for the second-order upwind scheme. The contribution of second-order partial derivatives in the expression of truncation error showed that the effect of this numerical error could not be neglected compared to the total kinetic energy dissipation rate. Transitions from laminar to turbulent flow are visualized considering the inviscid Taylor–Green Vortex (TGV test-case. The evolution in time of volumetrically-averaged kinetic energy and kinetic energy dissipation rate have been monitored for all numerical schemes and all grid levels. The dissipation mechanism has been compared to Direct Numerical Simulation (DNS data found in the literature at different Reynolds numbers. We found that the resolving power and the symmetry breaking property are enhanced with finer grid resolutions. The production of vorticity has been observed in terms of enstrophy and effective viscosity. The instantaneous kinetic energy spectrum has been computed using a three-dimensional Fast Fourier Transform (FFT. All combinations of numerical methods produce a k − 4 spectrum

  20. Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

    DEFF Research Database (Denmark)

    Henryon, M; Berg, P; Sørensen, A C

    2009-01-01

    We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stoch...

  1. A retrospective view on 'algorithms for radiative intensity calculations in moderately thick atmospheres using a truncation approximation' by Teruyuki Nakajima and Masayuki Tanaka (1988)

    International Nuclear Information System (INIS)

    Nakajima, Teruyuki

    2010-01-01

    I explain the motivation behind our paper 'Algorithms for radiative intensity calculations in moderately thick atmospheres using a truncation approximation' (JQSRT 1988;40:51-69) and discuss our results in a broader historical context.

  2. Generation of uniform light by use of diode lasers and a truncated paraboloid with a Lambertian scatterer.

    Science.gov (United States)

    Alahautala, Taito; Hernberg, Rolf

    2004-02-01

    Uniform illumination was generated by use of a large number of diode laser emitters and a single nonimaging paraboloid with a Lambertian scatterer in the truncation plane. Laser light traverses a path toward the Lambertian surface and back by total internal reflection. An overall efficiency of 69% was demonstrated. Improvements that would increase the efficiency to more than 85% are suggested. The illuminated area is circular, with 14-mm diameter. The spatial nonuniformity of the beam profile is less than +/- 2%.

  3. Development of a cysteine-deprived and C-terminally truncated GLP-1 receptor

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Knudsen, Lotte Bjerre; Garibay, Patrick W.

    2013-01-01

    The glucagon-like peptide-1 receptor (GLP-1R) belongs to family B of the G-protein coupled receptors (GPCRs), and has become a promising target for the treatment of type 2 diabetes. Here we describe the development and characterization of a fully functional cysteine-deprived and C......-terminally truncated GLP-1R. Single cysteines were initially substituted with alanine, and functionally redundant cysteines were subsequently changed simultaneously. Our results indicate that Cys174, Cys226, Cys296 and Cys403 are important for the GLP-1-mediated response, whereas Cys236, Cys329, Cys341, Cys347, Cys438...... that the membrane proximal part of the C-terminal is involved in receptor expression at the cell surface. The results show that seven cysteines and more than half of the C-terminal tail can be removed from GLP-1R without compromising GLP-1 binding or function....

  4. Germline RAD51B truncating mutation in a family with cutaneous melanoma

    DEFF Research Database (Denmark)

    Wadt, Karin A W; Aoude, Lauren G; Golmard, Lisa

    2015-01-01

    Known melanoma predisposition genes only account for around 40% of high-density melanoma families. Other rare mutations are likely to play a role in melanoma predisposition. RAD51B plays an important role in DNA repair through homologous recombination, and inactivation of RAD51B has been implicated...... in tumorigenesis. Thus RAD51B is a good candidate melanoma susceptibility gene, and previously, a germline splicing mutation in RAD51B has been identified in a family with early-onset breast cancer. In order to find genetic variants associated with melanoma predisposition, whole-exome sequencing was carried out...... on blood samples from a three-case cutaneous melanoma family. We identified a novel germline RAD51B nonsense mutation, and we demonstrate reduced expression of RAD51B in melanoma cells indicating inactivation of RAD51B. This is only the second report of a germline truncating RAD51B mutation. While...

  5. Formation of truncated proteins and high-molecular-mass aggregates upon soft illumination of photosynthetic proteins

    DEFF Research Database (Denmark)

    Rinalducci, Sara; Campostrini, Natascia; Antonioli, Paolo

    2005-01-01

    Different spot profiles were observed in 2D gel electrophoresis of thylakoid membranes performed either under complete darkness or by leaving the sample for a short time to low visible light. In the latter case, a large number of new spots with lower molecular masses, ranging between 15,000 and 25......,000 Da, were observed, and high-molecular-mass aggregates, seen as a smearing in the upper part of the gel, appeared in the region around 250 kDa. Identification of protein(s) contained in these new spots by MS/MS revealed that most of them are simply truncated proteins deriving from native ones...

  6. Prevalence of E/A wave fusion and A wave truncation in DDD pacemaker patients with complete AV block under nominal AV intervals.

    Directory of Open Access Journals (Sweden)

    Wolfram C Poller

    Full Text Available Optimization of the AV-interval (AVI in DDD pacemakers improves cardiac hemodynamics and reduces pacemaker syndromes. Manual optimization is typically not performed in clinical routine. In the present study we analyze the prevalence of E/A wave fusion and A wave truncation under resting conditions in 160 patients with complete AV block (AVB under the pre-programmed AVI. We manually optimized sub-optimal AVI.We analyzed 160 pacemaker patients with complete AVB, both in sinus rhythm (AV-sense; n = 129 and under atrial pacing (AV-pace; n = 31. Using Doppler analyses of the transmitral inflow we classified the nominal AVI as: a normal, b too long (E/A wave fusion or c too short (A wave truncation. In patients with a sub-optimal AVI, we performed manual optimization according to the recommendations of the American Society of Echocardiography.All AVB patients with atrial pacing exhibited a normal transmitral inflow under the nominal AV-pace intervals (100%. In contrast, 25 AVB patients in sinus rhythm showed E/A wave fusion under the pre-programmed AV-sense intervals (19.4%; 95% confidence interval (CI: 12.6-26.2%. A wave truncations were not observed in any patient. All patients with a complete E/A wave fusion achieved a normal transmitral inflow after AV-sense interval reduction (mean optimized AVI: 79.4 ± 13.6 ms.Given the rate of 19.4% (CI 12.6-26.2% of patients with a too long nominal AV-sense interval, automatic algorithms may prove useful in improving cardiac hemodynamics, especially in the subgroup of atrially triggered pacemaker patients with AV node diseases.

  7. Truncated borrelidin analogues: synthesis by sequential cross metathesis/olefination for the southern fragment and biological evaluation.

    Science.gov (United States)

    Gündemir-Durmaz, Tülay; Schmid, Fabian; El Baz, Yana; Häusser, Annette; Schneider, Carmen; Bilitewski, Ursula; Rauhut, Guntram; Garnier, Delphine; Baro, Angelika; Laschat, Sabine

    2016-09-21

    The construction of novel borrelidin analogues is reported in which the northern fragment is truncated to a simple hydroxyundecanecarboxylate and the original cyclopentanecarboxylic acid in the southern fragment is replaced with different six-membered rings. The required precursors were prepared by cross metathesis of the appropriate carbocycle-based homoallylic alcohol with crotonaldehyde followed by HWE olefination of the resulting enal with bromocyanophosphonate. The key aldehyde for intramolecular cross coupling was accessible by oxidation of the hydroxy group of the linked undecanecarboxylate unit. Grignard mediated macrocyclization finally yielded the borrelidin related products. The investigation is complemented by SAR studies and quantum-chemical calculations.

  8. Truncated ALK derived from chromosomal translocation t(2;5)(p23;q35) binds to the SH3 domain of p85-PI3K.

    Science.gov (United States)

    Polgar, Doris; Leisser, Christina; Maier, Susanne; Strasser, Stephan; Rüger, Beate; Dettke, Markus; Khorchide, Maya; Simonitsch, Ingrid; Cerni, Christa; Krupitza, Georg

    2005-02-15

    The chromosomal translocation t(2;5)(p23;q35) is associated with "Anaplastic large cell lymphomas" (ALCL), a Non Hodgkin Lymphoma occurring in childhood. The fusion of the tyrosine kinase gene-ALK (anaplastic lymphoma kinase) on chromosome 2p23 to the NPM (nucleophosmin/B23) gene on chromosome 5q35 results in a 80 kDa chimeric protein, which activates the "survival" kinase PI3K. However, the binding mechanism between truncated ALK and PI3K is poorly understood. Therefore, we attempted to elucidate the molecular interaction between ALK and the regulatory p85 subunit of PI3K. Here we provide evidence that the truncated ALK homodimer binds to the SH3 domain of p85. This finding may be useful for the development of a new target-specific intervention.

  9. Structure based modification of Bluetongue virus helicase protein VP6 to produce a viable VP6-truncated BTV

    Energy Technology Data Exchange (ETDEWEB)

    Matsuo, Eiko [Microbiology and Immunology, Division of Animal Science, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe-City 657-8501 (Japan); Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom); Leon, Esther; Matthews, Steve J. [Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ (United Kingdom); Roy, Polly, E-mail: polly.roy@lshtm.ac.uk [Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom)

    2014-09-05

    Highlights: • NMR analysis on BTV VP6 reveals two large loop regions. • The loss of a loop (aa 34–130) does not affect the overall fold of the protein. • A region of VP6 (aa 34–92) is not required for BTV replication. • A region of VP6 (aa 93–130) plays an essential role in the virus replication. - Abstract: Bluetongue virus core protein VP6 is an ATP hydrolysis dependent RNA helicase. However, despite much study, the precise role of VP6 within the viral capsid and its structure remain unclear. To investigate the requirement of VP6 in BTV replication, we initiated a structural and biological study. Multinuclear nuclear magnetic resonance spectra were assigned on his-tagged full-length VP6 (329 amino acid residues) as well as several truncated VP6 variants. The analysis revealed a large structured domain with two large loop regions that exhibit significant conformational exchange. One of the loops (amino acid position 34–130) could be removed without affecting the overall fold of the protein. Moreover, using a BTV reverse genetics system, it was possible to demonstrate that the VP6-truncated BTV was viable in BHK cells in the absence of any helper VP6 protein, suggesting that a large portion of this loop region is not absolutely required for BTV replication.

  10. TCP (truncated compound Poisson) process for multiplicity distributions in high energy collisions

    International Nuclear Information System (INIS)

    Srivastave, P.P.

    1990-01-01

    On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, the authors obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The TCP curves are narrower than NB at high multiplicity tail, look narrower at very high energy and develop shoulders and oscillations which become increasingly pronounced as the energy grows. At lower energies the distributions, of the data for fixed intervals of rapidity for UA5 data and for the data (at low energy) for e + e - annihilation and pion-proton, proton-proton and muon-proton scattering. A discussion of compound Poisson distribution, expression of reduced moments and Poisson transforms are also given. The TCP curves and curves of the reduced moments for different values of the parameters are also presented

  11. Accurate evolutions of inspiralling neutron-star binaries: assessment of the truncation error

    International Nuclear Information System (INIS)

    Baiotti, Luca; Giacomazzo, Bruno; Rezzolla, Luciano

    2009-01-01

    We have recently presented an investigation in full general relativity of the dynamics and gravitational-wave emission from binary neutron stars which inspiral and merge, producing a black hole surrounded by a torus (Baiotti et al 2008 Phys. Rev. D 78 084033). We discuss here in more detail the convergence properties of the results presented in Baiotti et al (2008 Phys. Rev. D 78 084033) and, in particular, the deterioration of the convergence rate at the merger and during the survival of the merged object, when strong shocks are formed and turbulence develops. We also show that physically reasonable and numerically convergent results obtained at low resolution suffer however from large truncation errors and hence are of little physical use. We summarize our findings in an 'error budget', which includes the different sources of possible inaccuracies we have investigated and provides a first quantitative assessment of the precision in the modelling of compact fluid binaries.

  12. Truncated Hilbert Space Approach for the 1+1D phi^4 Theory

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    (an informal seminar, not a regular string seminar) We used the massive analogue of the truncated conformal space approach to study the broken phase of the 1+1 dimensional scalar phi^4 model in finite volume, similarly to the work by S. Rychkov and L. Vitale. In our work, the finite size spectrum was determined numerically using an effective eigensolver routine, which was followed by a simple extrapolation in the cutoff energy. We analyzed both the periodic and antiperiodic sectors. The results were compared with semiclassical and Bethe-Yang results as well as perturbation theory. We obtained the coupling dependence of the infinite volume breather and kink masses for moderate couplings. The results fit well with semiclassics and perturbative estimations, and confirm the conjecture of Mussardo that at most two neutral excitations can exist in the spectrum. We believe that improving our method with the renormalization procedure of Rychkov et al. enables to measure further interesting quantities such as decay ra...

  13. The expression of a truncated HMGI-C gene induces gigantism associated with lipomatosis.

    Science.gov (United States)

    Battista, S; Fidanza, V; Fedele, M; Klein-Szanto, A J; Outwater, E; Brunner, H; Santoro, M; Croce, C M; Fusco, A

    1999-10-01

    Rearrangements of the HMGI-C gene have frequently been detected in human benign tumors of mesenchymal origin, including lipomas. The HMGI-C protein has three AT-hook domains and an acidic COOH-terminal tail. The HMGI-C modifications consist in the loss of the C-tail and the fusion with ectopic sequences. Recent results show that the loss of the COOH-terminal region, rather than the acquisition of new sequences, is sufficient to confer to HMGI-C the ability to transform NIH3T3 cells. Therefore, transgenic mice carrying a HMGI-C construct (HMGI-C/T), containing only the three AT-hook domains, were generated. The HMGI-C/T mice showed a giant phenotype, together with a predominantly abdominal/pelvic lipomatosis, suggesting a pivotal role of the HMGI-C truncation in the generation of human lipomas.

  14. Similarity and Difference between the South Atlantic Convergence Zone and the Baiu Frontal Zone Simulated by an AGCM

    OpenAIRE

    Kozo, NINOMIYA; Frontier Research Center for Global Change, Japan Agency for Marine-Earth Science and Technology

    2007-01-01

    Features of the South Atlantic convergence zone (SACZ) and the Baiu frontal zone (BFZ) simulated by an AGCM (T106L56: a primitive equation spectral model which has 56 σ-levels and triangular spectral truncation at wave-number 106) are studied. The 24-year integration, from 1979 to 2002, by the model constrained by observed sea-surface temperature and sea-ice distribution, is used for this study. The detailed analysis is made for the typical case of SACZ and BFZ selected from data in 1985-1996...

  15. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Science.gov (United States)

    Kanada, Ryo; Kuwata, Takeshi; Kenzaki, Hiroo; Takada, Shoji

    2013-01-01

    Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  16. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Directory of Open Access Journals (Sweden)

    Ryo Kanada

    Full Text Available Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  17. Simulation Analysis of Tilted Polyhedron-Shaped Thermoelectric Elements

    Science.gov (United States)

    Meng, Xiangning; Suzuki, Ryosuke O.

    2015-06-01

    The generation of thermoelectricity is considered a promising approach to harness the waste heat generated in industries, automobiles, gas fields, and other man-made processes. The waste heat can be converted to electricity via a thermoelectric (TE) generator. In this light, the generator performance depends on the geometric configuration of its constituent elements as well as their material properties. Our previous work reported TE behaviors for modules consisting of parallelogram-shaped elements, because elements with tilted laminate structures provide increased mechanical stability and efficient heat-transferring ability from the hot surface to the cold surface. Here, we study TE elements in the shape of a polyhedron that is obtained by mechanically truncating the edges of a parallelogram element in order to further enhance the generator performance and reduce TE material usage. The TE performance of the modules consisting of these polyhedron elements is numerically simulated by using the finite-volume method. The output power, voltage, and current of the polyhedral TE module are greater than those of the parallelogram-element module. The polyhedron shape positively affects heat transfer and the flow of electric charges in the light of increasing the efficiency of conversion from heat to electricity. By varying the shape of the truncated portions, we determine the optimal shape that enables homogeneous heat flux distribution and slow diffusion of thermal energy to obtain the better efficiency of conversion of heat into electricity. We believe that the findings of our study can significantly contribute to the design policy in TE generation.

  18. Expression and characterization of truncated human heme oxygenase (hHO-1) and a fusion protein of hHO-1 with human cytochrome P450 reductase.

    Science.gov (United States)

    Wilks, A; Black, S M; Miller, W L; Ortiz de Montellano, P R

    1995-04-04

    A human heme oxygenase (hHO-1) gene without the sequence coding for the last 23 amino acids has been expressed in Escherichia coli behind the pho A promoter. The truncated enzyme is obtained in high yields as a soluble, catalytically-active protein, making it available for the first time for detailed mechanistic studies. The purified, truncated hHO-1/heme complex is spectroscopically indistinguishable from that of the rat enzyme and converts heme to biliverdin when reconstituted with rat liver cytochrome P450 reductase. A self-sufficient heme oxygenase system has been obtained by fusing the truncated hHO-1 gene to the gene for human cytochrome P450 reductase without the sequence coding for the 20 amino acid membrane binding domain. Expression of the fusion protein in pCWori+ yields a protein that only requires NADPH for catalytic turnover. The failure of exogenous cytochrome P450 reductase to stimulate turnover and the insensitivity of the catalytic rate toward changes in ionic strength establish that electrons are transferred intramolecularly between the reductase and heme oxygenase domains of the fusion protein. The Vmax for the fusion protein is 2.5 times higher than that for the reconstituted system. Therefore, either the covalent tether does not interfere with normal docking and electron transfer between the flavin and heme domains or alternative but equally efficient electron transfer pathways are available that do not require specific docking.

  19. Furin is a chemokine-modifying enzyme: in vitro and in vivo processing of CXCL10 generates a C-terminally truncated chemokine retaining full activity.

    Science.gov (United States)

    Hensbergen, Paul J; Verzijl, Dennis; Balog, Crina I A; Dijkman, Remco; van der Schors, Roel C; van der Raaij-Helmer, Elizabeth M H; van der Plas, Mariena J A; Leurs, Rob; Deelder, André M; Smit, Martine J; Tensen, Cornelis P

    2004-04-02

    Chemokines comprise a class of structurally related proteins that are involved in many aspects of leukocyte migration under basal and inflammatory conditions. In addition to the large number of genes, limited processing of these proteins by a variety of enzymes enhances the complexity of the total spectrum of chemokine variants. We have recently shown that the native chemokine CXCL10 is processed at the C terminus, thereby shedding the last four amino acids. The present study was performed to elucidate the mechanism in vivo and in vitro and to study the biological activity of this novel isoform of CXCL10. Using a combination of protein purification and mass spectrometric techniques, we show that the production of C-terminally truncated CXCL10 by primary keratinocytes is inhibited in vivo by a specific inhibitor of pro-protein convertases (e.g. furin) but not by inhibition of matrix metalloproteinases. Moreover, CXCL10 is processed by furin in vitro, which is abrogated by a mutation in the furin recognition site. Using GTPgammaS binding, Ca(2+) mobilization, and chemotaxis assays, we demonstrate that the C-terminally truncated CXCL10 variant is a potent ligand for CXCR3. Moreover, the inverse agonist activity on the virally encoded receptor ORF74 and the direct antibacterial activity of CXCL10 are fully retained. Hence, we have identified furin as a novel chemokine-modifying enzyme in vitro and most probably also in vivo, generating a C-terminally truncated CXCL10, which fully retains its (inverse) agonistic properties.

  20. Probabilistic low-rank factorization accelerates tensor network simulations of critical quantum many-body ground states

    Science.gov (United States)

    Kohn, Lucas; Tschirsich, Ferdinand; Keck, Maximilian; Plenio, Martin B.; Tamascelli, Dario; Montangero, Simone

    2018-01-01

    We provide evidence that randomized low-rank factorization is a powerful tool for the determination of the ground-state properties of low-dimensional lattice Hamiltonians through tensor network techniques. In particular, we show that randomized matrix factorization outperforms truncated singular value decomposition based on state-of-the-art deterministic routines in time-evolving block decimation (TEBD)- and density matrix renormalization group (DMRG)-style simulations, even when the system under study gets close to a phase transition: We report linear speedups in the bond or local dimension of up to 24 times in quasi-two-dimensional cylindrical systems.

  1. Application of CPML to two-dimension numerical simulation of nuclear electromagnetic pulse from air explosions

    International Nuclear Information System (INIS)

    Gao Chunxia; Wang Lianghou

    2005-01-01

    The characteristics of different types of PML were analyzed and the convolutional PML was chosen to truncate the open boundaries in numerical simulation of nuclear electromagnetic pulse from air explosions. On the basis of the split-field PML and the plane-wave solution of electromagnetic field in free space, the unsplit-field PML was constructed. By applying the convolutional theorem of Fourier transform, the discrete iterative equations of electromagnetic field components were presented in the CPML media under the two-dimension prolate-spheroidal coordinate system. The numerical results indicate that the method of CPML can largely decrease calculation errors of boundary fields. (authors)

  2. Progranulin modulates zebrafish motoneuron development in vivo and rescues truncation defects associated with knockdown of Survival motor neuron 1

    Directory of Open Access Journals (Sweden)

    Bateman Andrew

    2010-10-01

    Full Text Available Abstract Background Progranulin (PGRN encoded by the GRN gene, is a secreted glycoprotein growth factor that has been implicated in many physiological and pathophysiological processes. PGRN haploinsufficiency caused by autosomal dominant mutations within the GRN gene leads to progressive neuronal atrophy in the form of frontotemporal lobar degeneration (FTLD. This form of the disease is associated with neuronal inclusions that bear the ubiquitinated TAR DNA Binding Protein-43 (TDP-43 molecular signature (FTLD-U. The neurotrophic properties of PGRN in vitro have recently been reported but the role of PGRN in neurons is not well understood. Here we document the neuronal expression and functions of PGRN in spinal cord motoneuron (MN maturation and branching in vivo using zebrafish, a well established model of vertebrate embryonic development. Results Whole-mount in situ hybridization and immunohistochemical analyses of zebrafish embryos revealed that zfPGRN-A is expressed within the peripheral and central nervous systems including the caudal primary (CaP MNs within the spinal cord. Knockdown of zfPGRN-A mRNA translation mediated by antisense morpholino oligonucleotides disrupted normal CaP MN development resulting in both truncated MNs and inappropriate early branching. Ectopic over-expression of zfPGRN-A mRNA resulted in increased MN branching and rescued the truncation defects brought about by knockdown of zfPGRN-A expression. The ability of PGRN to interact with established MN developmental pathways was tested. PGRN over-expression was found to reverse the truncation defect resulting from knockdown of Survival of motor neuron 1 (smn1. This is involved in small ribonucleoprotein biogenesis RNA processing, mutations of which cause Spinal Muscular Atrophy (SMA in humans. It did not reverse the MN defects caused by interfering with the neuronal guidance pathway by knockdown of expression of NRP-1, a semaphorin co-receptor. Conclusions Expression of

  3. The C-terminal subunit of artificially truncated human cathepsin B mediates its nuclear targeting and contributes to cell viability

    Directory of Open Access Journals (Sweden)

    Dallner Claudia

    2005-04-01

    Full Text Available Abstract Background Splicing variants of human cathepsinB primary transcripts (CB(-2,3 result in an expression product product which lacks the signal peptide and parts of the propeptide. This naturally truncated Δ51CB is thus unable to follow the regular CB processing and sorting pathway. It is addressed to the mitochondria through an activated N-terminal mitochondrial targeting signal instead. Although Δ51CB is supposed to be devoid of the typical CB enzymatic activity, it might play a role in malignancies and trigger cell death/apoptosis independent from the function of the regular enzyme. Cytoplasmic presence of the mature CB might occur as a result of lysosomal damage. Results We investigated such "aberrant" proteins by artificial CB-GFP chimeras covering various sequence parts in respect to their enzymatic activity, their localization in different cell types, and the effects on the cell viability. Unlike the entire full length CB form, the artificial single chain form was not processed and did not reveal typical enzymatic CB activity during transient overexpression in large cell lung carcinoma cells. Δ51CB was found predominantly in mitochondria. In contrast, the shorter artificial CB constructs localized in the cytoplasm, inside the cell nucleus, and in the midbodies of dividing cells. Bleaching experiments revealed both mobile and immobile fractions of these constructs in the nucleus. Nuclear accumulation of artificially truncated CB variants led to disintegration of nuclei, followed by cell death. Conclusion We propose that cell death associated with CB is not necessarily triggered by its regular enzymatic activity but alternatively by a yet unknown activity profile of truncated CB. Cytoplasmic CB might be able to enter the cell nucleus. According to a mutational analysis, the part of CB that mediates its nuclear import is a signal patch within its heavy chain domain. The results suggest that besides the N-terminal signal peptide also

  4. Charge-Spot Model for Electrostatic Forces in Simulation of Fine Particulates

    Science.gov (United States)

    Walton, Otis R.; Johnson, Scott M.

    2010-01-01

    The charge-spot technique for modeling the static electric forces acting between charged fine particles entails treating electric charges on individual particles as small sets of discrete point charges, located near their surfaces. This is in contrast to existing models, which assume a single charge per particle. The charge-spot technique more accurately describes the forces, torques, and moments that act on triboelectrically charged particles, especially image-charge forces acting near conducting surfaces. The discrete element method (DEM) simulation uses a truncation range to limit the number of near-neighbor charge spots via a shifted and truncated potential Coulomb interaction. The model can be readily adapted to account for induced dipoles in uncharged particles (and thus dielectrophoretic forces) by allowing two charge spots of opposite signs to be created in response to an external electric field. To account for virtual overlap during contacts, the model can be set to automatically scale down the effective charge in proportion to the amount of virtual overlap of the charge spots. This can be accomplished by mimicking the behavior of two real overlapping spherical charge clouds, or with other approximate forms. The charge-spot method much more closely resembles real non-uniform surface charge distributions that result from tribocharging than simpler approaches, which just assign a single total charge to a particle. With the charge-spot model, a single particle may have a zero net charge, but still have both positive and negative charge spots, which could produce substantial forces on the particle when it is close to other charges, when it is in an external electric field, or when near a conducting surface. Since the charge-spot model can contain any number of charges per particle, can be used with only one or two charge spots per particle for simulating charging from solar wind bombardment, or with several charge spots for simulating triboelectric charging

  5. Multidimensional Simulations of Colliding Outbursts from very Massive Stars

    Science.gov (United States)

    Chen, Ke-Jung; Woosley, Stan

    2015-08-01

    Massive stars that end their lives with helium cores in the range of 35 to 65 solar masses are known to produce repeated thermonuclear outbursts due to a recurring pair-instability. In some of these events, solar masses of material are ejected in repeated outbursts of several times 1050 erg each. Such models can be used to explain the strong mass loss rates at the last moment before the massive stars die. Collisions between these shells can sometimes produce very luminous transients. Previous 1D studies of these events produce thin,high-density shells as one ejection plows into another. We present the first multidimensional simulations of these collisions, we show that the development of a Rayleigh-Taylor instability truncates the growth of the high density spike and drives mixing between the shells.

  6. Simulation of light collection in calcium tungstate scintillation detectors

    Directory of Open Access Journals (Sweden)

    F. A. Danevich

    2015-12-01

    Full Text Available Due to high operational properties, the oxide scintillators are perspective for cryogenic scintillation experiments with aim of study rare nuclear processes. In order to optimize light yield and the energy resolution we performed calculations of the efficiency of light collection for different geometries of scintillation detector with CaWO4 crystal by Monte-Carlo method using Litrani, Geant4 and Zemax packages. The calculations were compared with experimental data in the same configurations, depending on the crystal shape, surface treatment, material and shape of the reflector and presence of optical contact. The best results were obtained with crystals shaped as the right prism with triangle base, with completely diffused surfaces, using mirror reflector shaped as a truncated cone. Simulations by using Litrani have shown the best agreement with experimental results.

  7. Experimental Study on GFRP Surface Cracks Detection Using Truncated-Correlation Photothermal Coherence Tomography

    Science.gov (United States)

    Wang, Fei; Liu, Junyan; Mohummad, Oliullah; Wang, Yang

    2018-04-01

    In this paper, truncated-correlation photothermal coherence tomography (TC-PCT) was used as a nondestructive inspection technique to evaluate glass-fiber reinforced polymer (GFRP) composite surface cracks. Chirped-pulsed signal that combines linear frequency modulation and pulse excitation was proposed as an excitation signal to detect GFRP composite surface cracks. The basic principle of TC-PCT and extraction algorithm of the thermal wave signal feature was described. The comparison experiments between lock-in thermography, thermal wave radar imaging and chirped-pulsed photothermal radar for detecting GFRP artificial surface cracks were carried out. Experimental results illustrated that chirped-pulsed photothermal radar has the merits of high signal-to-noise ratio in detecting GFRP composite surface cracks. TC-PCT as a depth-resolved photothermal imaging modality was employed to enable three-dimensional visualization of GFRP composite surface cracks. The results showed that TC-PCT can effectively evaluate the cracks depth of GFRP composite.

  8. Truncated form of VACM-1/cul-5 with an extended 3' untranslated region stimulates cell growth via a MAPK-dependent pathway

    International Nuclear Information System (INIS)

    Sartor, Ashleigh; Kossoris, J.B.; Wilcox, R.; Shearer, R.; Zeneberg, A.E.; Zhao, P.; Lazdins, I.; Burnatowska-Hledin, Maria A.

    2006-01-01

    We have sequenced a 4.9 kb clone (KLB22) which shares 99% sequence homology with the rabbit vasopressin-activated calcium mobilizing (VACM-1) protein. The 5' terminus sequence of KLB22 cDNA (nucleotides 1-1961) is continuous and overlapping with nucleotides 1226-3186 of the VACM-1 cDNA sequence. The 3'UTR of KLB22 cDNA extends beyond the 3'UTR of VACM-1 by 2999 nt. KLB22 cDNA encodes a 497 amino acid protein, which putatively begins at Met 284 of the 780 amino acid VACM-1 protein. The in vitro translation of KLB22 cDNA yields a 59 kDa protein. When expressed in cos-1 cells, the truncated VACM-1 protein localizes to the nucleus. KLB22 cDNA transfected cells show increased growth rates and increased levels of phosphorylated MAPK when compared to the vector or to VACM-1 cDNA transfected cells. Finally, in vivo, KLB22 protein expression is tissue specific and can be detected in kidney and in heart atrium. These results suggest that truncated VACM-1 cDNA (KLB22) increases cell proliferation through a MAPK pathway

  9. A comparative analysis of clustering algorithms: O{sub 2} migration in truncated hemoglobin I from transition networks

    Energy Technology Data Exchange (ETDEWEB)

    Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus, E-mail: m.meuwly@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel (Switzerland); Zheng, Wenwei; Clementi, Cecilia [Department of Chemistry, Rice University, 6100 Main St., Houston, Texas 77005 (United States); Prada-Gracia, Diego; Rao, Francesco [School of Soft Matter Research, Freiburg Institute for Advanced Studies, Albertstrasse 19, 79104 Freiburg im Breisgau (Germany)

    2015-01-14

    The ligand migration network for O{sub 2}–diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k–means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k–means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

  10. Distinguishing attack and second-preimage attack on encrypted message authentication codes (EMAC)

    Science.gov (United States)

    Ariwibowo, Sigit; Windarta, Susila

    2016-02-01

    In this paper we show that distinguisher on CBC-MAC can be applied to Encrypted Message Authentication Code (EMAC) scheme. EMAC scheme in general is vulnerable to distinguishing attack and second preimage attack. Distinguishing attack simulation on AES-EMAC using 225 message modifications, no collision have been found. According to second preimage attack simulation on AES-EMAC no collision found between EMAC value of S1 and S2, i.e. no second preimage found for messages that have been tested. Based on distinguishing attack simulation on truncated AES-EMAC we found collision in every message therefore we cannot distinguish truncated AES-EMAC with random function. Second-preimage attack is successfully performed on truncated AES-EMAC.

  11. A six-mode truncation of the Navier-Stokes equations on a two-dimensional torus: a numerical study

    International Nuclear Information System (INIS)

    Angelo, P.M.; Riela, G.

    1981-01-01

    We study a model obtained from a six-mode truncation of the Navier-Stokes equations for a two-dimensional incompressible fluid on a torus. We find that at low values of the Reynolds number R the dynamics is characterized by fixed points and, at large values of R, by two stable periodic orbits; at intermediate values of R two infinite sequences of bifurcations of periodic orbits into periodic orbits of doubled period lead to two regions of ''turbulent'' or ''chaotic'' behaviour. The turbulent regions end up for values of R for which stable periodic orbits appear. (author)

  12. USH1G with unique retinal findings caused by a novel truncating mutation identified by genome-wide linkage analysis

    Science.gov (United States)

    Taibah, Khalid; Bin-Khamis, Ghada; Kennedy, Shelley; Hemidan, Amal; Al-Qahtani, Faisal; Tabbara, Khalid; Mubarak, Bashayer Al; Ramzan, Khushnooda; Meyer, Brian F.; Al-Owain, Mohammed

    2012-01-01

    Purpose Usher syndrome (USH) is an autosomal recessive disorder divided into three distinct clinical subtypes based on the severity of the hearing loss, manifestation of vestibular dysfunction, and the age of onset of retinitis pigmentosa and visual symptoms. To date, mutations in seven different genes have been reported to cause USH type 1 (USH1), the most severe form. Patients diagnosed with USH1 are known to be ideal candidates to benefit from cochlear implantation. Methods Genome-wide linkage analysis using Affymetrix GeneChip Human Mapping 10K arrays were performed in three cochlear implanted Saudi siblings born from a consanguineous marriage, clinically diagnosed with USH1 by comprehensive clinical, audiological, and ophthalmological examinations. From the linkage results, the USH1G gene was screened for mutations by direct sequencing of the coding exons. Results We report the identification of a novel p.S243X truncating mutation in USH1G that segregated with the disease phenotype and was not present in 300 ethnically matched normal controls. We also report on the novel retinal findings and the outcome of cochlear implantation in the affected individuals. Conclusions In addition to reporting a novel truncating mutation, this report expands the retinal phenotype in USH1G and presents the first report of successful cochlear implants in this disease. PMID:22876113

  13. Sparse reconstruction for quantitative bioluminescence tomography based on the incomplete variables truncated conjugate gradient method.

    Science.gov (United States)

    He, Xiaowei; Liang, Jimin; Wang, Xiaorui; Yu, Jingjing; Qu, Xiaochao; Wang, Xiaodong; Hou, Yanbin; Chen, Duofang; Liu, Fang; Tian, Jie

    2010-11-22

    In this paper, we present an incomplete variables truncated conjugate gradient (IVTCG) method for bioluminescence tomography (BLT). Considering the sparse characteristic of the light source and insufficient surface measurement in the BLT scenarios, we combine a sparseness-inducing (ℓ1 norm) regularization term with a quadratic error term in the IVTCG-based framework for solving the inverse problem. By limiting the number of variables updated at each iterative and combining a variable splitting strategy to find the search direction more efficiently, it obtains fast and stable source reconstruction, even without a priori information of the permissible source region and multispectral measurements. Numerical experiments on a mouse atlas validate the effectiveness of the method. In vivo mouse experimental results further indicate its potential for a practical BLT system.

  14. Exponentially more precise quantum simulation of fermions in the configuration interaction representation

    Science.gov (United States)

    Babbush, Ryan; Berry, Dominic W.; Sanders, Yuval R.; Kivlichan, Ian D.; Scherer, Artur; Wei, Annie Y.; Love, Peter J.; Aspuru-Guzik, Alán

    2018-01-01

    We present a quantum algorithm for the simulation of molecular systems that is asymptotically more efficient than all previous algorithms in the literature in terms of the main problem parameters. As in Babbush et al (2016 New Journal of Physics 18, 033032), we employ a recently developed technique for simulating Hamiltonian evolution using a truncated Taylor series to obtain logarithmic scaling with the inverse of the desired precision. The algorithm of this paper involves simulation under an oracle for the sparse, first-quantized representation of the molecular Hamiltonian known as the configuration interaction (CI) matrix. We construct and query the CI matrix oracle to allow for on-the-fly computation of molecular integrals in a way that is exponentially more efficient than classical numerical methods. Whereas second-quantized representations of the wavefunction require \\widetilde{{ O }}(N) qubits, where N is the number of single-particle spin-orbitals, the CI matrix representation requires \\widetilde{{ O }}(η ) qubits, where η \\ll N is the number of electrons in the molecule of interest. We show that the gate count of our algorithm scales at most as \\widetilde{{ O }}({η }2{N}3t).

  15. 3D simulation of accelerator conventional magnets with end pole defined by an analytical approach controlling multipoles and magnetic length

    CERN Document Server

    Delferrière, O; Duperrier, R

    2000-01-01

    During the design of a magnet, people generally pay particular attention to get the largest transverse section with small contribution of undesirable multipoles, and the 2D cross-section is adjusted in that way with a good accuracy. But the poles are often cut with sharp ends in the beam direction. Otherwise, in order to minimize the stray field to avoid interaction with other elements on the beam lines and corner saturation, it is common to define a simple 45 degrees chamber. The such truncated poles will create an amount of multipoles that could exceed the magnet required tolerances. The magnetic length is also affected by the way that the truncation is done. We propose in this paper a handy analytical model that allows both to control integrated focusing forces and magnetic lengths for each type of conventional magnets (dipole, quadrupole, sextupole). The different end pole profiles are simulated with the 3D-program TOSCA for the dipole and the quadrupole cases. To estimate a possible damaging of optical q...

  16. Parametric instability analysis of truncated conical shells using the Haar wavelet method

    Science.gov (United States)

    Dai, Qiyi; Cao, Qingjie

    2018-05-01

    In this paper, the Haar wavelet method is employed to analyze the parametric instability of truncated conical shells under static and time dependent periodic axial loads. The present work is based on the Love first-approximation theory for classical thin shells. The displacement field is expressed as the Haar wavelet series in the axial direction and trigonometric functions in the circumferential direction. Then the partial differential equations are reduced into a system of coupled Mathieu-type ordinary differential equations describing dynamic instability behavior of the shell. Using Bolotin's method, the first-order and second-order approximations of principal instability regions are determined. The correctness of present method is examined by comparing the results with those in the literature and very good agreement is observed. The difference between the first-order and second-order approximations of principal instability regions for tensile and compressive loads is also investigated. Finally, numerical results are presented to bring out the influences of various parameters like static load factors, boundary conditions and shell geometrical characteristics on the domains of parametric instability of conical shells.

  17. Light neutron-rich hypernuclei from the importance-truncated no-core shell model

    Science.gov (United States)

    Wirth, Roland; Roth, Robert

    2018-04-01

    We explore the systematics of ground-state and excitation energies in singly-strange hypernuclei throughout the helium and lithium isotopic chains - from He5Λ to He11Λ and from Li7Λ to Li12Λ - in the ab initio no-core shell model with importance truncation. All calculations are based on two- and three-baryon interaction from chiral effective field theory and we employ a similarity renormalization group transformation consistently up to the three-baryon level to improve the model-space convergence. While the absolute energies of hypernuclear states show a systematic variation with the regulator cutoff of the hyperon-nucleon interaction, the resulting neutron separation energies are very stable and in good agreement with available data for both nucleonic parents and their daughter hypernuclei. We provide predictions for the neutron separation energies and the spectra of neutron-rich hypernuclei that have not yet been observed experimentally. Furthermore, we find that the neutron drip lines in the helium and lithium isotopic chains are not changed by the addition of a hyperon.

  18. Spline Truncated Multivariabel pada Permodelan Nilai Ujian Nasional di Kabupaten Lombok Barat

    Directory of Open Access Journals (Sweden)

    Nurul Fitriyani

    2017-12-01

    Full Text Available Regression model is used to analyze the relationship between dependent variable and independent variable. If the regression curve form is not known, then the regression curve estimation can be done by nonparametric regression approach. This study aimed to investigate the relationship between the value resulted by National Examination and the factors that influence it. The statistical analysis used was multivariable truncated spline, in order to analyze the relationship between variables. The research that has been done showed that the best model obtained by using three knot points. This model produced a minimum GCV value of 44.46 and the value of determination coefficient of 58.627%. The parameter test showed that all factors used were significantly influence the National Examination Score for Senior High School students in West Lombok Regency year 2017. The variables were as follows: National Examination Score of Junior High School; School or Madrasah Examination Score; the value of Student’s Report Card; Student’s House Distance to School; and Number of Student’s Siblings.

  19. Automatic, unstructured mesh optimization for simulation and assessment of tide- and surge-driven hydrodynamics in a longitudinal estuary: St. Johns River

    Science.gov (United States)

    Bacopoulos, Peter

    2018-05-01

    A localized truncation error analysis with complex derivatives (LTEA+CD) is applied recursively with advanced circulation (ADCIRC) simulations of tides and storm surge for finite element mesh optimization. Mesh optimization is demonstrated with two iterations of LTEA+CD for tidal simulation in the lower 200 km of the St. Johns River, located in northeast Florida, and achieves more than an over 50% decrease in the number of mesh nodes, relating to a twofold increase in efficiency, at a zero cost to model accuracy. The recursively generated meshes using LTEA+CD lead to successive reductions in the global cumulative truncation error associated with the model mesh. Tides are simulated with root mean square error (RMSE) of 0.09-0.21 m and index of agreement (IA) values generally in the 80s and 90s percentage ranges. Tidal currents are simulated with RMSE of 0.09-0.23 m s-1 and IA values of 97% and greater. Storm tide due to Hurricane Matthew 2016 is simulated with RMSE of 0.09-0.33 m and IA values of 75-96%. Analysis of the LTEA+CD results shows the M2 constituent to dominate the node spacing requirement in the St. Johns River, with the M4 and M6 overtides and the STEADY constituent contributing some. Friction is the predominant physical factor influencing the target element size distribution, especially along the main river stem, while frequency (inertia) and Coriolis (rotation) are supplementary contributing factors. The combination of interior- and boundary-type computational molecules, providing near-full coverage of the model domain, renders LTEA+CD an attractive mesh generation/optimization tool for complex coastal and estuarine domains. The mesh optimization procedure using LTEA+CD is automatic and extensible to other finite element-based numerical models. Discussion is provided on the scope of LTEA+CD, the starting point (mesh) of the procedure, the user-specified scaling of the LTEA+CD results, and the iteration (termination) of LTEA+CD for mesh optimization.

  20. Generalized Lorenz models and their routes to chaos. II. Energy-conserving horizontal mode truncations

    International Nuclear Information System (INIS)

    Roy, D.; Musielak, Z.E.

    2007-01-01

    All attempts to generalize the three-dimensional Lorenz model by selecting higher-order Fourier modes can be divided into three categories, namely: vertical, horizontal and vertical-horizontal mode truncations. The previous study showed that the first method allowed only construction of a nine-dimensional system when the selected modes were energy-conserving. The results presented in this paper demonstrate that a five-dimensional model is the lowest-order generalized Lorenz model that can be constructed by the second method and that its route to chaos is the same as that observed in the original Lorenz model. It is shown that the onset of chaos in both systems is determined by a number of modes that describe the vertical temperature difference in a convection roll. In addition, a simple rule that allows selecting modes that conserve energy for each method is derived

  1. Simulation of Logging-while-drilling Tool Response Using Integral Equation Fast Fourier Transform

    Directory of Open Access Journals (Sweden)

    Sun Xiang-Yang

    2017-01-01

    Full Text Available We rely on the volume integral equation (VIE method for the simulation of loggingwhile- drilling (LWG tool response using the integral equation fast Fourier transform (IE-FFT algorithm to accelerate the computation of the matrix-vector product in the iterative solver. Depending on the virtue of the Toeplitz structure of the interpolation of the Green’s function on the uniform Cartesian grids, this method uses FFT to calculate the matrix-vector multiplication. At the same time, this method reduce the memory requirement and CPU time. In this paper, IEFFT method is first used in the simulation of LWG. Numerical results are presented to demonstrate the accuracy and efficiency of this method. Compared with the Moment of Method (MOM and other fast algorithms, IE-FFT have distinct advantages in the fact of memory requirement and CPU time. In addition, this paper study the truncation, mesh elements, the size of the interpolation grids of IE-FFT and dip formation, and give some conclusion with wide applicability.

  2. Constitutional Tandem Duplication of 9q34 that Truncates EHMT1 in a Child with Ganglioglioma

    Science.gov (United States)

    Cheung, Hannah C.; Yatsenko, Svetlana A.; Kadapakkam, Meena; Legay, Hélène; Su, Jack; Lupski, James R.; Plon, Sharon E.

    2011-01-01

    Point mutations of EHMT1 or deletions and duplications of chromosome 9q34.3 are found in patients with variable neurologic and developmental disorders. Here, we present a child with congenital cataract, developmental and speech delay who developed a metastatic ganglioglioma with progression to anaplastic astrocytoma. Molecular analysis identified a novel constitutional tandem duplication in 9q34.3 with breakpoints in intron 1 of TRAF2 and intron 16 of EHMT1 generating a fusion transcript predicted to encode a truncated form of EHMT1. The ganglioglioma showed complex chromosomal aberrations with further duplication of the dup9q34. Thus, this unique tandem 9q34.3 duplication may impact brain tumor formation. PMID:21681934

  3. Stopping randomized trials early for benefit: a protocol of the Study Of Trial Policy Of Interim Truncation-2 (STOPIT-2)

    Science.gov (United States)

    Briel, Matthias; Lane, Melanie; Montori, Victor M; Bassler, Dirk; Glasziou, Paul; Malaga, German; Akl, Elie A; Ferreira-Gonzalez, Ignacio; Alonso-Coello, Pablo; Urrutia, Gerard; Kunz, Regina; Culebro, Carolina Ruiz; da Silva, Suzana Alves; Flynn, David N; Elamin, Mohamed B; Strahm, Brigitte; Murad, M Hassan; Djulbegovic, Benjamin; Adhikari, Neill KJ; Mills, Edward J; Gwadry-Sridhar, Femida; Kirpalani, Haresh; Soares, Heloisa P; Elnour, Nisrin O Abu; You, John J; Karanicolas, Paul J; Bucher, Heiner C; Lampropulos, Julianna F; Nordmann, Alain J; Burns, Karen EA; Mulla, Sohail M; Raatz, Heike; Sood, Amit; Kaur, Jagdeep; Bankhead, Clare R; Mullan, Rebecca J; Nerenberg, Kara A; Vandvik, Per Olav; Coto-Yglesias, Fernando; Schünemann, Holger; Tuche, Fabio; Chrispim, Pedro Paulo M; Cook, Deborah J; Lutz, Kristina; Ribic, Christine M; Vale, Noah; Erwin, Patricia J; Perera, Rafael; Zhou, Qi; Heels-Ansdell, Diane; Ramsay, Tim; Walter, Stephen D; Guyatt, Gordon H

    2009-01-01

    Background Randomized clinical trials (RCTs) stopped early for benefit often receive great attention and affect clinical practice, but pose interpretational challenges for clinicians, researchers, and policy makers. Because the decision to stop the trial may arise from catching the treatment effect at a random high, truncated RCTs (tRCTs) may overestimate the true treatment effect. The Study Of Trial Policy Of Interim Truncation (STOPIT-1), which systematically reviewed the epidemiology and reporting quality of tRCTs, found that such trials are becoming more common, but that reporting of stopping rules and decisions were often deficient. Most importantly, treatment effects were often implausibly large and inversely related to the number of the events accrued. The aim of STOPIT-2 is to determine the magnitude and determinants of possible bias introduced by stopping RCTs early for benefit. Methods/Design We will use sensitive strategies to search for systematic reviews addressing the same clinical question as each of the tRCTs identified in STOPIT-1 and in a subsequent literature search. We will check all RCTs included in each systematic review to determine their similarity to the index tRCT in terms of participants, interventions, and outcome definition, and conduct new meta-analyses addressing the outcome that led to early termination of the tRCT. For each pair of tRCT and systematic review of corresponding non-tRCTs we will estimate the ratio of relative risks, and hence estimate the degree of bias. We will use hierarchical multivariable regression to determine the factors associated with the magnitude of this ratio. Factors explored will include the presence and quality of a stopping rule, the methodological quality of the trials, and the number of total events that had occurred at the time of truncation. Finally, we will evaluate whether Bayesian methods using conservative informative priors to "regress to the mean" overoptimistic tRCTs can correct observed

  4. Stopping randomized trials early for benefit: a protocol of the Study Of Trial Policy Of Interim Truncation-2 (STOPIT-2

    Directory of Open Access Journals (Sweden)

    Mullan Rebecca J

    2009-07-01

    Full Text Available Abstract Background Randomized clinical trials (RCTs stopped early for benefit often receive great attention and affect clinical practice, but pose interpretational challenges for clinicians, researchers, and policy makers. Because the decision to stop the trial may arise from catching the treatment effect at a random high, truncated RCTs (tRCTs may overestimate the true treatment effect. The Study Of Trial Policy Of Interim Truncation (STOPIT-1, which systematically reviewed the epidemiology and reporting quality of tRCTs, found that such trials are becoming more common, but that reporting of stopping rules and decisions were often deficient. Most importantly, treatment effects were often implausibly large and inversely related to the number of the events accrued. The aim of STOPIT-2 is to determine the magnitude and determinants of possible bias introduced by stopping RCTs early for benefit. Methods/Design We will use sensitive strategies to search for systematic reviews addressing the same clinical question as each of the tRCTs identified in STOPIT-1 and in a subsequent literature search. We will check all RCTs included in each systematic review to determine their similarity to the index tRCT in terms of participants, interventions, and outcome definition, and conduct new meta-analyses addressing the outcome that led to early termination of the tRCT. For each pair of tRCT and systematic review of corresponding non-tRCTs we will estimate the ratio of relative risks, and hence estimate the degree of bias. We will use hierarchical multivariable regression to determine the factors associated with the magnitude of this ratio. Factors explored will include the presence and quality of a stopping rule, the methodological quality of the trials, and the number of total events that had occurred at the time of truncation. Finally, we will evaluate whether Bayesian methods using conservative informative priors to "regress to the mean" overoptimistic t

  5. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

    OpenAIRE

    Easton, Douglas Frederick; Lesueur, Fabienne; Decker, Brennan; Michailidou, Kyriaki; Li, Jun; Allen, Jamie; Luccarini, Craig; Pooley, Karen Anne; Shah, Mitulkumar Nandlal; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Ahmad, Jamil; Thompson, Ella R; Damiola, Francesca

    2016-01-01

    Background BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. Metho...

  6. A Bayesian zero-truncated approach for analysing capture-recapture count data from classical scrapie surveillance in France.

    Science.gov (United States)

    Vergne, Timothée; Calavas, Didier; Cazeau, Géraldine; Durand, Benoît; Dufour, Barbara; Grosbois, Vladimir

    2012-06-01

    Capture-recapture (CR) methods are used to study populations that are monitored with imperfect observation processes. They have recently been applied to the monitoring of animal diseases to evaluate the number of infected units that remain undetected by the surveillance system. This paper proposes three bayesian models to estimate the total number of scrapie-infected holdings in France from CR count data obtained from the French classical scrapie surveillance programme. We fitted two zero-truncated Poisson (ZTP) models (with and without holding size as a covariate) and a zero-truncated negative binomial (ZTNB) model to the 2006 national surveillance count dataset. We detected a large amount of heterogeneity in the count data, making the use of the simple ZTP model inappropriate. However, including holding size as a covariate did not bring any significant improvement over the simple ZTP model. The ZTNB model proved to be the best model, giving an estimation of 535 (CI(95%) 401-796) infected and detectable sheep holdings in 2006, although only 141 were effectively detected, resulting in a holding-level prevalence of 4.4‰ (CI(95%) 3.2-6.3) and a sensitivity of holding-level surveillance of 26% (CI(95%) 18-35). The main limitation of the present study was the small amount of data collected during the surveillance programme. It was therefore not possible to build complex models that would allow depicting more accurately the epidemiological and detection processes that generate the surveillance data. We discuss the perspectives of capture-recapture count models in the context of animal disease surveillance. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Functional defect of truncated hepatocyte nuclear factor-1{alpha} (G554fsX556) associated with maturity-onset diabetes of the young

    Energy Technology Data Exchange (ETDEWEB)

    Kooptiwut, Suwattanee, E-mail: S_kooptiwut@hotmail.com [Department of Physiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Sujjitjoon, Jatuporn [Department of Immunology and Immunology Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Plengvidhya, Nattachet [Department of Immunology and Immunology Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Boonyasrisawat, Watip; Chongjaroen, Nalinee; Jungtrakoon, Prapapron [Department of Immunology and Immunology Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Semprasert, Namoiy [Department of Physiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Furuta, Hiroto; Nanjo, Kishio [The First Department, Wakayama Medical University (Japan); Banchuin, Napatawn [Department of Immunology and Immunology Graduate Program, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Yenchitsomanus, Pa-thai [Division of Medical Molecular Biology, Medicine Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok (Thailand)

    2009-05-22

    A novel frameshift mutation attributable to 14-nucleotide insertion in hepatocyte nuclear factor-1{alpha} (HNF-1{alpha}) encoding a truncated HNF-1{alpha} (G554fsX556) with 76-amino acid deletion at its carboxyl terminus was identified in a Thai family with maturity-onset diabetes of the young (MODY). The wild-type and mutant HNF-1{alpha} proteins were expressed by in vitro transcription and translation (TNT) assay and by transfection in HeLa cells. The wild-type and mutant HNF-1{alpha} could similarly bind to human glucose-transporter 2 (GLUT2) promoter examined by electrophoretic mobility shift assay (EMSA). However, the transactivation activities of mutant HNF-1{alpha} on human GLUT2 and rat L-type pyruvate kinase (L-PK) promoters in HeLa cells determined by luciferase reporter assay were reduced to approximately 55-60% of the wild-type protein. These results suggested that the functional defect of novel truncated HNF-1{alpha} (G554fsX556) on the transactivation of its target-gene promoters would account for the {beta}-cell dysfunction associated with the pathogenesis of MODY.

  8. Functional defect of truncated hepatocyte nuclear factor-1α (G554fsX556) associated with maturity-onset diabetes of the young

    International Nuclear Information System (INIS)

    Kooptiwut, Suwattanee; Sujjitjoon, Jatuporn; Plengvidhya, Nattachet; Boonyasrisawat, Watip; Chongjaroen, Nalinee; Jungtrakoon, Prapapron; Semprasert, Namoiy; Furuta, Hiroto; Nanjo, Kishio; Banchuin, Napatawn; Yenchitsomanus, Pa-thai

    2009-01-01

    A novel frameshift mutation attributable to 14-nucleotide insertion in hepatocyte nuclear factor-1α (HNF-1α) encoding a truncated HNF-1α (G554fsX556) with 76-amino acid deletion at its carboxyl terminus was identified in a Thai family with maturity-onset diabetes of the young (MODY). The wild-type and mutant HNF-1α proteins were expressed by in vitro transcription and translation (TNT) assay and by transfection in HeLa cells. The wild-type and mutant HNF-1α could similarly bind to human glucose-transporter 2 (GLUT2) promoter examined by electrophoretic mobility shift assay (EMSA). However, the transactivation activities of mutant HNF-1α on human GLUT2 and rat L-type pyruvate kinase (L-PK) promoters in HeLa cells determined by luciferase reporter assay were reduced to approximately 55-60% of the wild-type protein. These results suggested that the functional defect of novel truncated HNF-1α (G554fsX556) on the transactivation of its target-gene promoters would account for the β-cell dysfunction associated with the pathogenesis of MODY.

  9. UNIPIC code for simulations of high power microwave devices

    International Nuclear Information System (INIS)

    Wang Jianguo; Zhang Dianhui; Wang Yue; Qiao Hailiang; Li Xiaoze; Liu Chunliang; Li Yongdong; Wang Hongguang

    2009-01-01

    In this paper, UNIPIC code, a new member in the family of fully electromagnetic particle-in-cell (PIC) codes for simulations of high power microwave (HPM) generation, is introduced. In the UNIPIC code, the electromagnetic fields are updated using the second-order, finite-difference time-domain (FDTD) method, and the particles are moved using the relativistic Newton-Lorentz force equation. The convolutional perfectly matched layer method is used to truncate the open boundaries of HPM devices. To model curved surfaces and avoid the time step reduction in the conformal-path FDTD method, CP weakly conditional-stable FDTD (WCS FDTD) method which combines the WCS FDTD and CP-FDTD methods, is implemented. UNIPIC is two-and-a-half dimensional, is written in the object-oriented C++ language, and can be run on a variety of platforms including WINDOWS, LINUX, and UNIX. Users can use the graphical user's interface to create the geometric structures of the simulated HPM devices, or input the old structures created before. Numerical experiments on some typical HPM devices by using the UNIPIC code are given. The results are compared to those obtained from some well-known PIC codes, which agree well with each other.

  10. UNIPIC code for simulations of high power microwave devices

    Science.gov (United States)

    Wang, Jianguo; Zhang, Dianhui; Liu, Chunliang; Li, Yongdong; Wang, Yue; Wang, Hongguang; Qiao, Hailiang; Li, Xiaoze

    2009-03-01

    In this paper, UNIPIC code, a new member in the family of fully electromagnetic particle-in-cell (PIC) codes for simulations of high power microwave (HPM) generation, is introduced. In the UNIPIC code, the electromagnetic fields are updated using the second-order, finite-difference time-domain (FDTD) method, and the particles are moved using the relativistic Newton-Lorentz force equation. The convolutional perfectly matched layer method is used to truncate the open boundaries of HPM devices. To model curved surfaces and avoid the time step reduction in the conformal-path FDTD method, CP weakly conditional-stable FDTD (WCS FDTD) method which combines the WCS FDTD and CP-FDTD methods, is implemented. UNIPIC is two-and-a-half dimensional, is written in the object-oriented C++ language, and can be run on a variety of platforms including WINDOWS, LINUX, and UNIX. Users can use the graphical user's interface to create the geometric structures of the simulated HPM devices, or input the old structures created before. Numerical experiments on some typical HPM devices by using the UNIPIC code are given. The results are compared to those obtained from some well-known PIC codes, which agree well with each other.

  11. Theoretical study of hydrogen storage in a truncated triangular pyramid molecule consisting of pyridine and benzene rings bridged by vinylene groups

    Science.gov (United States)

    Ishikawa, Shigeru; Nemoto, Tetsushi; Yamabe, Tokio

    2018-06-01

    Hydrogen storage in a truncated triangular pyramid molecule C33H21N3, which consists of three pyridine rings and one benzene ring bridged by six vinylene groups, is studied by quantum chemical methods. The molecule is derived by substituting three benzene rings in a truncated tetrahedron hydrocarbon C36H24 with pyridine rings. The optimized molecular structure under C 3v symmetry shows no imaginary vibrational modes at the B3LYP/cc-pVTZ level of theory. The hydrogen storage process is investigated based on the MP2/cc-pVTZ method. Like the structure before substitution, the C33H21N3 molecule has a cavity that stores a hydrogen molecule with a binding energy of - 140 meV. The Langmuir isotherm shows that this cavity can store hydrogen at higher temperatures and lower pressures than usual physisorption materials. The C33H21N3 molecule has a kinetic advantage over the C36H24 molecule because the former molecule has a lower barrier (+ 560 meV) for the hydrogen molecule entering the cavity compared with the latter molecule (+ 730 meV) owing to the lack of hydrogen atoms narrowing the opening.

  12. Power Adaptation Based on Truncated Channel Inversion for Hybrid FSO/RF Transmission With Adaptive Combining

    KAUST Repository

    Rakia, Tamer

    2015-07-23

    Hybrid free-space optical (FSO)/radio-frequency (RF) systems have emerged as a promising solution for high-data-rate wireless communications. In this paper, we consider power adaptation strategies based on truncated channel inversion for the hybrid FSO/RF system employing adaptive combining. Specifically, we adaptively set the RF link transmission power when FSO link quality is unacceptable to ensure constant combined signal-to-noise ratio (SNR) at the receiver. Two adaptation strategies are proposed. One strategy depends on the received RF SNR, whereas the other one depends on the combined SNR of both links. Analytical expressions for the outage probability of the hybrid system with and without power adaptation are obtained. Numerical examples show that the hybrid FSO/RF system with power adaptation achieves a considerable outage performance improvement over the conventional system.

  13. Power Adaptation Based on Truncated Channel Inversion for Hybrid FSO/RF Transmission With Adaptive Combining

    KAUST Repository

    Rakia, Tamer; Hong-Chuan Yang; Gebali, Fayez; Alouini, Mohamed-Slim

    2015-01-01

    Hybrid free-space optical (FSO)/radio-frequency (RF) systems have emerged as a promising solution for high-data-rate wireless communications. In this paper, we consider power adaptation strategies based on truncated channel inversion for the hybrid FSO/RF system employing adaptive combining. Specifically, we adaptively set the RF link transmission power when FSO link quality is unacceptable to ensure constant combined signal-to-noise ratio (SNR) at the receiver. Two adaptation strategies are proposed. One strategy depends on the received RF SNR, whereas the other one depends on the combined SNR of both links. Analytical expressions for the outage probability of the hybrid system with and without power adaptation are obtained. Numerical examples show that the hybrid FSO/RF system with power adaptation achieves a considerable outage performance improvement over the conventional system.

  14. Functional Characterization of a Novel Truncating Mutation in Lamin A/C Gene in a Family with a Severe Cardiomyopathy with Conduction Defects

    Directory of Open Access Journals (Sweden)

    Andrea Gerbino

    2017-12-01

    Full Text Available Background/Aims: Truncating LMNA gene mutations occur in many inherited cardiomyopathy cases, but the molecular mechanisms involved in the disease they cause have not yet been systematically investigated. Here, we studied a novel frameshift LMNA variant (p.D243Gfs*4 identified in three members of an Italian family co-segregating with a severe form of cardiomyopathy with conduction defects. Methods: HEK293 cells and HL-1 cardiomyocytes were transiently transfected with either Lamin A or D243Gfs*4 tagged with GFP (or mCherry. D243Gfs*4 expression, cellular localization and its effects on diverse cellular mechanisms were evaluated with western blotting, laser-scanning confocal microscopy and video-imaging analysis in single cells. Results: When expressed in HEK293 cells, GFP- (or mCherry-tagged LMNA D243Gfs*4 colocalized with calnexin within the ER. ER mislocalization of LMNA D243Gfs*4 did not significantly induce ER stress response, abnormal Ca2+ handling and apoptosis when compared with HEK293 cells expressing another truncated mutant of LMNA (R321X which similarly accumulates within the ER. Of note, HEK293-LMNA D243Gfs*4 cells showed a significant reduction of connexin 43 (CX43 expression level, which was completely rescued by activation of the WNT/β-catenin signaling pathway. When expressed in HL-1 cardiomyocytes, D243Gfs*4 significantly impaired the spontaneous Ca2+ oscillations recorded in these cells as result of propagation of the depolarizing waves through the gap junctions between non-transfected cells surrounding a cell harboring the mutation. Furthermore, mCh-D243Gfs*4 HL-1 cardiomyocytes showed reduced CX43-dependent Lucifer Yellow (LY loading and propagation. Of note, activation of β-catenin rescued both LY loading and LMNA D243Gfs*4 -HL-1 cells spontaneous activity propagation. Conclusion: Overall, the present results clearly indicate the involvement of the aberrant CX43 expression/activity as a pathogenic mechanism for the

  15. Comparison of acid ethanol extraction and acid gel filtration prior to IGF-I and IGF-II radioimmunoassays; Improvement of determinations in acid ethanol extracts by the use of truncated IGF-I as radioligand

    Energy Technology Data Exchange (ETDEWEB)

    Bang, P; Eriksson, U; Wivall, I -L; Hall, K [Department of Endocrinology, Karolinska Institute, Stockholm (Sweden); Sara, V [Department of Pathology, Karolinska Institute, Stockholm (Sweden)

    1991-01-01

    Insulin-like growth factor binding proteins interfere in the IGF-I and -II radioimmunoassays. In an attempt to overcome this problem, we have compared the use of truncated IGF-I, with reduced IGFBP affinity, and IGF-I as radioligands for IGF-I RIA measurements in serum separated by acid gel filtration or acid ethanol extraction followed by cryo-precipitation. With truncated IGF-I as radioligand the IGF-I measurements in acid gel filtrates and acid ethanol extracts were significantly correlated in healthy subjects (N=42, r=0.91, p<0.001) and in patients with acromegaly (N=10, r=0.85, p<0.01), GH deficiency (N=10, r=0.88, p<0.001) or Type I diabetes mellitus (N=10, r=0.90, p<0.001). In contrast, the IGF-I concentrations in acid ethanol extracts determined with IGF-I as radioligand did not correlate with those in acid gel filtrates using truncated IGF-I radioligand in patients with acromegaly (r=0.61, NS) or GH deficiency (r=0.46, NS). In the latter group the mean IGF-I concentrations measured in acid ethanol extracts were erroneously elevated by 112%. Low-affinity antibodies used for IGF-II RIA determinations failed to give reliable results in acid ethanol extracts from patients with Type I diabetes mellitus or GH deficiency. In conclusion, erroneously high IGF-I concentrations owing to binding of the radioligand to IGFBPs not completely removed by acid ethanol extraction can be avoided by the use of truncated IGF-I as radioligand. (author).

  16. Simulation of Tsunami Resistance of a Pinus Thunbergii tree in Coastal Forest in Japan

    Science.gov (United States)

    Nanko, K.; Suzuki, S.; Noguchi, H.; Hagino, H.

    2015-12-01

    Forests reduce fluid force of tsunami, whereas extreme tsunami sometimes breaks down the forest trees. It is difficult to estimate the interactive relationship between the fluid and the trees because fluid deform tree architecture and deformed tree changes flow field. Dynamic tree deformation and fluid behavior should be clarified by fluid-structure interaction analysis. For the initial step, we have developed dynamic simulation of tree sway and breakage caused by tsunami based on a vibrating system with multiple degrees of freedom. The target specie of the simulation was Japanese black pine (pinus thunbergii), which is major specie in the coastal forest to secure livelihood area from the damage by blown sand and salt in Japanese coastal area. For the simulation, a tree was segmented into 0.2 m long circular truncated cones. Turning moment induced by tsunami and self-weight was calculated at each segment bottom. Tree deformation was computed on multi-degree-of-freedom vibration equation. Tree sway was simulated by iterative calculation of the tree deformation with time step 0.05 second with temporally varied flow velocity of tsunami. From the calculation of bending stress and turning moment at tree base, we estimated resistance of a Pinus thunbergii tree from tsunami against tree breakage.

  17. Light neutron-rich hypernuclei from the importance-truncated no-core shell model

    Directory of Open Access Journals (Sweden)

    Roland Wirth

    2018-04-01

    Full Text Available We explore the systematics of ground-state and excitation energies in singly-strange hypernuclei throughout the helium and lithium isotopic chains — from HeΛ5 to HeΛ11 and from LiΛ7 to LiΛ12 — in the ab initio no-core shell model with importance truncation. All calculations are based on two- and three-baryon interaction from chiral effective field theory and we employ a similarity renormalization group transformation consistently up to the three-baryon level to improve the model-space convergence. While the absolute energies of hypernuclear states show a systematic variation with the regulator cutoff of the hyperon–nucleon interaction, the resulting neutron separation energies are very stable and in good agreement with available data for both nucleonic parents and their daughter hypernuclei. We provide predictions for the neutron separation energies and the spectra of neutron-rich hypernuclei that have not yet been observed experimentally. Furthermore, we find that the neutron drip lines in the helium and lithium isotopic chains are not changed by the addition of a hyperon. Keywords: Hypernuclei, Ab-initio methods, Neutron-rich nuclei, Neutron separation energies, Neutron drip line

  18. Effects of feeding Bt MON810 maize to pigs for 110 days on peripheral immune response and digestive fate of the cry1Ab gene and truncated Bt toxin.

    Directory of Open Access Journals (Sweden)

    Maria C Walsh

    Full Text Available BACKGROUND: The objective of this study was to evaluate potential long-term (110 days and age-specific effects of feeding genetically modified Bt maize on peripheral immune response in pigs and to determine the digestive fate of the cry1Ab gene and truncated Bt toxin. METHODOLOGY/PRINCIPAL FINDINGS: Forty day old pigs (n = 40 were fed one of the following treatments: 1 isogenic maize-based diet for 110 days (isogenic; 2 Bt maize-based diet (MON810 for 110 days (Bt; 3 Isogenic maize-based diet for 30 days followed by Bt maize-based diet for 80 days (isogenic/Bt; and 4 Bt maize-based diet (MON810 for 30 days followed by isogenic maize-based diet for 80 days (Bt/isogenic. Blood samples were collected during the study for haematological analysis, measurement of cytokine and Cry1Ab-specific antibody production, immune cell phenotyping and cry1Ab gene and truncated Bt toxin detection. Pigs were sacrificed on day 110 and digesta and organ samples were taken for detection of the cry1Ab gene and the truncated Bt toxin. On day 100, lymphocyte counts were higher (P<0.05 in pigs fed Bt/isogenic than pigs fed Bt or isogenic. Erythrocyte counts on day 100 were lower in pigs fed Bt or isogenic/Bt than pigs fed Bt/isogenic (P<0.05. Neither the truncated Bt toxin nor the cry1Ab gene were detected in the organs or blood of pigs fed Bt maize. The cry1Ab gene was detected in stomach digesta and at low frequency in the ileum but not in the distal gastrointestinal tract (GIT, while the Bt toxin fragments were detected at all sites in the GIT. CONCLUSIONS/SIGNIFICANCE: Perturbations in peripheral immune response were thought not to be age-specific and were not indicative of Th 2 type allergenic or Th 1 type inflammatory responses. There was no evidence of cry1Ab gene or Bt toxin translocation to organs or blood following long-term feeding.

  19. Truncating mutation in the NHS gene: phenotypic heterogeneity of Nance-Horan syndrome in an asian Indian family.

    Science.gov (United States)

    Ramprasad, Vedam Lakshmi; Thool, Alka; Murugan, Sakthivel; Nancarrow, Derek; Vyas, Prateep; Rao, Srinivas Kamalakar; Vidhya, Authiappan; Ravishankar, Krishnamoorthy; Kumaramanickavel, Govindasamy

    2005-01-01

    A four-generation family containing eight affected males who inherited X-linked developmental lens opacity and microcornea was studied. Some members in the family had mild to moderate nonocular clinical features suggestive of Nance-Horan syndrome. The purpose of the study was to map genetically the gene in the large 57-live-member Asian-Indian pedigree. PCR-based genotyping was performed on the X-chromosome, by using fluorescent microsatellite markers (10-cM intervals). Parametric linkage analysis was performed by using two disease models, assuming either recessive or dominant X-linked transmission by the MLINK/ILINK and FASTLINK (version 4.1P) programs (http:www.hgmp.mrc.ac.uk/; provided in the public domain by the Human Genome Mapping Project Resources Centre, Cambridge, UK). The NHS gene at the linked region was screened for mutation. By fine mapping, the disease gene was localized to Xp22.13. Multipoint analysis placed the peak LOD of 4.46 at DSX987. The NHS gene mapped to this region. Mutational screening in all the affected males and carrier females (heterozygous form) revealed a truncating mutation 115C-->T in exon 1, resulting in conversion of glutamine to stop codon (Q39X), but was not observed in unaffected individuals and control subjects. conclusions. A family with X-linked Nance-Horan syndrome had severe ocular, but mild to moderate nonocular, features. The clinical phenotype of the truncating mutation (Q39X) in the NHS gene suggests allelic heterogeneity at the NHS locus or the presence of modifier genes. X-linked families with cataract should be carefully examined for both ocular and nonocular features, to exclude Nance-Horan syndrome. RT-PCR analysis did not suggest nonsense-mediated mRNA decay as the possible mechanism for clinical heterogeneity.

  20. A new lattice Boltzmann equation to simulate density-driven convection of carbon dioxide

    KAUST Repository

    Allen, Rebecca

    2013-01-01

    The storage of CO2 in fluid-filled geological formations has been carried out for more than a decade in locations around the world. After CO2 has been injected into the aquifer and has moved laterally under the aquifer\\'s cap-rock, density-driven convection becomes an important transport process to model. However, the challenge lies in simulating this transport process accurately with high spatial resolution and low CPU cost. This issue can be addressed by using the lattice Boltzmann equation (LBE) to formulate a model for a similar scenario when a solute diffuses into a fluid and density differences lead to convective mixing. The LBE is a promising alternative to the traditional methods of computational fluid dynamics. Rather than discretizing the system of partial differential equations of classical continuum mechanics directly, the LBE is derived from a velocity-space truncation of the Boltzmann equation of classical kinetic theory. We propose an extension to the LBE, which can accurately predict the transport of dissolved CO2 in water, as a step towards fluid-filled porous media simulations. This is achieved by coupling two LBEs, one for the fluid flow and one for the convection and diffusion of CO2. Unlike existing lattice Boltzmann equations for porous media flow, our model is derived from a system of moment equations and a Crank-Nicolson discretization of the velocity-truncated Boltzmann equation. The forcing terms are updated locally without the need for additional central difference approximation. Therefore our model preserves all the computational advantages of the single-phase lattice Boltzmann equation and is formally second-order accurate in both space and time. Our new model also features a novel implementation of boundary conditions, which is simple to implement and does not suffer from the grid-dependent error that is present in the standard "bounce-back" condition. The significance of using the LBE in this work lies in the ability to efficiently

  1. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Ignacio Boron

    2015-07-01

    Full Text Available Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O2 and •ŸNO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify Ÿ•NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, Ÿ•NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

  2. Numerical Simulation with Experimental Validation of the Draping Behavior of Woven Fabrics

    Energy Technology Data Exchange (ETDEWEB)

    Rodgers, William [General Motors LLC; Pasupuleti, Praveen [ESI Group NA; Zhao, Selina [General Motors LLC; Wathen, Terry [General Motors LLC; Doroudian, Mark [ESI Group NA; Aitharaju, Venkat [General Motors LLC

    2017-10-23

    Woven fabric composites are extensively used in molding complex geometrical shapes due to their high conformability compared to other fabrics. Preforming is an important step in the overall process. In this step, the two-dimensional fabric is draped to become the three-dimensional shape of the part prior to resin injection. During preforming, the orientation of the tows may change significantly compared to the initial orientations. Accurate prediction of the tow orientations after molding is important for evaluating the structural performance of the final part. This paper investigates the fiber angle changes for carbon fiber woven fabrics during draping over a truncated pyramid tool designed and fabricated at the General Motors Research Labs. This aspect of study is a subset of the broad study conducted under the purview of a Department of Energy project funded to GM in developing state of the art computational tools for integrated manufacturing and structural performance prediction of carbon fiber composites. Fabric bending, picture frame testing, and bias-extension evaluations were carried out to determine the material parameters for these fabrics. The PAM-FORM computer program was used to model the draping behavior of these fabrics. Following deformation, fiber angle changes at different locations on the truncated pyramid were measured experimentally. The predicted angles matched the experimental results well as measured along the centerline and at several different locations on the deformed fabric. Details of the test methods used as well as the numerical results with various simulation parameters will be provided.

  3. Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method

    Directory of Open Access Journals (Sweden)

    Maziar Heidari

    2018-03-01

    Full Text Available The spatial block analysis (SBA method has been introduced to efficiently extrapolate thermodynamic quantities from finite-size computer simulations of a large variety of physical systems. In the particular case of simple liquids and liquid mixtures, by subdividing the simulation box into blocks of increasing size and calculating volume-dependent fluctuations of the number of particles, it is possible to extrapolate the bulk isothermal compressibility and Kirkwood–Buff integrals in the thermodynamic limit. Only by explicitly including finite-size effects, ubiquitous in computer simulations, into the SBA method, the extrapolation to the thermodynamic limit can be achieved. In this review, we discuss two of these finite-size effects in the context of the SBA method due to (i the statistical ensemble and (ii the finite integration domains used in computer simulations. To illustrate the method, we consider prototypical liquids and liquid mixtures described by truncated and shifted Lennard–Jones (TSLJ potentials. Furthermore, we show some of the most recent developments of the SBA method, in particular its use to calculate chemical potentials of liquids in a wide range of density/concentration conditions.

  4. Simulation Optimization of Search and Rescue in Disaster Relief Based on Distributed Auction Mechanism

    Directory of Open Access Journals (Sweden)

    Jian Tang

    2017-11-01

    Full Text Available In this paper, we optimize the search and rescue (SAR in disaster relief through agent-based simulation. We simulate rescue teams’ search behaviors with the improved Truncated Lévy walks. Then we propose a cooperative rescue plan based on a distributed auction mechanism, and illustrate it with the case of landslide disaster relief. The simulation is conducted in three scenarios, including “fatal”, “serious” and “normal”. Compared with the non-cooperative rescue plan, the proposed rescue plan in this paper would increase victims’ relative survival probability by 7–15%, increase the ratio of survivors getting rescued by 5.3–12.9%, and decrease the average elapsed time for one site getting rescued by 16.6–21.6%. The robustness analysis shows that search radius can affect the rescue efficiency significantly, while the scope of cooperation cannot. The sensitivity analysis shows that the two parameters, the time limit for completing rescue operations in one buried site and the maximum turning angle for next step, both have a great influence on rescue efficiency, and there exists optimal value for both of them in view of rescue efficiency.

  5. Metabolic fate of lactoferricin-based antimicrobial peptides: effect of truncation and incorporation of amino acid analogs on the in vitro metabolic stability.

    Science.gov (United States)

    Svenson, Johan; Vergote, Valentijn; Karstad, Rasmus; Burvenich, Christian; Svendsen, John S; De Spiegeleer, Bart

    2010-03-01

    A series of promising truncated antibacterial tripeptides derived from lactoferricin has been prepared, and their in vitro metabolic stability in the main metabolic compartments, plasma, liver, kidney, stomach, duodenum, and brain, has been investigated for the first time. The potential stabilizing effect of truncation, C-terminal capping, and introduction of the bulky synthetic amino acid biphenylalanine is also investigated. The drug-like peptides displayed large differences in half-lives in the different matrixes ranging from 4.2 min in stomach and duodenum to 355.9 min in liver. Kinetic analysis of the metabolites revealed that several different degrading enzymes simultaneously target the different peptide bonds and that the outcome of the tested strategies to increase the stability is clearly enzyme-specific. Some of the metabolic enzymes even prefer the synthetic modifications incorporated over the natural counterparts. Collectively, it is shown that the necessary antibacterial pharmacophore generates compounds that are not only potent antibacterial peptides, but excellent substrates for the main degrading enzymes. All the amide bonds are thus rapidly targeted by different enzymes despite the short peptidic sequences of the tested compounds. Hence, our results illustrate that several structural changes are needed before these compounds can be considered for oral administration. Strategies to overcome such metabolic challenges are discussed.

  6. Stable structures of Al510–800 clusters and lowest energy sequence of truncated octahedral Al clusters up to 10,000 atoms

    International Nuclear Information System (INIS)

    Wu, Xia; He, Chengdong

    2012-01-01

    Highlights: ► The stable structures of Al 510–800 clusters are obtained with the NP-B potential. ► Al 510–800 clusters adopt truncated octahedral (TO) growth pattern based on complete TOs at Al 405 , Al 586 , and Al 711 . ► The lowest energy sequence of complete TOs up to the size 10,000 is proposed. -- Abstract: The stable structures of Al 510–800 clusters are obtained using dynamic lattice searching with constructed cores (DLSc) method by the NP-B potential. According to the structural growth rule, octahedra and truncated octahedra (TO) configurations are adopted as the inner cores in DLSc method. The results show that in the optimized structures two complete TO structures are found at Al 586 and Al 711 . Furthermore, Al 510–800 clusters adopt TO growth pattern on complete TOs at Al 405 , Al 586 , and Al 711 , and the configurations of the surface atoms are investigated. On the other hand, Al clusters with complete TO motifs are studied up to the size 10,000 by the geometrical construction method. The structural characteristics of complete TOs are denoted by the term “family”, and the growth sequence of Al clusters is investigated. The lowest energy sequence of complete TOs is proposed.

  7. Numerical method for multigroup one-dimensional SN eigenvalue problems with no spatial truncation error

    International Nuclear Information System (INIS)

    Abreu, M.P.; Filho, H.A.; Barros, R.C.

    1993-01-01

    The authors describe a new nodal method for multigroup slab-geometry discrete ordinates S N eigenvalue problems that is completely free from all spatial truncation errors. The unknowns in the method are the node-edge angular fluxes, the node-average angular fluxes, and the effective multiplication factor k eff . The numerical values obtained for these quantities are exactly those of the dominant analytic solution of the S N eigenvalue problem apart from finite arithmetic considerations. This method is based on the use of the standard balance equation and two nonstandard auxiliary equations. In the nonmultiplying regions, e.g., the reflector, we use the multigroup spectral Green's function (SGF) auxiliary equations. In the fuel regions, we use the multigroup spectral diamond (SD) auxiliary equations. The SD auxiliary equation is an extension of the conventional auxiliary equation used in the diamond difference (DD) method. This hybrid characteristic of the SD-SGF method improves both the numerical stability and the convergence rate

  8. Optical colour image watermarking based on phase-truncated linear canonical transform and image decomposition

    Science.gov (United States)

    Su, Yonggang; Tang, Chen; Li, Biyuan; Lei, Zhenkun

    2018-05-01

    This paper presents a novel optical colour image watermarking scheme based on phase-truncated linear canonical transform (PT-LCT) and image decomposition (ID). In this proposed scheme, a PT-LCT-based asymmetric cryptography is designed to encode the colour watermark into a noise-like pattern, and an ID-based multilevel embedding method is constructed to embed the encoded colour watermark into a colour host image. The PT-LCT-based asymmetric cryptography, which can be optically implemented by double random phase encoding with a quadratic phase system, can provide a higher security to resist various common cryptographic attacks. And the ID-based multilevel embedding method, which can be digitally implemented by a computer, can make the information of the colour watermark disperse better in the colour host image. The proposed colour image watermarking scheme possesses high security and can achieve a higher robustness while preserving the watermark’s invisibility. The good performance of the proposed scheme has been demonstrated by extensive experiments and comparison with other relevant schemes.

  9. Analyzing heavy-ion-induced charge collection in Si devices by three-dimensional simulation

    International Nuclear Information System (INIS)

    Dodd, P.E.

    1994-01-01

    Properties of charge collection in Si devices in response to single-ion bombardment have been studied using transient three-dimensional drift-diffusion simulation. In unloaded Si diodes, the funnel effect is particularly strong in lightly-doped materials for high-density strikes such as 100 MeV Fe, and essentially all charge collection is by funnel-assisted drift. This drift collection may occur at time scales as late as several nanoseconds, much later than is traditionally associated with drift. For more heavily-doped materials or lower-density strikes, such as 5-MeV α-particles, drift and diffusion play more equal roles. In epitaxial structures the funnel is truncated by the heavily-doped substrate, collapses quickly, and a great deal of charge is collected at late times by diffusion. Charge collection in Si circuitry is influenced by the circuit external to the struck device. Loading effects on charge collection were studied using passive external circuit elements as well as by mixed-mode simulation, which allows modeling of active external circuitry. Simulations indicate that the funnel can be significantly affected by the inclusion of passive loads, while active loads may prevent any direct charge collection by funneling. Finally, the use of three-dimensional device simulators is presented as a method of analyzing results obtained from focused ion microbeam experiments

  10. Quantum dynamics calculations using symmetrized, orthogonal Weyl-Heisenberg wavelets with a phase space truncation scheme. II. Construction and optimization

    International Nuclear Information System (INIS)

    Poirier, Bill; Salam, A.

    2004-01-01

    In this paper, we extend and elaborate upon a wavelet method first presented in a previous publication [B. Poirier, J. Theo. Comput. Chem. 2, 65 (2003)]. In particular, we focus on construction and optimization of the wavelet functions, from theoretical and numerical viewpoints, and also examine their localization properties. The wavelets used are modified Wilson-Daubechies wavelets, which in conjunction with a simple phase space truncation scheme, enable one to solve the multidimensional Schroedinger equation. This approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where differential equations are involved

  11. Simulating transient dynamics of the time-dependent time fractional Fokker-Planck systems

    Science.gov (United States)

    Kang, Yan-Mei

    2016-09-01

    For a physically realistic type of time-dependent time fractional Fokker-Planck (FP) equation, derived as the continuous limit of the continuous time random walk with time-modulated Boltzmann jumping weight, a semi-analytic iteration scheme based on the truncated (generalized) Fourier series is presented to simulate the resultant transient dynamics when the external time modulation is a piece-wise constant signal. At first, the iteration scheme is demonstrated with a simple time-dependent time fractional FP equation on finite interval with two absorbing boundaries, and then it is generalized to the more general time-dependent Smoluchowski-type time fractional Fokker-Planck equation. The numerical examples verify the efficiency and accuracy of the iteration method, and some novel dynamical phenomena including polarized motion orientations and periodic response death are discussed.

  12. Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

    Science.gov (United States)

    Lippert, Ross A.; Predescu, Cristian; Ierardi, Douglas J.; Mackenzie, Kenneth M.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

    2013-10-01

    In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the additional variables along with the particle positions and momenta at each time step. We present a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostat and barostat updates to be applied infrequently. Such infrequent updates provide a particularly substantial performance advantage for simulations parallelized across many computer processors, because thermostat and barostat updates typically require communication among all processors. Infrequent updates can also improve accuracy by alleviating certain sources of error associated with limited-precision arithmetic. In addition, separating the barostat, thermostat, and particle motion update steps reduces certain truncation errors, bringing the time-average pressure closer to its target value. Finally, this framework, which we have implemented on both general-purpose and special-purpose hardware, reduces software complexity and improves software modularity.

  13. Charge neutralization as the major factor for the assembly of nucleocapsid-like particles from C-terminal truncated hepatitis C virus core protein

    OpenAIRE

    Theo Luiz Ferraz de Souza; Sheila Maria Barbosa de Lima; Vanessa L. de Azevedo Braga; David S. Peabody; Davis Fernandes Ferreira; M. Lucia Bianconi; Andre Marco de Oliveira Gomes; Jerson Lima Silva; Andréa Cheble de Oliveira

    2016-01-01

    Background Hepatitis C virus (HCV) core protein, in addition to its structural role to form the nucleocapsid assembly, plays a critical role in HCV pathogenesis by interfering in several cellular processes, including microRNA and mRNA homeostasis. The C-terminal truncated HCV core protein (C124) is intrinsically unstructured in solution and is able to interact with unspecific nucleic acids, in the micromolar range, and to assemble into nucleocapsid-like particles (NLPs) in vitro. The specific...

  14. Importance-truncated no-core shell model for fermionic many-body systems

    Energy Technology Data Exchange (ETDEWEB)

    Spies, Helena

    2017-03-15

    The exact solution of quantum mechanical many-body problems is only possible for few particles. Therefore, numerical methods were developed in the fields of quantum physics and quantum chemistry for larger particle numbers. Configuration Interaction (CI) methods or the No-Core Shell Model (NCSM) allow ab initio calculations for light and intermediate-mass nuclei, without resorting to phenomenology. An extension of the NCSM is the Importance-Truncated No-Core Shell Model, which uses an a priori selection of the most important basis states. The importance truncation was first developed and applied in quantum chemistry in the 1970s and latter successfully applied to models of light and intermediate mass nuclei. Other numerical methods for calculations for ultra-cold fermionic many-body systems are the Fixed-Node Diffusion Monte Carlo method (FN-DMC) and the stochastic variational approach with Correlated Gaussian basis functions (CG). There are also such method as the Coupled-Cluster method, Green's Function Monte Carlo (GFMC) method, et cetera, used for calculation of many-body systems. In this thesis, we adopt the IT-NCSM for the calculation of ultra-cold Fermi gases at unitarity. Ultracold gases are dilute, strongly correlated systems, in which the average interparticle distance is much larger than the range of the interaction. Therefore, the detailed radial dependence of the potential is not resolved, and the potential can be replaced by an effective contact interaction. At low energy, s-wave scattering dominates and the interaction can be described by the s-wave scattering length. If the scattering length is small and negative, Cooper-pairs are formed in the Bardeen-Cooper-Schrieffer (BCS) regime. If the scattering length is small and positive, these Cooper-pairs become strongly bound molecules in a Bose-Einstein-Condensate (BEC). In between (for large scattering lengths) is the unitary limit with universal properties. Calculations of the energy spectra

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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, CH 4 , NH 3 , H 2 O, SiH 4 , PH 3 , SH 2 , C 2 H 2 , C 2 H 4 , and C 2 H 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

  16. ERK and PI3K regulate different aspects of the epithelial to mesenchymal transition of mammary tumor cells induced by truncated MUC1

    International Nuclear Information System (INIS)

    Horn, Galit; Gaziel, Avital; Wreschner, Daniel H.; Smorodinsky, Nechama I.; Ehrlich, Marcelo

    2009-01-01

    Epithelial to mesenchymal transition (EMT) integrates changes to cell morphology and signaling pathways resulting from modifications to the cell's transcriptional response. Different combinations of stimuli ignite this process in the contexts of development or tumor progression. The human MUC1 gene encodes multiple alternatively spliced forms of a polymorphic oncoprotein that is aberrantly expressed in epithelial malignancies. MUC1 is endowed with various signaling modules and has the potential to mediate proliferative and morphological changes characteristic of the progression of epithelial tumors. The tyrosine-rich cytoplasmic domain and the heavily glycosylated extracellular domain both play a role in MUC1-mediated signal transduction. However, the attribution of function to specific domains of MUC1 is difficult due to the concomitant presence of multiple forms of the protein, which stem from alternative splicing and proteolytic cleavage. Here we show that DA3 mouse mammary tumor cells stably transfected with a truncated genomic fragment of human MUC1 undergo EMT. In their EMT, these cells demonstrate altered [i] morphology, [ii] signaling pathways and [iii] expression of epithelial and mesenchymal markers. Similarly to well characterized human breast cancer cell lines, cells transfected with truncated MUC1 show an ERK-dependent increased spreading on fibronectin, and a PI3K-dependent enhancement of their proliferative rate.

  17. Timing of the Cenozoic basins of Southern Mexico and its relationship with the Pacific truncation process: Subduction erosion or detachment of the Chortís block

    Science.gov (United States)

    Silva-Romo, Gilberto; Mendoza-Rosales, Claudia Cristina; Campos-Madrigal, Emiliano; Hernández-Marmolejo, Yoalli Bianii; de la Rosa-Mora, Orestes Antonio; de la Torre-González, Alam Israel; Bonifacio-Serralde, Carlos; López-García, Nallely; Nápoles-Valenzuela, Juan Ivan

    2018-04-01

    In the central sector of the Sierra Madre del Sur in Southern Mexico, between approximately 36 and 16 Ma ago and in the west to east direction, a diachronic process of the formation of ∼north-south trending fault-bounded basins occurred. No tectono-sedimentary event in the period between 25 and 20 Ma is recognized in the study region. A period during which subduction erosion truncated the continental crust of southern Mexico has been proposed. The chronology, geometry and style of the formation of the Eocene Miocene fault-bounded basins are more congruent with crustal truncation by the detachment of the Chortís block, thus bringing into question the crustal truncation hypothesis of the Southern Mexico margin. Between Taxco and Tehuacán, using seven new Laser Ablation- Inductively-coupled plasma mass spectrometry (LA-ICP-MS) U-Pb ages in magmatic zircons, we refine the stratigraphy of the Tepenene, Tehuitzingo, Atzumba and Tepelmeme basins. The analyzed basins present similar tectono-sedimentary evolutions as follows: Stage 1, depocenter formation and filling by clastic rocks accumulated as alluvial fans and Stage 2, lacustrine sedimentation characterized by calcareous and/or evaporite beds. Based on our results, we propose the following hypothesis: in Southern Mexico, during Eocene-Miocene times, the diachronic formation of fault-bounded basins with general north-south trend occurred within the framework of the convergence between the plates of North and South America, and once the Chortís block had slipped towards the east, the basins formed in the cortical crust were recently left behind. On the other hand, the beginning of the basins' formation process related to left strike slip faults during Eocene-Oligocene times can be associated with the thermomechanical maturation cortical process that caused the brittle/ductile transition level in the continental crust to shallow.

  18. Truncation studies of alpha-melanotropin peptides identify tripeptide analogues exhibiting prolonged agonist bioactivity.

    Science.gov (United States)

    Haskell-Luevano, C; Sawyer, T K; Hendrata, S; North, C; Panahinia, L; Stum, M; Staples, D J; Castrucci, A M; Hadley, M F; Hruby, V J

    1996-01-01

    Truncation studies of alpha-melanotropin peptides identify tripeptide analogues exhibiting prolonged agonist bioactivity: PEPTIDES 17(6) 995-1002, 1996.-Systematic analysis of fragment derivatives of the superpotent alpha-MSH analogue. Ac-Ser.Tyr-Ser-Nle4-Glu- His-DPhe7-Arg-Trp-Gly-Lys-Pro-Val-NH2(NDP-MSH), led to the discovery of tripeptide agonists possessing prolonged bioactivity in the frog skin assay. Of particular significance to this discovery was Ac-DPhe-Arg-DTrp-NH2, which was the most potent tripeptide in this series exhibiting sustained melanotropic activity. Different pharmacophore models appear to exist that are dependent on the substructure and stereochemistry of the MSH(6-9) "active site." The tripeptides Ac-DPhe-Arg-Trp-NH2, Ac-DPhe-Arg-DTrp-NH2, and Ac-DPhe-DArg-Trp-NH2 stereo-chemical combinations require only Phe7-Xaa8-Trp9, whereas Ac-DPhe-DArg-DTrp-NH2, Ac-Phe-Arg-DTrp-NH2, and Ac-Phe-Arg-Trp-NH2 additionally require His4 for minimal biological activity. Ac-DPhe-Arg-DTrp-NH2 represents a novel prototype lead for the development of MSH-based peptidomimetic agonists.

  19. Simulation of nucleation and growth of atomic layer deposition phosphorus for doping of advanced FinFETs

    International Nuclear Information System (INIS)

    Seidel, Thomas E.; Goldberg, Alexander; Halls, Mat D.; Current, Michael I.

    2016-01-01

    Simulations for the nucleation and growth of phosphorus films were carried out using density functional theory. The surface was represented by a Si 9 H 12 truncated cluster surface model with 2 × 1-reconstructured (100) Si-OH terminations for the initial reaction sites. Chemistries included phosphorous halides (PF 3 , PCl 3 , and PBr 3 ) and disilane (Si 2 H 6 ). Atomic layer deposition (ALD) reaction sequences were illustrated with three-dimensional molecular models using sequential PF 3 and Si 2 H 6 reactions and featuring SiFH 3 as a byproduct. Exothermic reaction pathways were developed for both nucleation and growth for a Si-OH surface. Energetically favorable reactions for the deposition of four phosphorus atoms including lateral P–P bonding were simulated. This paper suggests energetically favorable thermodynamic reactions for the growth of elemental phosphorus on (100) silicon. Phosphorus layers made by ALD are an option for doping advanced fin field-effect transistors (FinFETs). Phosphorus may be thermally diffused into the silicon or recoil knocked in; simulations of the recoil profile of phosphorus into a FinFET surface are illustrated

  20. MHD simulations of ram pressure stripping of a disc galaxy

    Science.gov (United States)

    Ramos-Martínez, Mariana; Gómez, Gilberto C.; Pérez-Villegas, Ángeles

    2018-05-01

    The removal of the interstellar medium (ISM) of disc galaxies through ram pressure stripping (RPS) has been extensively studied in numerous simulations. Nevertheless, the role of magnetic fields (MFs) on the gas dynamics in this process has been hardly studied, although the MF influence on the large-scale disc structure is well established. With this in mind, we present a 3D magnetohydrodynamic simulation of face-on RPS of a disc galaxy to study the impact of the galactic MF in the gas stripping. The main effect of including a galactic MF is a flared disc. When the intracluster medium wind hits this flared disc, oblique shocks are produced at the interaction interface, where the ISM is compressed, generating a gas inflow from large radii towards the central regions of the galaxy. This inflow is observed for {˜ } 150 {Myr} and may supply the central parts of the galaxy with material for star formation while the outskirts of the disc are being stripped of gas, thus the oblique shocks can induce and enhance the star formation in the remaining disc. We also observed that the MF alters the shape and structure of the swept gas, giving a smooth appearance in the magnetized case and clumpier and filamentary-like morphology in the hydro case. Finally, we estimated the truncation radius expected for our models using the Gunn-Gott criterion and found that that is in agreement with the simulations.